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Sample records for intact soil-core microcosms

  1. Hydrocarbon biodegradation kinetics in an intact unsaturated zone soil core

    SciTech Connect

    Moyer, E.E.; Ostendorf, D.W.; Richards, R.J.; Goodwin, S.

    1995-12-31

    Aerobic biodegradation of vapor-phase petroleum hydrocarbons was evaluated in an intact soil core from the site of an aviation gasoline release. A mid-depth unsaturated zone soil core was subjected to a flow of nitrogen gas, oxygen, water vapor, and vapor-phase hydrocarbons in a configuration analogous to a biofilter or an in situ bioventing or sparging situation. The vertical profiles of vapor-phase hydrocarbon concentration in the soil core were determined by gas chromatography of vapor samples. Steady-state concentrations were input to a simple analytical model balancing advection and first-order biodegradation of hydrocarbons. First-order rate constants for each major hydrocarbon compound were used to calibrate the model to the concentration profiles. Compounds with lower molecular weights, fewer methyl groups, and no quaternary carbons tended to have higher rate constants. The first-order rate constants were consistent with kinetic parameters determined from microcosm studies at the same field site, suggesting that both estimation methods were effective.

  2. Petroleum hydrocarbon bioventing kinetics determined in soil core, microcosm, and tubing cluster studies

    SciTech Connect

    Moyer, E.E.; Ostendorf, D.W.; Richards, R.J.; Goodwin, S.

    1996-05-01

    Aerobic biodegradation of vapor-phase petroleum hydrocarbons was evaluated in an intact soil core from the site of an aviation gasoline release. An unsaturated zone soil core was subjected to a flow of nitrogen gas, oxygen, water vapor, and vapor-phase hydrocarbons in a configuration analogous to a biofilter or an in situ bioventing or sparging situation. The vertical profiles of vapor-phase hydrocarbon concentration in the soil core were determined by gas chromatography of vapor samples. Biodegradation reduced low influent hydrocarbon concentrations by 45 to 92% over a 0.6-m interval of an intact soil core. The estimated total hydrocarbon concentration was reduced by 75% from 26 to 7 parts per million. Steady-state concentrations were input to a simple analytical model balancing advection and first-order biodegradation of hydrocarbons. First-order rate constants for the major hydrocarbon compounds were used to calibrate the model to the concentration profiles. Rate constants for the seven individual hydrocarbon compounds varied by a factor of 4. Compounds with lower molecular weights, fewer methyl groups, and no quaternary carbons tended to have higher rate constants. The first-order rate constants were consistent with kinetic parameters determined from both microcosm and tubing cluster studies at the field site.

  3. Field calibration of soil-core microcosms for evaluating fate and effects of genetically engineered microorganisms in terrestrial ecosystems

    SciTech Connect

    Bolton, H Jr; Fredrickson, J K; Bentjen, S A; Workman, D J; Li, S W; Thomas, J M

    1991-04-01

    Pacific Northwest Laboratory compared intact soil-core microcosms and the field for ecosystem structural and functional properties after the introduction of a model genetically engineered microorganism (GEM). This project used two distinct microbial types as model GEMs, Gram-negative Pseudomonas sp. RC1, which was an aggressive root colonizer, and Gram-positive Streptomyces lividans TK24. The model GEMs were added to surface soil in separate studies, with RC1 studied throughout the growth of winter wheat (Triticum aestivum), while TK24 was studied throughout a ten month period. Also, RC1 was used in studies conducted during two consecutive field seasons (1988 to 1990) to determine how year-to-year field variability influenced the calibration of microcosms with the field. The main conclusions of this research were that intact soil-core microcosms can be useful to simulate the field for studies of microbial fate and effects on ecosystem structural and functional properties. In general, microcosms in the growth chamber, which simulated average field variations, were similar to the field for most parameters or differences could be attributed to the great extremes in temperature that occurred in the field compared to the microcosms. Better controls of environmental variables including temperature and moisture will be necessary to more closely simulate the field for future use of microcosms for risk assessment. 126 refs., 13 figs., 12 tabs.

  4. An improved method for field extraction and laboratory analysis of large, intact soil cores

    USGS Publications Warehouse

    Tindall, J.A.; Hemmen, K.; Dowd, J.F.

    1992-01-01

    Various methods have been proposed for the extraction of large, undisturbed soil cores and for subsequent analysis of fluid movement within the cores. The major problems associated with these methods are expense, cumbersome field extraction, and inadequate simulation of unsaturated flow conditions. A field and laboratory procedure is presented that is economical, convenient, and simulates unsaturated and saturated flow without interface flow problems and can be used on a variety of soil types. In the field, a stainless steel core barrel is hydraulically pressed into the soil (30-cm diam. and 38 cm high), the barrel and core are extracted from the soil, and after the barrel is removed from the core, the core is then wrapped securely with flexible sheet metal and a stainless mesh screen is attached to the bottom of the core for support. In the laboratory the soil core is set atop a porous ceramic plate over which a soil-diatomaceous earth slurry has been poured to assure good contact between plate and core. A cardboard cylinder (mold) is fastened around the core and the empty space filled with paraffin wax. Soil cores were tested under saturated and unsaturated conditions using a hanging water column for potentials ???0. Breakthrough curves indicated that no interface flow occurred along the edge of the core. This procedure proved to be reliable for field extraction of large, intact soil cores and for laboratory analysis of solute transport.

  5. Controlled Environment Soil-Core Microcosm Unit (CESMU) for Investigating Fate, Transport, and Transformation of Chemicals in Site-Specific Soils

    DTIC Science & Technology

    1994-06-01

    34 Acid Rain," Environment Vol. 14, pp 33-44 (1972). 12. The Soil Core Microcosm - A Potential Screening Tool, EPA-600/3-79-089, U.S. Environmental...AD-A284 768 EDGEWOOD U A CN DEMW APUENT & •ENGCWR Dh Ct ZER U.& ARMY CXZWCAL AND WOLOGICAL DErzNu COwLAND ERDEC-TR-088 CONTROLLED ENVIRONMENT SOIL ...CORE MICROCOSM UNIT (CESMU) FOR INVESTIGATING FATE, TRANSPORT, AND TRANSFORMATION OF CHEMICALS IN SITE-SPECIFIC SOILS Ronald T. Checkal Randall S

  6. Improved Methods for Estimating Microbial Activity and Moisture Characteristic Curves in Intact Unsaturated Soil Cores

    NASA Astrophysics Data System (ADS)

    Thompson, D. N.; Baker, K. E.

    2001-12-01

    Estimation of microbial activity in soils is a complex and often difficult process. In this work, we describe several new and innovative methods we have developed to measure microbial respiration in intact cores of unsaturated soils. The ultimate goal of this work is to predict the effect of microbial activity on contaminant mobility via CO2 generation in variably saturated vadose zone soils. This goal requires estimation of the effect of available water (i.e. in pores accessible to the microbes) on the microbial activity, and thus a homogeneous distribution of substrate throughout the soil water. Prior studies have added substrate solution drop wise to the soil, and then distributed the substrate throughout the soil by mixing. While this method distributes the substrate well, it alters the in situ pore volume distribution and has been shown to result in an anomalously high degree of microbial activity shortly after mixing. Traditional methods for uniformly distributing substrate in intact unsaturated soils require days to weeks to reach equilibrium. Since the substrate would be completely consumed in this time frame, an innovative approach is being used in this study to drain intact soil cores to the desired moisture contents in a matter of hours. This approach involves the use of the Unsaturated Flow Apparatus (UFAT). In the method, the samples are vacuum saturated under refrigeration to uniformly distribute a 14C-labeled substrate throughout the soil water, drained to various pressures in the UFA, and transferred to a sealed container and incubated. The labeled 14CO2 is then trapped and counted after incubation to determine microbial activity. Since the soil used in this study contains a high percentage of swelling clays, the cores tend to compact in the UFA, altering the macropore volume distribution. To address this alteration, we developed a correction function to correct the UFA-measured pore volume distribution at each rotational speed. Finally, the high

  7. Experimental terrestrial soil-core microcosm test protocol. A method for measuring the potential ecological effects, fate, and transport of chemicals in terrestrial ecosystems

    SciTech Connect

    Van Voris, P.; Tolle, D.A.; Arthur, M.F.

    1985-06-01

    In order to protect the environment properly and have a realistic appraisal of how a chemical will act in the environment, tests of ecological effects and chemical fate must be performed on complex assemblages of biotic and abiotic components (i.e., microcosms) as well as single species. This protocol is one which could be added to a series of tests recently developed as guidelines for Section 4 of the Toxic Substances Control Act (P.L. 94-469; U.S.C., Section 2601-2629). The terrestrial soil-core microcosm is designed to supply site-specific and possibly regional information on the probable chemical fate and ecological effects resulting from release of a chemical substance to a terrestrial ecosystem. The EPA will use the data resulting from this test system to compare the potential hazards of a chemical with others that have been previously evaluated.

  8. Leaching of Cryptosporidium parvum Oocysts, Escherichia coli, and a Salmonella enterica Serovar Typhimurium Bacteriophage through Intact Soil Cores following Surface Application and Injection of Slurry▿

    PubMed Central

    Forslund, Anita; Markussen, Bo; Toenner-Klank, Lise; Bech, Tina B.; Jacobsen, Ole Stig; Dalsgaard, Anders

    2011-01-01

    Increasing amounts of livestock manure are being applied to agricultural soil, but it is unknown to what extent this may be associated with contamination of aquatic recipients and groundwater if microorganisms are transported through the soil under natural weather conditions. The objective of this study was therefore to evaluate how injection and surface application of pig slurry on intact sandy clay loam soil cores influenced the leaching of Salmonella enterica serovar Typhimurium bacteriophage 28B, Escherichia coli, and Cryptosporidium parvum oocysts. All three microbial tracers were detected in the leachate on day 1, and the highest relative concentration was detected on the fourth day (0.1 pore volume). Although the concentration of the phage 28B declined over time, the phage was still found in leachate at day 148. C. parvum oocysts and chloride had an additional rise in the relative concentration at a 0.5 pore volume, corresponding to the exchange of the total pore volume. The leaching of E. coli was delayed compared with that of the added microbial tracers, indicating a stronger attachment to slurry particles, but E. coli could be detected up to 3 months. Significantly enhanced leaching of phage 28B and oocysts by the injection method was seen, whereas leaching of the indigenous E. coli was not affected by the application method. Preferential flow was the primary transport vehicle, and the diameter of the fractures in the intact soil cores facilitated transport of all sizes of microbial tracers under natural weather conditions. PMID:21948848

  9. Transport of Residual Nitrogen and Carbon through Intact Soil Cores Amended with Stockpiled Feedlot Manure with Wood-Chip or Straw Bedding.

    PubMed

    Miller, J J; Beasley, B W; Drury, C F; Hao, X; Larney, F J

    2013-11-01

    The environmental impact of using wood chips instead of straw bedding with feedlot manure on transport and leaching potential from feedlot manure is unknown. Our main objective was to determine if transport of total N, total organic N, NO-N, and nonpurgeable organic C (NPOC) to subsurface soil was lower for soils amended with feedlot manure if combined with wood chips compared with straw. A secondary objective was to compare transport of N and NPOC with organic amendments versus inorganic fertilizer. Stockpiled feedlot manure (SM) with wood chip (SM-WD) or barley straw (SM-ST) bedding at 39 Mg (dry wt.) ha, and inorganic fertilizer (IN) at 100 kg N ha, was applied annually for 13 yr to a clay loam soil in a replicated field experiment in southern Alberta, Canada. Intact soil cores were taken in fall 2011 (0-30 cm depth) from the three treatments, and the residual N and NPOC were eluted from the soil cores. Total N, total organic N, and NPOC were determined on filtered (1.0 μm) effluent samples that are primarily dissolved fraction but may contain some small particulate N and C. Peak concentrations, flow-weighted mean concentrations, and mass loss of total N, total organic N, NO-N, and NPOC were significantly ( ≤ 0.05) lower by 35 to 86% for SM-WD compared with SM-ST. Mean recoveries were also significantly lower for SM-WD than SM-ST by 0.07 to 8% (absolute difference). The transport behavior was similar for SM-WD and IN treatment, but solute transport was greater for SM-ST than for IN. Application of stockpiled feedlot manure with wood chips instead of straw bedding may be a beneficial management practice to reduce transport and leaching potential of N fractions and NPOC.

  10. N2O, NO, N2, and CO2 emissions from tropical savanna and grassland of Northern Australia: an incubation experiment with intact soil cores

    NASA Astrophysics Data System (ADS)

    Werner, C.; Reiser, K.; Dannenmann, M.; Hutley, L. B.; Jacobeit, J.; Butterbach-Bahl, K.

    2014-06-01

    Strong seasonal variability of hygric and thermal soil conditions are a defining environmental feature in Northern Australia. However, how such changes affect the soil-atmosphere exchange of nitrous oxide (N2O), nitric oxide (NO) and dinitrogen (N2) is still not well explored. By incubating intact soil cores from four sites (3 savanna, 1 pasture) under controlled soil temperatures (ST) and soil moisture (SM) we investigated the release of the trace gas fluxes of N2O, NO and carbon dioxide (CO2). Furthermore, the release of N2 due to denitrification was measured using the helium gas flow soil core technique. Under dry pre-incubation conditions NO and N2O emission were very low (<7.0 ± 5.0 μg NO-N m-2 h-1; <0.0 ± 1.4 μg N2O-N m-2 h-1) or in case of N2O, even a net soil uptake was observed. Substantial NO (max: 306.5 μg N m-2 h-1) and relatively small N2O pulse emissions (max: 5.8 ± 5.0 μg N m-2 h-1) were recorded following soil wetting, but these pulses were short-lived, lasting only up to 3 days. The total atmospheric loss of nitrogen was dominated by N2 emissions (82.4-99.3% of total N lost), although NO emissions contributed almost 43.2% at 50% SM and 30 °C ST. N2O emissions were systematically higher for 3 of 12 sample locations, which indicates substantial spatial variability at site level, but on average soils acted as weak N2O sources or even sinks. Emissions were controlled by SM and ST for N2O and CO2, ST and pH for NO, and SM and pH for N2.

  11. Evaluating the mobility of polymer-stabilised zero-valent iron nanoparticles and their potential to co-transport contaminants in intact soil cores.

    PubMed

    Chekli, L; Brunetti, G; Marzouk, E R; Maoz-Shen, A; Smith, E; Naidu, R; Shon, H K; Lombi, E; Donner, E

    2016-09-01

    The use of zero-valent iron nanoparticles (nZVI) has been advocated for the remediation of both soils and groundwater. A key parameter affecting nZVI remediation efficacy is the mobility of the particles as this influences the reaction zone where remediation can occur. However, by engineering nZVI particles with increased stability and mobility we may also inadvertently facilitate nZVI-mediated contaminant transport away from the zone of treatment. Previous nZVI mobility studies have often been limited to model systems as the presence of background Fe makes detection and tracking of nZVI in real systems difficult. We overcame this problem by synthesising Fe-59 radiolabelled nZVI. This enabled us to detect and quantify the leaching of nZVI-derived Fe-59 in intact soil cores, including a soil contaminated by Chromated-Copper-Arsenate. Mobility of a commercially available nZVI was also tested. The results showed limited mobility of both nanomaterials; <1% of the injected mass was eluted from the columns and most of the radiolabelled nZVI remained in the surface soil layers (the primary treatment zone in this contaminated soil). Nevertheless, the observed breakthrough of contaminants and nZVI occurred simultaneously, indicating that although the quantity transported was low in this case, nZVI does have the potential to co-transport contaminants. These results show that direct injection of nZVI into the surface layers of contaminated soils may be a viable remediation option for soils such as this one, in which the mobility of nZVI below the injection/remediation zone was very limited. This Fe-59 experimental approach can be further extended to test nZVI transport in a wider range of contaminated soil types and textures and using different application methods and rates. The resulting database could then be used to develop and validate modelling of nZVI-facilitated contaminant transport on an individual soil basis suitable for site specific risk assessment prior to n

  12. Evaluation of terrestrial microcosms for assessing the fate and effects of genetically engineered microorganisms on ecological processes

    SciTech Connect

    Fredrickson, J.K.; Bentjen, S.A.; Bolton, H. Jr.; Li, S.W.; Ligotke, M.W.; McFadden, K.M.; Van Voris, P.

    1989-04-01

    This project evaluates and modifies the existing US Environmental Protection Agency's Office of Pesticides and Toxic Substances (EPA/OPTS) terrestrial microcosm test system and test protocols such that they can be used to determine the environmental fate and ecological hazards of genetically engineered microorganisms (GEMs). The intact soil-core microcosm represents terrestrial ecosystems, and when coupled with appropriate test protocols, such microcosms may be appropriate to define and limit risks associated with the intentional release of GEMs. The terrestrial microcosm test system was used to investigate the survival and transport of two model GEMs (Azospirillum lipoferum and Pseudomonas sp. Tn5 mutants) to various trophic levels and niches and through intact soil cores. Subsequent effects on nutrient cycling and displacement of indigenous microorganisms were evaluated. The model organisms were a diazotrophic root-colonizing bacterium (A. lipoferum) and a wheat root growth-inhibiting rhizobacterium (Pseudomonas sp.). The transposable element Tn5 was used as a genetic marker for both microorganisms in two separate experiments. The organisms were subjected to transposon mutagenesis using a broad host-range-mobilizable suicide plasmid. The transposon Tn5 conferred levels of kanamycin resistance up to 500 ..mu..g/ml (Pseudomonas sp.), which allowed for selection of the bacteria from environmental samples. The presence of Tn5 DNA in the genome of the model GEMs also allowed the use of Tn5 gene probes to confirm and enumerate the microorganisms in different samples from the microcosms. Two types of root growth-inhibiting Pseudomonas sp. Tn5 mutants were obtained and used in microcosm studies: those that lacked the ability to inhibit either wheat root growth or the growth of other microorganisms in vitro (tox/sup /minus//) and those which retained these properties (tox/sup +/). 53 refs., 7 figs., 6 tabs.

  13. Evaluation of terrestrial microcosms for detection, fate, and survival analysis of genetically engineered microorganisms and their recombinant genetic material

    SciTech Connect

    Fredrickson, J.K.; Seidler, R.J.

    1989-02-01

    The research included in this document represents the current scientific information available regarding the applicability of terrestrial microcosms and related methodologies for evaluating detection methods and the fate and survival of microorganisms in the environment. The three terrestrial microcosms described in this document were used to evaluate the survival and fate of recombinant bacteria in soils and in association with plant surfaces and insects and their transport through soil with percolating water and root systems, and to test new methods and procedures to improve detection and enumeration of bacteria in soil. Simple (potting soil composed of peat mix and perlite, lacking environmental control and monitoring) and complex microcosms (agricultural soil with partial control and monitoring of environmental conditions) were demonstrated to be useful tools for preliminary assessments of microbial viability in terrestrial ecosystems. These studies evaluated the survival patterns of Enterobacter cloacae (pBR322) in soil and on plant surfaces and the ingestion of this same microorganism by cutworms and survival in the foregut and frass. The Versacore microcosm design was used to monitor the fate and competitiveness of genetically engineered bacteria in soil. Both selective media and gene probes were used successfully to follow the fate of two recombinant Pseudomonas sp. introduced into Versacore microcosms. Intact soil-core microcosms were employed to evaluate the fate and transport of genetically altered Azospirillum sp. and Pseudomonas sp. in soil and the plant rhizosphere. The usefulness of these various microcosms as a tool for risk assessment is underscored by the ease in obtaining soil from a proposed field release site to evaluate subsequent GEM fate and survival.

  14. Temperature effects on propylene glycol-contaminated soil cores

    SciTech Connect

    Davis-Hoover, W.J.; Vesper, S.J.

    1995-12-31

    The authors are examining the effect of temperature on the biodegradation of propylene glycol (PPG) in subsurface soil cores. Subsurface soils were contaminated in situ with PPG and allowed to diffuse into the soil for 30 days. The treated soil was reexposed, and intact were incubated for 30 days at temperatures ranging from 9 to 39 C in a temperature gradient incubator. At 30 days, soil moisture, soil pH, microbial activity [fluorescein diacetate (FDA) test], R2A plate counts, and plate counts of PPG degraders were studied. Although the soil moisture and pH remained relatively unchanged, the parameters of microbial activity varied rather consistently with temperature. Multiple populations or subpopulations of bacteria appear to exist between temperatures of 9 and 39 C in these soils.

  15. The University as Microcosm

    ERIC Educational Resources Information Center

    Kaldis, Byron

    2009-01-01

    This paper puts forward the model of "microcosm-macrocosm" isomorphism encapsulated in certain philosophical views on the form of university education. The human being as a "microcosm" should reflect internally the external "macrocosm". Higher Education is a socially instituted attempt to guide human beings into forming themselves as microcosms of…

  16. Apollo rocks, fines and soil cores

    NASA Astrophysics Data System (ADS)

    Allton, J.; Bevill, T.

    Apollo rocks and soils not only established basic lunar properties and ground truth for global remote sensing, they also provided important lessons for planetary protection (Adv. Space Res ., 1998, v. 22, no. 3 pp. 373-382). The six Apollo missions returned 2196 samples weighing 381.7 kg, comprised of rocks, fines, soil cores and 2 gas samples. By examining which samples were allocated for scientific investigations, information was obtained on usefulness of sampling strategy, sampling devices and containers, sample types and diversity, and on size of sample needed by various disciplines. Diversity was increased by using rakes to gather small rocks on the Moon and by removing fragments >1 mm from soils by sieving in the laboratory. Breccias and soil cores are diverse internally. Per unit weight these samples were more often allocated for research. Apollo investigators became adept at wringing information from very small sample sizes. By pushing the analytical limits, the main concern was adequate size for representative sampling. Typical allocations for trace element analyses were 750 mg for rocks, 300 mg for fines and 70 mg for core subsamples. Age-dating and isotope systematics allocations were typically 1 g for rocks and fines, but only 10% of that amount for core depth subsamples. Historically, allocations for organics and microbiology were 4 g (10% for cores). Modern allocations for biomarker detection are 100mg. Other disciplines supported have been cosmogenic nuclides, rock and soil petrology, sedimentary volatiles, reflectance, magnetics, and biohazard studies . Highly applicable to future sample return missions was the Apollo experience with organic contamination, estimated to be from 1 to 5 ng/g sample for Apollo 11 (Simonheit &Flory, 1970; Apollo 11, 12 &13 Organic contamination Monitoring History, U.C. Berkeley; Burlingame et al., 1970, Apollo 11 LSC , pp. 1779-1792). Eleven sources of contaminants, of which 7 are applicable to robotic missions, were

  17. Inorganic and suspended/dissolved-organic nitrogen in Sierra Nevada soil core leachates

    SciTech Connect

    Marcus, J.A.; Miller, W.W.; Blank, R.R.

    1998-07-01

    Watershed disturbance has been suggested as a possible mechanism for accelerated nutrient input into Lake Tahoe, California/Nevada. However, little is known regarding how nutrient discharge is coupled to physicochemical watershed processes. Recent investigations in the Lake Tahoe Basin have suggested that suspended/dissolved-organic nutrient transport may play an important role in lake and tributary water quality. The mobility of inorganic and suspended/dissolved-organic N in soils of a Lake Tahoe watershed was assessed using constant head permeameter leaching experiments with intact soil cores. The authors evaluated the interaction of plot condition on magnitude and form of N discharge. Incremental leachate discharge was analyzed for concentrations of inorganic (NH{sub 4}-N and NO{sub 3}-N) and suspended/dissolved-organic N. Leachate from the riparian soil cores had significantly higher concentrations and total discharge NO{sub 3}-N than that from the nonforested or forested areas. Loading of NH{sub 4}-N was more consistent among vegetative cover types, but the riparian leachate again contributed a significantly greater amount. Suspended/dissolved-organic N was mobile and the most dominant form of N for nonforested and forested soil cores with discharge loading ratios of 17:1 and 7:1, respectively. Although the loading ratio was approximately 1:1 for the riparian soil cores, the amount of suspended/dissolved-organic N discharged was greatest. The mobility and presence of significant amounts of suspended/dissolved-organic N indicate that this once unrecognized nutrient form is an important component in at least one Sierra Nevada watershed, and should be more fully investigated elsewhere.

  18. A Protocol for Collecting and Constructing Soil Core Lysimeters.

    PubMed

    Saporito, Louis S; Bryant, Ray B; Kleinman, Peter J A

    2016-06-06

    Leaching of nutrients from land applied fertilizers and manure used in agriculture can lead to accelerated eutrophication of surface water. Because the landscape has complex and varied soil morphology, an accompanying disparity in flow paths for leachate through the soil macropore and matrix structure is present. The rate of flow through these paths is further affected by antecedent soil moisture. Lysimeters are used to quantify flow rate, volume of water and concentration of nutrients leaching downward through soils. While many lysimeter designs exist, accurately determining the volume of water and mass balance of nutrients is best accomplished with bounded lysimeters that leave the natural soil structure intact. Here we present a detailed method for the extraction and construction of soil core lysimeters equipped with soil moisture sensors at 5 cm and 25 cm depths. Lysimeters from four different Coastal Plain soils (Bojac, Evesboro, Quindocqua and Sassafras) were collected on the Delmarva Peninsula and moved to an indoor climate controlled facility. Soils were irrigated once weekly with the equivalent of 2 cm of rainfall to draw down soil nitrate-N concentrations. At the end of the draw down period, poultry litter was applied (162 kg TN ha(-1)) and leaching was resumed for an additional five weeks. Total recovery of applied irrigation water varied from 71% to 85%. Nitrate-N concentration varied over the course of the study from an average of 27.1 mg L(-1) before litter application to 40.3 mg L(-1) following litter application. While greatest flux of nutrients was measured in soils dominated by coarse sand (Sassafras) the greatest immediate flux occurred from the finest textured soil with pronounced macropore development (Quindocqua).

  19. Extending the Marine Microcosm Laboratory

    ERIC Educational Resources Information Center

    Ryswyk, Hal Van; Hall, Eric W.; Petesch, Steven J.; Wiedeman, Alice E.

    2007-01-01

    The traditional range of marine microcosm laboratory experiments is presented as an ideal environment to teach the entire analysis process. The microcosm lab provides student-centered approach with opportunities for collaborative learning and to develop critical communication skills.

  20. Atmospheric carbonyl sulfide exchange in bog microcosms

    SciTech Connect

    Fried, A.; Klinger, L.F.; Erickson, D.J. III )

    1993-01-22

    Measurements of Carbonyl sulfide (OCS) fluxes were carried out on bog microcosms using chamber sampling and tunable diode laser analysis. Intact bog microcosms (vascular plants, mosses, and peat) removed ambient levels of OCS in the light and dark with rates from [minus]2.4 to [minus]8.1 ng S min[sup [minus]1] m[sup [minus]2]. Peat and peat plus mosses emitted OCS in the light with rates of 17.4 and 10.9 ng S min[sup [minus]1] m[sup [minus]2], respectively. In the dark, the mosses apparently removed OCS at a rate equivalent to the peat emissions. A 3-D numerical tracer model using this data indicated that boreal bog ecosystems remove at most 1% of ambient OCS, not sufficient to account for an observed OCS depletion in boreal air masses. 13 refs., 1 fig., 1 tab.

  1. A Natal Microcosm

    NASA Technical Reports Server (NTRS)

    2004-01-01

    In the quest to better understand the birth of stars and the formation of new worlds, astronomers have used NASA's Spitzer Space Telescope to examine the massive stars contained in a cloudy region called Sharpless 140. This cloud is a fascinating microcosm of a star-forming region since it exhibits, within a relatively small area, all of the classic manifestations of stellar birth.

    Sharpless 140 lies almost 3000 light-years from Earth in the constellation Cepheus. At its heart is a cluster of three deeply embedded young stars, which are each several thousand times brighter than the Sun. Though they are strikingly visible in this image from Spitzer's infrared array camera, they are completely obscured in visible light, buried within the core of the surrounding dust cloud.

    The extreme youth of at least one of these stars is indicated by the presence of a stream of gas moving at high velocities. Such outflows are signatures of the processes surrounding a star that is still gobbling up material as part of its formation.

    The bright red bowl, or arc, seen in this image traces the outer surface of the dense dust cloud encasing the young stars. This arc is made up primarily of organic compounds called polycyclic aromatic hydrocarbons, which glow on the surface of the cloud. Ultraviolet light from a nearby bright star outside of the image is 'eating away' at these molecules. Eventually, this light will destroy the dust envelope and the masked young stars will emerge.

    This false-color image was taken on Oct. 11, 2003 and is composed of photographs obtained at four wavelengths: 3.6 microns (blue), 4.5 microns (green), 5.8 microns (orange) and 8 microns (red).

  2. Atrazine remediation in wetland microcosms.

    PubMed

    Runes, H B; Bottomley, P J; Lerch, R N; Jenkins, J J

    2001-05-01

    Laboratory wetland microcosms were used to study treatment of atrazine in irrigation runoff by a field-scale-constructed wetland under controlled conditions. Three experiments, in which 1 ppm atrazine was added to the water column of three wetland, one soil control, and one water control microcosm, were conducted. Atrazine dissipation from the water column and degradate formation (deethylatrazine [DEA]; deisopropylatrazine [DIA]; and hydroxyatrazine [HA]) were monitored. Atrazine dissipation from the water column of wetland microcosms was biphasic. Less than 12% of the atrazine applied to wetland microcosms remained in the water column on day 56. Atrazine degradates were observed in water and sediment, with HA the predominant degradate. Analysis of day 56 sediment samples indicated that a significant portion of the initial application was detected as the parent compound and HA. Most probable number (MPN) assays demonstrated that atrazine degrader populations were small in wetland sediment. Wetland microcosms were able to reduce atrazine concentration in the water column via sorption and degradation. Based on results from this study, it is hypothesized that plant uptake contributed to atrazine dissipation from the water column.

  3. Using Microcosms To Teach about the Environment.

    ERIC Educational Resources Information Center

    Kaufman, Donald G.; Taylor, Lisa

    A microcosm is a small, completely sealed, self-sustaining ecosystem. Once a microcosm has been sealed in a transparent container, only light and some heat can enter and only excess heat can leave. This manual describes how to set up aquatic microcosms using glass jars and little or no collecting equipment. The activities can be tailored to suit…

  4. Know Thyself: Macrocosm and Microcosm

    ERIC Educational Resources Information Center

    Tubbs, Nigel

    2011-01-01

    There was a time when, in the Liberal Arts, philosophy and education enjoyed the most intimate and productive relationship. Drawing together philosophy and nature they sought to understand the greatest of human mysteries. This meant thinking about both the macrocosm and the microcosm and especially the relation between them. In this relation lies…

  5. Infiltration characteristics of non-aqueous phase liquids in undisturbed loessal soil cores.

    PubMed

    Wang, Yunqiang; Shao, Ming'an

    2009-01-01

    The widespread contamination of soils and aquifers by non-aqueous phase liquids (NAPL), such as crude oil, poses serious environmental and health hazards globally. Understanding the infiltration characteristics of NAPL in soil is crucial in mitigating or remediating soil contamination. The infiltration characteristics of crude and diesel oils into undisturbed loessal soil cores, collected in polymethyl methacrylate cylindrical columns, were investigated under a constant fluid head (3 cm) of either crude oil or diesel oil. The infiltration rate of both crude and diesel oils decreased exponentially as wetting depth increased with time. Soil core size and bulk density both had significant effects on NAPL infiltration through the undisturbed soil cores; a smaller core size or a greater bulk density could reduce oil penetration to depth. Compacting soil in areas susceptible to oil spills may be an effective stratage to reduce contamination. The infiltration of NAPL into soil cores was spatially anisotropic and heterogeneous, thus recording the data at four points on the soil core is a good stratage to improve the accuracy of experimental results. Our results revealed that crude and diesel oils, rather than their components, have a practical value for remediation of contaminated loessal soils.

  6. A portable fluorescence spectroscopy imaging system for automated root phenotyping in soil cores in the field.

    PubMed

    Wasson, Anton; Bischof, Leanne; Zwart, Alec; Watt, Michelle

    2016-02-01

    Root architecture traits are a target for pre-breeders. Incorporation of root architecture traits into new cultivars requires phenotyping. It is attractive to rapidly and directly phenotype root architecture in the field, avoiding laboratory studies that may not translate to the field. A combination of soil coring with a hydraulic push press and manual core-break counting can directly phenotype root architecture traits of depth and distribution in the field through to grain development, but large teams of people are required and labour costs are high with this method. We developed a portable fluorescence imaging system (BlueBox) to automate root counting in soil cores with image analysis software directly in the field. The lighting system was optimized to produce high-contrast images of roots emerging from soil cores. The correlation of the measurements with the root length density of the soil cores exceeded the correlation achieved by human operator measurements (R (2)=0.68 versus 0.57, respectively). A BlueBox-equipped team processed 4.3 cores/hour/person, compared with 3.7 cores/hour/person for the manual method. The portable, automated in-field root architecture phenotyping system was 16% more labour efficient, 19% more accurate, and 12% cheaper than manual conventional coring, and presents an opportunity to directly phenotype root architecture in the field as part of pre-breeding programs. The platform has wide possibilities to capture more information about root health and other root traits in the field.

  7. Mutational hot spots in the mitochondrial microcosm

    SciTech Connect

    Paeaebo, S.

    1996-09-01

    Human mitochondria can be seen as a genetic microcosm, located within the macrocosm of the entire cell. In each cell, this microcosm contains a few thousand copies of a circular DNA genome of 16,569 bp that is transmitted between generations, almost exclusively from mother to child. The study of this genetic microcosm holds particular fascination, since it may fore-shadow the coming genetics of the nuclear genome. In the mitochondrial microcosm, the {open_quotes}Human Genome Project{close_quotes} was completed years ago, with the publication of the DNA sequence of an entire mitochondrial genome. In the microcosm, one is thus well into the {open_quotes}postgenomic era.{close_quotes} It therefore may be instructive to ask what the first 15 years of postgenomics has brought within the microcosmic field of mitochondrial genetics. The availability of a complete genome sequence obviously brought great benefits to the study of physiological process in the mitochondria. However, in addition, many insights in the immediately postgenomic phase seem to come from the study of genomic variation. 26 refs.

  8. A portable fluorescence spectroscopy imaging system for automated root phenotyping in soil cores in the field

    PubMed Central

    Wasson, Anton; Bischof, Leanne; Zwart, Alec; Watt, Michelle

    2016-01-01

    Root architecture traits are a target for pre-breeders. Incorporation of root architecture traits into new cultivars requires phenotyping. It is attractive to rapidly and directly phenotype root architecture in the field, avoiding laboratory studies that may not translate to the field. A combination of soil coring with a hydraulic push press and manual core-break counting can directly phenotype root architecture traits of depth and distribution in the field through to grain development, but large teams of people are required and labour costs are high with this method. We developed a portable fluorescence imaging system (BlueBox) to automate root counting in soil cores with image analysis software directly in the field. The lighting system was optimized to produce high-contrast images of roots emerging from soil cores. The correlation of the measurements with the root length density of the soil cores exceeded the correlation achieved by human operator measurements (R 2=0.68 versus 0.57, respectively). A BlueBox-equipped team processed 4.3 cores/hour/person, compared with 3.7 cores/hour/person for the manual method. The portable, automated in-field root architecture phenotyping system was 16% more labour efficient, 19% more accurate, and 12% cheaper than manual conventional coring, and presents an opportunity to directly phenotype root architecture in the field as part of pre-breeding programs. The platform has wide possibilities to capture more information about root health and other root traits in the field. PMID:26826219

  9. Effect of elevated temperature and enhanced drainage on carbon balance of tundra microcosms

    SciTech Connect

    Johnson, L.C.; Shaver, G.R.; Giblin, A.E.; Nadelhoffer, K.J.; Rastetter, E.B.; Laundre, J.A.; Murray, G.L. )

    1994-06-01

    We tested effects of temperature and drainage on C balance of intact soil and tundra vegetation over a simulated season. We measured C budgets (CO[sub 2] and CH[sub 4] emissions and dissolved CO[sub 2], CH[sub 4] and DOC in soil water) of Eriophorum vaginatum tussock and moss-dominated interussock microcosms at two temperatures (7[degrees] and 15[degrees]C, season maxima) and two water regimes (saturated and field capacity). Net ecosystem productivity was strongly affected by water. Averaged over temperature and microhabitat, the rate of net C loss from microcosms at field capacity was [approximately]5[times] the saturated microcosms. Only saturated, 15[degrees]C tussock microcosms showed net C storage integrated over the whole season. Ecosystem respiration was strongly affected by water and less by temperature. Respiration rates at field capacity were [approximately]2[times] the rates under saturated conditions. Elevated temperature caused a 1.5[times] increase. Other C components were <20% of gaseous CO[sub 2] losses. Results indicate that C in tundra exists in a fragile balance between storage and release that is controlled mainly by water regime.

  10. MODELING EUTROPHICATION KINETICS IN RESERVOIR MICROCOSMS

    EPA Science Inventory

    This study addresses the question of how a general seasonal eutrophication model, WASP5, can handle daily phytoplankton and nutrient dynamics in perturbed microcosms for 1-to 2-week periods of time. It is intended to explore both the interpretative and the predictive capabilities...

  11. Depth-resolved microbial community analyses in two contrasting soil cores contaminated by antimony and arsenic.

    PubMed

    Xiao, Enzong; Krumins, Valdis; Xiao, Tangfu; Dong, Yiran; Tang, Song; Ning, Zengping; Huang, Zhengyu; Sun, Weimin

    2017-02-01

    Investigation of microbial communities of soils contaminated by antimony (Sb) and arsenic (As) is necessary to obtain knowledge for their bioremediation. However, little is known about the depth profiles of microbial community composition and structure in Sb and As contaminated soils. Our previous studies have suggested that historical factors (i.e., soil and sediment) play important roles in governing microbial community structure and composition. Here, we selected two different types of soil (flooded paddy soil versus dry corn field soil) with co-contamination of Sb and As to study interactions between these metalloids, geochemical parameters and the soil microbiota as well as microbial metabolism in response to Sb and As contamination. Comprehensive geochemical analyses and 16S rRNA amplicon sequencing were used to shed light on the interactions of the microbial communities with their environments. A wide diversity of taxonomical groups was present in both soil cores, and many were significantly correlated with geochemical parameters. Canonical correspondence analysis (CCA) and co-occurrence networks further elucidated the impact of geochemical parameters (including Sb and As contamination fractions and sulfate, TOC, Eh, and pH) on vertical distribution of soil microbial communities. Metagenomes predicted from the 16S data using PICRUSt included arsenic metabolism genes such as arsenate reductase (ArsC), arsenite oxidase small subunit (AoxA and AoxB), and arsenite transporter (ArsA and ACR3). In addition, predicted abundances of arsenate reductase (ArsC) and arsenite oxidase (AoxA and AoxB) genes were significantly correlated with Sb contamination fractions, These results suggest potential As biogeochemical cycling in both soil cores and potentially dynamic Sb biogeochemical cycling as well.

  12. Cometabolic biodegradation of trichloroethylene in microcosms

    USGS Publications Warehouse

    Kane, Allen C.; Wilson, Timothy P.; Fischer, Jeffrey M.

    1997-01-01

    Laboratory microcosms were used to determine the concentrations of oxygen (O2) and methane (CH4) that optimize trichloroethylene (TCE) biodegradation in sediment and ground-water samples from a TCE-contaminated aquifer at Picatinny Arsenal, Morris County, New Jersey. The mechanism for degradation is the cometabolic activity of methanotrophic bacteria. The laboratory data will be used to support a field study designed to demonstrate the effectiveness of combining air sparging with cometabolic degradation of TCE for the purpose of aquifer remediation. Microcosms were constructed in autoclaved 250-mL (milliliter) amber glass bottles with valves for repeated headspace sampling. Equal volumes (25 mL) of sediment and ground water, collected from a depth of 40 feet, were added. TCE was added to attain initial aqueous concentrations equal to the field level of 1,400 mu g/L (micrograms per liter). Nine microcosms were constructed with initial headspace O2 concentrations of 5%, 10%, or 14% and CH4 concentrations of 0.5%, 3%, or 5%, with nitrogen making up the balance. Sterile controls, controls without CH4, and controls without sediment were also constructed. A 4-mL gas sample was removed periodically and TCE, O2 , CH4 , and carbon dioxide (CO2) concentrations were measured by using gas chromatography. As biodegradation proceeded, the decrease in O2, CH4 , and TCE concentrations and the production of CO2 were monitored. An initial acclimation period of at least 100 days was observed in those microcosms in which significant microbial activity occurred, as determined from decreases in O2 and CH4 concentrations and an increase in CO2 content. Degradation of TCE occurred with O2 concentrations of 2.7 to 8.7% and CH4 concentrations of 0.5 to 3.5%. Microcosms that initially contained 10% O2 and 3% CH4 showed the greatest microbial activity and the greatest amount of TCE degradation. The greatest rates of TCE degradation occurred when O2 and CH4 headspace concentrations reached

  13. Transport of bromide measured by soil coring, suction plates, and lysimeters under transient flow conditions.

    NASA Astrophysics Data System (ADS)

    Kasteel, R.; Pütz, Th.; Vereecken, H.

    2003-04-01

    Lysimeter studies are one step within the registration procedure of pesticides. Flow and transport in these free-draining lysimeters do not reflect the field situation mainly because of the occurence of a zone of local saturation at the lower boundary (seepage face). The objective of this study is to evaluate the impact of flow and transport behaviour of bromide detected with different measuring devices (lysimeters, suction plates, and soil coring) by comparing experimental results with numerical simulations in heterogeneous flow domains. We applied bromide as a small pulse to the bare soil surface (Orthic Luvisol) of the three devices and the displacement of bromide was regurlarly sampled for three years under natural wheather conditions. Based on the mean breakthrough curves we observe experimentally that lysimeters have a lower effective pore-water velocity and exhibit more solute spreading resulting in a larger dispersivity than the suction plates. This can be ascribed to the artefact of the lower boundary. We performed numerical transport simulations in 2-D heterogeneous flow fields (scaling approach) choosing appropriate boundary conditions for the various devices. The simulations allow to follow the temporal evolution of flow and transport processes in the various devices and to gain additional process understanding. We conclude that the model is essentially capable to reproduce the main experimental findings only if we account for the spatial correlation structure of the hydraulic properties, i.e. soil heterogeneity.

  14. Measurement of effective air diffusion coefficients for trichloroethene in undisturbed soil cores.

    PubMed

    Bartelt-Hunt, Shannon L; Smith, James A

    2002-06-01

    In this study, we measure effective diffusion coefficients for trichloroethene in undisturbed soil samples taken from Picatinny Arsenal, New Jersey. The measured effective diffusion coefficients ranged from 0.0053 to 0.0609 cm2/s over a range of air-filled porosity of 0.23-0.49. The experimental data were compared to several previously published relations that predict diffusion coefficients as a function of air-filled porosity and porosity. A multiple linear regression analysis was developed to determine if a modification of the exponents in Millington's [Science 130 (1959) 100] relation would better fit the experimental data. The literature relations appeared to generally underpredict the effective diffusion coefficient for the soil cores studied in this work. Inclusion of a particle-size distribution parameter, d10, did not significantly improve the fit of the linear regression equation. The effective diffusion coefficient and porosity data were used to recalculate estimates of diffusive flux through the subsurface made in a previous study performed at the field site. It was determined that the method of calculation used in the previous study resulted in an underprediction of diffusive flux from the subsurface. We conclude that although Millington's [Science 130 (1959) 100] relation works well to predict effective diffusion coefficients in homogeneous soils with relatively uniform particle-size distributions, it may be inaccurate for many natural soils with heterogeneous structure and/or non-uniform particle-size distributions.

  15. Measurement of effective air diffusion coefficients for trichloroethene in undisturbed soil cores

    NASA Astrophysics Data System (ADS)

    Bartelt-Hunt, Shannon L.; Smith, James A.

    2002-06-01

    In this study, we measure effective diffusion coefficients for trichloroethene in undisturbed soil samples taken from Picatinny Arsenal, New Jersey. The measured effective diffusion coefficients ranged from 0.0053 to 0.0609 cm 2/s over a range of air-filled porosity of 0.23-0.49. The experimental data were compared to several previously published relations that predict diffusion coefficients as a function of air-filled porosity and porosity. A multiple linear regression analysis was developed to determine if a modification of the exponents in Millington's [Science 130 (1959) 100] relation would better fit the experimental data. The literature relations appeared to generally underpredict the effective diffusion coefficient for the soil cores studied in this work. Inclusion of a particle-size distribution parameter, d10, did not significantly improve the fit of the linear regression equation. The effective diffusion coefficient and porosity data were used to recalculate estimates of diffusive flux through the subsurface made in a previous study performed at the field site. It was determined that the method of calculation used in the previous study resulted in an underprediction of diffusive flux from the subsurface. We conclude that although Millington's [Science 130 (1959) 100] relation works well to predict effective diffusion coefficients in homogeneous soils with relatively uniform particle-size distributions, it may be inaccurate for many natural soils with heterogeneous structure and/or non-uniform particle-size distributions.

  16. Arbuscular-mycorrhizal networks inhibit Eucalyptus tetrodonta seedlings in rain forest soil microcosms.

    PubMed

    Janos, David P; Scott, John; Aristizábal, Catalina; Bowman, David M J S

    2013-01-01

    Eucalyptus tetrodonta, a co-dominant tree species of tropical, northern Australian savannas, does not invade adjacent monsoon rain forest unless the forest is burnt intensely. Such facilitation by fire of seedling establishment is known as the "ashbed effect." Because the ashbed effect might involve disruption of common mycorrhizal networks, we hypothesized that in the absence of fire, intact rain forest arbuscular mycorrhizal (AM) networks inhibit E. tetrodonta seedlings. Although arbuscular mycorrhizas predominate in the rain forest, common tree species of the northern Australian savannas (including adult E. tetrodonta) host ectomycorrhizas. To test our hypothesis, we grew E. tetrodonta and Ceiba pentandra (an AM-responsive species used to confirm treatments) separately in microcosms of ambient or methyl-bromide fumigated rain forest soil with or without severing potential mycorrhizal fungus connections to an AM nurse plant, Litsea glutinosa. As expected, C. pentandra formed mycorrhizas in all treatments but had the most root colonization and grew fastest in ambient soil. E. tetrodonta seedlings also formed AM in all treatments, but severing hyphae in fumigated soil produced the least colonization and the best growth. Three of ten E. tetrodonta seedlings in ambient soil with intact network hyphae died. Because foliar chlorosis was symptomatic of iron deficiency, after 130 days we began to fertilize half the E. tetrodonta seedlings in ambient soil with an iron solution. Iron fertilization completely remedied chlorosis and stimulated leaf growth. Our microcosm results suggest that in intact rain forest, common AM networks mediate belowground competition and AM fungi may exacerbate iron deficiency, thereby enhancing resistance to E. tetrodonta invasion. Common AM networks-previously unrecognized as contributors to the ashbed effect-probably help to maintain the rain forest-savanna boundary.

  17. Coaxial atomizer liquid intact lengths

    NASA Technical Reports Server (NTRS)

    Eroglu, Hasan; Chigier, Norman; Farago, Zoltan

    1991-01-01

    Average intact lengths of round liquid jets generated by airblast coaxial atomizer were measured from over 1500 photographs. The intact lengths were studied over a jet Reynolds number range of 18,000 and Weber number range of 260. Results are presented for two different nozzle geometries. The intact lengths were found to be strongly dependent on Re and We numbers. An empirical equation was derived as a function of these parameters. A comparison of the intact lengths for round jets and flat sheets shows that round jets generate shorter intact lengths.

  18. (Photosynthesis in intact plants)

    SciTech Connect

    Not Available

    1990-01-01

    Progress in the two years since the last renewal application has been excellent. We have made substantial contributions on both main fronts of the projects, and are particularly happy with the progress of our research on intact plants. The approach of basing our field work on a sound foundation of laboratory studies has enabled is to use methods which provide unambiguous assays of well characterized reactions. We have also made excellent progress in several laboratory studies which will have direct applications in future field work, and have introduced to the laboratory a range of molecular genetics techniques which will allow us to explore new options in the attempt to understand function at the level of molecular structure.

  19. Effect of organic loading on nitrification and denitrification in a marine sediment microcosm

    USGS Publications Warehouse

    Caffrey, J.M.; Sloth, N.P.; Kaspar, H.F.; Blackburn, T.H.

    1993-01-01

    The effects of organic additions on nitrification and denitrification were examined in sediment microcosms. The organic material, heat killed yeast, had a C/N ratio of 7.5 and was added to sieved, homogenized sediments. Four treatments were compared: no addition (control, 30 g dry weight (dw) m-2 mixed throughout the 10 cm sediment column (30 M), 100 g dw m-2 mixed throughout sediments (100M), and 100 g dw m-2 mixed into top 1 cm (100S). After the microcosms had been established for 7-11 days, depth of O2 penetration, sediment-water fluxes and nitrification rates were measured. Nitrification rates were measured using three different techniques: N-serve and acetylene inhibition in intact cores, and nitrification potentials in slurries. Increased organic additions decreased O2 penetration from 2.7 to 0.2 mm while increasing both O2 consumption, from 30 to 70 mmol O2 m-2 d-1, and NO3- flux into sediments. Nitrification rates in intact cores were similar for the two methods. Highest rates occurred in the 30 M treatment, while the lowest rate was measured in the 100S treatment. Total denitrification rates (estimated from nitrification and nitrate fluxes) increased with increased organic addition, because of the high concentrations of NO3- (40 ??M) in the overlying water. The ratio of nitrification: denitrification was used as an indication of the importance of nitrification as the NO3- supply for denitrification. This ratio decreased from 1.55 to 0.05 with increased organic addition.

  20. The physics of intact capture

    NASA Technical Reports Server (NTRS)

    Tsou, Peter; Griffiths, D. J.; Albee, A. L.

    1994-01-01

    The ability to capture projectiles intact at hypervelocities in underdense media open a new area of study in physics. Underdense material behaves markedly different than solid, liquid, or gas upon hypervelocity impact. This new phenomenon enables applications in science that would either not be possible or would be very costly by other means. This phenomenon has been fully demonstrated in the laboratory and validated in space. Even more interesting is the fact that this hypervelocity intact capture was accomplished passively. A better understanding of the physics of intact capture will lead to improvements in intact capture. A collection of physical observations of this phenomenon is presented here.

  1. Space research with intact organisms

    NASA Technical Reports Server (NTRS)

    Phillips, Robert W.; Haddy, Francis J.

    1992-01-01

    Effects of space exposure on intact organisms are briefly reviewed, and examples of future experiments that might provide new information on the role of gravity in the evolution of life are suggested. It is noted that long term experiments with intact plant and animals for studying gravitational thresholds will provide important new insights.

  2. Determination of uranium isotopes in soil core samples collected on the JCO grounds after the criticality accident.

    PubMed

    Yoshida, S; Muramatsu, Y; Tagami, K

    2001-11-01

    To evaluate the impact of the 1999 criticality accident in Tokai-mura on the U isotope composition in soils, U isotopes (235U and 238U) were determined with inductively coupled plasma-mass spectrometry (ICP-MS) for soil core samples collected on the JCO grounds after the accident. The 235U/238U ratios were higher than the natural ratio in most samples. The highest ratio observed was 0.0262. Although vertical profiles of the 235U/238U ratio differed among the soil cores, the ratios tended to be high at the surface and decreased with depth. The U concentration also changed with depth. The percentages of 235U in the excess U, estimated from the positive correlation between U concentration and the 235U/238U ratio in soil samples, were less than 4% by mass (mostly 1-3%) and were much lower than the enrichment of the U used in the uranium conversion building at the time of the criticality accident (18.8%). These findings indicate that enriched U had been released before the criticality accident during the U processing at JCO in connection with the reconversion of light water reactor fuel. Since the range of the U concentrations found was comparable to the range of uncontaminated Japanese surface soils, the amount of U added to the soil was judged negligible from a radiation protection viewpoint.

  3. Reduction of nitrate in aquifer microcosms by carbon additions

    USGS Publications Warehouse

    Obenhuber, Donald C.; Lowrance , Richard

    1991-01-01

    Aquifer microcosms were used to examine the effects of NO−3 and C amendments on groundwater from the Claiborne aquifer. Nitrate concentrations of 12.17 mg L−1 in aquifer microcosms were reduced 0.92%/d to 5.84 mg L−1 by the addition of 10 mg C L−1 for 35 d. Nitrate disappearance correlated with increases in number of denitrifiers and dissolved N2O concentration and decreases in dissolved oxygen, suggesting biological denitrification. Nitrate/chloride ratios decreased in microcosms with 10 mg C L−1 added and then increased when the C addition was removed. Carbon additions of 0.4 mg C L−1 had no effect on the microbial or chemical properties of the microcosms. Nitrous oxide levels in wells sampling the Claiborne aquifer showed an increase with depth, indicating N2O production within the aquifer. Microcosms are useful tools to examine biological transformations of chemical contaminants in unconsolidated aquifer material. The remediation of NO−3 contaminated aquifers by organic infusion is possible and appears to be a function of microbial denitrification.

  4. Long Term Thawing Experiments on Intact Cores of Arctic Mineral Cryosol: Implications for Greenhouse Gas Feedbacks from Global Warming

    NASA Astrophysics Data System (ADS)

    Onstott, T. C.; Stackhouse, B. T.; Lau, C. Y. M.; Whyte, L. G.; Pfiffner, S. M.; Vishnivetskaya, T. A.

    2015-12-01

    Mineral cryosols comprise >87% of Arctic tundra. Much attention has focused on high-organic carbon cryosols and how they will respond to global warming. The biogeochemical processes related to the greenhouse gas release from mineral cryosols, however, have not been fully explored. To this end, seventeen intact cores of active layer and underlying permafrost of mineral cryosol from Axel Heiberg Island, Nunavut, Canada, were subjected to 85 weeks of thawing at 4.5°C under various treatment regimes. The fluxes of CO2 and CH4 across the atmosphere-soil boundary and vertical profiles of the gas and water chemistry and the metagenomes were determined. The flux measurements were compared to those of microcosms and field measurements. The main conclusions were as follows: 1) CO2 emission rates from the intact cores do not behave in the typical fast to slow carbon pool fashion that typify microcosm experiments. The CO2 emission rates from the intact cores were much slower than those from the microcosm initially, but steadily increased with time, overtaking and then exceeding microcosm release rates after one year. 2) The increased CO2 flux from thawing permafrost could not be distinguished from that of control cores until after a full year of thawing. 3) Atmospheric CH4 oxidation was present in all intact cores regardless of whether they are water saturated or not, but after one year it had diminished to the point of being negligible. Over that same time the period the metagenomic data recorded a significant decline in the proportion of high-affinity methanotrophs. 4) Thaw slumps in the cores temporarily increased the CH4 oxidation and the CO2 emission rates. 5) The microbial community structures varied significantly by depth with methanotrophs being more abundant in above 35 cm depth than below 35 cm depth. 6) Other than the diminishment of Type II methanotrophs, the microbial community structure varied little after one week of thawing, nor even after 18 months of thaw.

  5. Effectiveness of intact capture media

    SciTech Connect

    Tsou, P.; Aubert, J.; Brownlee, D.; Hrubesh, L.; Williams, J.; Albee, A.

    1989-01-01

    The possibility of capturing cosmic dust at hypervelocity has been demonstrated in the laboratory and in the unintended Solar Max spacecraft. This technology will enable a comet coma sample return mission and be important for the earth orbital cosmic dust collection mission, i.e., the Space Station Cosmic Dust Collection Facility. Since the only controllable factor in an intact capture of cosmic dust is the capturing medium, characterizing the effectiveness and properties of available capture media would be very important in the development of the technique for capturing hypervelocity cosmic dust intact. We have evaluated various capture underdense media for the relative effectiveness for intact capture. 2 refs., 2 figs.

  6. PCB dechlorination enhancement in Anacostia River sediment microcosms.

    PubMed

    Krumins, Valdis; Park, Joong-Wook; Son, Eun-Kyeu; Rodenburg, Lisa A; Kerkhof, Lee J; Häggblom, Max M; Fennell, Donna E

    2009-10-01

    In situ treatment of PCB contaminated sediments via microbial dechlorination is a promising alternative to dredging, which may be reserved for only the most contaminated areas. Reductive dechlorination of low levels of weathered PCB mixtures typical of urban environments may occur at slow rates. Here, we report that biostimulation and bioaugmentation enhanced dechlorination of low concentration (2.1 mg PCBs/kg dry weight) historical PCBs in microcosms prepared with Anacostia River, Washington, DC, sediment. Treatments included electron donors butyrate, lactate, propionate and acetate (1 mM each); alternate halogenated electron acceptors (haloprimers) tetrachlorobenzene (TeCB, 25 microM), pentachloronitrobenzene (PCNB, 25 microM), or 2,3,4,5,6-PCB (PCB116, 2.0 microM); and/or bioaugmentation with a culture containing Dehalococcoides ethenogenes strain 195 (3 x 10(6)cells/mL). Dechlorination rates were enhanced in microcosms receiving bioaugmentation, PCNB and PCNB plus bioaugmentation, compared to other treatments. Microcosm subcultures generated after 415 days and spiked with PCB116 showed sustained capacity for dechlorination of PCB116 in PCNB, PCNB plus bioaugmentation, and TeCB treatments, relative to other treatments. Analysis of Chloroflexi 16S rRNA genes showed that TeCB and PCNB increased native Dehalococcoides spp. from the Pinellas subgroup; however this increase was correlated to enhanced dechlorination of low concentration weathered PCBs only in PCNB-amended microcosms. D. ethenogenes strain 195 was detected only in bioaugmented microcosms and decreased over 281 days. Bioaugmentation with D. ethenogenes strain 195 increased PCB dechlorination rates initially, but enhanced capacity for dechlorination of a model congener, PCB116, after 415 days occurred only in microcosms with enhanced native Dehalococcoides spp.

  7. Soil coring at multiple field environments can directly quantify variation in deep root traits to select wheat genotypes for breeding

    PubMed Central

    Wasson, A. P.; Rebetzke, G. J.; Kirkegaard, J. A.; Christopher, J.; Richards, R. A.; Watt, M.

    2014-01-01

    We aim to incorporate deep root traits into future wheat varieties to increase access to stored soil water during grain development, which is twice as valuable for yield as water captured at younger stages. Most root phenotyping efforts have been indirect studies in the laboratory, at young plant stages, or using indirect shoot measures. Here, soil coring to 2 m depth was used across three field environments to directly phenotype deep root traits on grain development (depth, descent rate, density, length, and distribution). Shoot phenotypes at coring included canopy temperature depression, chlorophyll reflectance, and green leaf scoring, with developmental stage, biomass, and yield. Current varieties, and genotypes with breeding histories and plant architectures expected to promote deep roots, were used to maximize identification of variation due to genetics. Variation was observed for deep root traits (e.g. 111.4–178.5cm (60%) for depth; 0.09–0.22cm/°C day (144%) for descent rate) using soil coring in the field environments. There was significant variation for root traits between sites, and variation in the relative performance of genotypes between sites. However, genotypes were identified that performed consistently well or poorly at both sites. Furthermore, high-performing genotypes were statistically superior in root traits than low-performing genotypes or commercial varieties. There was a weak but significant negative correlation between green leaf score (–0.5), CTD (0.45), and rooting depth and a positive correlation for chlorophyll reflectance (0.32). Shoot phenotypes did not predict other root traits. This study suggests that field coring can directly identify variation in deep root traits to speed up selection of genotypes for breeding programmes. PMID:24963000

  8. In-situ 1-D and 2-D mapping of soil core and rock samples using the LIBS long spark

    SciTech Connect

    Rodolfa, C. T.; Cremers, D. A.; Ebinger, M. H.

    2004-01-01

    LIBS is being developed for stand-off interrogation of samples up to 20 m from a lander or rover. Stand-off capability is important to access targets not conveniently located for in-situ analysis. On the other hand, in-situ techniques are still important and are being developed for future missions such as MSL. Retrieved samples may consist of loose soils, subsurface soil cores, drilled rock cores, and ice cores. For these sample types, it is possible to employ LIBS analysis and take advantage of LIBS capabilities. These include: (1) rapid analysis, (2) good detection sensitivity for many elements, (3) good spatial resolution (3-100 microns), and (4) ability to clean a surface prior to analysis. Using LIBS, it is possible to perform a 1-dimensional analysis, for example, determining element concentrations along a soil core, or a 2-dimensional mapping of the sample surface using a unique 'long' spark. Two-dimensional sampling has been developed previously by focusing the laser pulses as small spots on the sample and then moving the sample a short distance between sampling locations. Although demonstrated, this method is time consuming, requiring a large number of shots to span even a small region (for 3 micron resolution, an area 600 x 480 microns sampled in {approx} 30 min using a 20 Hz laser). For a spacecraft instrument, the ability to more rapidly prepare a 2D elemental spatial map will be desirable. Here they discuss the use of LIBS for sampling along a core in 1D (detection of carbon) and for 2D mapping of a rock face.

  9. Soil coring at multiple field environments can directly quantify variation in deep root traits to select wheat genotypes for breeding.

    PubMed

    Wasson, A P; Rebetzke, G J; Kirkegaard, J A; Christopher, J; Richards, R A; Watt, M

    2014-11-01

    We aim to incorporate deep root traits into future wheat varieties to increase access to stored soil water during grain development, which is twice as valuable for yield as water captured at younger stages. Most root phenotyping efforts have been indirect studies in the laboratory, at young plant stages, or using indirect shoot measures. Here, soil coring to 2 m depth was used across three field environments to directly phenotype deep root traits on grain development (depth, descent rate, density, length, and distribution). Shoot phenotypes at coring included canopy temperature depression, chlorophyll reflectance, and green leaf scoring, with developmental stage, biomass, and yield. Current varieties, and genotypes with breeding histories and plant architectures expected to promote deep roots, were used to maximize identification of variation due to genetics. Variation was observed for deep root traits (e.g. 111.4-178.5cm (60%) for depth; 0.09-0.22cm/°C day (144%) for descent rate) using soil coring in the field environments. There was significant variation for root traits between sites, and variation in the relative performance of genotypes between sites. However, genotypes were identified that performed consistently well or poorly at both sites. Furthermore, high-performing genotypes were statistically superior in root traits than low-performing genotypes or commercial varieties. There was a weak but significant negative correlation between green leaf score (-0.5), CTD (0.45), and rooting depth and a positive correlation for chlorophyll reflectance (0.32). Shoot phenotypes did not predict other root traits. This study suggests that field coring can directly identify variation in deep root traits to speed up selection of genotypes for breeding programmes.

  10. Metal binding in soil cores and sediments in the vicinity of a dammed agricultural and industrial watershed.

    PubMed

    Kanbar, Hussein Jaafar; Hanna, Nour; El Samrani, Antoine G; Kazpard, Véronique; Kobaissi, Ahmad; Harb, Nafez; Amacha, Nabil

    2014-12-01

    The environment is witnessing a downgrade caused by the amelioration of the industrial and agricultural sectors, namely, soil and sediment compartments. For those reasons, a comparative study was done between soil cores and sediments taken from two locations in the Qaraaoun reservoir, Lebanon. The soil cores were partitioned into several layers. Each layer was analyzed for several physicochemical parameters, such as functional groups, particle size distribution, ζ-potential, texture, pH, electric conductivity, total dissolved solids, organic matter, cation exchange capacity, active and total calcareous, available sodium and potassium, and metal content (cadmium, copper, and lead). The metal content of each site was linked to soil composition and characteristics. The two sites showed distinguishable characteristics for features such as organic matter, pH, mineral fraction, calcareous, and metal content. The samples taken toward the south site (Q1), though contain lower organic matter than the other but are more calcareous, showed higher metal content in comparison to the other site (Q2) (average metal content of Q1 > Q2; for Cd 3.8 > 1.8 mg/kg, Cu 28.6 > 21.9 mg/kg, Pb 26.7 > 19 mg/kg). However, the metal content in this study did not correlate as much to the organic matter; rather, it was influenced by the location of the samples with respect to the dam, the reservoir's hydrodynamics, the calcareous nature of the soil, and the variation of the industrial and agricultural influence on each site.

  11. Metagenome and metatranscriptome data for Rifle CMT-03 laboratory microcosm experiment completed in April 2014

    DOE Data Explorer

    Jewell, Talia [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Karaoz, Ulas [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Bill, Markus [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Chakraborty, Romy [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Brodie, Eoin L [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Williams, Kenneth Hurst [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Beller, Harry R [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2014-04-01

    Sediment samples were collected during installation of monitoring borehole CMT-03. Microcosms were constructed and inoculated under anerobic conditions with these sediments and anaerobic Rifle artificial groundwater. Microcosm metagenomes and metatranscriptomes were sampled every 5 days for a period of 20 days. The dataset gives gene-level annotations, binning, metagenomic and metatranscriptomic coverages for these microcosms.

  12. Influence of water table on carbon dioxide, carbon monoxide, and methane fluxes from taiga bog microcosms

    SciTech Connect

    Funk, D.W.; Pullmann, E.R.; Peterson, K.M.

    1994-09-01

    Hydrological changes, particularly alterations in water table level, may largely overshadow the more direct effects of global temperature increase upon carbon cycling in arctic and subarctic wetlands. Frozen cores (n=40) of intact soils and vegetation were collected from a bog near Fairbanks, Alaska, and fluxes of CO{sub 2}, CH{sub 4}, and Co in response to water table variation were studied under controlled conditions in the Duke University phytotron. Core microcosms thawed to a 20-cm depth over 30 days under a 20 hour photoperiod with a day/night temperature regime of 20/10{degrees}C. After 30 days the water table in 20 microcosms was decreased from the soil surface to -15 cm and maintained at the soil surface in 20 control cores. Outward fluxes of CO{sub 2} (9-16 g m{sup -2}d{sup -1}) and CO (3-4 mg m{sup -2}d{sup -1}) were greatest during early thaw and decreased to near zero for both gases before the water table treatment started. Lower water table tripled CO{sub 2} flux to the atmosphere when compared with control cores. Carbon monoxide was emitted at low rates from high water table cores and consumed by low water table cores. Methane fluxes were low (<1 mg m{sup -2}d{sup -1}) in all cores during thaw. High water table cores increased CH{sub 4} flux to 8-9 mg m{sup -2}d{sup -1} over 70 days and remained high relative to the low water table cores (<0.74 mg m{sup -2}d{sup -1}). Although drying of wetland taiga soils may decrease CH{sub 4} emissions to the atmosphere, the associated increase in CO{sub 2} due to aerobic respiration will likely increase the global warming potential of gas emissions from these soils. 43 refs., 4 figs.

  13. Comparison of laboratory batch and flow-through microcosm bioassays.

    PubMed

    Clément, Bernard J P; Delhaye, Hélène L; Triffault-Bouchet, Gaëlle G

    2014-10-01

    Since 1997, we have been developing a protocol for ecotoxicological bioassays in 2-L laboratory microcosms and have applied it to the study of various pollutants and ecotoxicological risk assessment scenarios in the area of urban facilities and transport infrastructures. The effects on five different organisms (micro-algae, duckweeds, daphnids, amphipods, chironomids) are assessed using biological responses such as growth, emergence (chironomids), reproduction (daphnids) and survival, with a duration of exposure of 3 weeks. This bioassay has mainly been used as a batch bioassay, i.e., the water was not renewed during the test. A flow-through microcosm bioassay has been developed recently, with the assumption that conditions for the biota should be improved, variability reduced, and the range of exposure patterns enlarged (e.g., the possibility of maintaining constant exposure in the water column). This paper compares the results obtained in batch and flow-through microcosm bioassays, using cadmium as a model toxicant. As expected, the stabilization of physico-chemical parameters, increased organism fitness and reduced variability were observed in the flow-through microcosm bioassay.

  14. ANAEROBIC BIODEGRADATION OF ALKYLBENZENES IN LABORATORY MICROCOSMS REPRESENTING AMBIENT CONDITIONS

    EPA Science Inventory

    A microcosm study was performed to document the anaerobic biodegradation of benzene, toluene, ethylbenzene, m- xylene, and/or o-xylene in petroleum-contaminated aquifer sediment from sites in Michigan (MI) and North Carolina (NC) and relate the results to previous field investiga...

  15. METRICS OF PERFORMANCE FOR THE SABRE MICROCOSM STUDY (ABSTRACT ONLY)

    EPA Science Inventory

    The SABRE (Source Area BioREmediation) project will evaluate accelerated anaerobic bioremediation of chlorinated solvents in areas of high concentration, such as DNAPL source areas. In preparation for a field scale pilot test, a laboratory microcosm study was conducted to provide...

  16. CHARACTERIZING THE MICROBIAL COMMUNITY IN SABRE MICROCOSM STUDIES (ABSTRACT ONLY)

    EPA Science Inventory

    The SABRE (Source Area BioREmediation) project will evaluate accelerated anaerobic bioremediation of chlorinated solvents in areas of high concentration, such as DNAPL source areas. In preparation for a field scale pilot test, laboratory microcosm and column studies were conducte...

  17. Intact capture of hypervelocity particles

    NASA Technical Reports Server (NTRS)

    Tsou, P.; Brownlee, D. E.; Albee, A. L.

    1986-01-01

    Knowledge of the phase, structure, and crystallography of cosmic particles, as well as their elemental and isotopic compositions, would be very valuable information toward understanding the nature of our solar system. This information can be obtained from the intact capture of large mineral grains of cosmic particles from hypervelocity impacts. Hypervelocity experiments of intact capture in underdense media have indicated realistic potential in this endeaver. The recovery of the thermal blankets and louvers from the Solar Max spacecraft have independently verified this potential in the unintended capture of cosmic materials from hypervelocity impacts. Passive underdense media will permit relatively simple and inexpensive missions to capture cosmic particles intact, either by going to a planetary body or by waiting for the particles to come to the Shuttle or the Space Station. Experiments to explore the potential of using various underdense media for an intact comet sample capture up to 6.7 km/s were performed at NASA Ames Research Center Vertical Gun Range. Explorative hypervelocity experiments up to 7.9 km/s were also made at the Ernst Mach Institute. These experiments have proven that capturing intact particles at hypervelocity impacts is definitely possible. Further research is being conducted to achieve higher capture ratios at even higher hypervelocities for even smaller projectiles.

  18. Intact capture of hypervelocity particles

    NASA Astrophysics Data System (ADS)

    Tsou, P.; Brownlee, D. E.; Albee, A. L.

    Knowledge of the phase, structure, and crystallography of cosmic particles, as well as their elemental and isotopic compositions, would be very valuable information toward understanding the nature of our solar system. This information can be obtained from the intact capture of large mineral grains of cosmic particles from hypervelocity impacts. Hypervelocity experiments of intact capture in underdense media have indicated realistic potential in this endeaver. The recovery of the thermal blankets and louvers from the Solar Max spacecraft have independently verified this potential in the unintended capture of cosmic materials from hypervelocity impacts. Passive underdense media will permit relatively simple and inexpensive missions to capture cosmic particles intact, either by going to a planetary body or by waiting for the particles to come to the Shuttle or the Space Station. Experiments to explore the potential of using various underdense media for an intact comet sample capture up to 6.7 km/s were performed at NASA Ames Research Center Vertical Gun Range. Explorative hypervelocity experiments up to 7.9 km/s were also made at the Ernst Mach Institute. These experiments have proven that capturing intact particles at hypervelocity impacts is definitely possible. Further research is being conducted to achieve higher capture ratios at even higher hypervelocities for even smaller projectiles.

  19. Intact capture of cosmic dust

    NASA Technical Reports Server (NTRS)

    Tsou, P.

    1991-01-01

    The focus of this development effort is to capture dust particles at hypervelocities intact and unmelted in order to preserve volatile organics. At the same time, the capture process must minimize any organic elemental or compound contamination to prevent any compromise of exobiological analyses. Inorganic silicate aerogel has been developed as a successful capture medium to satisfy both requirements of intact capture and minimal organic contamination. Up to 6 km/s, silicate projectiles from a few microns up to 100 microns have been captured intact without any melting and with minimal loss of mass. Carbon in silicate aerogel can be reduced to less than 1 part in 1000 and hydrogen 3 parts in 1000 when baked in air. Under controlled inert gas environments, additional hydrocarbon reduction can be achieved.

  20. Bioaccumulation and toxicity of copper in outdoor freshwater microcosms.

    PubMed

    Hoang, Tham C; Pryor, Rachel L; Rand, Gary M; Frakes, Robert A

    2011-05-01

    This study characterizes the effects of copper (Cu) on Florida apple snails (Pomacea paludosa) and mosquito fish (Gambusia affinis) using a replicated outdoor microcosm design. Soils used in this study were collected from two Cu-enriched citrus agricultural sites in South Florida (Agler property (AGLR) in St. Lucie County and Sunrise Boys property (SRB) in Palm Beach County) and a reference site (Equus property) in St. Lucie County. The study included a 5-week aging phase, an 11 month exposure phase, and a 3 month post-treatment (exposure) phase. The aging phase was initiated by flooding agricultural soils with rainwater in 4 m(3) fiberglass microcosm tanks. Introducing juvenile apple snails (≤7 d old) and mosquito fish (2-3 cm) into the microcosm tanks initiated the exposure phase. Survival, growth, and reproduction of apple snails and fish, and Cu uptake in apple snails, fish, and periphyton were determined in this study. Water chemistry (e.g., dissolved Cu concentration, dissolved organic carbon and dissolved oxygen concentrations, pH, hardness, alkalinity, etc.) was measured daily or weekly during the study. Initial soil Cu concentrations in Equus, SRB, and AGLR microcosms were 7, 55, and 99 mg/kg dw, respectively. Dissolved Cu concentrations in Equus, SRB and AGLR microcosms at the beginning of the study were 3, 82, and 43 μg/L, respectively and decreased to low saturation levels of about ≤9 μg/L Cu after the first 3 months of the study. The decrease of dissolved Cu concentrations was likely due to the dilution of rainwater. Snail and fish mortality appeared to be higher in SRB microcosms than in Equus and AGLR microcosms. There was no significant difference in growth of the snails between treatments. Snail growth data followed the von Bertalanffy Model. The maximum shell length, shell height, and shell width of the snails calculated by the von Bertalanffy Model (L(∞)) were 2.76, 2.05, and 2.18 cm, respectively. The maximum wet weight was 9.38 g

  1. Modeling of penconazole and metalaxyl mobility in undisturbed vineyard soil cores, unamended and amended with spent mushroom substrate

    NASA Astrophysics Data System (ADS)

    Marin-Benito, Jesus Maria; Mamy, Laure; Rodriguez-Cruz, Maria Sonia; Sanchez-Martin, Maria Jesus

    2013-04-01

    In Spain, one of the main producers of mushrooms in the world, a huge amount of the substrates used for the growth of mushrooms have to be eliminated after harvest. However, this substrate represents a promising amendment because of its high organic matter content and, in particular, it could be used in vineyard soils because they generally are poor in organic matter. But the effect of this amendment on the fate in soils of fungicides that are massively used in vineyards is unknown. Therefore, the objectives of this work were to model the mobility of two fungicides, penconazole and metalaxyl, in undisturbed vineyard soil columns using the PRZM3 (Pesticide Root Zone Model) parameterized with laboratory data, and to compare the simulations with the experimental results obtained in mobility studies. Soil cores (40 cm x 9 cm d.i.) were collected from experimental plots in three different vineyard soils of La Rioja (Spain). Three different treatments were tested in each soil: natural (control) soil, soil amended with fresh spent mushroom substrate, and soil amended with composted spent mushroom substrate. The leaching of fungicides was studied in non-incubated and incubated (outdoors for 77 days) soil cores under unsaturated flow conditions. In general, the addition of mushroom substrates decreased the leaching of fungicides compared to control soils. For the most hydrophobic fungicide, penconazole, the predictions obtained by the model were highly correlated (r > 0.88) with the experimental results. Penconazole was never observed in the leachates, its vertical distribution was similar within all soil profiles, and retention of almost all the fungicide was into the topsoil (0-8cm). For the less hydrophobic fungicide, metalaxyl, and the CGA 62826 metabolite generated from its degradation during the experimental period, PRZM3 was not able to reproduce the observations and it was necessary to calibrate the model. After calibration, the correlation between model predictions

  2. Modelling of Genetically Engineered Microorganisms Introduction in Closed Artificial Microcosms

    NASA Astrophysics Data System (ADS)

    Pechurkin, N. S.; Brilkov, A. V.; Ganusov, V. V.; Kargatova, T. V.; Maksimova, E. E.; Popova, L. Yu.

    1999-01-01

    The possibility of introducing genetically engineered microorganisms (GEM) into simple biotic cycles of laboratory water microcosms was investigated. The survival of the recombinant strain Escherichia coli Z905 (Apr, Lux+) in microcosms depends on the type of model ecosystems. During the absence of algae blooming in the model ecosystem, the part of plasmid-containing cells E. coli decreased fast, and the structure of the plasmid was also modified. In conditions of algae blooming (Ankistrodesmus sp.) an almost total maintenance of plasmid-containing cells was observed in E.coli population. A mathematics model of GEM's behavior in water ecosystems with different level of complexity has been formulated. Mechanisms causing the difference in luminescent exhibition of different species are discussed, and attempts are made to forecast the GEM's behavior in water ecosystems.

  3. Vertical distributions of organochlorine pesticides and polychlorinated biphenyls in an agricultural soil core from the Guanzhong Basin, China.

    PubMed

    Lu, Hongxuan; Liu, Weiguo

    2015-01-01

    The concentrations and distributions of hexachlorocyclohexanes (HCHs), dichlorodiphenyltrichloroethanes (DDTs), and polychlorinated biphenyls (PCBs) in an agricultural soil core in the Guanzhong Basin, China were determined. Overall, p,p'-DDT and p,p'-DDE were dominant contaminants and accounted for approximately 48.4 and 23.3% of the total detected DDTs. Low chlorinated PCBs (PCB 28 and PCB 52) were generally detected at higher concentrations and more frequently than high chlorinated PCBs. The peak values of ∑DDT (12.92 ng/g), ∑HCH (2.25 ng/g), and ∑PCB (3.44 ng/g) occurred in the 10-15, 15-20, and 5-10 cm sections, respectively. The negative correlation between the organochlorine pesticide (OCP) concentrations and the soil depths and the relatively high p,p'-DDT/p,p'-DDE ratios in the surface soils indicated that these chemicals were recently used illegally, despite their official ban in 1983. The increase in the ratio of α-/γ-HCH with increasing soil depth indicated that the use of lindane decreased relative to the use of technical HCHs in recent years.

  4. Plant bioindicators for polycyclic aromatic hydrocarbon toxicity in aquatic microcosms

    SciTech Connect

    Gensemer, R.W.; Solomon, K.R.; Day, K.E.; Hodson, P.V.; Servos, M.R.; Greenberg, B.M.

    1994-12-31

    Plant bioindicators are being developed to assess the effects of polycyclic aromatic hydrocarbons (PAHs) in experimental aquatic ecosystems. The approach is to develop and test biomarker assays that are specifically predictive of ecological events at the population and/or community levels of organization in artificial aquatic microcosms. PAH mixtures were introduced into a series of aquatic microcosms using the wood preservative creosote as a PAH source. The authors applied creosote at five dosage levels designed to simulate conductions observed at highly contaminated sites. The growth and biomass of phytoplankton, periphyton, and macrophytes were then measured throughout the growing season, and compared to one or more biomarker assays used to detect PAH contamination. Preliminary results using fluorescence induction on aquatic macrophytes suggest that PAHs can significantly inhibit photosynthesis at even modest concentrations 1--4 hours after exposure. This assay thus is not only a sensitive indicator of PAH exposure, but may also describe mechanisms of PAH toxicity that ultimately reduce biomass or population growth for aquatic plants in these microcosms.

  5. Monitoring Intact Viruses Using Aptamers.

    PubMed

    Kumar, Penmetcha K R

    2016-08-04

    Viral diagnosis and surveillance are necessary steps in containing the spread of viral diseases, and they help in the deployment of appropriate therapeutic interventions. In the past, the commonly employed viral detection methods were either cell-culture or molecule-level assays. Most of these assays are laborious and expensive, require special facilities, and provide a slow diagnosis. To circumvent these limitations, biosensor-based approaches are becoming attractive, especially after the successful commercialization of glucose and other biosensors. In the present article, I have reviewed the current progress using the biosensor approach for detecting intact viruses. At the time of writing this review, three types of bioreceptor surfaces (antibody-, glycan-, and aptamer-based) have been explored on different sensing platforms for detecting intact viruses. Among these bioreceptors, aptamer-based sensors have been increasingly explored for detecting intact viruses using surface plasmon resonance (SPR) and other platforms. Special emphasis is placed on the aptamer-based SPR platform in the present review.

  6. Monitoring Intact Viruses Using Aptamers

    PubMed Central

    Kumar, Penmetcha K. R.

    2016-01-01

    Viral diagnosis and surveillance are necessary steps in containing the spread of viral diseases, and they help in the deployment of appropriate therapeutic interventions. In the past, the commonly employed viral detection methods were either cell-culture or molecule-level assays. Most of these assays are laborious and expensive, require special facilities, and provide a slow diagnosis. To circumvent these limitations, biosensor-based approaches are becoming attractive, especially after the successful commercialization of glucose and other biosensors. In the present article, I have reviewed the current progress using the biosensor approach for detecting intact viruses. At the time of writing this review, three types of bioreceptor surfaces (antibody-, glycan-, and aptamer-based) have been explored on different sensing platforms for detecting intact viruses. Among these bioreceptors, aptamer-based sensors have been increasingly explored for detecting intact viruses using surface plasmon resonance (SPR) and other platforms. Special emphasis is placed on the aptamer-based SPR platform in the present review. PMID:27527230

  7. Nitrogen Transformations in Wetland Soil Cores Measured by (sup15)N Isotope Pairing and Dilution at Four Infiltration Rates

    PubMed Central

    Stepanauskas, R.; Davidsson, E. T.; Leonardson, L.

    1996-01-01

    The effect of water infiltration rate (IR) on nitrogen cycling in a saturated wetland soil was investigated by applying a (sup15)N isotope dilution and pairing method. Water containing [(sup15)N]nitrate was infiltrated through 10-cm-long cores of sieved and homogenized soil at rates of 72, 168, 267, and 638 mm day(sup-1). Then the frequencies of (sup30)N(inf2), (sup29)N(inf2), (sup15)NO(inf3)(sup-), and (sup15)NH(inf4)(sup+) in the outflow water were measured. This method allowed simultaneous determination of nitrification, coupled and uncoupled denitrification, and nitrate assimilation rates. From 3% (at the highest IR) to 95% (at the lowest IR) of nitrate was removed from the water, mainly by denitrification. The nitrate removal was compensated for by the net release of ammonium and dissolved organic nitrogen. Lower oxygen concentrations in the soil at lower IRs led to a sharper decrease in the nitrification rate than in the ammonification rate, and, consequently, more ammonium leaked from the soil. The decreasing organic-carbon-to-nitrogen ratio (from 12.8 to 5.1) and the increasing light A(inf250)/A(inf365) ratio (from 4.5 to 5.2) indicated an increasing bioavailability of the outflowing dissolved organic matter with increasing IR. The efflux of nitrous oxide was also very sensitive to IR and increased severalfold when a zone of low oxygen concentration was close to the outlet of the soil cores. N(inf2)O then constituted 8% of the total gaseous N lost from the soil. PMID:16535352

  8. Isomer-specific investigation of PCDD/F mobility and other fate processes in deep soil cores.

    PubMed

    Grant, Sharon; Stevenson, Gavin; Malcolm, Don; Zennegg, Markus; Gaus, Caroline

    2015-10-01

    Polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) are highly hydrophobic compounds with low migration potential in soil-water. Nevertheless, they have been occasionally reported in subsurface soils hypothesised as the result of facilitated transport processes with colloids or surfactants, or yet unidentified in-situ formation processes. To date, however, the prevalence of deep soil contamination, involved processes and their kinetics remain poorly understood. This study investigated PCDD/F concentrations and isomer profiles through deep soil cores (to 20 m) from agricultural, industrial and urban sites in Queensland, Australia. Based on isomer profiles, a unique source common to all core soils (regardless of depth) was identified, dominated by octachlorodibenzo-p-dioxin (OCDD). The source was consistent with contamination resulting from pesticide impurities. Elevated PCDD concentrations (μg/kg range) to depths up to ∼4-17 m and a continuous increase of peri-chlorinated (1,4,6,9-substituted) isomers through the cores suggested that vertical transport and lateral dechlorination were key post-depositional processes at these sites. The mobility of PCDDs in the present study is far greater than previously reported in soils in general. High estimated mass transport rates for OCDD in four agricultural cores (3.0-6.2% year(-1)) likely reflect significant levels of facilitating species, including surfactants, and intensive rainfall at these sites. The implications of such extensive subsurface transport of PCDD/Fs for groundwater contamination and load estimates may be significant. If the cores of the present study are assumed representative of the region, a total PCDD/F load in the order of 800 tonnes (1.6 tonnes TEQ) could be present in subsurface Queensland coastal soils.

  9. Naphthenic acids and surrogate naphthenic acids in methanogenic microcosms.

    PubMed

    Holowenko, F M; Mackinnon, M D; Fedorak, P M

    2001-08-01

    Naphthenic acids (NAs) are a complex mixture of naturally occurring acyclic and cyclic aliphatic carboxylic acids in petroleum. In the Athabasca oil sands. NAs have been identified as the largest component of dissolved organic matter in the tailings waters from oils sands extraction processes. They are the major contributor to the acute toxicity of the fine tailings wastewaters at the oil sands extraction plants in northeastern Alberta, Canada. In this study, three sources of NAs were studied, including commercially available NAs, those extracted from oil sands process-affected waters, and individual naphthenic-like surrogate compounds. Analysis by gas chromatography-mass spectrometry demonstrated differences between the commercial and extracted NAs. The NAs derived from the process-affected waters showed a short-term inhibition of methanogenesis from H2 or acetate, but with time the populations resumed methane production. It has been postulated that microbial metabolism of the carboxylated side chains of NAs would lead to methane production. The two NA mixtures failed to stimulate methanogenesis in microcosms that contained either oil sands fine tailings or domestic sewage sludge. However, in microcosms with sewage sludge, methanogenesis was stimulated by some surrogate NAs including 3-cyclohexylpropanoic acid at 400-800 mg/L, 5-cyclohexylpentanoic acid at 200 mg/L or 6-phenylhexanoic acid at 200 and 400 mg/L. When added at 200 mg/L to methanogenic microcosms containing fine tailings, 3-cyclohexylpropanoic and 4-cyclohexylbutanoic acids produced methane yields that suggested mineralization of the side chain and the ring.

  10. Biotransformations of Aroclor 1242 in Hudson River test tube microcosms

    SciTech Connect

    Fish, K.M.; Principe, J.M.

    1994-12-01

    Polychlorinated biphenyls (PCBs) are relatively unreactive and hydrophobic, are widely used commercially, and have accumulated in soils, sediments, and biota. The researchers partially simulated environmental conditions in the laboratory to examine the fate of Aroclor 1242 in the Upper Hudson River. The test tube microcosms developed both aerobic and anaerobic compartments. This paper reports on the patterns and rates of anaerobic and aerobic PCB transformations for a single set of conditions in static, unamended microosms to model the environmental fate of Aroclor 1242 in river sediments. 23 refs., 5 figs.

  11. Microcosm experiments of oil degradation by microbial mats.

    PubMed

    de Oteyza, Tirso García; Grimalt, Joan O; Llirós, Marc; Esteve, Isabel

    2006-03-15

    Several microcosm experiments were run in parallel to evaluate the efficiency of microbial mats for crude oil degradation as compared with physico-chemical weathering. The oils used in the experiments constituted representative examples of those currently used for commercial purposes. One was aliphatic and of low viscosity (33.4 American Petroleum Institute degrees, degrees API) and the other was predominantly aromatic, with high sulphur content (ca. 2.7%) and viscosity (16.6 degrees API). After crude oil introduction, the microcosms were kept under cyclic changes in water level to mimic coastal tidal movements. The transformations observed showed that water weathering leads to more effective and rapid elimination of low molecular weight hydrocarbons than microbial mat metabolism, e.g. n-alkanes with chain length shorter than n-pentadecane or n-heptadecane, regular isoprenoid hydrocarbons with chain length lower than C16 or C18 or lower molecular weight naphthalenes. Microbial mats preserved these hydrocarbons from volatilization and water washing. However, hydrocarbons of lower volatility such as the C24-C30 n-alkanes or containing nitrogen atoms, e.g. carbazoles, were eliminated in higher proportion by microbial mats than by water weathering. The strong differences in composition between the two oils used for the experiments were also reflected in significant differences between water weathering and microbial mat biodegradation. Higher oil viscosity seemed to hinder the former but not the later.

  12. Ecological changes in oral microcosm biofilm during maturation

    NASA Astrophysics Data System (ADS)

    Kim, Young-Seok; Kang, Si-Mook; Lee, Eun-Song; Lee, Ji Hyun; Kim, Bo-Ra; Kim, Baek-Il

    2016-10-01

    The aim of this study was to evaluate the ecological changes in the biofilm at different stages of maturation using 16S rDNA gene amplicon sequencing and to identify correlations between red/green (R/G) fluorescence ratio and ecological changes. An oral microcosm biofilm was initiated from the saliva of a single donor and grown anaerobically for up to 10 days in basal medium mucin. Quantitative light-induced fluorescence analysis was shown that the R/G ratio of the biofilm increased consistently, but the slope rapidly decreased after six days. The bacterial compositions of 10 species also consistently changed over time. However, there was no significant correlation between each bacteria and red fluorescence. The monitoring of the maturation process of oral microcosm biofilm over 10 days revealed that the R/G ratio and the bacterial composition within biofilm consistently changed. Therefore, the R/G fluorescence ratio of biofilm may be related with its ecological change rather than specific bacteria.

  13. Alteration of Rock Fragments from Columbia River Basalt Microcosms

    NASA Technical Reports Server (NTRS)

    Wentworth, Susan J.; Thomas-Keprta, Kathie L.; Velbel, Michael A.; McKay, David S.; Stevens, Todd O.

    1999-01-01

    During an earlier study, microorganisms were grown microcosms consisting of sterilized chips of Columbia River Basalt (CRB) and natural CRB ground water with its natural microflora; environmental conditions simulated a deep subsurface, anaerobic, dark environment. Subsequent scanning and transmission electron microscope (SEM and TEM) studies revealed the presence of several types of bacteria and biofilm, some of which were mineralized. Some of these biological features are very similar to possible biogenic features found in two meteorites from Mars, ALH84001 (found in Antarctica) and Nakhla (observed to fall in Egypt). Both ALH84001 and Nakhla contain traces of low-temperature aqueous alteration of silicates, oxides, and sulfides. The goals of this study are to use high-resolution field-emission SEM (FE-SEM) to examine the CRB samples for evidence of alteration features similar to those in the martian meteorites, to determine the extent of alteration during the CRB microcosm experiments, and to determine whether effects of biological activity can be distinguished from inorganic effects.

  14. Intact capture of hypervelocity projectiles

    NASA Technical Reports Server (NTRS)

    Tsou, P.

    1990-01-01

    The ability to capture projectiles intact at hypervelocities opens new applications in science and technology that would either not be possible or would be very costly by other means. This capability has been demonstrated in the laboratory for aluminum projectiles of 1.6 mm diameter, captured at 6 km/s, in one unmelted piece, and retaining up to 95% of the original mass. Furthermore, capture was accomplished passively using microcellular underdense polymer foam. Another advantage of capturing projectiles in an underdense medium is the ability of such a medium to preserve a record of the projectile's original velocity components of speed and direction. A survey of these experimental results is described in terms of a dozen parameters which characterize the amount of capture and the effect on the projectile due to different capture media.

  15. Intact capture of hypervelocity projectiles.

    PubMed

    Tsou, P

    1990-01-01

    The ability to capture projectiles intact at hypervelocities opens new applications in science and technology that would either not be possible or would be very costly by other means. This capability has been demonstrated in the laboratory for aluminum projectiles of 1.6 mm diameter, captured at 6 km/s, in one unmelted piece, and retaining up to 95% of the original mass. Furthermore, capture was accomplished passively using microcellular underdense polymer foam. Another advantage of capturing projectiles in an underdense medium is the ability of such a medium to preserve a record of the projectile's original velocity components of speed and direction. A survey of these experimental results is described in terms of a dozen parameters which characterize the amount of capture and the effect on the projectile due to different capture media.

  16. EFFECTS OF SEDIMENT TYPE ON BENTHIC MACROINFAUNAL COLONIZATION OF LABORATORY MICROCOSMS

    EPA Science Inventory

    We tested the effects of four different sediment types on macroinfaunal colonization and community development in our laboratory flow-thru microcosm system (all microcosms were 20 cm side-1 and sediment depth was 5 cm) over a period of 41 days. Sediments included Santa Rosa Islan...

  17. Triton shells of intact erythrocytes.

    PubMed

    Sheetz, M P; Sawyer, D

    1978-01-01

    About 40% of human erythrocyte membrane protein is resistant to solubilization in 0.5% Triton X-114. These components comprise a structure called a Triton shell roughly similar in size and shape to the original erythrocyte and thus constitute a cytoskeleton. With increasing concentrations of Triton the lipid content of the Triton shell decreases dramatically, whereas the majority of the protein components remain constant. Exceptions to this rule include proteins contained in band 3, the presumed anion channel, and in band 4 which decrease with increasing Triton concentration. The Triton-insoluble complex includes spectrin (bands 1 and 2), actin (band 5), and bands 3' and 7. Component 3' has an apparent molecular weight of 88,000 daltons as does 3; but unlike 3, it is insensitive to protease treatment of the intact cell, has a low extinction coefficient at 280 nm, and is solubilized from the shells in alkaline water solutions. Component 7 also has a low extinction coefficient at 280 nm. Spectrin alone is solubilized from the Triton shells in isotonic media. The solubilized spectrin contains no bound Triton and coelectrophoreses with spectrin eluted in hypotonic solutions from ghosts. Electron micrographs of fixed Triton shells stained with uranyl acetate show the presence of numerous filaments which appear beaded and are 80--120 A in diameter. The filaments cannot be composed mainly af actin, but enough spectrin is present to form the filaments. Triton shells may provide an excellent source of material useful in the investigation of the erythrocyte cytoskeleton.

  18. Starvation survival of Candida albicans in various water microcosms.

    PubMed

    Chaieb, Kamel; Kouidhi, Bochra; Zmantar, Tarek; Mahdouani, Kacem; Bakhrouf, Amina

    2011-08-01

    Candida is a major Human pathogen causing a variety of infections and can survive for extended period of time in aquatic environment including marine and fresh water. In this study we compared a colorimetric XTT assay to colony forming units (CFU) count to evaluate the survival potential of Candida albicans incubated in water microcosms. Our results showed that cells maintain cultivability within a long period followed by a decline in cultivability and a drop of plate counts to less than 20 cell ml(-1) after 150 days in tap water, 190 days in rain water and 200 days in seawater. In addition we noted that 10% of cells viability was reached after 150 days in seawater, 180 days in rain water and 210 days in tap water. Molecular method confirms the persistence of C. albicans cells in water during long time starvation period.

  19. Population dynamics of Vibrio spp. associated with marine sponge microcosms.

    PubMed

    Hoffmann, Maria; Fischer, Markus; Ottesen, Andrea; McCarthy, Peter J; Lopez, Jose V; Brown, Eric W; Monday, Steven R

    2010-12-01

    Vibrio is a diverse genus of marine-associated bacteria with at least 74 species and more expected as additional marine ecospheres are interrogated. This report describes a phylogenetic reconstruction of Vibrio isolates derived from one such unique ecosystem, marine sponges (Phylum Porifera) collected from depths of 150 to 1242 feet. 16S rRNA gene sequencing along with molecular typing of 16S-23S rRNA intergenic spacer regions clustered many sponge-associated Vibrio (spp) with current known species. That is, several benthic Vibrio species commensal with Porifera sponges seemed genetically linked to vibrios associated with coastal or shallow-water communities, signalling a panmictic population structure among seemingly ecologically disparate strains. Conversely, phylogenetic analysis provided evidence for at least two novel Vibrio speciation events within this specific sponge microcosm. Collectively, these findings earmark this still relatively unknown environment as a bastion of taxonomic and phylogenetic variability for the genus and probably other bacterial taxa.

  20. Habitat Complexity in Aquatic Microcosms Affects Processes Driven by Detritivores

    PubMed Central

    Flores, Lorea; Bailey, R. A.; Elosegi, Arturo; Larrañaga, Aitor; Reiss, Julia

    2016-01-01

    Habitat complexity can influence predation rates (e.g. by providing refuge) but other ecosystem processes and species interactions might also be modulated by the properties of habitat structure. Here, we focussed on how complexity of artificial habitat (plastic plants), in microcosms, influenced short-term processes driven by three aquatic detritivores. The effects of habitat complexity on leaf decomposition, production of fine organic matter and pH levels were explored by measuring complexity in three ways: 1. as the presence vs. absence of habitat structure; 2. as the amount of structure (3 or 4.5 g of plastic plants); and 3. as the spatial configuration of structures (measured as fractal dimension). The experiment also addressed potential interactions among the consumers by running all possible species combinations. In the experimental microcosms, habitat complexity influenced how species performed, especially when comparing structure present vs. structure absent. Treatments with structure showed higher fine particulate matter production and lower pH compared to treatments without structures and this was probably due to higher digestion and respiration when structures were present. When we explored the effects of the different complexity levels, we found that the amount of structure added explained more than the fractal dimension of the structures. We give a detailed overview of the experimental design, statistical models and R codes, because our statistical analysis can be applied to other study systems (and disciplines such as restoration ecology). We further make suggestions of how to optimise statistical power when artificially assembling, and analysing, ‘habitat complexity’ by not confounding complexity with the amount of structure added. In summary, this study highlights the importance of habitat complexity for energy flow and the maintenance of ecosystem processes in aquatic ecosystems. PMID:27802267

  1. Fate of pathogenic bacteria in microcosms mimicking human body sites.

    PubMed

    Castellani, Francesco; Ghidini, Valentina; Tafi, Maria Carla; Boaretti, Marzia; Lleo, Maria M

    2013-07-01

    During the infectious process, pathogens may reach anatomical sites where they are exposed to substances interfering with their growth. These substances can include molecules produced by the host, and his resident microbial population, as well as exogenous antibacterial drugs. Suboptimal concentrations of inhibitory molecules and stress conditions found in vivo (high or low temperatures, lack of oxygen, extreme pH) might induce in bacteria the activation of survival mechanisms blocking their division capability but allowing them to stay alive. These "dormant" bacteria can be reactivated in particular circumstances and would be able to express their virulence traits. In this study, it was evaluated the effect of some environmental conditions, such as optimal and suboptimal temperatures, direct light and antibiotic sub-inhibitory concentrations doses of antibiotic, on the human pathogens Escherichia coli and Enterococcus faecalis when incubated in fluids accumulated in the body of patients with different pathologies. It is shown that inoculation in a number of accumulated body fluids and the presence of gentamicin, reliable conditions encountered during pathological states, induce stress-responding strategies enabling bacteria to persist in microcosms mimicking the human body. Significant differences were detected in Gram-negative and Gram-positive species with E. faecalis surviving, as starved or viable but non-culturable forms, in any microcosm and condition tested and E. coli activating a viable but non-culturable state only in some clinical samples. The persistence of bacteria under these conditions, being non-culturable, might explain some recurrent infections without isolation of the causative agent after application of the standard microbiological methods.

  2. [Exploration of microcosmic Chinese medicine used by western medicine].

    PubMed

    Zheng, Zhi-jing

    2015-02-01

    "Microcosmic syndrome", "treatment based on syndrome differentiation", and "combination of disease identification and syndrome differentiation" generally refer to a mode: following the syndrome if with no disease identified, following the disease if with no syndrome type differentiated. For example, Chinese medical treatment of hypertension, high blood lipids, increased transaminase, and so on candirectly use Chinese recipes, but no longer with syndrome differentiation. Clinical application of Chinese patent medicine can also obtain favorable clinical. Western doctors need not follow syndrome differentiation. The invention of artemisinin was screened from more than 40 000 kinds of compounds and herbs, but with no reference of any traditional Chinese medical theory. A lot of folk remedy and empirical recipes have obtained effective efficacy but unnecessarily with profound Chinese medical theories. Various evidences showed that disease can also be cured without syndrome differentiation. I held that it might be associated with the same mechanism of Chinese medicine and Western medicine. Any disease can be cured or alleviated by Chinese medicine is a result from its modern pharmacological effect, which is achieved by improving etiologies, and pathogeneses. I was inspired by whether we can directly use traditional Chinese medicine with modern pharmacological effects to treat symptomatic disease. So I raised an idea of microcosmic Chinese medicine used by Western medicine, i.e., we find and use Chinese herbs with relatively effective modern pharmacological effect to treat diseases targeting at patients' clinical symptoms and signs, as well as various positive laboratory results (collectively called as microscopic dialectical indicators). More Western doctors would use it to treat disease due to omission of complicated and mysterious syndrome differentiation. This will promote extensive application and expansion of Chi- nese medicine and pharmacy, enlarge the team of

  3. Introduction of anaerobic dechlorinating bacteria into soil slurry microcosms and nested-PCR monitoring.

    PubMed Central

    el Fantroussi, S; Mahillon, J; Naveau, H; Agathos, S N

    1997-01-01

    Desulfomonile tiedjei and Desulfitobacterium dehalogenans were chosen as model bacteria to demonstrate the introduction of an anaerobic microbia reductive dechlorination activity into nonsterile soil slurry microcosms by inoculation. De novo 3-chlorobenzoate dechlorination activity was established with the bacterium D. tiedjei in microcosms normally devoid of this dechlorination capacity. The addition of D. tiedjei to microcosms supplemented with 20 mM pyruvate as the cosubstrate resulted in total biotransformation of 1.5 mM 3-chlorobenzoate within 7 days. The introduction of the bacterium Desulfitobacterium dehalogenans into nonsterile microcosms resulted in a shortening of the period required for dechlorination activity to be established. In microcosms inoculated with Desulfitobacterium dehalogenans, total degradation of 6 mM 3-chloro-4-hydroxy phenoxyacetic acid (3-Cl-4-OHPA) was observed after 4 days in contrast to the result in noninoculated microcosms, where the total degradation of 3-Cl-4-OHPA by indigenous microorganisms was observed after 11 days. Both externally introduced bacterial strains were detected in soil slurry microcosms by a nested-PCR methodology. PMID:9023963

  4. Microbial community analysis of switchgrass planted and unplanted soil microcosms displaying PCB dechlorination

    PubMed Central

    Liang, Yi; Meggo, Richard; Hu, Dingfei; Schnoor, Jerald L.; Mattes, Timothy E.

    2015-01-01

    Polychlorinated biphenyls (PCBs) pose potential risks to human and environmental health because they are carcinogenic, persistent and bioaccumulative. In this study we investigated bacterial communities in soil microcosms spiked with PCB 52, 77 and 153. Switchgrass (Panicum virgatum) was employed to improve overall PCB removal and redox cycling (i.e. sequential periods of flooding followed by periods of no flooding) was performed in an effort to promote PCB dechlorination. Lesser chlorinated PCB transformation products were detected in all microcosms, indicating the occurrence of PCB dechlorination. Terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis showed that PCB spiking, switchgrass planting and redox cycling affected the microbial community structure. Putative organohalide-respiring Chloroflexi populations, which were not found in unflooded microcosms, were enriched after two weeks of flooding in the redox-cycled microcosms. Sequences classified as Geobacter sp. were detected in all microcosms, and were most abundant in the switchgrass-planted microcosm spiked with PCB congeners. The presence of possible organohalide-respiring bacteria in these soil microcosms suggests they play a role in PCB dechlorination therein. PMID:25820643

  5. BIODEGRADATION OF POLYCYCLIC AROMATIC HYDROCARBONS (PAH) FROM CRUDE OIL IN SANDY-BEACH MICROCOSMS.

    EPA Science Inventory

    Though the lower n-alkanes are considered the most degradable components of crude oil, our experiments with microcosms simulating oiled beaches showed substantial depletion of fluorene, phenanthrene, dibenzothiophene, and other PAH in control treatments consisting of raw seawater...

  6. Arsenic mobilization from sediments in microcosms under sulfate reduction.

    PubMed

    Sun, Jing; Quicksall, Andrew N; Chillrud, Steven N; Mailloux, Brian J; Bostick, Benjamin C

    2016-06-01

    Arsenic is often assumed to be immobile in sulfidic environments. Here, laboratory-scale microcosms were conducted to investigate whether microbial sulfate reduction could control dissolved arsenic concentrations sufficiently for use in groundwater remediation. Sediments from the Vineland Superfund site and the Coeur d'Alene mining district were amended with different combination of lactate and sulfate and incubated for 30-40 days. In general, sulfate reduction in Vineland sediments resulted in transient and incomplete arsenic removal, or arsenic release from sediments. Sulfate reduction in the Coeur d'Alene sediments was more effective at removing arsenic from solution than the Vineland sediments, probably by arsenic substitution and adsorption within iron sulfides. X-ray absorption spectroscopy indicated that the Vineland sediments initially contained abundant reactive ferrihydrite, and underwent extensive sulfur cycling during incubation. As a result, arsenic in the Vineland sediments could not be effectively converted to immobile arsenic-bearing sulfides, but instead a part of the arsenic was probably converted to soluble thioarsenates. These results suggest that coupling between the iron and sulfur redox cycles must be fully understood for in situ arsenic immobilization by sulfate reduction to be successful.

  7. Antiseptics and microcosm biofilm formation on titanium surfaces.

    PubMed

    Verardi, Georgia; Cenci, Maximiliano Sérgio; Maske, Tamires Timm; Webber, Bruna; Santos, Luciana Ruschel dos

    2016-01-01

    Oral rehabilitation with osseointegrated implants is a way to restore esthetics and masticatory function in edentulous patients, but bacterial colonization around the implants may lead to mucositis or peri-implantitis and consequent implant loss. Peri-implantitis is the main complication of oral rehabilitation with dental implants and, therefore, it is necessary to take into account the potential effects of antiseptics such as chlorhexidine (CHX), chloramine T (CHT), triclosan (TRI), and essential oils (EO) on bacterial adhesion and on biofilm formation. To assess the action of these substances, we used the microcosm technique, in which the oral environment and periodontal conditions are simulated in vitro on titanium discs with different surface treatments (smooth surface - SS, acid-etched smooth surface - AESS, sand-blasted surface - SBS, and sand-blasted and acid-etched surface - SBAES). Roughness measurements yielded the following results: SS: 0.47 µm, AESS: 0.43 µm, SB: 0.79 µm, and SBAES: 0.72 µm. There was statistical difference only between SBS and AESS. There was no statistical difference among antiseptic treatments. However, EO and CHT showed lower bacterial counts compared with the saline solution treatment (control group). Thus, the current gold standard (CHX) did not outperform CHT and EO, which were efficient in reducing the biofilm biomass compared with saline solution.

  8. Stereoselective biodegradation of amphetamine and methamphetamine in river microcosms.

    PubMed

    Bagnall, John; Malia, Louis; Lubben, Anneke; Kasprzyk-Hordern, Barbara

    2013-10-01

    Here presented for the first time is the enantioselective biodegradation of amphetamine and methamphetamine in river microcosm bioreactors. The aim of this investigation was to test the hypothesis that mechanisms governing the fate of amphetamine and methamphetamine in the environment are mostly stereoselective and biological in nature. Several bioreactors were studied over the duration of 15 days (i) in both biotic and abiotic conditions, (ii) in the dark or exposed to light and (iii) in the presence or absence of suspended particulate matter. Bioreactor samples were analysed using SPE-chiral-LC-(QTOF)MS methodology. This investigation has elucidated the fundamental mechanism for degradation of amphetamine and methamphetamine as being predominantly biological in origin. Furthermore, stereoselectivity and changes in enantiomeric fraction (EF) were only observed under biotic conditions. Neither amphetamine nor methamphetamine appeared to demonstrate adsorption to suspended particulate matter. Our experiments also demonstrated that amphetamine and methamphetamine were photo-stable. Illicit drugs are present in the environment at low concentrations but due to their pseudo-persistence and non-racemic behaviour, with two enantiomers revealing significantly different potency (and potentially different toxicity towards aquatic organisms) the risk posed by illicit drugs in the environment should not be under- or over-estimated. The above results demonstrate the need for re-evaluation of the procedures utilised in environmental risk assessment, which currently do not recognise the importance of the phenomenon of chirality in pharmacologically active compounds.

  9. 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

  10. Non-destructive Analysis of Oil-Contaminated Soil Core Samples by X-ray Computed Tomography and Low-Field Nuclear Magnetic Resonance Relaxometry: a Case Study.

    PubMed

    Nakashima, Yoshito; Mitsuhata, Yuji; Nishiwaki, Junko; Kawabe, Yoshishige; Utsuzawa, Shin; Jinguuji, Motoharu

    2011-01-01

    Non-destructive measurements of contaminated soil core samples are desirable prior to destructive measurements because they allow obtaining gross information from the core samples without touching harmful chemical species. Medical X-ray computed tomography (CT) and time-domain low-field nuclear magnetic resonance (NMR) relaxometry were applied to non-destructive measurements of sandy soil core samples from a real site contaminated with heavy oil. The medical CT visualized the spatial distribution of the bulk density averaged over the voxel of 0.31 × 0.31 × 2 mm(3). The obtained CT images clearly showed an increase in the bulk density with increasing depth. Coupled analysis with in situ time-domain reflectometry logging suggests that this increase is derived from an increase in the water volume fraction of soils with depth (i.e., unsaturated to saturated transition). This was confirmed by supplementary analysis using high-resolution micro-focus X-ray CT at a resolution of ∼10 μm, which directly imaged the increase in pore water with depth. NMR transverse relaxation waveforms of protons were acquired non-destructively at 2.7 MHz by the Carr-Purcell-Meiboom-Gill (CPMG) pulse sequence. The nature of viscous petroleum molecules having short transverse relaxation times (T2) compared to water molecules enabled us to distinguish the water-saturated portion from the oil-contaminated portion in the core sample using an M(0)-T2 plot, where M(0) is the initial amplitude of the CPMG signal. The present study demonstrates that non-destructive core measurements by medical X-ray CT and low-field NMR provide information on the groundwater saturation level and oil-contaminated intervals, which is useful for constructing an adequate plan for subsequent destructive laboratory measurements of cores.

  11. Automated online measurement of N2, N2O, NO, CO2, and CH4 emissions based on a gas-flow-soil-core technique.

    PubMed

    Liao, Tingting; Wang, Rui; Zheng, Xunhua; Sun, Yang; Butterbach-Bahl, Klaus; Chen, Nuo

    2013-11-01

    The gas-flow-soil-core (GFSC) technique allows to directly measure emission rates of denitrification gases of incubated soil cores. However, the technique was still suffering some drawbacks such as inadequate accuracy due to asynchronous detection of dinitrogen (N2) and other gases and low measurement frequency. Furthermore, its application was limited due to intensive manual operation. To overcome these drawbacks, we updated the GFSC system as described by Wang et al. (2011) by (a) using both a chemiluminescent detector and a gas chromatograph detector to measure nitric oxide (NO), (b) synchronizing the measurements of N2, NO, nitrous oxide (N2O), carbon dioxide (CO2) and methane (CH4), and (c) fully automating the sampling/analysis of all the gases. These technical modifications significantly reduced labor demands by at least a factor of two, increased the measurement frequency from 3 to 6 times per day and resulted in remarkable improvements in measurement accuracy (with detection limits of 0.5, 0.01, 0.05, 2.3 and 0.2μgN or Ch(-1)kg(-1)ds, or 17, 0.3, 1.8, 82, and 6μgN or Cm(-2)h(-1), for N2, N2O, NO, CO2, and CH4, respectively). In some circumstances, the modified system measured significantly more N2 and CO2 and less N2O and NO because of the enhanced measurement frequency. The modified system distinguished the differences in emissions of the denitrification gases and CO2 due to a 20% change in initial carbon supplies. It also remarkably recovered approximately 90% of consumed nitrate during incubation. These performances validate the technical improvement, and indicate that the improved GFSC system may provide a powerful research tool for obtaining deeper insights into the processes of soil carbon and nitrogen transformation during denitrification.

  12. Gradients in intact polar diacylglycerolipids across the Mediterranean Sea are related to phosphate availability

    NASA Astrophysics Data System (ADS)

    Popendorf, K. J.; Tanaka, T.; Pujo-Pay, M.; Lagaria, A.; Courties, C.; Conan, P.; Oriol, L.; Sofen, L. E.; Moutin, T.; van Mooy, B. A. S.

    2011-12-01

    Intact polar membrane lipids compose a significant fraction of cellular material in plankton and their synthesis imposes a substantial constraint on planktonic nutrient requirements. As a part of the Biogeochemistry from the Oligotrophic to the Ultraoligotrophic Mediterranean (BOUM) cruise we examined the distribution of several classes of intact polar diacylglycerolipids (IP-DAGs) across the Mediterranean, and found that phospholipid concentration as a percent of total lipids correlated with phosphate concentration. In addition, the ratios of non-phosphorus lipids to phospholipids - sulfoquinovosyldiacylglycerol (SQDG) to phosphatidylglycerol (PG), and betaine lipids to phosphatidylcholine (PC) - were also found to increase from west to east across the Mediterranean. Additionally, microcosm incubations from across the Mediterranean were amended with phosphate and ammonium, and in the course of several days nutrient amendments elicited a shift in the ratios of IP-DAGs. These experiments were used to assess the relative contribution of community shifts and physiological response to the observed change in IP-DAGs across the Mediterranean. The ratio of SQDG to chlorophyll-a was also explored as an indicator of phytoplankton response to nitrogen availability. This study is the first to demonstrate the dynamic response of membrane lipid composition to changes in nutrients in a natural, mixed planktonic community.

  13. Gradients in intact polar diacylglycerolipids across the Mediterranean Sea are related to phosphate availability

    NASA Astrophysics Data System (ADS)

    Popendorf, K. J.; Tanaka, T.; Pujo-Pay, M.; Lagaria, A.; Courties, C.; Conan, P.; Oriol, L.; Sofen, L. E.; Moutin, T.; van Mooy, B. A. S.

    2011-08-01

    Intact polar membrane lipids compose a significant fraction of cellular material in plankton and their synthesis imposes a substantial constraint on planktonic nutrient requirements. As a part of the Biogeochemistry from the Oligotrophic to the Ultraoligtrophic Mediterranean (BOUM) cruise we examined the distribution of several classes of intact polar diacylglycerolipids (IP-DAGs) across the Mediterranean, and found that phospholipid concentration as a percent of total lipids correlated with phosphate concentration. In addition, the ratios of non-phosphorus lipids to phospholipids - sulfoquinovosyldiacylglycerol (SQDG) to phosphatidylglycerol (PG), and betaine lipids to phosphatidylcholine (PC) - were also found to increase from west to east across the Mediterranean. Additionally, microcosm incubations from across the Mediterranean were amended with phosphate and ammonium, and in the course of several days nutrient amendments elicited a shift in the ratios of IP-DAGs. These experiments were used to assess the relative contribution of community shifts and physiological response to the observed change in IP-DAGs across the Mediterranean. The ratio of SQDG to chlorophyll a was also explored as an indicator of phytoplankton response to nitrogen availability. This study is the first to demonstrate the dynamic response of membrane lipid composition to changes in nutrients in a natural, mixed planktonic community.

  14. Bacterial Community Response to Petroleum Hydrocarbon Amendments in Freshwater, Marine, and Hypersaline Water-Containing Microcosms

    PubMed Central

    Jurelevicius, Diogo; Alvarez, Vanessa Marques; Marques, Joana Montezano; de Sousa Lima, Laryssa Ribeiro Fonseca; Dias, Felipe de Almeida

    2013-01-01

    Hydrocarbon-degrading bacterial communities from freshwater, marine, and hypersaline Brazilian aquatic ecosystems (with water salinities corresponding to 0.2%, 4%, and 5%, respectively) were enriched with different hydrocarbons (heptadecane, naphthalene, or crude oil). Changes within the different microcosms of bacterial communities were analyzed using cultivation approaches and molecular methods (DNA and RNA extraction, followed by genetic fingerprinting and analyses of clone libraries based on the 16S rRNA-coding gene). A redundancy analysis (RDA) of the genetic fingerprint data and a principal component analysis (PCA) of the clone libraries revealed hydrocarbon-enriched bacterial communities specific for each ecosystem studied. However, within the same ecosystem, different bacterial communities were selected according to the petroleum hydrocarbon used. In general, the results demonstrated that Acinetobacter and Cloacibacterium were the dominant genera in freshwater microcosms; the Oceanospirillales order and the Marinobacter, Pseudomonas, and Cycloclasticus genera predominated in marine microcosms; and the Oceanospirillales order and the Marinobacter genus were selected in the different hydrocarbon-containing microcosms in hypersaline water. Determination of total petroleum hydrocarbons (TPHs) in all microcosms after 32 days of incubation showed a decrease in the hydrocarbon concentration compared to that for the controls. A total of 50 (41.3%) isolates from the different hydrocarbon-contaminated microcosms were associated with the dominant operational taxonomic units (OTUs) obtained from the clone libraries, and their growth in the hydrocarbon contaminating the microcosm from which they were isolated as the sole carbon source was observed. These data provide insight into the general response of bacterial communities from freshwater, marine, and hypersaline aquatic ecosystems to petroleum hydrocarbon contamination. PMID:23872573

  15. Bacterial community response to petroleum hydrocarbon amendments in freshwater, marine, and hypersaline water-containing microcosms.

    PubMed

    Jurelevicius, Diogo; Alvarez, Vanessa Marques; Marques, Joana Montezano; de Sousa Lima, Laryssa Ribeiro Fonseca; Dias, Felipe de Almeida; Seldin, Lucy

    2013-10-01

    Hydrocarbon-degrading bacterial communities from freshwater, marine, and hypersaline Brazilian aquatic ecosystems (with water salinities corresponding to 0.2%, 4%, and 5%, respectively) were enriched with different hydrocarbons (heptadecane, naphthalene, or crude oil). Changes within the different microcosms of bacterial communities were analyzed using cultivation approaches and molecular methods (DNA and RNA extraction, followed by genetic fingerprinting and analyses of clone libraries based on the 16S rRNA-coding gene). A redundancy analysis (RDA) of the genetic fingerprint data and a principal component analysis (PCA) of the clone libraries revealed hydrocarbon-enriched bacterial communities specific for each ecosystem studied. However, within the same ecosystem, different bacterial communities were selected according to the petroleum hydrocarbon used. In general, the results demonstrated that Acinetobacter and Cloacibacterium were the dominant genera in freshwater microcosms; the Oceanospirillales order and the Marinobacter, Pseudomonas, and Cycloclasticus genera predominated in marine microcosms; and the Oceanospirillales order and the Marinobacter genus were selected in the different hydrocarbon-containing microcosms in hypersaline water. Determination of total petroleum hydrocarbons (TPHs) in all microcosms after 32 days of incubation showed a decrease in the hydrocarbon concentration compared to that for the controls. A total of 50 (41.3%) isolates from the different hydrocarbon-contaminated microcosms were associated with the dominant operational taxonomic units (OTUs) obtained from the clone libraries, and their growth in the hydrocarbon contaminating the microcosm from which they were isolated as the sole carbon source was observed. These data provide insight into the general response of bacterial communities from freshwater, marine, and hypersaline aquatic ecosystems to petroleum hydrocarbon contamination.

  16. Responses of meiofauna and nematode communities to crude oil contamination in a laboratory microcosm experiment

    NASA Astrophysics Data System (ADS)

    Kang, Teawook; Oh, Je Hyeok; Hong, Jae-Sang; Kim, Dongsung

    2016-09-01

    We examined the effects of crude oil contamination on community assemblages of meiofauna and nematodes after exposure to total petroleum hydrocarbons in the laboratory. We administered a seawater solution that had been contaminated with total petroleum hydrocarbons to seven treatment groups at different concentrations, while the control group received uncontaminated filtered seawater. The average density of total meiofauna in the experimental microcosms diluted with 0.5%, 1%, 2%, and 4% contaminated seawater was higher than the density in the control. The average density of total meiofauna in the 8%, 15%, and 20% microcosms was lower than the density in the control. The density of nematodes was similar to that of the total meiofauna. Cluster analysis divided the microcosms into group 1 (control, 0.5%, 1%, 2%, and 4% microcosms) and group 2 (8%, 15%, and 20% microcosms). However, SIMPROF analysis showed no significant difference between the two groups ( p > 0.05). Bolbolaimus spp. (37.1%) were dominant among the nematodes. Cluster analysis showed similar results for nematode and meiofaunal communities. The total meiofaunal density, nematode density, and number of Bolbolaimus spp. individuals were significantly negatively associated with the concentration of total petroleum hydrocarbons (Spearman correlation coefficients, p < 0.05). Within the nematodes, epistrate feeders (group 2A: 46%) were the most abundant trophic group. Among the treatment groups, the abundance of group 2A increased in low-concentration microcosms and decreased in high-concentration microcosms. Thus, our findings provide information on the effects of oil pollution on meiofauna in the intertidal zones of sandy beaches.

  17. Microcosms metacommunities in river network: niche effects and biodiversity

    NASA Astrophysics Data System (ADS)

    Giometto, A.; Carrara, F.; Altermatt, F.; Rinaldo, A.

    2012-04-01

    Many highly diverse landscapes exhibit hierarchical spatial structures that are shaped by geomorphological processes. Riverine ecosystems, among the most diverse habitats on Earth, represent an outstanding example of such mechanisms. In these landscapes, in which connectivity directly influences metacommunity processes, habitat capacity contributes to control biodiversity at several levels. A previous study has already highlighted the effect of connectivity on species distribution at local and regional scales, but habitat capacity was kept uniform. We studied the interaction of connectivity and habitat capacity in an aquatic microcosm experiment, in which microbial communities were grown in 36-well culture plates connected by dispersal. Dispersal occurred by periodic transfer of culture medium among connected local communities, following river network topology. The effect of habitat capacity in these landscapes was investigated by comparing three different spatial configurations of local community volumes: 1. Power law distributed volumes, according to drainage area. 2. Spatial random permutation of the volumes in the above configuration. 3. Equal distribution of volumes (preserving the total volume with respect to the above configurations). The net effect of habitat capacity on community composition was isolated in a control treatment in which communities were kept isolated for the whole duration of the experiment. In all treatments we observed that varying volumes induced niche effects: some protozoan species preferentially occupied larger nodes (systematically in isolation). Nevertheless, there is evidence that position along the network played a significant role in shaping biodiversity patterns. Size distribution measurements for each community were taken with a CASY cell counter, and species abundances data on log scale precision were collected by direct microscope observation.

  18. Carbazole degradation in the soil microcosm by tropical bacterial strains

    PubMed Central

    Salam, Lateef B.; Ilori, Matthew O.; Amund, Olukayode O.

    2015-01-01

    In a previous study, three bacterial strains isolated from tropical hydrocarbon-contaminated soils and phylogenetically identified as Achromobacter sp. strain SL1, Pseudomonas sp. strain SL4 and Microbacterium esteraromaticum strain SL6 displayed angular dioxygenation and mineralization of carbazole in batch cultures. In this study, the ability of these isolates to survive and enhance carbazole degradation in soil were tested in field-moist microcosms. Strain SL4 had the highest survival rate (1.8 x 107 cfu/g) after 30 days of incubation in sterilized soil, while there was a decrease in population density in native (unsterilized) soil when compared with the initial population. Gas chromatographic analysis after 30 days of incubation showed that in sterilized soil amended with carbazole (100 mg/kg), 66.96, 82.15 and 68.54% were degraded by strains SL1, SL4 and SL6, respectively, with rates of degradation of 0.093, 0.114 and 0.095 mg kg−1 h−1. The combination of the three isolates as inoculum in sterilized soil degraded 87.13% carbazole at a rate of 0.121 mg kg−1 h−1. In native soil amended with carbazole (100 mg/kg), 91.64, 87.29 and 89.13% were degraded by strains SL1, SL4 and SL6 after 30 days of incubation, with rates of degradation of 0.127, 0.121 and 0.124 mg kg−1 h−1, respectively. This study successfully established the survivability (> 106 cfu/g detected after 30 days) and carbazole-degrading ability of these bacterial strains in soil, and highlights the potential of these isolates as seed for the bioremediation of carbazole-impacted environments. PMID:26691461

  19. Biostimulation of indigenous microorganisms for bioremediation of oily hypersaline microcosms from the Arabian Gulf Kuwaiti coasts.

    PubMed

    Al-Mailem, Dina M; Al-Deieg, Maha; Eliyas, Mohamed; Radwan, Samir S

    2017-05-15

    Hypersaline soil and water samples were collected in summer and winter from the "sabkha" area at the Kuwaiti shore of the Arabian Gulf. Physicochemical parameters were analyzed, and found suitable for microbial oil-removal. Summer- and winter-microcosms were treated with individual cation (K(+), Ca(2+), Mg(2+), Fe(3+)) salts, and with animal blood and commercial yeast, as cost-effective vitamin sources. Those microcosms were exposed to the open environment for six winter and six summer months, and analyzed for their hydrocarbonoclastic microorganisms at time zero and in two month intervals. The hydrocarbonoclastic microbial communities in the microcosms consisted of halophilic bacteria and haloarchaea. The constituent bacterial species varied according to the season. Three species, Dietzia kunjamensis, Marinobacter lacisalsi and Halomonas oxialensis consistently occurred both in summer- and winter-samples, but the remaining species were different. On the other hand, the haloarchaeal communities in summer and winter were quite similar, and consisted mainly of Haloferax spp and Halobacterium spp. Treating the microcosms with cations and with vitamin-containing natural products enhanced microbial numbers and oil-removal. The effectiveness of the cations in oil-removal was in the order; Fe(3+) (94%) > Ca(2+) (89%) > Mg(2+) (85%) > K(+) (82%). Thus, oily microcosms amended with trivalent and divalent cations lost most of the oil, and those amended with commercial yeast and with animal blood, as vitamin sources, lost 78% and 72% oil, respectively.

  20. Plant growth and the performance of mangrove wetland microcosms for mariculture effluent depuration.

    PubMed

    Su, Yung-Ming; Lin, Ying-Feng; Jing, Shuh-Ren; Hou, Ping-Chun Lucy

    2011-07-01

    This study established wetland microcosms that were either unplanted or planted in monoculture with native mangrove species in Taiwan (Avicennia marina, Rhizophora stylosa, and Lumnitzera racemosa) for the purpose of receiving high-salinity mariculture effluents; additionally, the microcosms operated at different hydraulic retention times (HRTs). Plant growth and the performance of the microcosms with respect to pollutant removal were investigated. The results showed that seedlings of all three mangrove species survived and grew sufficiently well under continuous flooding. The presence of mangroves consistently improved SS, BOD(5), and TP removal, particularly under short HRT conditions. The mangrove microcosms removed pollutants from the mariculture effluents with efficiencies of 5.7-27.1% (SS), 4.9-36.3% (BOD(5)), 18.7-29.9% (TP), 21.2-49.8% (NH(4)-N), and 5.4-37.7% (NO(x)-N). A. marina and L. racemosa were more tolerant of continuous flooding than R. stylosa. However, no species displayed consistently superior performance in decreasing all pollutant-related parameters investigated. For all pollutants, microcosms operating at a 2-d HRT exhibited a higher removal efficiency than those operating at a 0.5-d HRT.

  1. Autism Spectrum Disorder and intact executive functioning.

    PubMed

    Ferrara, R; Ansermet, F; Massoni, F; Petrone, L; Onofri, E; Ricci, P; Archer, T; Ricci, S

    2016-01-01

    Earliest notions concerning autism (Autism Spectrum Disorders, ASD) describe the disturbance in executive functioning. Despite altered definition, executive functioning, expressed as higher cognitive skills required complex behaviors linked to the prefrontal cortex, are defective in autism. Specific difficulties in children presenting autism or verbal disabilities at executive functioning levels have been identified. Nevertheless, the developmental deficit of executive functioning in autism is highly diversified with huge individual variation and may even be absent. The aim of the present study to examine the current standing of intact executive functioning intact in ASD.

  2. Microbial abundance and community in subsurface flow constructed wetland microcosms: role of plant presence.

    PubMed

    Wang, Qian; Xie, Huijun; Ngo, Huu Hao; Guo, Wenshan; Zhang, Jian; Liu, Cui; Liang, Shuang; Hu, Zhen; Yang, Zhongchen; Zhao, Congcong

    2016-03-01

    In this research, the role of plants in improving microorganism growth conditions in subsurface flow constructed wetland (CW) microcosms was determined. In particular, microbial abundance and community were investigated during summer and winter in Phragmites australis-planted CW microcosms (PA) and unplanted CW microcosms (control, CT). Results revealed that the removal efficiencies of pollutants and microbial community structure varied in winter with variable microbial abundance. During summer, PA comprised more dominant phyla (e.g., Proteobacteria, Actinobacteria, and Bacteroidetes), whereas CT contained more Cyanobacteria and photosynthetic bacteria. During winter, the abundance of Proteobacteria was >40 % in PA but dramatically decreased in CT. Moreover, Cyanobacteria and photosynthetic bacterial dominance in CT decreased. In both seasons, bacteria were more abundant in root surfaces than in sand. Plant presence positively affected microbial abundance and community. The potential removal ability of CT, in which Cyanobacteria and photosynthetic bacteria were abundant during summer, was more significantly affected by temperature reduction than that of PA with plant presence.

  3. Quick stimulation of Alcanivorax sp. by bioemulsificant EPS2003 on microcosm oil spill simulation

    PubMed Central

    Cappello, Simone; Genovese, Maria; Denaro, Renata; Santisi, Santina; Volta, Anna; Bonsignore, Martina; Mancini, Giuseppe; Giuliano, Laura; Genovese, Lucrezia; Yakimov, Michail M.

    2014-01-01

    Oil spill microcosms experiments were carried out to evaluate the effect of bioemulsificant exopolysaccharide (EPS2003) on quick stimulation of hydrocarbonoclastic bacteria. Early hours of oil spill, were stimulated using an experimental seawater microcosm, supplemented with crude oil and EPS2003 (SW+OIL+EPS2003); this system was monitored for 2 days and compared to control microcosm (only oil-polluted seawater, SW+OIL). Determination of bacterial abundance, heterotrophic cultivable and hydrocarbon-degrading bacteria were carried out. Community composition of marine bacterioplankton was determined by 16S rRNA gene clone libraries. Data obtained indicated that bioemulsificant addition stimulated an increase of total bacterial abundance and, in particular, selection of bacteria related to Alcanivorax genus; confirming that EPS2003 could be used for the dispersion of oil slicks and could stimulate the selection of marine hydrocarbon degraders thus increasing bioremediation process. PMID:25763036

  4. Toxicity to freshwater organisms from oils and oil spill chemical treatments in laboratory microcosms.

    PubMed

    Bhattacharyya, S; Klerks, P L; Nyman, J A

    2003-01-01

    Toxicity and temporal changes in toxicity of freshwater-marsh-microcosms containing South Louisiana Crude (SLC) or diesel fuel and treated with a cleaner or dispersant, were investigated using Chironomus tentans, Daphnia pulex, and Oryzias latipes. Bioassays used microcosm water (for D. pulex and O. latipes) or soil slurry (for C. tentans) taken 1,7, 31, and 186 days after treatment. SLC was less toxic than diesel, chemical additives enhanced oil toxicity, the dispersant was more toxic than the cleaner, and toxicities were greatly reduced by day 186. Toxicities were higher in the bioassay with the benthic species than in those with the two water-column species. A separate experiment showed that C. tentans' sensitivity was intermediate to that of Tubifex tubifex and Hyallela azteca. Freshwater organisms, especially benthic invertebrates, thus appear seriously effected by oil under the worst-case-scenario of our microcosms. Moreover, the cleaner and dispersant tested were poor response options under those conditions.

  5. Synergistic relationships in algal-bacterial microcosms for the treatment of aromatic pollutants.

    PubMed

    Borde, Xavier; Guieysse, Benoît; Delgado, Osvaldo; Muñoz, Raúl; Hatti-Kaul, Rajni; Nugier-Chauvin, Caroline; Patin, Henri; Mattiasson, Bo

    2003-02-01

    The potential of algal-bacterial microcosms was studied for the biodegradation of salicylate, phenol and phenanthrene. The isolation and characterization of aerobic bacterial strains capable of mineralizing each pollutant were first conducted. Ralstonia basilensis was isolated for salicylate degradation, Acinetobacter haemolyticus for phenol and Pseudomonas migulae and Sphingomonas yanoikuyae for phenanthrene. The green alga Chlorella sorokiniana was then cultivated in the presence of the pollutants at different concentrations, showing increasing inhibitory effects in the following order: salicylate < phenol < phenanthrene. The synergistic relationships in the algal-bacterial microcosms were clearly demonstrated, since for the three contaminants tested, a substantial removal (>85%) was recorded only in the systems inoculated with both algae and bacteria and incubated under continuous lighting. This study presents, to our knowledge, the first reported case of photosynthesis-enhanced biodegradation of toxic aromatic pollutants by algal-bacterial microcosms in a one-stage treatment.

  6. HYDROCARBON VAPOR DIFFUSION IN INTACT CORE SLEEVES

    EPA Science Inventory

    The diffusion of 2,2,4-trimethylpentane (TMP) and 2,2,5-trimethylhexane (TMH) vapors put of residually contaminated sandy soil from the U.S. Environmental Protection Agency (EPA) field research site at Traverse City, Michigan, was measured and modeled. The headspace of an intact ...

  7. The recovery of heat-stressed Escherichia coli in lake water microcosms.

    PubMed

    Lim, C H; Flint, K P

    1995-12-01

    Escherichia coli was heat stressed at 55 degrees, 60 degrees or 65 degrees C in sterile flasks of lake water. After 6 h at these temperatures the viable count on nutrient agar had dropped below the limits of detection (1 colony in 100 ml). The flasks were transferred to a 15 degrees C incubator and left for 7 d. Recovery of the stressed E. coli was shown to occur within 48 h at this temperature. Recovery also occurred in microcosms amended with 5% (v/v) synthetic sewage. The stressed E. coli multiplied in the amended but not in the unamended microcosms.

  8. Stimulation of Mercury Methylation by Coal Ash in Anaerobic Sediment Microcosms

    NASA Astrophysics Data System (ADS)

    Schwartz, G.; Hsu-Kim, H.; Redfern, L.; Gunsch, C.; Vengosh, A.

    2015-12-01

    Coal combustion products (coal ash) represent one of the largest industrial waste streams in the United States. Coal ash contains elevated levels of toxic, bioaccumulative elements such as mercury (Hg), yet the majority of coal ash waste is stored in unlined impoundments and landfills. These impoundments have a long history of environmental degradation, including: groundwater contamination, surface water contamination through impoundment effluent discharge, and impoundment failures resulting in catastrophic ash release events. The fate of toxic elements associated with coal ash is greatly influenced by environmental parameters, such as redox potential and microbial activity, which induce transformations and leaching of contaminants. Here we used anaerobic sediment-ash microcosms to determine how coal ash impacts methyl mercury (MeHg) production in a simulated benthic aquatic environment. We used two coal ash types in the microcosms: a weathered ash with low sulfate/Hg content and a fresh fly ash that was relatively enriched in sulfate/Hg compared to the weathered ash. Two different sediments were used in the microcosms: one was a pristine sediment (containing 0.03 mg/kg Hg) and the other was a relatively Hg-contaminated sediment (containing 0.29 mg/kg Hg). Results showed that microcosms amended with the low sulfate/low Hg ash had no net MeHg production. In contrast, microcosms amended with high sulfate/high Hg ash showed increases in MeHg concentrations that were 2 to 3 times greater than control microcosms without ash, indicating that coal ash can stimulate MeHg production by providing spikes of Hg and labile sulfate to the aquatic system. MeHg production in ash-amended microcosms containing contaminated sediment was no greater than in the ash-amended pristine sediment microcosms. This may indicate that Hg associated with coal ash is more bioavailable than the Hg present in historically contaminated sediments. Illumina sequencing is underway to investigate the

  9. The Use of Microcosms as an Experimental Approach to Understanding Terrestrial Ecosystem Functioning

    NASA Astrophysics Data System (ADS)

    Fraser, L. H.

    1999-01-01

    Since 1986, a series of microcosm experiments has been conducted at the Unit of Comparative Plant Ecology (UCPE) in an attempt to test our understanding of the principles controlling the structure and dynamics of plant communities and ecosystems. In each experiment microcosms have been seeded with a common pool of organisms, and systems have been allowed to assemble under replicated controlled conditions. Experiment variables have included mineral nutrient supply, temperature, moisture supply, soil depth, carbon dioxide concentration, mycorrhizas, rhizobia, herbivores and carnivores. Results from these experiments are presented to illustrate the value of synthesised ecosystems in ecological research.

  10. Anaerobic Degradation of Pristane in Nitrate-Reducing Microcosms and Enrichment Cultures

    PubMed Central

    Bregnard, T. P.; Haner, A.; Hohener, P.; Zeyer, J.

    1997-01-01

    Microcosm studies were conducted under nitrate-reducing conditions with diesel fuel-contaminated aquifer material from a site treated by in situ bioremediation. In the microcosms, the consumption of nitrate and the production of inorganic carbon were strongly stimulated by the addition of the isoprenoid alkane pristane (2,6,10,14-tetramethylpentadecane). Within 102 days enrichment cultures degraded more than 90% of the pristane supplied as coatings on reticulated sinter glass rings. The study demonstrates that pristane can no longer be regarded as recalcitrant under anaerobic conditions. PMID:16535616

  11. MICROCOSM AND IN-SITU FIELD STUDIES OF ENHANCED BIOTRANSFORMATION OF TRICHLOROETHYLENE BY PHENOL-UTILIZING MICROORGANISMS

    EPA Science Inventory

    The ability of different aerobic groundwater microorganisms to cometabolically degrade trichloroethylene (TCE), 1,2-cis-dichloroethylene (c-DCE), and 1,2-trans-dichloroethylene (t-DCE) was evaluated both in groundwater-fed microcosms and in situ in a shallow aquifer. Microcosms a...

  12. Small Particles Intact Capture Experiment (SPICE)

    NASA Technical Reports Server (NTRS)

    Nishioka, Ken-Ji; Carle, G. C.; Bunch, T. E.; Mendez, David J.; Ryder, J. T.

    1994-01-01

    The Small Particles Intact Capture Experiment (SPICE) will develop technologies and engineering techniques necessary to capture nearly intact, uncontaminated cosmic and interplanetary dust particles (IDP's). Successful capture of such particles will benefit the exobiology and planetary science communities by providing particulate samples that may have survived unaltered since the formation of the solar system. Characterization of these particles may contribute fundamental data to our knowledge of how these particles could have formed into our planet Earth and, perhaps, contributed to the beginnings of life. The term 'uncontaminated' means that captured cosmic and IDP particles are free of organic contamination from the capture process and the term 'nearly intact capture' means that their chemical and elemental components are not materially altered during capture. The key to capturing cosmic and IDP particles that are organic-contamination free and nearly intact is the capture medium. Initial screening of capture media included organic foams, multiple thin foil layers, and aerogel (a silica gel); but, with the exception of aerogel, the requirements of no contamination or nearly intact capture were not met. To ensure no contamination of particles in the capture process, high-purity aerogel was chosen. High-purity aerogel results in high clarity (visual clearness), a useful quality in detection and recovery of embedded captured particles from the aerogel. P. Tsou at the Jet Propulsion Laboratory (JPL) originally described the use of aerogel for this purpose and reported laboratory test results. He has flown aerogel as a 'GAS-can Lid' payload on STS-47 and is evaluating the results. The Timeband Capture Cell Experiment (TICCE), a Eureca 1 experiment, is also flying aerogel and is scheduled for recovery in late April.

  13. The MBA in Singapore: A Microcosm of Communication Training for Management

    ERIC Educational Resources Information Center

    Rogers, Priscilla S.; Wong, Irene F. H.

    2005-01-01

    This study assesses communication training provided in MBA and executive MBA programs in Singapore. The authors found that Singapore is a microcosm in terms of (a) requirements for English competency, (b) the variety of communication offerings, and (c) the lack of uniformity in the delivery of communication training. Whereas Singaporean MBA/EMBA…

  14. Effect of isobutanol on toluene biodegradation in nitrate amended, sulfate amended and methanogenic enrichment microcosms.

    PubMed

    Jayamani, Indumathy; Cupples, Alison M

    2013-09-01

    Isobutanol is an alternate fuel additive that is being considered because of economic and lower emission benefits. However, future gasoline spills could result in co-contamination of isobutanol with gasoline components such as benzene, toluene, ethyl-benzene and xylene. Hence, isobutanol could affect the degradability of gasoline components thereby having an effect on contaminant plume length and half-life. In this study, the effect of isobutanol on the biodegradation of a model gasoline component (toluene) was examined in laboratory microcosms. For this, toluene and isobutanol were added to six different toluene degrading laboratory microcosms under sulfate amended, nitrate amended or methanogenic conditions. While toluene biodegradation was not greatly affected in the presence of isobutanol in five out of the six different experimental sets, toluene degradation was completely inhibited in one set of microcosms. This inhibition occurred in sulfate amended microcosms constructed with inocula from wastewater treatment plant activated sludge. Our data suggest that toluene degrading consortia are affected differently by isobutanol addition. These results indicate that, if co-contamination occurs, in some cases the in situ half-life of toluene could be significantly extended.

  15. EFFECTS OF MICROCOSM PREPARATION ON RATES OF TOLUENE BIODEGRADATION UNDER DENITRIFYING CONDITIONS

    EPA Science Inventory

    Microcosms were prepared with subsurface material from two aquifers to examine the effects of preparation methods on rates of toluene biodegradation under denitrifying conditions. In both cases, the data fit a zero-order kinetics plot. However, rates of removal were generally pro...

  16. AEROBIC SOIL MICROCOSMS FOR LONG-TERM BIODEGRADATION OF HYDROCARBON VAPORS

    EPA Science Inventory

    The aims of this research project included the development of laboratory protocols for the preparation of aerobic soil microcosms using aseptic field soil samples, and for the gas chromatographic analysis of hydrocarbon vapor biodegradation based on vapor samples obtained from th...

  17. Direct and indirect effects of pollutants on algae and algivorous ciliates in an aquatic indoor microcosm.

    PubMed

    Liebig, Markus; Schmidt, Gunnar; Bontje, Daniel; Kooi, Bob W; Streck, Georg; Traunspurger, Walter; Knacker, Thomas

    2008-06-23

    An aquatic indoor microcosm was used to study effects of the pesticides parathion-methyl and prometryn on phototrophic flagellates (Cryptomonas sp.) and predatory ciliates (Urotricha furcata). Parathion-methyl caused effects to flagellates and ciliates at the range of low mg L(-1), regardless of whether the organisms were exposed separately or combined in the multi-species test system. Prometryn caused effects on the flagellates at low microg L(-1) concentrations, resulting in a NOEC of 6.9 microg L(-1) in the single-species test and a NOEC of 15.2 microg L(-1) in the multi-species microcosm. For ciliates the NOEC decreased by factor 145 in the multi-species test compared to the NOEC of 2.2 mg L(-1) in the single-species test when exposed to prometryn. The lower NOEC for ciliates exposed to prometryn in the microcosm was most likely caused by an indirect effect due to reduced availability of flagellates as food. The measurement of nutrient concentrations in the test media and organisms facilitated the modelling of effects. The presented aquatic indoor microcosm is considered as a tool which could be standardised and applied as an instrument to provide data for higher tier risk assessment.

  18. Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene.

    PubMed

    Offre, Pierre; Prosser, James I; Nicol, Graeme W

    2009-10-01

    Autotrophic ammonia-oxidizing bacteria were considered to be responsible for the majority of ammonia oxidation in soil until the recent discovery of the autotrophic ammonia-oxidizing archaea. To assess the relative contributions of bacterial and archaeal ammonia oxidizers to soil ammonia oxidation, their growth was analysed during active nitrification in soil microcosms incubated for 30 days at 30 degrees C, and the effect of an inhibitor of ammonia oxidation (acetylene) on their growth and soil nitrification kinetics was determined. Denaturing gradient gel electrophoresis (DGGE) analysis of bacterial ammonia oxidizer 16S rRNA genes did not detect any change in their community composition during incubation, and quantitative PCR (qPCR) analysis of bacterial amoA genes indicated a small decrease in abundance in control and acetylene-containing microcosms. DGGE fingerprints of archaeal amoA and 16S rRNA genes demonstrated changes in the relative abundance of specific crenarchaeal phylotypes during active nitrification. Growth was also indicated by increases in crenarchaeal amoA gene copy number, determined by qPCR. In microcosms containing acetylene, nitrification and growth of the crenarchaeal phylotypes were suppressed, suggesting that these crenarchaea are ammonia oxidizers. Growth of only archaeal but not bacterial ammonia oxidizers occurred in microcosms with active nitrification, indicating that ammonia oxidation was mostly due to archaea in the conditions of the present study.

  19. Responses of microbial activity and decomposer organisms to contamination in microcosms containing coniferous forest soil.

    PubMed

    Salminen, J; Liiri, M; Haimi, J

    2002-09-01

    Soil respiration from microcosms contaminated with pentachlorophenol, 2-ethanolhexanoate, creosote, CuSO4, and benomyl was measured in order to evaluate usefulness of soil microcosms and microbial respiration rate monitoring as a toxicity test in soils with high organic matter content. Coniferous forest soil and its organisms were used as test objects. In addition, how a short-term low temperature period including frost affects respiration dynamics in stressed soils was studied, i.e., whether contaminants reduce resistance of the community to other (also natural) stresses. In addition, at the end of the experiment, effects of contaminants on faunal and microbial community structures were analyzed. Soil respiration measurements from the microcosms appeared to be a sensitive parameter for testing community-level effects of chemicals in the soil with high organic matter content. An 84-day exposure had acute effects, long-term effects, delaying effects, and total recovery of community respiration. Direct negative and indirect positive effects of chemical contamination on the community of soil organisms were found. Responses to contamination of soil respiration rate and structure of the soil community were parallel. Addition of pentachlorophenol, 2-ethanolhexane, and Cu into the soil reduced frost resistance of the decomposer community. It was concluded that soil respiration monitoring of artificially contaminated soil microcosms seems to be a useful tool for testing community-level toxic effects of chemicals.

  20. Effects Of Nutrient Source And Supply On Crude Oil Biodegradation In Continuous-Flow Beach Microcosms

    EPA Science Inventory

    Ammonium and nitrate were used as nitrogen sources to support microbial biodegradation of crude oil in continuous-flow beach microcosms to determine whether either nutrient was more effective in open systems, such as intertidal shorelines. No differences in the rate or the exten...

  1. Methanogenic degradation kinetics of phenolic compounds in aquifer-derived microcosms

    USGS Publications Warehouse

    Godsy, E.M.; Goerlitz, D.F.; Grbic-Galic, D.

    1992-01-01

    In this segment of a larger multidisciplinary study of the movement and fate of creosote derived compounds in a sand-and-gravel aquifer, we present evidence that the methanogenic degradation of the major biodegradable phenolic compounds and concomitant microbial growth in batch microcosms derived from contaminated aquifer material can be described using Monod kinetics. Substrate depletion and bacterial growth curves were fitted to the Monod equations using nonlinear regression analysis. The method of Marquardt was used for the determination of parameter values that best fit the experimental data by minimizing the residual sum of squares. The Monod kinetic constants (??max, Ks, Y, and kd) that describe phenol, 2-, 3-, and 4-methylphenol degradation and concomitant microbial growth were determined under conditions that were substantially different from those previously reported for microcosms cultured from sewage sludge. The Ks values obtained in this study are approximately two orders of magnitude lower than values obtained for the anaerobic degradation of phenol in digesting sewage sludge, indicating that the aquifer microorganisms have developed enzyme systems that are adapted to low nutrient conditions. The values for kd are much less than ??max, and can be neglected in the microcosms. The extremely low Y values, approximately 3 orders of magnitude lower than for the sewage sludge derived cultures, and the very low numbers of microorganisms in the aquifer derived microcosms suggest that these organisms use some unique strategies to survive in the subsurface environment. ?? 1992 Kluwer Academic Publishers.

  2. Dynamics of microbial community during bioremediation of phenanthrene and chromium(VI)-contaminated soil microcosms.

    PubMed

    Ibarrolaza, Agustín; Coppotelli, Bibiana M; Del Panno, María T; Donati, Edgardo R; Morelli, Irma S

    2009-02-01

    The combined effect of phenanthrene and Cr(VI) on soil microbial activity, community composition and on the efficiency of bioremediation processes has been studied. Biometer flask systems and soil microcosm systems contaminated with 2,000 mg of phenanthrene per kg of dry soil and different Cr(VI) concentrations were investigated. Temperature, soil moisture and oxygen availability were controlled to support bioremediation. Cr(VI) inhibited the phenanthrene mineralization (CO(2) production) and cultivable PAH degrading bacteria at levels of 500-2,600 mg kg(-1). In the bioremediation experiments in soil microcosms the degradation of phenanthrene, the dehydrogenase activity and the increase in PAH degrading bacteria counts were retarded by the presence of Cr(VI) at all studied concentrations (25, 50 and 100 mg kg(-1)). These negative effects did not show a correlation with Cr(VI) concentration. Whereas the presence of Cr(VI) had a negative effect on the phenanthrene elimination rate, co-contamination with phenanthrene reduced the residual Cr(VI) concentration in the water exchangeable Cr(VI) fraction (WEF) in comparison with the soil microcosm contaminated only with Cr(VI). Clear differences were found between the denaturing gradient gel electrophoresis (DGGE) patterns of each soil microcosm, showing that the presence of different Cr(VI) concentrations did modulate the community response to phenanthrene and caused perdurable changes in the structure of the microbial soil community.

  3. The Institution of Carlisle School: A Microcosm of 500 Years of Indian Policy.

    ERIC Educational Resources Information Center

    Fine, Mike

    The history of the Carlisle Indian Boarding School is a microcosm of 500 years of Indian policy. Established through the efforts of career military man Richard Pratt in 1879, the school symbolized the emerging view of assimilation, an important change from earlier attempts at genocide and prior militant attitudes towards the Indians. Long…

  4. The influence of sediment resuspension on the degradation of phenanthrene in flow-through microcosms.

    PubMed

    LeBlanc, Lawrence A; Gulnick, Jeanne D; Brownawell, Bruce J; Taylor, Gordon T

    2006-03-01

    The effect of sediment resuspension on the mineralization of phenanthrene was examined in microcosms and sediment slurries. In computer-controlled, flow-through microcosms, 14C-phenanthrene-amended sediments were resuspended into overlying oxic water at frequencies of 12, 4, 1, 0.25 and 0 d(-1). In slurry bottle experiments 14C-phenanthrene-amended sediments were continuously resuspended under oxic (excess air headspace) and anoxic (N2 headspace) conditions and mineralization was measured at periods from 2 h to 7 days. Our main findings were: (1) mineralization rate constants from the microcosms ranged from 0.001 to 0.01 d(-1) and increased with frequency of resuspension, (2) these rates fell between those measured in oxic and anoxic slurries and were predicted within a factor of 2.5 by a model in which mineralization depended on the degree of oxygen exposure, and (3) the phenanthrene-degrading bacterial community was more active in resuspended sediments incubated in the microcosms than in sediments which were not resuspended, or which were stored under refrigeration. We conclude from these experiments that the effects of sediment resuspension on phenanthrene degradation are consistent with a primary role of average oxygen exposure, and also an alteration in the PAH-degrading activity of microbial populations.

  5. Fate of Sulfamethazine in Surface Water Microcosms and Bioaccumulation in Sediment-dwelling Invertebrates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The antibiotic sulfamethazine can be transported from manured fields to surface water bodies. We investigated the degradation and fate of sulfamethazine in small pond water microcosms using 14C-phenyl-sulfamethazine, and found a 2.7-d half-life in pond water and 4.2-d half-life when added to the wat...

  6. STIMULATION OF THE REDUCTIVE DECHLORINATION OF TETRACHLOROETHENE IN ANAEROBIC AQUIFER MICROCOSMS BY THE ADDITION OF TOLUENE

    EPA Science Inventory

    In this study, the biologically mediated interactions of toluene and PCE under anaerobic conditions were investigated by using microcosms constructed with aquifer solids from an area that was exposed to both alkylbenzenes and chlorinated ethenes at the U.S. Coast Guard Air Statio...

  7. Persistence and renaturation efficiency of thermally treated waste recombinant DNA in defined aquatic microcosms.

    PubMed

    Fu, Xiao H; Wang, Lei; Le, Yi Q; Hu, Jia J

    2012-01-01

    To validate the possibility of horizontal gene transfer (HGT) from thermally denatured recombinant DNA discharged into the eco-system, a constructed plasmid was used to investigate the persistence and renaturation efficiency of thermally denatured recombinant DNA in defined aquatic microcosms. The results revealed that there was undecayed recombinant plasmid pMDLKJ material being discharged into the aquatic microcosms even after thermal treatment at either 100°C (using boiling water) or at 120°C (using an autoclave). The plasmid had a relatively long persistence time. At least 10(2) copies μL(-1) of a specific 245 bp fragment of the plasmid could be detected after 12 h and a specific 628 bp fragment could be detected up to 2 h. The thermally denatured recombinant DNA could efficiently renature and recover its functional double stranded structure in aquatic microcosms and the highest concentration of double-stranded DNA (dsDNA) occurred around 1 h after the thermally denatured DNA was added to the system. These results imply that when thermally treated recombinant DNAs are discharged into aquatic environments, they have enough time to renature and possibly transfer to other organisms. In addition, the recombinant DNA added to aquatic microcosms could be absorbed by the seston particles in water, such as mineral, organic and colloids particles with a maximum absorption value of about 5.18 ng L(-1). This absorbed DNA could persist longer in aquatic environments than free recombinant DNA, thus further favoring HGT.

  8. Xenopus egg cytoplasm with intact actin.

    PubMed

    Field, Christine M; Nguyen, Phuong A; Ishihara, Keisuke; Groen, Aaron C; Mitchison, Timothy J

    2014-01-01

    We report optimized methods for preparing Xenopus egg extracts without cytochalasin D, that we term "actin-intact egg extract." These are undiluted egg cytoplasm that contains abundant organelles, and glycogen which supplies energy, and represents the least perturbed cell-free cytoplasm preparation we know of. We used this system to probe cell cycle regulation of actin and myosin-II dynamics (Field et al., 2011), and to reconstitute the large, interphase asters that organize early Xenopus embryos (Mitchison et al., 2012; Wühr, Tan, Parker, Detrich, & Mitchison, 2010). Actin-intact Xenopus egg extracts are useful for analysis of actin dynamics, and interaction of actin with other cytoplasmic systems, in a cell-free system that closely mimics egg physiology, and more generally for probing the biochemistry and biophysics of the egg, zygote, and early embryo. Detailed protocols are provided along with assays used to check cell cycle state and tips for handling and storing undiluted egg extracts.

  9. Silica Aerogel Captures Cosmic Dust Intact

    NASA Technical Reports Server (NTRS)

    Tsou, P.

    1994-01-01

    The mesostructure of silica aerogel resembles stings of grapes, ranging in size from 10 to 100 angstrom. This fine mesostructure transmits nearly 90 percent of incident light in the visible, while providing sufficiently gentle dissipation of the kinetric energy of hypervelocity cosmic dust particles to permit their intact capture. We introduced silica aerogel in 1987 as capture medium to take advantage of its low density, fine mesostruicture and most importantly, its transparency, allowing optical location of captured micron sized particles.

  10. Exposure of Sink Drain Microcosms to Triclosan: Population Dynamics and Antimicrobial Susceptibility

    PubMed Central

    McBain, Andrew J.; Bartolo, Robert G.; Catrenich, Carl E.; Charbonneau, Duane; Ledder, Ruth G.; Price, Bradford B.; Gilbert, Peter

    2003-01-01

    Recent concern that the increased use of triclosan (TCS) in consumer products may contribute to the emergence of antibiotic resistance has led us to examine the effects of TCS dosing on domestic-drain biofilm microcosms. TCS-containing domestic detergent (TCSD) markedly lowered biofouling at 50% (wt/vol) but was poorly effective at use levels. Long-term microcosms were established and stabilized for 6 months before one was subjected to successive 3-month exposures to TCSD at sublethal concentrations (0.2 and 0.4% [wt/vol]). Culturable bacteria were identified by 16S rDNA sequence analysis, and their susceptibilities to four biocides and six antibiotics were determined. Microcosms harbored ca. 10 log10 CFU/g of biofilm, representing at least 27 species, mainly gamma proteobacteria, and maintained dynamic stability. Viable cell counts were largely unaffected by TCSD exposure, but species diversity was decreased, as corroborated by denaturing gradient gel electrophoresis analysis. TCS susceptibilities ranged widely within bacterial groups, and TCS-tolerant strains (including aeromonads, pseudomonads, stenotrophomonads, and Alcaligenes spp.) were isolated before and after TCSD exposure. Several TCS-tolerant bacteria related to Achromobacter xylosoxidans became clonally expanded during dosing. TCSD addition did not significantly affect the community profiles of susceptibility to the test biocides or antibiotics. Several microcosm isolates, as well as reference bacteria, caused clearing of particulate TCS in solid media. Incubations of consortia and isolates with particulate TCS in liquid led to putative TCS degradation by the consortia and TCS solubilization by the reference strains. Our results support the view that low-level exposure of environmental microcosms to TCS does not affect antimicrobial susceptibility and that TCS is degradable by common domestic biofilms. PMID:12957932

  11. Mineralogical, chemical, organic and microbial properties of subsurface soil cores from Mars Desert Research Station (Utah, USA): Phyllosilicate and sulfate analogues to Mars mission landing sites

    NASA Astrophysics Data System (ADS)

    Stoker, Carol R.; Clarke, Jonathan; Direito, Susana O. L.; Blake, David; Martin, Kevin R.; Zavaleta, Jhony; Foing, Bernard

    2011-07-01

    We collected and analysed soil cores from four geologic units surrounding Mars Desert Research Station (MDRS) Utah, USA, including Mancos Shale, Dakota Sandstone, Morrison formation (Brushy Basin member) and Summerville formation. The area is an important geochemical and morphological analogue to terrains on Mars. Soils were analysed for mineralogy by a Terra X-ray diffractometer (XRD), a field version of the CheMin instrument on the Mars Science Laboratory (MSL) mission (2012 landing). Soluble ion chemistry, total organic content and identity and distribution of microbial populations were also determined. The Terra data reveal that Mancos and Morrison soils are rich in phyllosilicates similar to those observed on Mars from orbital measurements (montmorillonite, nontronite and illite). Evaporite minerals observed include gypsum, thenardite, polyhalite and calcite. Soil chemical analysis shows sulfate the dominant anion in all soils and SO4>>CO3, as on Mars. The cation pattern Na>Ca>Mg is seen in all soils except for the Summerville where Ca>Na. In all soils, SO4 correlates with Na, suggesting sodium sulfates are the dominant phase. Oxidizable organics are low in all soils and range from a high of 0.7% in the Mancos samples to undetectable at a detection limit of 0.1% in the Morrison soils. Minerals rich in chromium and vanadium were identified in Morrison soils that result from diagenetic replacement of organic compounds. Depositional environment, geologic history and mineralogy all affect the ability to preserve and detect organic compounds. Subsurface biosphere populations were revealed to contain organisms from all three domains (Archaea, Bacteria and Eukarya) with cell density between 3.0×106 and 1.8×107 cells ml-1 at the deepest depth. These measurements are analogous to data that could be obtained on future robotic or human Mars missions and results are relevant to the MSL mission that will investigate phyllosilicates on Mars.

  12. Microcosm study for revegetation of barren land with wild plants by some plant growth-promoting rhizobacteria.

    PubMed

    Ahn, Tae-Seok; Ka, Jong-Ok; Lee, Geon-Hyoung; Song, Hong-Gyu

    2007-01-01

    Growth promotion of wild plants by some plant growth-promoting rhizobacteria (PGPR) was examined in the microcosms composed of soils collected separately from a grass-covered site and a nongrass-covered site in a lakeside barren area at Lake Paro, Korea. After sowing the seeds of eight kinds of wild plants and inoculation of several strains of PGPR, the total bacterial number and microbial activity were measured during 5 months of study period, and the plant biomasses grown were compared at the end of the study. Acridine orange direct counts in the inoculated microcosms, 1.3-9.8 x 10(9) cells x g soil(-1) in the soil from the grass-covered area and 0.9-7.2 x 10(9) cells x g soil(-1) in the soil from the nongrass-covered site, were almost twice higher than those in the uninoculated microcosms. The number of Pseudomonas sp., well-known bacteria as PGPR, and the soil dehydrogenase activity were also higher in the inoculated soils than the uninoculated soils. The first germination of sowed seeds in the inoculated microcosm was 5 days earlier than the uninoculated microcosm. Average lengths of all plants grown during the study period were 26% and 29% longer in the inoculated microcosms starting with the grass-covered soil and the nongrass-covered soil, respectively, compared with those in the uninoculated microcosms. Dry weights of whole plants grown were 67-82% higher in the inoculated microcosms than the uninoculated microcosms. Microbial population and activity and growth promoting effect by PGPR were all higher in the soils collected from the grass-covered area than in the nongrass-covered area. The growth enhancement of wild plants seemed to occur by the activities of inoculated microorganisms, and this capability of PGPR may be utilized for rapid revegetation of some barren lands.

  13. 50 CFR 622.493 - Landing Caribbean queen conch intact.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... conch intact. (a) A Caribbean queen conch in or from the Caribbean EEZ must be maintained with meat and shell intact. (b) The operator of a vessel that fishes in the EEZ is responsible for ensuring...

  14. 50 CFR 622.493 - Landing Caribbean queen conch intact.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... conch intact. (a) A Caribbean queen conch in or from the Caribbean EEZ must be maintained with meat and shell intact. (b) The operator of a vessel that fishes in the EEZ is responsible for ensuring...

  15. Calcium Signaling in Intact Dorsal Root Ganglia

    PubMed Central

    Gemes, Geza; Rigaud, Marcel; Koopmeiners, Andrew S.; Poroli, Mark J.; Zoga, Vasiliki; Hogan, Quinn H.

    2013-01-01

    Background Ca2+ is the dominant second messenger in primary sensory neurons. In addition, disrupted Ca2+ signaling is a prominent feature in pain models involving peripheral nerve injury. Standard cytoplasmic Ca2+ recording techniques use high K+ or field stimulation and dissociated neurons. To compare findings in intact dorsal root ganglia, we used a method of simultaneous electrophysiologic and microfluorimetric recording. Methods Dissociated neurons were loaded by bath-applied Fura-2-AM and subjected to field stimulation. Alternatively, we adapted a technique in which neuronal somata of intact ganglia were loaded with Fura-2 through an intracellular microelectrode that provided simultaneous membrane potential recording during activation by action potentials (APs) conducted from attached dorsal roots. Results Field stimulation at levels necessary to activate neurons generated bath pH changes through electrolysis and failed to predictably drive neurons with AP trains. In the intact ganglion technique, single APs produced measurable Ca2+ transients that were fourfold larger in presumed nociceptive C-type neurons than in nonnociceptive Aβ-type neurons. Unitary Ca2+ transients summated during AP trains, forming transients with amplitudes that were highly dependent on stimulation frequency. Each neuron was tuned to a preferred frequency at which transient amplitude was maximal. Transients predominantly exhibited monoexponential recovery and had sustained plateaus during recovery only with trains of more than 100 APs. Nerve injury decreased Ca2+ transients in C-type neurons, but increased transients in Aβ-type neurons. Conclusions Refined observation of Ca2+ signaling is possible through natural activation by conducted APs in undissociated sensory neurons and reveals features distinct to neuronal types and injury state. PMID:20526180

  16. Sodium Absorption by Intact Sugar Beet Plants

    PubMed Central

    El-Sheikh, Adel M; Ulrich, Albert

    1971-01-01

    Sodium absorption by intact sugar beet plants (Beta vulgaris) was found to be mediated by at least two distinct mechanisms when uptake was studied over a wide range of Na and K concentrations. The first mechanism operates at low Na concentrations (<1 milliequivalent per liter); presence of K completely blocks this mechanism for Na. The second mechanism operates at high Na concentrations (>1 milliequivalent per liter), transporting Na as well as K; but apparently this mechanism is not active for Na absorption in young sugar beet plants up to the 10-leaf stage. PMID:16657872

  17. Fate and effects of the insecticide-miticide chlorfenapyr in outdoor aquatic microcosms.

    PubMed

    Rand, Gary M

    2004-05-01

    The concentrations of chlorfenapyr in water and sediment in a lentic pond following early and late applications in a Florida crop treatment program were predicted using PRZM and EXAMS modeling and incorporating 30 years of actual rainfall data. An outdoor microcosm study was also conducted to determine the fate of chlorfenapyr and its effects on zooplankton, macroinvertebrates, phytoplankton, and fish in a freshwater system under exposure conditions representing simulated surface runoff and/or spray drift. The microcosm design used a regression model with five treatments (i.e., 300 microg/L spray, 30 microg/L spray, 15 microg/L spray and 30 microg/L runoff, 1.2 microg/L spray and 2.5 microg/L runoff, 30 microg/L runoff) plus a control. Chlorfenapyr was applied as an aqueous suspension concentrate (36% a.i.) to six microcosm tanks (30.9 m3). The no-observed-effect-concentration (NOEC) for zooplankton was the water concentration produced from the combination 1.2 microg/L spray and 2.5 microg/L runoff treatment. The NOEC for bluegill sunfish was the water concentration produced from the 30 microg/L runoff, which was significantly higher than the exposure concentrations from the lowest combination treatment. Chlorfenapyr was more toxic via spray to the water than via an exposure simulating surface runoff. The 96-h time weighted average concentrations (TWAs) from the lowest joint treatment and the 30 microg/L runoff treatment in the microcosm study were similar to model-predicted water 96-h TWA concentrations from early and late applications. The toxicity data from laboratory and microcosm studies along with water exposure data indicate low hazard to zooplankton species in the water column. Although chlorfenapyr remained in sediment, TWAs concentrations from the microcosm study along with model-predicted concentrations indicate low hazard to benthic invertebrate species based on acute toxicity to amphipods in the laboratory. Results from this assessment indicate that

  18. Response of zooplankton and phytoplankton communities to creosote-impregnated Douglas fir pilings in freshwater microcosms.

    PubMed

    Sibley, P K; Harris, M L; Bestari, K T; Steele, T A; Robinson, R D; Gensemer, R W; Day, K E; Solomon, K R

    2004-07-01

    Creosote has been used extensively as an industrial wood preservative for the protection of marine pilings, railway ties, and utility poles and is a common source of polycyclic aromatic hydrocarbons (PAHs) into aquatic environments. At present, there is little information by which to judge the potential for creosote leached from impregnated pilings to cause toxicity to biota in aquatic environments. The objective of the current study was to assess the effects of creosote on zooplankton and phytoplankton populations in freshwater microcosms in relation to changes in the concentration and composition of PAHs leached from creosote-impregnated Douglas fir pilings during an 83-day exposure period. The study consisted of single microcosms containing one half, one, two, three, four, and six treated pilings. Two microcosms that received untreated pilings were used as controls. The total surface area of pilings in each microcosm was normalized by adding the appropriate number of untreated pilings. Samples were collected periodically between -14 and 83 days pre- and postexposure to determine aqueous concentrations of 15 priority PAHs and to assess the response of zooplankton and phytoplankton communities. Plankton community response to creosote was analyzed using principle responses curves. Peak aqueous concentrations of sigmaPAH occurred at day 7, ranging from 7.3 to 97.3 microg/L. Zooplankton abundance decreased in all microcosms after introduction of the impregnated pilings, with the magnitude of response varying as a function of aqueous creosote concentration. Using inverse regression, a no-observed-effect concentration for the zooplankton community of 11.1 microg/L was estimated. In contrast, algal abundance and diversity increased in all treatments between 7 and 21 days and attained levels up to twice that in control microcosms. This trend most likely reflected decreased grazing pressure because of the decrease in zooplankton populations, but it may also have reflected

  19. Molecular Analysis of Microbial Community Structures in Pristine and Contaminated Aquifers: Field and Laboratory Microcosm Experiments

    PubMed Central

    Shi, Y.; Zwolinski, M. D.; Schreiber, M. E.; Bahr, J. M.; Sewell, G. W.; Hickey, W. J.

    1999-01-01

    This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminated (NC) and (ii) examine alterations in microbial community structures resulting from exposure to toluene and/or electron acceptor supplementation (nitrate). The latter objective was addressed by using the NC and FC aquifer materials for anaerobic microcosm studies in which phylogenetic probe analysis was complemented by microbial activity assays. Domain probe analysis of the aquifer samples showed that the communities were predominantly Bacteria; Eucarya and Archaea were not detectable. At the phylum and subclass levels, the FC and NC aquifer material had similar relative abundance distributions of 43 to 65% β- and γ-Proteobacteria (B+G), 31 to 35% α-Proteobacteria (ALF), 15 to 18% sulfate-reducing bacteria, and 5 to 10% high G+C gram positive bacteria. Compared to that of the NC region, the community structure of the FC material differed mainly in an increased abundance of B+G relative to that of ALF. The microcosm communities were like those of the field samples in that they were predominantly Bacteria (83 to 101%) and lacked detectable Archaea but differed in that a small fraction (2 to 8%) of Eucarya was detected regardless of the treatment applied. The latter result was hypothesized to reflect enrichment of anaerobic protozoa. Addition of nitrate and/or toluene stimulated microbial activity in the microcosms, but only supplementation of toluene alone significantly altered community structures. For the NC material, the dominant subclass shifted from B+G to ALF, while in the FC microcosms 55 to 65% of the Bacteria community was no longer identifiable by the phylum or subclass probes used. The latter result suggested that toluene exposure fostered the proliferation of phylotype(s) that were otherwise minor constituents of the

  20. Short-term emissions of ammonia and carbon dioxide from cattle urine contaminated tropical grassland microcosm.

    PubMed

    Majumdar, Deepanjan; Patel, Manoj; Drabar, Reena; Vyas, Manish

    2006-11-01

    The study was designed to understand the emissions of ammonia (NH(3)) and carbon dioxide (CO(2)) from a single cattle urination event on a tropical grassland and underline the significance of the emissions in the context of huge animal population grazing on large pasture areas in some countries. Emissions of ammonia (NH(3)) and carbon dioxide (CO(2)) were monitored for three weeks from a tropical grassland (dominated by Cynodon dactylon Pers.) microcosm contaminated with cow and buffalo urine. The grassland microcosms were treated with urine (50 and 100 ml of each) only once and irrigated with water once every week. Ammonia was sampled by an automatic sampling system comprising of a vacuum pump, three-way stopcocks and rubber tubing and an impinger containing suitable absorbing solution (H(2)SO(4)), connected to the tubing suitably. The sampled gas, after sucked by the vacuum pump and absorbed in H(2)SO(4), was allowed to enter the closed microcosm again maintaining internal pressure of the microcosm. Carbon dioxide was sampled by absorption in an alkali (NaOH) trap inside the microcosm. Both NH(3) and CO(2) emissions were highly variable temporally and there was no continuous increasing or decreasing emission trend with time. Respectively, 45 and 46% of total NH(3)-N were emitted within first 48 h from 50 and 100 ml cow urine application while the corresponding values for buffalo urine were 34 and 32%. Total NH(3)-N emissions, integrated for sampling days (i.e. 1, 2, 3, 4, 6, 15, 18 and 21st) were 11 and 6% in cow and 8 and 5% in buffalo urine, of the total-N added through 50 and 100 ml urine samples. Carbon dioxide emissions were standardized at 25 degrees C by using a suitable formula which were lower than actual emissions at actual soil temperature (> 25 degrees C). Carbon dioxide emission rates were classified on the basis of soil repiratory classification and classes ranged from moderately low soil activity up to unusually high soil activity, the latter

  1. 7 CFR 160.29 - Containers to remain intact.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Containers to remain intact. 160.29 Section 160.29... STANDARDS FOR NAVAL STORES Analysis, Inspection, and Grading on Request § 160.29 Containers to remain intact... the containers holding such naval stores remain intact as sampled until the analysis,...

  2. Rapid isolation of intact chloroplasts from spinach leaves.

    PubMed

    Joly, David; Carpentier, Robert

    2011-01-01

    In this chapter, a rapid method to isolate intact chloroplasts from spinach leaves is described. Intact chloroplasts are isolated using two short centrifugation steps and avoiding the use of percoll gradient. Intactness of chloroplast is evaluated by the inability of potassium ferricyanide to enter inside the chloroplasts and to act as an electron acceptor for photosystem II.

  3. A simple, inexpensive, and field-relevant microcosm tidal simulator for use in marsh macrophyte studies1

    PubMed Central

    MacTavish, Rachel M.; Cohen, Risa A.

    2014-01-01

    • Premise of the study: A microcosm unit with tidal simulation was developed to address the challenge of maintaining ecologically relevant tidal regimes while performing controlled greenhouse experiments on smooth cordgrass, Spartina alterniflora. • Methods and Results: We designed a simple, inexpensive, easily replicated microcosm unit with tidal simulation and tested whether S. alterniflora growth in microcosms with tidal simulation was similar to that of tidally influenced plants in the field on Sapelo Island, Georgia. After three months of exposure to either natural or simulated tidal treatment, plants in microcosms receiving tidal simulation had similar stem density, height, and above- and belowground biomass to plants in field plots. • Conclusions: The tidal simulator developed may provide an inexpensive, effective method for conducting studies on S. alterniflora and other tidally influenced plants in controlled settings to be used not only to complement field studies, but also in locations without coastal access. PMID:25383265

  4. Microbial community dynamics associated with veterinary antibiotics removal in constructed wetlands microcosms.

    PubMed

    Fernandes, Joana P; Almeida, C Marisa R; Pereira, Ana C; Ribeiro, Iolanda L; Reis, Izabela; Carvalho, Pedro; Basto, M Clara P; Mucha, Ana P

    2015-04-01

    This study aimed to evaluate the response of the microbial community from CWs microcosms tested for the removal of two veterinary antibiotics, enrofloxacin (ENR) and tetracycline (TET), from livestock industry wastewater. Three treatments were tested (control, ENR or TET (100 μg L(-1))) over 12 weeks in microcosms unplanted and planted with Phragmites australis. CWs removal efficiency was relatively stable along time, with removals higher than 98% for ENR and 94% for TET. In addition, CWs were able to reduce wastewater toxicity, independently of antibiotics presence. Despite no significant differences were observed in terms of microbial abundance, bacterial richness or diversity, analysis of similarities (two-way crossed ANOSIM) showed a significant effect of both time and treatments in bacterial community structure. This study points to CWs applicability for veterinary antibiotics removal from livestock wastewaters, showing that CWs microbial communities were able to adapt without significant changes in their diversity or depuration capacity.

  5. Recollections of Parent Characteristics and Attachment Patterns for College Women of Intact vs. Non-Intact Families

    ERIC Educational Resources Information Center

    Kilmann, Peter R.; Carranza, Laura V.; Vendemia, Jennifer M. C.

    2006-01-01

    This study contrasted offsprings' attachment patterns and recollections of parent characteristics in two college samples: 147 females from intact biological parents and 157 females of parental divorce. Secure females from intact or non-intact families rated parents positively, while insecure females rated parents as absent, distant, and demanding.…

  6. Direct and indirect effects of the fungicide azoxystrobin in outdoor brackish water microcosms.

    PubMed

    Gustafsson, Kerstin; Blidberg, Eva; Elfgren, Irene Karlsson; Hellström, Anna; Kylin, Henrik; Gorokhova, Elena

    2010-02-01

    The effects of the strobilurin fungicide azoxystrobin were studied in brackish water microcosms, with natural plankton communities and sediment. Two experiments were conducted: Experiment 1 (nominal conc. 0, 15 and 60 microg/L, 24-L outdoor microcosms for 21 days) and a second, follow-up, Experiment 2 (nominal conc. 0, 3, 7.5, 15 microg/L, 4-L indoor microcosms for 12 days). The microcosms represent a simplified brackish water community found in shallow semi-enclosed coastal areas in agricultural districts in the Baltic Sea region. Measured water concentrations of the fungicide (Experiment 1) were, on average, 83 and 62% of nominal concentrations directly after application, and 25 and 30% after 21 days, for the low and high dose treatments, respectively, corresponding to mean DT50-values of 15.1 and 25.8 days, for low and high dose treatments, respectively. In Experiment 1, direct toxic effects on calanoid copepods at both test concentrations were observed. Similarly, in Experiment 2, the copepod abundance was significantly reduced at all tested concentrations. There were also significant secondary effects on zooplankton and phytoplankton community structure, standing stocks and primary production. Very few ecotoxicological studies have investigated effects of plant protection products on Baltic organisms in general and effects on community structure and function specifically. Our results show that azoxystrobin is toxic to brackish water copepods at considerably lower concentrations than previously reported from single species tests on freshwater crustaceans, and that direct toxic effects on this ecologically important group may lead to cascade effects altering lower food webs and ecosystem functioning.

  7. Polychlorinated biphenyl (PCB) anaerobic degradation in marine sediments: microcosm study and role of autochthonous microbial communities.

    PubMed

    Matturro, Bruna; Ubaldi, Carla; Grenni, Paola; Caracciolo, Anna Barra; Rossetti, Simona

    2016-07-01

    Polychlorobiphenyl (PCB) biodegradation was followed for 1 year in microcosms containing marine sediments collected from Mar Piccolo (Taranto, Italy) chronically contaminated by this class of hazardous compounds. The microcosms were performed under strictly anaerobic conditions with or without the addition of Dehalococcoides mccartyi, the main microorganism known to degrade PCBs through the anaerobic reductive dechlorination process. Thirty PCB congeners were monitored during the experiments revealing that the biodegradation occurred in all microcosms with a decrease in hepta-, hexa-, and penta-chlorobiphenyls (CBs) and a parallel increase in low chlorinated PCBs (tri-CBs and tetra-CBs). The concentrations of the most representative congeners detected in the original sediment, such as 245-245-CB and 2345-245-CB, and of the mixture 2356-34-CB+234-245-CB, decreased by 32.5, 23.8, and 46.7 %, respectively, after only 70 days of anaerobic incubation without any bioaugmentation treatment. Additionally, the structure and population dynamics of the microbial key players involved in the biodegradative process and of the entire mixed microbial community were accurately defined by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) in both the original sediment and during the operation of the microcosm. The reductive dehalogenase genes of D. mccartyi, specifically involved in PCB dechlorination, were also quantified using real-time PCR (qPCR). Our results demonstrated that the autochthonous microbial community living in the marine sediment, including D. mccartyi (6.32E+06 16S rRNA gene copy numbers g(-1) sediment), was able to efficiently sustain the biodegradation of PCBs when controlled anaerobic conditions were imposed.

  8. Direct Link between Toluene Degradation in Contaminated-Site Microcosms and a Polaromonas Strain ▿

    PubMed Central

    Sun, Weimin; Xie, Shuguang; Luo, Chunling; Cupples, Alison M.

    2010-01-01

    Stable isotope probing (SIP) was used to identify the aerobic toluene-degrading microorganism in soil microcosms. Several approaches (terminal restriction fragment length polymorphism, 16S rRNA gene sequencing, and quantitative PCR) provided evidence that the microorganism responsible was a member of the genus Polaromonas and could grow on toluene. This microorganism also transformed benzene, but not m-xylene or cis-dichloroethene. PMID:20008173

  9. Methyl t-Butyl Ether Mineralization in Surface-Water Sediment Microcosms under Denitrifying Conditions

    USGS Publications Warehouse

    Bradley, P.M.; Chapelle, F.H.; Landmeyer, J.E.

    2001-01-01

    Mineralization of [U-14C] methyl t-butyl ether (MTBE) to 14CO2 without accumulation of t-butyl alcohol (TBA) was observed in surface-water sediment microcosms under denitrifying conditions. Methanogenic activity and limited transformation of MTBE to TBA were observed in the absence of denitrification. Results indicate that bed sediment microorganisms can effectively degrade MTBE to nontoxic products under denitrifying conditions.

  10. Naturally-Derived Microcosms for Estimating Stress Effects in Aquatic Ecosystems

    DTIC Science & Technology

    1991-05-31

    responses and the responses of standard test species. However, a heavy ash basin considered non -toxic to daphnids and fish adversely affected microcosms...artificial substrates to examine stress responses of biological systems using non -taxonomic measures cf adverse effect based on energy flow ’production...mobile laboratory test systems. To ensure that existing work in developing automated data collection and non -taxonomic methods for evaluating system

  11. Impact of imidacloprid on life-cycle development of Coccinella septempunctata in laboratory microcosms.

    PubMed

    Yu, Caihong; Lin, Ronghua; Fu, Maoran; Zhou, Yanming; Zong, Fulin; Jiang, Hui; Lv, Ning; Piao, Xiuying; Zhang, Jia; Liu, Yongquan; Brock, Theo C M

    2014-12-01

    Long-term effects of a single application of imidacloprid on ladybird beetle, Coccinella septempunctata L., were studied in indoor laboratory microcosms, starting with the 2nd instar larvae of C. septempunctata but covering the full life cycle. The microcosms comprised enclosures containing a pot with soil planted with broad bean plants and black bean aphid, Aphis craccivora Koch, as food. Exposure doses (0.85-13.66g a.i. ha(-1)) in the long-term microcosm experiment were based on a preliminary short-term (72h) toxicity test with 2nd instar larvae. The measurement endpoints used to calculate NOERs (No Observed Effect application Rates) included development time, hatching, pupation, adult emergence, survival and number of eggs produced. Furthermore, for these endpoints ER50 (application rate causing 50 percent effect) and LR50 (application rate causing 50 percent mortality) values were calculated when possible. The single imidacloprid application affected survival (lowest LR50 4.07g a.i. ha(-1); NOER 3.42g a.i. ha(-1)), egg production (ER50 26.63g a.i. ha(-1)) and egg hatching (NOER 6.83g a.i. ha(-1)). Statistically significant treatment-related effects on the whole development duration, pupation and adult emergence could not be demonstrated (NOER≥13.66g a.i. ha(-1)). The lowest L(E)R50 values and NOERs derived from the laboratory microcosm test with C. septempunctata are lower than the reported field application rates of imidacloprid (15-60g a.i. ha(-1)) in cotton cultivation in China, suggesting potential risks to beneficial arthropods.

  12. Mercury Distribution, Methylation and Volatilization in Microcosms with and without the Sea Anemone Bunodosoma caissarum

    NASA Astrophysics Data System (ADS)

    Ansari, N. R.; Correia, R. R. S.; Fernandez, M. A. S.; Cordeiro, R. C.; Guimarães, J. R. D.

    2014-12-01

    Mercury (Hg) can be a dangerous contaminant and has a complex biogeochemical cycling in aquatic environments. The sea anemone Bunodosoma caissarum is an endemic species in Brazil capable of bioaccumulating Hg from the ambient seawater. The radiotracer 203Hg was used in order to investigate mechanisms of Hg uptake and depuration of B. caissarum and the distribution of Hg in laboratory model systems, with and without B. caissarum. A single initial spike of 203Hg was added to each microcosm. Microcosms had continuous air renovation and trapping of Hg volatile forms. Total Hg in different compartments was measured by gamma spectrometry. In the uptake experiment 203Hg activity was determined periodically in seawater and specimens for 6 days. At the end, specimens had an average bioconcentration factor of 70. After the uptake experiment, methylmercury (MeHg) in seawater was extracted and measured by liquid scintillation. In microcosms with and without B. caissarum, respectively 0.05% and 0.32% of the initial spike was found as MeHg. Hg was probably less available for methylation in the first because of bioaccumulation and higher concentrations of suspended particulate matter that could form complexes with Hg. After that, specimens were transferred to unspiked microcosms. After a 48 day depuration specimens still retained 35 - 70% of the previously bioaccumulated Hg and 0.2 - 2.4% of the total Hg was MeHg. The presence of B. caissarum resulted in an unexpected higher volatilization of Hg (58%) compared to controls (17%). This increased volatilization is possibly a result of Hg2+ reduction mediated by microorganisms associated with its tissues and mucus secretions and/or an unknown defense mechanism of this species.

  13. Oligodeoxynucleotide Probes for Detecting Intact Cells

    NASA Technical Reports Server (NTRS)

    Rosson, Reinhardt A.; Maurina-Brunker, Julie; Langley, Kim; Pynnonen, Christine M.

    2004-01-01

    A rapid, sensitive test using chemiluminescent oligodeoxynucleotide probes has been developed for detecting, identifying, and enumerating intact cells. The test is intended especially for use in detecting and enumerating bacteria and yeasts in potable water. As in related tests that have been developed recently for similar purposes, the oligodeoxynucleotide probes used in this test are typically targeted at either singlecopy deoxyribonucleic acid (DNA) genes (such as virulence genes) or the multiple copies (10,000 to 50,000 copies per cell) of 16S ribosomal ribonucleic acids (rRNAs). Some of those tests involve radioisotope or fluorescent labeling of the probes for reporting hybridization of probes to target nucleic acids. Others of those tests involve labeling with enzymes plus the use of chemiluminescent or chromogenic substrates to report hybridization via color or the emission of light, respectively. The present test is of the last-mentioned type. The chemiluminescence in the present test can be detected easily with relatively simple instrumentation. In developing the present test, the hybridization approach was chosen because hybridization techniques are very specific. Hybridization detects stable, inheritable genetic targets within microorganisms. These targets are not dependent on products of gene expression that can vary with growth conditions or physiological states of organisms in test samples. Therefore, unique probes can be designed to detect and identify specific genera or species of bacteria or yeast (in terms of rRNA target sequences) or can be designed to detect and identify virulence genes (genomic target sequences). Because of the inherent specificity of this system, there are few problems of cross-reactivity. Hybridization tests are rapid, but hybridization tests now available commercially lack sensitivity; typically, between 10(exp 6) and 10(exp 7) cells of the target organism are needed to ensure a reliable test. Consequently, the numbers of

  14. U(VI) bioreduction with emulsified vegetable oil as the electron donor--microcosm tests and model development.

    PubMed

    Tang, Guoping; Wu, Wei-Min; Watson, David B; Parker, Jack C; Schadt, Christopher W; Shi, Xiaoqing; Brooks, Scott C

    2013-04-02

    We conducted microcosm tests and biogeochemical modeling to study U(VI) reduction in contaminated sediments amended with emulsified vegetable oil (EVO). Indigenous microorganisms in the sediments degraded EVO and stimulated Fe(III), U(VI), and sulfate reduction, and methanogenesis. Acetate concentration peaked in 100-120 days in the EVO microcosms versus 10-20 days in the oleate microcosms, suggesting that triglyceride hydrolysis was a rate-limiting step in EVO degradation and subsequent reactions. Acetate persisted 50 days longer in oleate- and EVO- than in ethanol-amended microcosms, indicating that acetate-utilizing methanogenesis was slower in the oleate and EVO than ethanol microcosms. We developed a comprehensive biogeochemical model to couple EVO hydrolysis, production, and oxidation of long-chain fatty acids (LCFA), glycerol, acetate, and hydrogen, reduction of Fe(III), U(VI) and sulfate, and methanogenesis with growth and decay of multiple functional microbial groups. By estimating EVO, LCFA, and glycerol degradation rate coefficients, and introducing a 100 day lag time for acetoclastic methanogenesis for oleate and EVO microcosms, the model approximately matched observed sulfate, U(VI), and acetate concentrations. Our results confirmed that EVO could stimulate U(VI) bioreduction in sediments and the slow EVO hydrolysis and acetate-utilizing methanogens growth could contribute to longer term bioreduction than simple substrates (e.g., ethanol, acetate, etc.) in the subsurface.

  15. Enhanced and stabilized arsenic retention in microcosms through the microbial oxidation of ferrous iron by nitrate.

    PubMed

    Sun, Jing; Chillrud, Steven N; Mailloux, Brian J; Stute, Martin; Singh, Rajesh; Dong, Hailiang; Lepre, Christopher J; Bostick, Benjamin C

    2016-02-01

    Magnetite strongly retains As, and is relatively stable under Fe(III)-reducing conditions common in aquifers that release As. Here, laboratory microcosm experiments were conducted to investigate a potential As remediation method involving magnetite formation, using groundwater and sediments from the Vineland Superfund site. The microcosms were amended with various combinations of nitrate, Fe(II) (aq) (as ferrous sulfate) and lactate, and were incubated for more than 5 weeks. In the microcosms enriched with 10 mM nitrate and 5 mM Fe(II) (aq), black magnetic particles were produced, and As removal from solution was observed even under sustained Fe(III) reduction stimulated by the addition of 10 mM lactate. The enhanced As retention was mainly attributed to co-precipitation within magnetite and adsorption on a mixture of magnetite and ferrihydrite. Sequential chemical extraction, X-ray absorption spectroscopy and magnetic susceptibility measurements showed that these minerals formed at pH 6-7 following nitrate-Fe(II) addition, and As-bearing magnetite was stable under reducing conditions. Scanning electron microscopy and X-ray diffraction indicated that nano-particulate magnetite was produced as coatings on fine sediments, and no aging effect was detected on morphology over the course of incubation. These results suggest that a magnetite based strategy may be a long-term remedial option for As-contaminated aquifers.

  16. Gonadal development of larval male Xenopus laevis exposed to atrazine in outdoor microcosms

    USGS Publications Warehouse

    Jooste, A.M.; Du Preez, L.H.; Carr, J.A.; Giesy, J.P.; Gross, T.S.; Kendall, R.J.; Smith, E.E.; Van Der Kraak, G. L.; Solomon, K.R.

    2005-01-01

    The potential effects of atrazine on gonadal development in metamorphs and subadults of the African clawed frog (Xenopus laevis) were studied under conditions of natural photoperiod and temperatures in outdoor microcosms from August 2002 to June 2003 in South Africa. Triplicate 1100 L microcosms for each nominal concentration of 0.0, 1, 10, and 25 ??g of atrazine/L were used. Measured atrazine concentrations varied <25% throughout the study, and no atrazine was detected in the control microcosms. Tadpoles developed well at all concentrations. On the basis of histological examination of testes of recently metamorphosed stage 66 frogs, 57% of the individuals in the reference group exhibited testicular oocytes as compared with 57, 59, and 39% of the 1, 10, and 25 ??g/L atrazine groups, respectively. The average prevalence of testicular oocytes for all of the treatments including the controls was 54% in a single testis, while, in 35% of individuals, testicular oocytes were observed in both testes. The number of testicular oocytes per individual ranged from 0 to 58 with means of 9.5, 9.8, 8.5, and 11.1 for the 0.0, 1, 10, and 25 ??g of atrazine/L groups, respectively. Ten months after metamorphosis, another subset of juveniles was examined, and the maximum number of testicular oocytes observed was five in one animal. The presence of testicular oocytes was not related to exposure to atrazine and may be a natural phenomenon during ontogeny. ?? 2005 American Chemical Society.

  17. Emissions of NO and N2O in wetland microcosms for swine wastewater treatment.

    PubMed

    Zhang, Shunan; Liu, Feng; Xiao, Runlin; Li, Yong; Zhou, Juan; Wu, Jinshui

    2015-12-01

    Nitric oxide (NO) and nitrous oxide (N2O) emitted from wetland systems contribute an important proportion to the global warming effect. In this study, four wetland microcosms vegetated with Myriophyllum elatinoides (WM), Alternanthera philoxeroides (WA), Eichhornia crassipes (WE), or without vegetation (NW) were compared to investigate the emissions of NO and N2O during nitrogen (N) removal process when treating swine wastewater. After 30-day incubation, TN removal rates of 96.4, 74.2, 97.2, and 47.3 % were observed for the WM, WA, WE, and NW microcosms, respectively. Yet, no significant difference was observed in WM and WE (p > 0.05). The average NO and N2O emissions in WE was significantly higher than those in WM, WA, and NW (p < 0.05). In addition, the emission of N2O in WE accounted for 2.10 % of initial TN load and 2.17 % of the total amount of TN removal, compared with less than 1 % in the other microcosms. These findings indicate that wetland vegetated with M. elatinoides may be an optimal system for swine wastewater treatment, based on its higher removal of N and lower emissions of NO and N2O.

  18. The use of outdoor freshwater pond microcosms. III. Responses of phytoplankton and periphyton to pyridaben

    USGS Publications Warehouse

    Ross, R.M.; Krise, W.F.; Redell, L.A.; Bennett, R.M.

    2001-01-01

    An outdoor freshwater microcosm study was conducted in which pyridaben, an insecticide-miticide, was directly applied to water to determine its biological effects on phytoplankton and periphyton. Twenty-four microcosms (24 m3 each) were monitored for 11 months, then four treatments of pyridaben were applied two times at three concentrations (0.34, 34.0 ??g/L), including an untreated control. The succession of algal groups observed and the major genera found in microcosms during the baseline phase of the study were typical of oligo-mesotrophic systems in Florida. Following application of pyridaben, the most remarkable effect was a positive correlation of phytoplankton abundance with pyridaben concentrations in water; indicating increased abundance as a result of exposure. Both Chlorophyta and Pyrrophyta exhibited a significant increase (p=0.05) in population abundance at 3.4 and 34.0 ??g/L pyridaben. Chrysophyta also elicited a trend of increased abundance at 34.0 ??g/L, although the effect was not significant. The effects on phytoplankton populations were associated with the decline of zooplankton populations as a result of a direct effect of pyridaben exposure. There were no effects of pyridaben on periphyton communities or on functional endpoints. ?? 2001 by John Wiley & Sons, Inc.

  19. Magnetotactic bacteria in microcosms originating from the French Mediterranean Coast subjected to oil industry activities.

    PubMed

    Postec, Anne; Tapia, Nicolas; Bernadac, Alain; Joseph, Manon; Davidson, Sylvain; Wu, Long-Fei; Ollivier, Bernard; Pradel, Nathalie

    2012-01-01

    Magnetotactic bacteria (MTB) mineralize nanosized magnetite or greigite crystals within cells and thus play an important role in the biogeochemical process. Despite decades of research, knowledge of MTB distribution and ecology, notably in areas subjected to oil industry activities, is still limited. In the present study, we investigated the presence of MTB in the Gulf of Fos, French Mediterranean coast, which is subjected to intensive oil industry activities. Microcosms containing sediments/water (1:2, v/v) from several sampling sites were monitored over several weeks. The presence of MTB was revealed in five of eight sites. Diverse and numerous MTB were revealed particularly from one site (named CAR), whilst temporal variations of a homogenous magnetotactic cocci population was shown within the LAV site microcosm over a 4-month period. Phylogenetic analysis revealed that they belonged to Alphaproteobacteria, and a novel genus from the LAV site was evidenced. Among the physicochemical parameters measured, a correlation was shown between the variation of MTB abundance in microcosms and the redox state of sulphur compounds.

  20. Biosorbent, a promising material for remediation of eutrophic environments: studies in microcosm.

    PubMed

    Pantano, Glaucia; Ferreira, Josilei S; Aquino, Francisco W B; Pereira-Filho, Edenir R; Mozeto, Antonio A; Fadini, Pedro S

    2017-01-01

    Eutrophication is considered a global environmental problem that causes economic and biodiversity loss. Together with excess phosphorus in some aquatic environments, there is the depletion of phosphate rock deposits, which can directly affect fertilizer production and therefore global food security. Thus, the present work aimed to study a new remediation technique for eutrophic environments that enables the recovery of these environments through phosphorus adsorption in sawdust, creating the possibility to apply the phosphorus-enriched material as an agricultural fertilizer. The study was conducted in 36 microcosm flasks with water and sediment samples from a eutrophic reservoir in Ibirité/MG. The experiment was carried out using 18 control flasks and 18 others as treatment, consisting of water and eutrophic environment sediment and, additionally, two bags, containing 10 g of sawdust in each bag. The phosphorus adsorption on sawdust was more intense after 49 days of immersion in the microcosm, and reductions of 90% in the concentration of reactive soluble phosphorus were observed in the water column of the microcosm treatment at 159 days of the experiment. Based on the results, it can be concluded that, although the phosphorus concentration adsorbed on sawdust (16.2 μg g(-1)) is considered low, the use of the biosorbent is a particularly promising technique for remediation of eutrophic environments, as well as the possible reuse of the adsorbed phosphorus as a fertilizer in agriculture.

  1. [The impact of macro- and microcosm on the perception of illness and patient].

    PubMed

    Kalemba, Z

    1998-01-01

    The orgins of the idea of macro- and microcosm date back to the Ancient Greek thought. And however often that idea recurred in historically different epochs always carrying the sign of time it invariably assumed there was a correspondence between the universe (macrocosm) and man (microcosm). This type of correlation of both worlds was viewed as a reflection of cosmic harmony and common material (6/5th century BC) or the unity of what is created with the emphasis put on the uniqueness of man (Middle Ages). The philosophical consequence of such approach was the belief that the knowledge of one reality allows one to explain another. Most often such reasoning led from understanding the macrocosm (allowing for stars) to reflections on man. Advocates of such an approach to the perception of man and nature were two great scientific doctors Hippocrates (5th century BC) and Paracelsus (16th century). They both claimed that man retained communication with the whole universe. Paracelsus perceived the world and man in a unity that permitted to recognize an equivalent of anatomy in astronomy. This exceptional link between both cosms was a guarantee for health. Illness occurred as a result of the disturbance of harmony between both worlds. In this context, the task of medical science was to consist in such understanding of the forces present in macro- and microcosm that could restore the line between the nature and man inflicted with illness.

  2. Microcosm enrichment of biphenyl-degrading microbial communities from soils and sediments

    SciTech Connect

    Wagner-Doebler, I.; Bennasar, A.; Stroempl, C.; Bruemmer, I.; Eichner, C.; Grammel, I.; Moore, E.R.B.; Vancanneyt, M.

    1998-08-01

    A microcosm enrichment approach was employed to isolate bacteria which are representative of long-term biphenyl-adapted microbial communities. Growth of microorganisms was stimulated by incubating soil and sediment samples from polluted and nonpolluted sites with biphenyl crystals. After 6 months, stable population densities between 8 {times} 10{sup 9} and 2 {times} 10{sup 11} CFU/ml were established in the microcosms, and a large percentage of the organisms were able to grow on biphenyl-containing minimal medium plates. A total of 177 biphenyl-degrading strains were subsequently isolated and characterized by their ability to grow on biphenyl in liquid culture and to accumulate a yellow meta cleavage product when they were sprayed with dihydroxy-biphenyl. Isolates were identified by using a polyphasic approach, including fatty acid methyl ester (FAME) analysis, 16S rRNA gene sequence comparison, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell proteins, and genomic fingerprinting based on sequence variability in the 16S-23S ribosomal DNA intergenic spacer region. In all of the microcosms, isolates identified as Rhodococcus opacus dominated the cultivable microbial community, comprising a cluster of 137 isolates with very similar FAME profiles (Euclidean distances, <10) and identical 16S rRNA gene sequences.

  3. Jarosite-related chemical processes and water ecotoxicity in simplified anaerobic microcosm wetlands

    NASA Astrophysics Data System (ADS)

    Zhu, L.; Lin, C.; Wu, Y.; Lu, W.; Liu, Y.; Ma, Y.; Chen, A.

    2008-02-01

    Simulation experiments were conducted to examine whether jarosite is decomposed and toxic products are produced under anaerobic microcosm wetland conditions. The results show that jarosite was stable under water inundation in the microcosm wetland for a period of at least 56 days when no organic substance was added. However, jarosite became increasingly unstable with increasing amount of added organic matter. This resulted in entry of ferrous Fe into the soil solutions. Concentration of other heavy metals in the leachates was extremely low except for Mn. This is attributed to the maintenance of a high pH in the microcosm wetlands, which might cause re-precipitation of originally jarosite-borne heavy metals, if any. No acute toxicity was observed for leachate from the control (non organic matter-added treatment). However, leachates from various organic matter-added treatments show varying degrees of toxicity to the test organism and soluble Fe was likely to be the dominant metal of potential toxicity. Atmospheric exposure of leachate led to oxidation of ferrous Fe and precipitation of iron hydroxide, which caused a drop in leachate pH. This, in turn, inhibited further oxidation of ferrous Fe.

  4. Enhanced and stabilized arsenic retention in microcosms through the microbial oxidation of ferrous iron by nitrate

    DOE PAGES

    Sun, Jing; Chillrud, Steven N.; Mailloux, Brian J.; ...

    2015-10-23

    Magnetite strongly retains As, and is relatively stable under Fe(III)-reducing conditions common in aquifers that release As. In this paper, laboratory microcosm experiments were conducted to investigate a potential As remediation method involving magnetite formation, using groundwater and sediments from the Vineland Superfund site. The microcosms were amended with various combinations of nitrate, Fe(II) (aq) (as ferrous sulfate) and lactate, and were incubated for more than 5 weeks. In the microcosms enriched with 10 mM nitrate and 5 mM Fe(II) (aq), black magnetic particles were produced, and As removal from solution was observed even under sustained Fe(III) reduction stimulated bymore » the addition of 10 mM lactate. The enhanced As retention was mainly attributed to co-precipitation within magnetite and adsorption on a mixture of magnetite and ferrihydrite. Sequential chemical extraction, X-ray absorption spectroscopy and magnetic susceptibility measurements showed that these minerals formed at pH 6–7 following nitrate-Fe(II) addition, and As-bearing magnetite was stable under reducing conditions. Scanning electron microscopy and X-ray diffraction indicated that nano-particulate magnetite was produced as coatings on fine sediments, and no aging effect was detected on morphology over the course of incubation. Finally, these results suggest that a magnetite based strategy may be a long-term remedial option for As-contaminated aquifers.« less

  5. Identification of active oxalotrophic bacteria by Bromodeoxyuridine DNA labeling in a microcosm soil experiments.

    PubMed

    Bravo, Daniel; Martin, Gaëtan; David, Maude M; Cailleau, Guillaume; Verrecchia, Eric; Junier, Pilar

    2013-11-01

    The oxalate-carbonate pathway (OCP) leads to a potential carbon sink in terrestrial environments. This process is linked to the activity of oxalotrophic bacteria. Although isolation and molecular characterizations are used to study oxalotrophic bacteria, these approaches do not give information on the active oxalotrophs present in soil undergoing the OCP. The aim of this study was to assess the diversity of active oxalotrophic bacteria in soil microcosms using the Bromodeoxyuridine (BrdU) DNA labeling technique. Soil was collected near an oxalogenic tree (Milicia excelsa). Different concentrations of calcium oxalate (0.5%, 1%, and 4% w/w) were added to the soil microcosms and compared with an untreated control. After 12 days of incubation, a maximal pH of 7.7 was measured for microcosms with oxalate (initial pH 6.4). At this time point, a DGGE profile of the frc gene was performed from BrdU-labeled soil DNA and unlabeled soil DNA. Actinobacteria (Streptomyces- and Kribbella-like sequences), Gammaproteobacteria and Betaproteobacteria were found as the main active oxalotrophic bacterial groups. This study highlights the relevance of Actinobacteria as members of the active bacterial community and the identification of novel uncultured oxalotrophic groups (i.e. Kribbella) active in soils.

  6. Enhanced and Stabilized Arsenic Retention in Microcosms through the Microbial Oxidation of Ferrous Iron by Nitrate

    PubMed Central

    SUN, JING; CHILLRUD, STEVEN N.; MAILLOUX, BRIAN J.; STUTE, MARTIN; SINGH, RAJESH; DONG, HAILIANG; LEPRE, CHRISTOPHER J.; BOSTICK, BENJAMIN C.

    2016-01-01

    Magnetite strongly retains As, and is relatively stable under Fe(III)-reducing conditions common in aquifers that release As. Here, laboratory microcosm experiments were conducted to investigate a potential As remediation method involving magnetite formation, using groundwater and sediments from the Vineland Superfund site. The microcosms were amended with various combinations of nitrate, Fe(II)(aq)(as ferrous sulfate) and lactate, and were incubated for more than 5 weeks. In the microcosms enriched with 10 mM nitrate and 5 mM Fe(II)(aq), black magnetic particles were produced, and As removal from solution was observed even under sustained Fe(III) reduction stimulated by the addition of 10 mM lactate. The enhanced As retention was mainly attributed to co-precipitation within magnetite and adsorption on a mixture of magnetite and ferrihydrite. Sequential chemical extraction, X-ray absorption spectroscopy and magnetic susceptibility measurements showed that these minerals formed at pH 6 – 7 following nitrate-Fe(II) addition, and As-bearing magnetite was stable under reducing conditions. Scanning electron microscopy and X-ray diffraction indicated that nano-particulate magnetite was produced as coatings on fine sediments, and no aging effect was detected on morphology over the course of incubation. These results suggest that a magnetite based strategy may be a long-term remedial option for As-contaminated aquifers. PMID:26454120

  7. Enhanced and stabilized arsenic retention in microcosms through the microbial oxidation of ferrous iron by nitrate

    SciTech Connect

    Sun, Jing; Chillrud, Steven N.; Mailloux, Brian J.; Stute, Martin; Singh, Rajesh; Dong, Hailiang; Lepre, Christopher J.; Bostick, Benjamin C.

    2015-10-23

    Magnetite strongly retains As, and is relatively stable under Fe(III)-reducing conditions common in aquifers that release As. In this paper, laboratory microcosm experiments were conducted to investigate a potential As remediation method involving magnetite formation, using groundwater and sediments from the Vineland Superfund site. The microcosms were amended with various combinations of nitrate, Fe(II) (aq) (as ferrous sulfate) and lactate, and were incubated for more than 5 weeks. In the microcosms enriched with 10 mM nitrate and 5 mM Fe(II) (aq), black magnetic particles were produced, and As removal from solution was observed even under sustained Fe(III) reduction stimulated by the addition of 10 mM lactate. The enhanced As retention was mainly attributed to co-precipitation within magnetite and adsorption on a mixture of magnetite and ferrihydrite. Sequential chemical extraction, X-ray absorption spectroscopy and magnetic susceptibility measurements showed that these minerals formed at pH 6–7 following nitrate-Fe(II) addition, and As-bearing magnetite was stable under reducing conditions. Scanning electron microscopy and X-ray diffraction indicated that nano-particulate magnetite was produced as coatings on fine sediments, and no aging effect was detected on morphology over the course of incubation. Finally, these results suggest that a magnetite based strategy may be a long-term remedial option for As-contaminated aquifers.

  8. Protein methylation reactions in intact pea chloroplasts

    SciTech Connect

    Niemi, K.J. )

    1989-04-01

    Post-translational protein methylation was investigated in Pisum sativum chloroplasts. Intact pea chloroplasts were incubated with ({sup 3}H-methyl)-S-adenosylmethionine under various conditions. The chloroplasts were then separated into stromal and thylakoid fractions and analyzed for radioactivity transferred to protein. Light enhanced the magnitude of labeling in both fractions. One thylakoid polypeptide with an apparent molecular mass of 43 kDa was labeled only in the light. Several other thylakoid and stromal proteins were labeled in both light and dark-labeling conditions. Both base-labile methylation, carboxy-methylesters and base-stable groups, N-methylations were found. Further characterization of the methyl-transfer reactions will be presented.

  9. Drilling to gabbro in intact ocean crust.

    PubMed

    Wilson, Douglas S; Teagle, Damon A H; Alt, Jeffrey C; Banerjee, Neil R; Umino, Susumu; Miyashita, Sumio; Acton, Gary D; Anma, Ryo; Barr, Samantha R; Belghoul, Akram; Carlut, Julie; Christie, David M; Coggon, Rosalind M; Cooper, Kari M; Cordier, Carole; Crispini, Laura; Durand, Sedelia Rodriguez; Einaudi, Florence; Galli, Laura; Gao, Yongjun; Geldmacher, Jörg; Gilbert, Lisa A; Hayman, Nicholas W; Herrero-Bervera, Emilio; Hirano, Nobuo; Holter, Sara; Ingle, Stephanie; Jiang, Shijun; Kalberkamp, Ulrich; Kerneklian, Marcie; Koepke, Jürgen; Laverne, Christine; Vasquez, Haroldo L Lledo; Maclennan, John; Morgan, Sally; Neo, Natsuki; Nichols, Holly J; Park, Sung-Hyun; Reichow, Marc K; Sakuyama, Tetsuya; Sano, Takashi; Sandwell, Rachel; Scheibner, Birgit; Smith-Duque, Chris E; Swift, Stephen A; Tartarotti, Paola; Tikku, Anahita A; Tominaga, Masako; Veloso, Eugenio A; Yamasaki, Toru; Yamazaki, Shusaku; Ziegler, Christa

    2006-05-19

    Sampling an intact sequence of oceanic crust through lavas, dikes, and gabbros is necessary to advance the understanding of the formation and evolution of crust formed at mid-ocean ridges, but it has been an elusive goal of scientific ocean drilling for decades. Recent drilling in the eastern Pacific Ocean in Hole 1256D reached gabbro within seismic layer 2, 1157 meters into crust formed at a superfast spreading rate. The gabbros are the crystallized melt lenses that formed beneath a mid-ocean ridge. The depth at which gabbro was reached confirms predictions extrapolated from seismic experiments at modern mid-ocean ridges: Melt lenses occur at shallower depths at faster spreading rates. The gabbros intrude metamorphosed sheeted dikes and have compositions similar to the overlying lavas, precluding formation of the cumulate lower oceanic crust from melt lenses so far penetrated by Hole 1256D.

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

    NASA Astrophysics Data System (ADS)

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

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

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

    NASA Technical Reports Server (NTRS)

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

    2005-01-01

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

  12. Influence of sediment on the fate and toxicity of a polyethoxylated tallowamine surfactant system (MON 0818) in aquatic microcosms

    USGS Publications Warehouse

    Wang, N.; Besser, J.M.; Buckler, D.R.; Honegger, J.L.; Ingersoll, C.G.; Johnson, B.T.; Kurtzweil, M.L.; MacGregor, J.; McKee, M.J.

    2005-01-01

    The fate and toxicity of a polyethoxylated tallowamine (POEA) surfactant system, MON 0818, was evaluated in water-sediment microcosms during a 4-d laboratory study. A surfactant solution of 8 mg l-1 nominal concentration was added to each of nine 72-l aquaria with or without a 3-cm layer of one of two natural sediments (total organic carbon (TOC) 1.5% or 3.0%). Control well water was added to each of nine additional 72-l aquaria with or without sediment. Water samples were collected from the microcosms after 2, 6, 24, 48, 72, and 96 h of aging to conduct 48-h toxicity tests with Daphnia magna and to determine surfactant concentrations. Elevated mortality of D. magna (43-83%) was observed in overlying water sampled from water-only microcosms throughout the 96-h aging period, whereas elevated mortality (23-97%) was only observed in overlying water sampled from water-sediment microcosms during the first 24 h of aging. Measured concentrations of MON 0818 in water-only microcosms remained relatively constant (4-6 mg l-1) during the 96-h period, whereas the concentrations in overlying water from microcosms containing either of the two types of sediment dissipated rapidly, with half-lives of 13 h in the 3.0% TOC sediment and 18 h in the 1.5% TOC sediment. Both toxicity and the concentration of MON 0818 in overlying water decreased more rapidly in microcosms containing sediment with the higher percent TOC and clay and with a higher microbial biomass. Mortality of D. magna was significantly correlated with surfactant concentrations in the overlying water. These results indicate that the toxicity of the POEA surfactant in water rapidly declines in the presence of sediment due to a reduction in the surfactant concentration in the overlying water above the sediment.

  13. Uranium migration through intact sandstone cores

    NASA Astrophysics Data System (ADS)

    Read, D.; Lawless, T. A.; Sims, R. J.; Butter, K. R.

    1993-06-01

    Uranium is often considered to be a mobile radioelement in the natural environment owing to its tendency to form stable complexes with a number of aqueous anions, particularly in oxidising milieu. A series of infiltration experiments were devised to investigate this migration behaviour under rigidly controlled laboratory conditions. Intact cores of Permo-Triassic Clashach Sandstone were pre-equilibrated with synthetic groundwater solutions and continuous flow-through of uranium monitored together with pH and concentrations of other ions. Prior to performing each experiment a simulation was carried out using a one-dimensional coupled chemical transport code, encompassing a thermodynamic description of the electrical double layer. These calculations together with electron microscopy indicated the potential role played by iron oxyhydroxide grain coatings in retarding the uranium plume. Thus, a second series of experiments was initiated on pre-acidified cores from which all surface exposed iron had been removed, allowing an assessment of the retention capacity of non-ferric components. Taken together, the data clearly illustrate the strong affinity of aqueous uranium species for natural surfaces even under strongly oxidising conditions. The success of the model in predicting a priori the dominant trends in uranium migration behaviour is encouraging and may aid in prioritising analytical requirements for investigations in more complex geochemical situations than those studied here.

  14. Assessing microbial responses to iron enrichment in the Subarctic Northeast Pacific: Do microcosms reproduce the in situ condition?

    NASA Astrophysics Data System (ADS)

    Scarratt, M. G.; Marchetti, A.; Hale, M. S.; Rivkin, R. B.; Michaud, S.; Matthews, P.; Levasseur, M.; Sherry, N.; Merzouk, A.; Li, W. K. W.; Kiyosawa, H.

    2006-10-01

    A microcosm experiment was conducted in the NE Pacific in July 2002 to compare the microbial response between microcosms and the Subarctic Ecosystem Response to Iron-Enrichment Study (SERIES) in situ iron-enrichment experiment. Seawater microcosms (20 L) were incubated aboard ship under natural light using three treatments: (1) low-iron seawater amended with 4 nmol l -1 FeSO 4 (+Fe); (2) low-iron seawater amended with 4 nmol l -1 FeSO 4 and 86 nmol l -1 GeO 2 (+Fe+Ge); (3) seawater collected from the in situ Fe-enriched patch (PW). The +Fe+Ge treatment used germanium to control diatom growth to assess the role of diatoms in dimethylsulfoniopropionate (DMSP) production. The following variables were measured in the microcosms and in situ: chlorophyll a (chl a), nitrate ( NO3-), silicic acid (Si(OH) 4), phytoplankton abundance and species identification, bacterial abundance (including estimates of low- and high-DNA bacteria), bacterial production, bacterial specific growth rate, particulate and dissolved DMSP and dimethylsulfide (DMS) concentrations. There was little or no significant difference (ANCOVA) in the response of most variables between the +Fe and PW microcosms, but large differences were observed between both these treatments and the in situ data from the enriched patch. Chl a in all microcosms increased from ambient levels (approx. 0.5-1 μg l -1) to approx. 4.5-6.2 μg l -1 after 11 d incubation, when NO3- was fully depleted from all microcosms. During this same period, in situ chl a increased more slowly to a maximum of 2.9 μg l -1 on day 11. Nanophytoplankton and picophytoplankton were more abundant in the microcosms relative to the in situ community, which became dominated by large diatoms. Bacterial abundance was similar in the microcosms and in situ, but bacterial production was significantly higher in the microcosms. While neither DMSP d nor DMS accumulation showed significant differences between the microcosms and in situ , particulate DMSP

  15. Transgenic strain Escherichia coli Z905/pPHL7 survival in aquatic microcosms with different salinity

    NASA Astrophysics Data System (ADS)

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

    The population dynamics and expression variability of transgenic microorganism (TM) Escherichia coli Z905/pPHL7 (AprLux+) bioluminescence genes cloned in recombinant plasmid have been studied in the artificial aquatic ecosystems with different salinity and bacterial species composition. It was shown that in competition with indigenous microflora the TM population was 2-4 times lower than in sterile fresh-water and brackish microcosms. Higher salt concentration in the medium led to the differencies in displaying plasmid genes expression as compared to fresh-water microcosms, independent of their complexity. Particularly, in brackish medium the bioluminescence expression reduced to a greater extent and was revealed only at plating into TM accumulative cultures with high content of selective factor (50-200 μ kg/ml ampicillin). TM clones isolated from fresh-water microcosms maintained higher bioluminescence level, at that for sterile microcosms it was higher than for non-sterile. Many clones could be seen during the plating of microcosm water samples on the selective media.

  16. Agar-block microcosms for controlled plant tissue decomposition by aerobic fungi.

    PubMed

    Schilling, Jonathan S; Jacobson, K Brook

    2011-02-03

    The two principal methods for studying fungal biodegradation of lignocellulosic plant tissues were developed for wood preservative testing (soil-block; agar-block). It is well-accepted that soil-block microcosms yield higher decay rates, fewer moisture issues, lower variability among studies, and higher thresholds of preservative toxicity. Soil-block testing is thus the more utilized technique and has been standardized by American Society for Testing and Materials (ASTM) (method D 1413-07). The soil-block design has drawbacks, however, using locally-variable soil sources and in limiting the control of nutrients external (exogenous) to the decaying tissues. These drawbacks have emerged as a problem in applying this method to other, increasingly popular research aims. These modern aims include degrading lignocellulosics for bioenergy research, testing bioremediation of co-metabolized toxics, evaluating oxidative mechanisms, and tracking translocated elements along hyphal networks. Soil-blocks do not lend enough control in these applications. A refined agar-block approach is necessary. Here, we use the brown rot wood-degrading fungus Serpula lacrymans to degrade wood in agar-block microcosms, using deep Petri dishes with low-calcium agar. We test the role of exogenous gypsum on decay in a time-series, to demonstrate the utility and expected variability. Blocks from a single board rip (longitudinal cut) are conditioned, weighed, autoclaved, and introduced aseptically atop plastic mesh. Fungal inoculations are at each block face, with exogenous gypsum added at interfaces. Harvests are aseptic until the final destructive harvest. These microcosms are designed to avoid block contact with agar or Petri dish walls. Condensation is minimized during plate pours and during incubation. Finally, inoculum/gypsum/wood spacing is minimized but without allowing contact. These less technical aspects of agar-block design are also the most common causes of failure and the key source of

  17. Monitoring of soil bacterial community and some inoculated bacteria after prescribed fire in microcosm.

    PubMed

    Song, Hong-Gyu; Kim, Ok-Sun; Yoo, Jae-Jun; Jeon, Sun-Ok; Hong, Sun-Hee; Lee, Dong-Hun; Ahn, Tae-Seok

    2004-12-01

    The soil bacterial community and some inoculated bacteria were monitored to assess the microbial responses to prescribed fire in their microcosm. An acridine orange direct count of the bacteria in the unburned control soil were maintained at a relatively stable level (2.0 approximately 2.7 x 10(9) cells/g(-1).soil) during the 180 day study period. The number of bacteria in the surface soil was decreased by fire, but was restored after 3 months. Inoculation of some bacteria increased the number of inoculated bacteria several times and these elevated levels lasted several months. The ratios of eubacteria detected by a fluorescent in situ hybridization (FISH) method to direct bacterial count were in the range of 60 approximately 80% during the study period, with the exception of some lower values at the beginning, but there were no definite differences between the burned and unburned soils or the inoculated and uninoculated soils. In the unburned control soil, the ratios of alpha-, beta- and gamma-subgroups of the proteobacteria, Cytophaga-Flavobacterium and other eubacteria groups to that of the entire eubacteria were 13.7, 31.7, 17.1, 16.8 and 20.8%, respectively, at time 0. The overall change on the patterns of the ratios of the 5 subgroups of eubacteria in the uninoculated burned and inoculated soils were similar to those of the unburned control soil, with the exception of some minor variations during the initial period. The proportions of each group of eubacteria became similar in the different microcosms after 6 months, which may indicate the recovery of the original soil microbial community structure after fire or the inoculation of some bacteria. The populations of Azotobacter vinelandii, Bacillus megaterium and Pseudomonas fluorescens, which had been inoculated to enhance the microbial activities, and monitored by FISH method, showed similar changes in the microcosms, and maintained high levels for several months.

  18. Donor-dependent extent of uranium reduction for bioremediation of contaminated sediment microcosms.

    PubMed

    Madden, Andrew S; Palumbo, Anthony V; Ravel, Bruce; Vishnivetskaya, Tatiana A; Phelps, Tommy J; Schadt, Christopher W; Brandt, Craig C

    2009-01-01

    Bioremediation of uranium was investigated in microcosm experiments containing contaminated sediments from Oak Ridge, Tennessee to explore the importance of electron donor selection for uranium reduction rate and extent. In these experiments, all of the electron donors, including ethanol, glucose, methanol, and methanol with added humic acids, stimulated the reduction and immobilization of aqueous uranium by the indigenous microbial community. Uranium loss from solution began after the completion of nitrate reduction but essentially concurrent with sulfate reduction. When electron donor concentrations were normalized for their equivalent electron donor potential yield, the rates of uranium reduction were nearly equivalent for all treatments (0.55-0.95 micromol L(-1) d(-1)). Uranium reduction with methanol proceeded after a 15-d longer lag time relative to that of ethanol or glucose. Significant differences were not found with the inclusion of humic acids. The extent of U reduction in sediment slurries measured by XANES at various time periods after the start of the experiment increased in the order of ethanol (5-7% reduced at 77 and 153 d), glucose (49% reduced at 53 d), and methanol (93% reduced at 90 d). The microbial diversity of ethanol- and methanol-amended microcosms in their late stage of U reduction was analyzed with 16S rRNA gene amplification. Members of the Geobacteraceae were found in all microcosms as well as other potential uranium-reducing organisms, such as Clostridium and Desulfosporosinus. The effectiveness of methanol relative to ethanol at reducing aqueous and sediment-hosted uranium suggests that bioremediation strategies that encourage fermentative poising of the subsurface to a lower redox potential may be more effective for long-term uranium immobilization as compared with selecting an electron donor that is efficiently metabolized by known uranium-reducing microorganisms.

  19. Tracking the Response of Burkholderia cepacia G4 5223-PR1 in Aquifer Microcosms.

    PubMed

    Winkler, J; Timmis, K N; Snyder, R A

    1995-02-01

    The introduction of bacteria into the environment for bioremediation purposes (bioaugmentation) requires analysis and monitoring of microbial population dynamics to define persistence and activity from both efficacy and risk assessment perspectives. Burkholderia cepacia G4 5223-PR1 is a Tn5 insertion mutant which constitutively expresses a toluene ortho-monooxygenase that degrades trichloroethylene (TCE). This ability of G4 5223-PR1 to degrade TCE without aromatic induction may be useful for bioremediation of TCE-containing aquifers and groundwater. Thus, a simulated aquifer sediment system and groundwater microcosms were used to monitor the survival of G4 5223-PR1. The fate of G4 5223-PR1 in sediment was monitored by indirect immunofluorescence microscopy, a colony blot assay, and growth on selective medium. G4 5223-PR1 was detected immunologically by using a highly specific monoclonal antibody which reacted against the O-specific polysaccharide chain of the lipopolysaccharides of this organism. G4 5223-PR1 survived well in sterilized groundwater, although in nonsterile groundwater microcosms rapid decreases in the G4 5223-PR1 cell population were observed. Ten days after inoculation no G4 5223-PR1 cells could be detected by selective plating or immunofluorescence. G4 5223-PR1 survival was greater in a nonsterile aquifer sediment microcosm, although after 22 days of elution the number of G4 5223-PR1 cells was low. Our results demonstrate the utility of monoclonal antibody tracking methods and the importance of biotic interactions in determining the persistence of introduced microorganisms.

  20. Factors Influencing TCE Anaerobic Dechlorination Investigated via Simulations of Microcosm Experiments

    NASA Astrophysics Data System (ADS)

    Mao, X.; Harkness, M.; Lee, M. D.; Mack, E. E.; Dworatzek, S.; Acheson, C.; McCarty, P.; Barry, D. A.; Gerhard, J. I.

    2006-12-01

    SABRE (Source Area BioREmediation) is a public-private consortium whose charter is to determine if enhanced anaerobic bioremediation can result in effective and quantifiable treatment of chlorinated solvent DNAPL source areas. The focus of this 4-year, $5.7 million research project is a field site in the United Kingdom containing a TCE DNAPL source area. In preparation, a microcosm study was performed to determine the optimal combination of factors to support reductive dechlorination of TCE in site soil and groundwater. The study consisted of 168 bottles distributed between four laboratories (Dupont, GE, SiREM, and Terra Systems) and tested the impact of six carbon substrates (lactate, acetate, methanol, SRS (soybean oil), hexanol, butyl acetate), bioaugmentation with KB-1 bacterial culture, three TCE levels (100 mg/L, 400 mg/L, and 800 mg/L) and two sulphate levels (200 mg/L, >500 mg/L) on TCE dechlorination. This research presents a numerical model designed to simulate the main processes occurring in the microcosms, including substrate fermentation, sequential dechlorination, toxic inhibition, and the influence of sulphate concentration. In calibrating the model to over 60 of the microcosm experiments, lumped parameters were employed to quantify the effect of key factors on the conversion rate of each chlorinated ethene in the TCE degradation sequence. Results quantify the benefit (i.e., increased stepwise dechlorination rate) due to both bioaugmentation and the presence of higher sulphate concentrations. Competitive inhibition is found to increase in significance as TCE concentrations increase; however, inclusion of Haldane inhibition is not supported. Over a wide range of experimental conditions and dechlorination steps, SRS appears to induce relatively little hydrogen limitation, thereby facilitating relatively quick conversion of TCE to ethene. In general, hydrogen limitation is found to increase with increasing TCE concentration and with bioaugmentation, and

  1. Donor-dependent Extent of Uranium Reduction for Bioremediation of Contaminated Sediment Microcosms

    SciTech Connect

    Madden, Andrew S.; Palumbo, Anthony V.; Ravel, Bruce; Vishnivetskaya, Tatiana A.; Phelps, Tommy J.; Schadt, Christopher W.; Brandt, Craig C.

    2009-03-16

    Bioremediation of uranium was investigated in microcosm experiments containing contaminated sediments from Oak Ridge, Tennessee to explore the importance of electron donor selection for uranium reduction rate and extent. In these experiments, all of the electron donors, including ethanol, glucose, methanol, and methanol with added humic acids, stimulated the reduction and immobilization of aqueous uranium by the indigenous microbial community. Uranium loss from solution began after the completion of nitrate reduction but essentially concurrent with sulfate reduction. When electron donor concentrations were normalized for their equivalent electron donor potential yield, the rates of uranium reduction were nearly equivalent for all treatments (0.55-0.95 {micro}mol L{sup -1} d{sup -1}). Uranium reduction with methanol proceeded after a 15-d longer lag time relative to that of ethanol or glucose. Significant differences were not found with the inclusion of humic acids. The extent of U reduction in sediment slurries measured by XANES at various time periods after the start of the experiment increased in the order of ethanol (5-7% reduced at 77 and 153 d), glucose (49% reduced at 53 d), and methanol (93% reduced at 90 d). The microbial diversity of ethanol- and methanol-amended microcosms in their late stage of U reduction was analyzed with 16S rRNA gene amplification. Members of the Geobacteraceae were found in all microcosms as well as other potential uranium-reducing organisms, such as Clostridium and Desulfosporosinus. The effectiveness of methanol relative to ethanol at reducing aqueous and sediment-hosted uranium suggests that bioremediation strategies that encourage fermentative poising of the subsurface to a lower redox potential may be more effective for long-term uranium immobilization as compared with selecting an electron donor that is efficiently metabolized by known uranium-reducing microorganisms.

  2. Donor-dependent Extent of Uranium Reduction for Bioremediation of Contaminated Sediment Microcosms

    SciTech Connect

    Palumbo, Anthony Vito; Ravel, Bruce; Phelps, Tommy Joe; Schadt, Christopher Warren; Brandt, Craig C

    2009-01-01

    Bioremediation of uranium was investigated in microcosm experiments containing contaminated sediments from Oak Ridge, Tennessee to explore the importance of electron donor selection for uranium reduction rate and extent. In these experiments, all of the electron donors, including ethanol, glucose, methanol, and methanol with added humic acids, stimulated the reduction and immobilization of aqueous uranium by the indigenous microbial community. Uranium loss from solution began after the completion of nitrate reduction but essentially concurrent with sulfate reduction. When electron donor concentrations were normalized for their equivalent electron donor potential yield, the rates of uranium reduction were nearly equivalent for all treatments (0.55-0.95 {micro}mol L{sup -1} d{sup -1}). Uranium reduction with methanol proceeded after a 15-d longer lag time relative to that of ethanol or glucose. Significant differences were not found with the inclusion of humic acids. The extent of U reduction in sediment slurries measured by XANES at various time periods after the start of the experiment increased in the order of ethanol (5-7% reduced at 77 and 153 d), glucose (49% reduced at 53 d), and methanol (93% reduced at 90 d). The microbial diversity of ethanol- and methanol-amended microcosms in their late stage of U reduction was analyzed with 16S rRNA gene amplification. Members of the Geobacteraceae were found in all microcosms as well as other potential uranium-reducing organisms, such as Clostridium and Desulfosporosinus. The effectiveness of methanol relative to ethanol at reducing aqueous and sediment-hosted uranium suggests that bioremediation strategies that encourage fermentative poising of the subsurface to a lower redox potential may be more effective for long-term uranium immobilization as compared with selecting an electron donor that is efficiently metabolized by known uranium-reducing microorganisms.

  3. Zostera marina seed burial can be enhanced by Manila clam Ruditapes philippinarum: A microcosm study

    NASA Astrophysics Data System (ADS)

    Li, Chang-Jun; Li, Wen-Tao; Liu, Jianying; Zhang, Xiumei; Zhang, Peidong

    2017-03-01

    Seagrass seed bank plays a key role in the regeneration of new vegetation when seagrasses are removed by the natural or man-made disaster. Various factors may affect the development of sediment seed bank. We conducted a microcosm experiment to test the effects of burrowing and feeding activities of Manila clam, Ruditapes philippinarum on the burial of Zostera marina seeds in sediments. The effects of lasting time (3-hour, 1-day, 3-day, 7-day, 14-day and 28-day), clam density (0, 2, 4 and 8 clams with shell length of 3 cm in each microcosm) and clam size (shell length of 2, 3 and 4 cm at 4-clam density) on seed burial were examined in plastic microcosm cores (30 cm high × 10 in inner diameter) in a 28-day period. Results showed that the seed burial depth significantly increased with time, the density and the size of clams. No seeds were buried in the sediment in the cores without clams during the whole experiment period. For the 3-cm clams, about 91.61% of the seeds were buried in the sediment at the end of the experiment in the high-density treatment (8 clams at each core); while in the medium and low-density treatments (4 and 2 clams in each core, respectively), about 76.93% and 60.61% of the seeds were buried in the sediment, respectively. For the size treatments, large (4 cm) clams buried 89.56% of the seeds at the end of the experiment, much more than those of medium (3 cm, 76.93%) and small (2 cm, 61.50%) size clams. During the whole experiment period, nearly all of the buried seeds were at a depth of from 0 cm to 5 cm. These results suggested that Manila clam Ruditapes philippinarum may play an important positive role in seagrass seed bank dynamics in the field.

  4. Plasmid Introduction in Metal-Stressed, Subsurface-Derived Microcosms: Plasmid Fate and Community Response

    PubMed Central

    Smets, Barth F.; Morrow, Jayne B.; Arango Pinedo, Catalina

    2003-01-01

    The nonconjugal IncQ plasmids pMOL187 and pMOL222, which contain the metal resistance-encoding genes czc and ncc, were introduced by using Escherichia coli as a transitory delivery strain into microcosms containing subsurface-derived parent materials. The microcosms were semicontinuously dosed with an artificial groundwater to set a low-carbon flux and a target metal stress (0, 10, 100, and 1,000 μM CdCl2), permitting long-term community monitoring. The broad-host-range IncPα plasmid RP4 was also transitorily introduced into a subset of microcosms. No novel community phenotype was detected after plasmid delivery, due to the high background resistances to Cd and Ni. At fixed Cd doses, however, small but consistent increases in Cdr or Nir density were measured due to the introduction of a single pMOL plasmid, and this effect was enhanced by the joint introduction of RP4; the effects were most significant at the highest Cd doses. The pMOL plasmids introduced could, however, be monitored via czc- and ncc-targeted infinite-dilution PCR (ID-PCR) methods, because these genes were absent from the indigenous community: long-term presence of czc (after 14 or 27 weeks) was contingent on the joint introduction of RP4, although RP4 cointroduction was not yet required to ensure retention of ncc after 8 weeks. Plasmids isolated from Nir transconjugants further confirmed the presence and retention of a pMOL222-sized plasmid. ID-PCR targeting the RP4-specific trafA gene revealed retention of RP4 for at least 8 weeks. Our findings confirm plasmid transfer and long-term retention in low-carbon-flux, metal-stressed subsurface communities but indicate that the subsurface community examined has limited mobilization potential for the IncQ plasmids employed. PMID:12839785

  5. Dissimilatory Iron Reduction and Odor Indicator Abatement by Biofilm Communities in Swine Manure Microcosms

    PubMed Central

    Castillo-Gonzalez, Hugo A.; Bruns, Mary Ann

    2005-01-01

    Animal waste odors arising from products of anaerobic microbial metabolism create community relations problems for livestock producers. We investigated a novel approach to swine waste odor reduction: the addition of FeCl3, a commonly used coagulant in municipal wastewater treatment, to stimulate degradation of odorous compounds by dissimilatory iron-reducing bacteria (DIRB). Two hypotheses were tested: (i) FeCl3 is an effective source of redox-active ferric iron (Fe3+) for dissimilatory reduction by bacteria indigenous to swine manure, and (ii) dissimilatory iron reduction results in significant degradation of odorous compounds within 7 days. Our results demonstrated that Fe3+ from FeCl3 was reduced biologically as well as chemically in laboratory microcosms prepared with prefiltered swine manure slurry and limestone gravel, which provided pH buffering and a substrate for microbial biofilm development. Addition of a 1-g liter−1 equivalent concentration of Fe3+ from FeCl3, but not from presynthesized ferrihydrite, caused initial, rapid solids flocculation, chemical Fe3+ reduction, and Eh increase, followed by a 2-day lag period. Between 2 and 6 days of incubation, increases in Fe2+ concentrations were accompanied by significant reductions in concentrations of volatile fatty acids used as odor indicators. Increases in Fe2+ concentrations between 2 and 6 days did not occur in FeCl3-treated microcosms that were sterilized by gamma irradiation or amended with NaN3, a respiratory inhibitor. DNA sequences obtained from rRNA gene amplicons of bacterial communities in FeCl3-treated microcosms were closely related to Desulfitobacterium spp., which are known representatives of DIRB. Use of iron respiration to abate wastewater odors warrants further investigation. PMID:16151075

  6. Plasmid Transfer between Spatially Separated Donor and Recipient Bacteria in Earthworm-Containing Soil Microcosms

    PubMed Central

    Daane, L. L.; Molina, J.; Sadowsky, M. J.

    1997-01-01

    Most gene transfer studies have been performed with relatively homogeneous soil systems in the absence of soil macrobiota, including invertebrates. In this study we examined the influence of earthworm activity (burrowing, casting, and feeding) on transfer of plasmid pJP4 between spatially separated donor (Alcaligenes eutrophus) and recipient (Pseudomonas fluorescens) bacteria in nonsterile soil columns. A model system was designed such that the activity of earthworms would act to mediate cell contact and gene transfer. Three different earthworm species (Aporrectodea trapezoides, Lumbricus rubellus, and Lumbricus terrestris), representing each of the major ecological categories (endogeic, epigeic, and anecic), were evaluated. Inoculated soil microcosms, with and without added earthworms, were analyzed for donor, recipient, and transconjugant bacteria at 5-cm-depth intervals by using selective plating techniques. Transconjugants were confirmed by colony hybridization with a mer gene probe. The presence of earthworms significantly increased dispersal of the donor and recipient strains. In situ gene transfer of plasmid pJP4 from A. eutrophus to P. fluorescens was detected only in earthworm-containing microcosms, at a frequency of (symbl)10(sup2) transconjugants per g of soil. The depth of recovery was dependent on the burrowing behavior of each earthworm species; however, there was no significant difference in the total number of transconjugants among the earthworm species. Donor and recipient bacteria were recovered from earthworm feces (casts) of all three earthworm species, with numbers up to 10(sup6) and 10(sup4) bacteria per g of cast, respectively. A. trapezoides egg capsules (cocoons) formed in the inoculated soil microcosms contained up to 10(sup7) donor and 10(sup6) recipient bacteria per g of cocoon. No transconjugant bacteria, however, were recovered from these microhabitats. To our knowledge, this is the first report of gene transfer between physically

  7. Combining rapid bioassessment and field-based microcosms for identifying impacts in an urban river.

    PubMed

    O'Brien, Matthew L; Pettigrove, Vincent; Carew, Melissa E; Hoffmann, Ary A

    2010-08-01

    Rapid bioassessment indices based on macroinvertebrates are the most commonly used tools for assessing stream condition. However, once stream degradation has been detected, it is often difficult to identify which environmental stressors are most important because of changes in multiple correlated factors. In this study, we examined eight sites in an urban river watershed using a field-based microcosm experiment and the rapid bioassessment-based biotic index, SIGNAL. The experiment assessed the effects of polluted river sediment by examining the macroinvertebrate taxa that colonized sediments at an unpolluted wetland. Results were compared with an assessment of field-collected macroinvertebrates using SIGNAL, a biotic index that assigns pollution sensitivity scores to macroinvertebrate families, and environmental data, to determine whether sediment pollution or other factors such as habitat deterioration were likely to be influencing riverine macroinvertebrate communities. The microcosm results indicated that common species (Tanytarsus fuscithorax, Procladius paludicola, and Ablabesmyia notabilis) and the overall macroinvertebrate assemblage did not significantly change among sediments from different sites, with the exception of local effects on a few uncommon taxa (Chironomus pseudoppositus, Kiefferulus martini, Cladotanytarsus australomancus, Chaoboridae, Polypedilum "S1," and Tanytarsus belairensis). In contrast, SIGNAL showed a gradual trend of deterioration from upstream to downstream, decreasing from a score of 6.5 in upstream areas (unimpacted) to a score of 4.4 in the downstream sites (moderately impacted). This result combined with a significant correlation of SIGNAL scores to habitat data suggested that habitat deterioration rather than polluted sediment was likely to be responsible for the declining stream condition detected with the rapid bioassessment approach. The addition of the microcosms to other monitoring approaches could be useful for determining

  8. Alkaline phosphatase activity of Escherichia coli starved in sterile lake water microcosms.

    PubMed

    Ozkanca, R; Flint, K P

    1996-03-01

    Escherichia coli grown in high or low phosphate medium was inoculated into a lake water starvation medium. The viable count decreased at 37 degrees C but not at the lower temperatures over 70 d. Alkaline phosphatase was monitored using a colorimetric assay with pNPP as the substrate. Derepression of the enzyme occurred in cultures starved for > 30 d in the lake water and within 5 d in lake water microcosms supplemented with carbon and nitrogen sources where there was rarely an increase in viable count. Chloramphenicol prevented the synthesis of alkaline phosphatase suggesting that, even under starvation conditions, de novo synthesis of the enzyme occurs.

  9. Microcosm experiments to study the interaction of solid and solute phases during initial soil development

    NASA Astrophysics Data System (ADS)

    Zimmermann, C.; Chabbi, S.; Schaaf, W.

    2009-04-01

    During the initial phase of soil formation mineral weathering, interactions between the solid and liquid phases as well as accumulation of organic matter play an important role for the development of soil properties and for the establishment of vegetation and the colonization of soil biota. Our study is part of the Transregional Collaborative Research Centre (SFB/TRR 38) ‘Patterns and processes of initial ecosystem development in an artificial catchment' funded by the Deutsche Forschungsgemeinschaft (DFG). The catchment ´Chicken Creeḱ close to Cottbus (Germany) has a size of 6 ha and is composed of a 3-4 m layer of Quaternary loamy to sandy sediments overlying a 1-2 m clay layer. To connect interactions between the soil solid phase and soil solution at the micro-scale with observed processes at the catchment scale we perform microcosm experiments with soil samples from the catchment under controlled laboratory conditions. The microcosm experiments are carried out in a climate chamber at constant 10 °C corresponding to the mean annual temperature of the region. In total 48 soil columns with a diameter of 14.4 cm and height of 30 cm were filled with substrates of two textural compositions reflecting the gradients observed at the catchment and a bulk density of 1.4-1.5 g*cm3. Within the microcosms it is possible to control the gaseous phase and the water fluxes by artificial irrigation. The irrigation runs automated and quasi-continuously four times a day with 6.6 ml each (in total 600 mm*yr-1). Irrigation amount and chemical composition of the artificial rainwater are based on the annual mean at the field site. Litter of two different plant species occurring at the catchment site (Lotus corniculatus, Calamagrostis epigejos) labelled with stable isotopes (δ13C; δ15N) is used for the experiments. All treatments including a control run with four replicates. The gaseous phase in the headspace of the microcosms is analysed continuously for CO2 and N2O contents

  10. Evaluation of Graphite for Environmental Toxicity Using the Standard Aquatic Microcosm

    DTIC Science & Technology

    1988-08-01

    suspended as possible. The exposure concentrations were set so that a no effect and an effect level could be expected as estimated by Daphnia magna 48-hr...development. 2 ,3,4,5#6 During the last 3 years, we participated in the Food and Drug Administration (FDA) supported round-robin evaluation of the method...F.B., and Read, P.L., Standardized Aauatic Microcosm Protocol, Contract No. 223-80-2352, Vol I1, Food and Drug Administration, Washington, DC, 1983. 9

  11. Comparison of the effects of two herbicides and an insecticide on tropical freshwater plankton in microcosms.

    PubMed

    Leboulanger, C; Bouvy, M; Carré, C; Cecchi, P; Amalric, L; Bouchez, A; Pagano, M; Sarazin, G

    2011-11-01

    Natural plankton communities from a tropical freshwater reservoir (Combani Reservoir, Mayotte Island, Mozambique Channel) were exposed, in 20-l nutrient-enriched microcosms, to two nominal concentrations of three pesticides: the herbicides diuron (2.2 and 11 μg/l) and paraquat (10 and 40.5 μg/l) and the insecticide fenitrothion (10 and 100 μg/l), commonly used in the tropics for agriculture and disease vector control. Bacterioplankton, phytoplankton, and zooplankton communities were monitored for 5 days after exposure, and the concentrations of toxicant and major nutrients were measured. Bacterioplankton growth was noticeable in all systems and was slightly affected by pesticide at any concentration. A transitory increase in thymidine-based bacterial production was observed in diuron- and fenitrothion-treated microcosms, followed by a marked decrease in all microcosms after 5 days. The functional diversity of bacterioplankton, evaluated using BIOLOG ECO(®) microplates, was reduced by exposure to the highest pesticide concentrations. Phytoplankton was affected by pesticides in different ways. Chlorophyll biomass and biovolumes were increased by diuron addition and decreased by paraquat, whereas fenitrothion-treated microcosms remained unaffected relative to controls. Phytoplankton taxonomic diversity was decreased by paraquat and high doses of fenitrothion but was unaffected by addition of diuron. The decrease in diversity was due to a reduction in the number of species, whereas the density of small cells increased, especially after addition of paraquat. Heterotrophic flagellates were sensitive to paraquat and to the highest diuron concentration; a reduction in biomass of up to 90% was observed for 40.5 μg/l paraquat. Zooplankton, dominated by Thermocyclops decipiens and Diaphanosoma excisum, was slightly sensitive to diuron, and very sensitive to paraquat. High concentrations of the insecticide fenitrothion were effective only on young stages. The potential

  12. Biomarker response and biomass change of earthworms exposed to chlorpyrifos in microcosms.

    PubMed

    Reinecke, S A; Reinecke, A J

    2007-01-01

    Background levels of chlorpyrifos and earthworm abundance were determined in an orchard and adjacent areas on a farm in the Western Cape, South Africa before these areas were again sprayed with this organophosphate. The background concentrations ranged from 0.2 microg/kg dm in the spray drift area adjacent to the orchard to 10.18 microg/kg dm on the slope in the run off area. In the target area the chlorpyrifos concentrations varied from a mean of 15.25 +/- 10.0 microg/kg directly after spraying to a mean of 7.0 +/- 0.9 microg/kg 6 months later and in the nontarget area they varied from a mean of 55.0 +/- 35 microg/kg to 12.0 +/- 5 microg/kg after 6 months. Chlorpyrifos was therefore still present in the field soils, but at lower concentrations, up to 6 months after the last spraying event. Earthworm abundance and population densities were very low. Only Aporrectodea caliginosa was found and the densities were much lower in the orchards (22 per m(2)) than in the nontarget areas (98.3 per m(2)). Microcosm studies were undertaken to relate biomarker responses to chlorpyrifos with biomass changes. Microcosms were filled with soil from the same areas and earthworms of the species A. caliginosa were introduced. The microcosms were treated with a series of concentrations of chlorpyrifos in the laboratory under controlled conditions. These concentrations were chosen to fall within the background ranges found in the soils. The biomass of the worms was determined regularly for a period of 5 weeks and worms in a state of estivation were noted. Earthworms were removed from the microcosms for biomarker tests: for cholinesterase (ChE) inhibition assays every week and for a neutral red retention determination 2 weeks after the exposures started. The most prominent biomass loss was noted in earthworms exposed to the highest pesticide concentration of 8.0 microg/kg. Estivation was higher among earthworms exposed to higher exposure concentrations. Inhibition of ChE increased with

  13. Experimental serpentinization of intact dunite cores

    NASA Astrophysics Data System (ADS)

    Luhmann, A. J.; Tutolo, B. M.; Kong, X. Z.; Bagley, B. C.; Schaen, A. T.; Saar, M. O.; Seyfried, W. E., Jr.

    2014-12-01

    Serpentinization in ultramafic-hosted hydrothermal systems, such as Lost City, produces relatively cool and alkaline fluids that support diverse ecosystems. To simulate serpentinization in such systems, we conducted single-pass, flow-through experiments on dunite cores cut out of a sample from Jackson County, North Carolina. Experimental seawater prepared using laboratory-grade reagents and standards was pumped through a core at 150ºC and 150 bar pore-fluid outlet pressure at a flow rate of 0.01 ml/min. An additional experiment will be conducted at 200ºC. At 150ºC, permeability decreased by 2.3 times with reaction progress over the course of the 36 day experiment. Fluid-rock reaction generally produced CO2, H2, CH4, and CO concentrations of 100 μmol/kg, up to 40 μmol/kg, 2 μmol/kg, and less than 1 μmol/kg, respectively. Outlet fluid chemistry was relatively stable, except for initial peaks in Al, Ba, Fe, Mn, and Si. pH of outlet fluids increased with reaction progress, but it was always lower (6.9-7.4) than the initial seawater (7.8). X-ray computed tomography scans were/will be collected for both pre- and post-experimental cores. The combination of flow-through experiments on solid, intact rock cores cut out of natural samples and X-ray tomography permits visualization and quantification of mineralogical changes and flow path evolution during serpentinization. This approach further permits physical and chemical processes to be documented on a fine scale to better understand feedbacks between chemical reactions and flow fields, with implications for ultramafic-hosted hydrothermal systems.

  14. 46 CFR 28.570 - Intact righting energy.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 1 2011-10-01 2011-10-01 false Intact righting energy. 28.570 Section 28.570 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY UNINSPECTED VESSELS REQUIREMENTS FOR COMMERCIAL FISHING INDUSTRY VESSELS Stability § 28.570 Intact righting energy. (a) Except as provided in paragraph (c) of...

  15. 46 CFR 28.570 - Intact righting energy.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 1 2010-10-01 2010-10-01 false Intact righting energy. 28.570 Section 28.570 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY UNINSPECTED VESSELS REQUIREMENTS FOR COMMERCIAL FISHING INDUSTRY VESSELS Stability § 28.570 Intact righting energy. (a) Except as provided in paragraph (c) of...

  16. 50 CFR 622.186 - Landing fish intact.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...-Grouper Fishery of the South Atlantic Region § 622.186 Landing fish intact. (a) South Atlantic snapper-grouper in or from the South Atlantic EEZ must be maintained with head and fins intact, except as..., snapper-grouper lawfully harvested in Bahamian waters are exempt from the requirement that they...

  17. 50 CFR 622.186 - Landing fish intact.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...-Grouper Fishery of the South Atlantic Region § 622.186 Landing fish intact. (a) South Atlantic snapper-grouper in or from the South Atlantic EEZ must be maintained with head and fins intact, except as..., snapper-grouper lawfully harvested in Bahamian waters are exempt from the requirement that they...

  18. 50 CFR 622.455 - Landing spiny lobster intact.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 12 2014-10-01 2014-10-01 false Landing spiny lobster intact. 622.455... ATLANTIC Spiny Lobster Fishery of Puerto Rico and the U.S. Virgin Islands § 622.455 Landing spiny lobster intact. (a) A Caribbean spiny lobster in or from the Caribbean EEZ must be maintained with head...

  19. 50 CFR 622.455 - Landing spiny lobster intact.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 50 Wildlife and Fisheries 12 2013-10-01 2013-10-01 false Landing spiny lobster intact. 622.455... ATLANTIC Spiny Lobster Fishery of Puerto Rico and the U.S. Virgin Islands § 622.455 Landing spiny lobster intact. (a) A Caribbean spiny lobster in or from the Caribbean EEZ must be maintained with head...

  20. 46 CFR 28.570 - Intact righting energy.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 1 2014-10-01 2014-10-01 false Intact righting energy. 28.570 Section 28.570 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY UNINSPECTED VESSELS REQUIREMENTS FOR COMMERCIAL FISHING INDUSTRY VESSELS Stability § 28.570 Intact righting energy. (a) Except as provided in paragraph (c) of...

  1. 46 CFR 28.570 - Intact righting energy.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 1 2012-10-01 2012-10-01 false Intact righting energy. 28.570 Section 28.570 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY UNINSPECTED VESSELS REQUIREMENTS FOR COMMERCIAL FISHING INDUSTRY VESSELS Stability § 28.570 Intact righting energy. (a) Except as provided in paragraph (c) of...

  2. 46 CFR 28.570 - Intact righting energy.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 1 2013-10-01 2013-10-01 false Intact righting energy. 28.570 Section 28.570 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY UNINSPECTED VESSELS REQUIREMENTS FOR COMMERCIAL FISHING INDUSTRY VESSELS Stability § 28.570 Intact righting energy. (a) Except as provided in paragraph (c) of...

  3. 50 CFR 622.10 - Landing fish intact--general.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE FISHERIES OF THE CARIBBEAN, GULF OF MEXICO, AND SOUTH... landing fish intact that are broadly applicable to finfish in the Gulf EEZ and Caribbean EEZ, as specified... intact. (a) Finfish in or from the Gulf EEZ or Caribbean EEZ, except as specified in paragraphs (b)...

  4. 50 CFR 622.10 - Landing fish intact--general.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE FISHERIES OF THE CARIBBEAN, GULF OF MEXICO, AND SOUTH... landing fish intact that are broadly applicable to finfish in the Gulf EEZ and Caribbean EEZ, as specified... intact. (a) Finfish in or from the Gulf EEZ or Caribbean EEZ, except as specified in paragraphs (b)...

  5. Quick stimulation of Alcanivorax sp. by bioemulsificant EPS₂₀₀₃ on microcosm oil spill simulation.

    PubMed

    Cappello, Simone; Genovese, Maria; Denaro, Renata; Santisi, Santina; Volta, Anna; Bonsignore, Martina; Mancini, Giuseppe; Giuliano, Laura; Genovese, Lucrezia; Yakimov, Michail M

    2014-01-01

    Oil spill microcosms experiments were carried out to evaluate the effect of bioemulsificant exopolysaccharide (EPS₂₀₀₃) on quick stimulation of hydrocarbonoclastic bacteria. Early hours of oil spill, were stimulated using an experimental seawater microcosm, supplemented with crude oil and EPS₂₀₀₃ (SW+OIL+EPS₂₀₀₃); this system was monitored for 2 days and compared to control microcosm (only oil-polluted seawater, SW+OIL). Determination of bacterial abundance, heterotrophic cultivable and hydrocarbon-degrading bacteria were carried out. Community composition of marine bacterioplankton was determined by 16S rRNA gene clone libraries. Data obtained indicated that bioemulsificant addition stimulated an increase of total bacterial abundance and, in particular, selection of bacteria related to Alcanivorax genus; confirming that EPS₂₀₀₃ could be used for the dispersion of oil slicks and could stimulate the selection of marine hydrocarbon degraders thus increasing bioremediation process.

  6. Development of spatial database on intact forest landscapes of India

    NASA Astrophysics Data System (ADS)

    Sudhakar Reddy, C.; Singh, Jyoti; Jha, C. S.; Diwakar, P. G.; Dadhwal, V. K.

    2017-01-01

    There is an increased interest in identifying the status of biodiversity in different spatial and temporal scales. The objective of the current research is to prepare a consistent spatial database of intact forest landscapes of India. The intact forest landscapes are located in the Himalayas, Andaman & Nicobar Islands, Western Ghats and Sunderbans. At national level 237 forest landscapes and 5.4% of the total natural forest remained as intact in India. Current intact forest landscapes of India consists of blocks larger than 10 km2 covering an area of 34,061 km2. Of the total area under intact forest landscapes, Eastern Himalayas represent 76.7% of the area, followed by Western Himalayas (8.8%), Andaman & Nicobar Islands (6.2%) and Western Ghats (5.7%). The largest intact forest landscape block occupies an area of 3342.9 km2 (9.8%) is found in western Arunachal Pradesh. Temperate forest zone represents the highest intactness (56.6%), followed by subtropical zone (19.2%), tropical zone (18.6%) and alpine zone (5.6%). Himalayan moist temperate forests represent the highest area (39.1%) of intact forest landscapes followed by subtropical broad-leaved hill forests, wet evergreen forests, and montane wet temperate forests. It is estimated that 4.4% of the area of intact forest landscapes fall inside the existing 47 protected areas. The results of the analysis best suited as input for the process of identification of new protected areas. The study recommends fine-scale mapping of biodiversity within the intact forest landscapes and to prepare efficient conservation plans.

  7. Vesta Is Not an Intact Protoplanet

    NASA Astrophysics Data System (ADS)

    Consolmagno, Guy; Turrini, Diego; Golabeck, Gregor; Jutzi, Martin; Sirono, Sin-iti; Svetsov, Vladimir; Tsiganis, Kleomenis

    2014-11-01

    Asteroid 4 Vesta has been identified as the likely source of howardite, eucrite, and diogenite (HED) basaltic achondrite meteorites, whose parent body differentiated and started solidifying within 3 Ma after the condensation of the Ca-Al-rich inclusions (CAIs). The formation of Jupiter and the disk-driven migration of the giant planets also occurred during this period; thus it was expected that Vesta could provide an intact record of large-scale early episodes of planetary migration and bombardment as in the proposed Jovian Early Bombardment and the “Grand Tack” scenarios. However, the results of the Dawn mission detailing Vesta’s mass, volume, density, and surface characteristics provide challenges for modeling the structure and evolution of this asteroid. All proposed models for the generation of the HEDs require the presence of a substantial olivine-rich mantle. But recent work on the depth of excavation of the large basins at the south pole of Vesta suggests that because there is not abundant mantle olivine visible on Vesta or in the Vestoid family asteroids, the crust of Vesta must be at least 80 km thick. Such a thick crust is radically at odds with previous models; should it exist, it ought to manifest itself in other ways such as Vesta’s density structure and bulk chemical composition. However, we find that no Vesta model of iron core, olivine-rich mantle, and HED crust can match the joint constraints of (a) Vesta’s density as derived from the gravity field observed by Dawn; (b) the observed depletion of sodium and potassium and trace element enrichments of the HED meteorites; and (c) the absence of exposed olivine on Vesta’s surface, among Vestoid asteroids, or in our collection of basaltic meteorites. Either Vesta was subjected to a radical change in composition, presumably due to the intense collisional environment where and when it formed, or the asteroid we see today is in fact a reaccretion of material formed elsewhere from now

  8. A microcosm system and an analytical protocol to assess PAH degradation and metabolite formation in soils.

    PubMed

    Arias, Lida; Bauzá, Jorge; Tobella, Joana; Vila, Joaquim; Grifoll, Magdalena

    2008-06-01

    During bioremediation of polycyclic aromatic hydrocarbon (PAH)-polluted soils accumulation of polar metabolites resulting from the biological activity may occur. Since these polar metabolites are potentially more toxic than the parental products, a better understanding of the processes involved in the production and fate of these oxidation products in soil is needed. In the present work we describe the design and set-up of a static soil microcosm system and an analytical methodology for detection of PAHs and their oxidation products in soils. When applied to a soil contaminated with phenanthrene, as a model PAH, and 1-hydroxy-2-naphthoic acid, diphenic acid, and phthalic acid as putative metabolites, the extraction and fractionation procedures resulted in recoveries of 93%, 89%, 100%, and 89%, respectively. The application of the standardized system to study the biodegradation of phenanthrene in an agricultural soil with and without inoculation of the high molecular weight PAH-degrading strain Mycobacterium sp. AP1, demonstrates its suitability for determining the environmental fate of PAHs in polluted soils and for evaluating the effect of bioremediative treatments. In inoculated microcosms 35% of the added phenanthrene was depleted, 19% being recovered as CO(2) and 3% as diphenic acid. The latter, together with other two unidentified metabolites, accumulated in soil.

  9. Temporal dynamics of microbial communities in microcosms in response to pollutants.

    PubMed

    Jiao, Shuo; Zhang, Zhengqing; Yang, Fan; Lin, Yanbing; Chen, Weimin; Wei, Gehong

    2017-02-01

    Elucidating the mechanisms underlying microbial succession is a major goal of microbial ecology research. Given the increasing human pressure on the environment and natural resources, responses to the repeated introduction of organic and inorganic pollutants are of particular interest. To investigate the temporal dynamics of microbial communities in response to pollutants, we analysed the microbial community structure in batch microcosms that were inoculated with soil bacteria following exposure to individual or combined pollutants (phenanthrene, n-octadecane, phenanthrene + n-octadecane and phenanthrene + n-octadecane + CdCl2 ). Subculturing was performed at 10-day intervals, followed by high-throughput sequencing of 16S rRNA genes. The dynamics of microbial communities in response to different pollutants alone and in combination displayed similar patterns during enrichment. Specifically, the repression and induction of microbial taxa were dominant, and the fluctuation was not significant. The rate of appearance for new taxa and the temporal turnover within microbial communities were higher than the rates reported in other studies of microbial communities in air, water and soil samples. In addition, conditionally rare taxa that were specific to the treatments exhibited higher betweenness centrality values in the co-occurrence network, indicating a strong influence on other interactions in the community. These results suggest that the repeated introduction of pollutants could accelerate microbial succession in microcosms, resulting in the rapid re-equilibration of microbial communities.

  10. [Microcosm Simulation Study and Methylmercury Forming Mechanism at Landscape Water of City].

    PubMed

    Liu, Xiao-hong; Si, You-bin; Guo, Zi-wei; Du, Cheng-zhu; Zhu, Cong-cong

    2016-04-15

    Mercury is harmful to the environment, which has gradually become one of the research hotspots. Sediments, as a main repository of pollutants, have an important impact on water quality and the internal organisms, which deserves our research. In this paper, we focused on Hefei landscape water sediment and tried to investigate the status of inorganic mercury and methylmercury pollutions in the sediment. To study the conversion process from inorganic mercury to methylmercury and their enrichment levels and mechanism, we established the ecological chain of "sediment-water-grass-fish" through analog microcosm examination. The results were as follows: from ten water and sediment samples in Hefei landscape water sediment, we found that the contents of inorganic mercury and methylmercury ranged 11.74-13.12 µg · kg⁻¹ and 0.37-2.23 µg · kg⁻¹, respectively. The microcosm examination showed that: with increasing culture time, inorganic mercury in sediments gradually decreased. There was a phenomenon that the content of methylmercury increased at first and then decreased to reach the balance later. Both the inorganic mercury and methylmercury in water change showed an increasing trend. The enrichment contents of inorganic mercury in Egeria densa Planch, and golden mandarin fish (Siniperca scherzeri Steindachner) were low while their enrichment of methylmercury could he great. In addition, we found that both the bioaccumulation ability and the enrichment coefficient of methylmercury in the body of golden mandarin fish were the maximum during the same period.

  11. A comparison of zooplankton sampling methods in evaluating copper sulfate toxicity in outdoor microcosms

    SciTech Connect

    Hellenbrandt, S.; La Point, T.W.; Shaw, J.L.; Marshall, S.J.; Ratte, H.T.

    1994-12-31

    Six outdoor microcosms (2m{sup 3}) were used to determine copper sulfate effects on epibenthic and planktonic zooplankton community structure. Microcosms were treated three times with CuSO{sub 4} at 0, 50, 100, 200, 350, 550 {mu}g Cu/L, respectively. Zooplankton was sampled biweekly from July through October 1993. Epibenthic zooplankton was collected with an inverted funnel trap, whereas planktonic zooplankton was sampled with an integrated water column sampler. Samples were sieved through a 35 {mu}m mesh and organisms preserved with 1% Lugol`s solution and later identified to genus or species level. Both communities initially decreased in total abundance at high copper rates. However, recovery started shortly after the final Cu application. Species richness was lowest at high copper concentrations, particularly in the epi-benthic community. Epibenthic zooplankton diversity decreased at high copper rates, whereas planktonic zooplankton diversity did not. Epi-benthic zooplankton may be a sensitive indicator of chemical stress and therefore be used to assess the bioavailability of sediment-bound xenobiotics.

  12. Understanding the controllability of complex networks from the microcosmic to the macrocosmic

    NASA Astrophysics Data System (ADS)

    Sun, Peng Gang; Ma, Xiaoke

    2017-01-01

    From a microcosmic perspective, nodes as meta-structures (or ‘smallest units’) for the constitution of a graph are of great importance for understanding complex network-based systems. In this paper, we develop a new framework, which first of all defines the meta-structures of a graph in different levels and tries to depict a graph from a low to a high level of abstraction. Further, based on this framework we study the meta-structure-driven control model and try to understand the controllability of complex networks from a microcosmic to a macrocosmic perspective. Finally, we analyze the impact of the community strength of networks on meta-structure-driven control. The results for artificial networks and real-world networks indicate that for meta-structure-driven control, the number of driver nodes is dependent on the networks’ degree distribution, and the dependence weakens as the level of the meta-structures increases. In addition, the networks are easier to control as the community strength increases, while this monotonicity is not preserved as the level of the meta-structures increases. We also find that it is harder to control sparse and inhomogeneous networks as the level of the meta-structures increases.

  13. Inhibition of nitrate reduction by chromium (VI) in anaerobic soil microcosms

    SciTech Connect

    Kourtev, P. S.; Nakatsu, C. H.; Konopka, Allan

    2009-10-01

    Chromium (VI) is often found as a co-contaminant at sites polluted with organic compounds. We used microcosms amended with glucose or protein, nitrate and increasing concentrations of chromium to study nitrate reduction in Cr(VI) polluted soils. Organic carbon stimulated bacterial activity, but the addition of Cr(VI) caused a lag and then slower rates 5 of CO2 accumulation. Nitrate reduction only occurred after Cr(VI) had been reduced. Bacterial activity was again inhibited when Cr(VI) was added a second time; thus not all Cr-sensitive bacteria were removed in the first phase. Glucose and protein selected for relatively similar bacterial communities, as assayed by PCR-DGGE of the 16S rRNA gene; this selection was modified by the addition of 10 Cr(VI). Cr-resistant bacteria isolated from microcosms were closely related to members of Bacillus, Enterococcus and Propionibacterium sp. Our results indicate that carbon utilization and nitrate reduction in these soils in the presence of Cr(VI) are contingent upon the reduction of the added heavy metal by a limited subset of the bacterial community. The amount of Cr(VI) required to inhibit nitrate reduction was 10-fold less than for aerobic catabolism of the same 15 substrate. We hypothesize that the resistance level of a microbial process is directly related to the diversity of microbes capable of conducting it.

  14. Effects of two lubricant oils on marine nematode assemblages in a laboratory microcosm experiment.

    PubMed

    Beyrem, H; Louati, H; Essid, N; Aïssa, P; Mahmoudi, E

    2010-05-01

    The effects of two lubricating oils on nematode assemblages of a Tunisian lagoon were investigated in a microcosm experiment. Sediment from a pristine site in Ghar El Melh lagoon (Western Mediterranean) was treated with either mineral oil (Mobil 20 W-50), a synthetic lubricant (Mobil 0 W-40), the same two lubricants after use in a vehicle, and effects were examined after 5 weeks. Univariate analysis showed significant differences between most univariate indices of the nematode assemblages in all the lubricant treatments as compared to the control. Total nematode abundance (I), species richness (d) and number of species (S) decreased significantly in all lubricant contaminated microcosms. However, evenness was not affected in all treated replicates except in used mineral lubricant treatment where it was significantly higher than in the control. Diversity (H') was only altered in synthetic lubricant treatments. Results from multivariate analyses of the species abundance data demonstrated that responses of nematode species to the two lubricants treatments were varied: Daptonema trabeculosum was eliminated in all lubricant treatments and seemed to be an intolerant species to oil contamination. Spirinia gerlachi increased in mineral lubricant treatments ("clean" and used) but was eliminated in all synthetic lubricant treatments. This species could be categorized as "resistant" to mineral oil contamination and intolerant to synthetic lubricant contamination. Terschellingia longicaudata increased only in synthetic lubricant treatments ("clean" and used) and appeared to be a "synthetic oil-resistant" species.

  15. Investigation into ammonia stress on Cyperus alternifolius and its impact on nutrient removal in microcosm experiments.

    PubMed

    Tao, Wendong; Han, Jianqiu; Li, Hanyan

    2015-11-01

    Ammonia stress on plants has been investigated at discrete ammonia concentrations in constructed wetlands. This study introduced a Gaussian model to simulate the kinetics of ammonia stress and investigated reversible and irreversible ammonia stress on Cyperus alternifolius in wetland-like microcosms. Ammonia stress on plant weight increase and oxygen release potential started at weekly ammonia concentrations of 27 and 28 mg N/L, reached 50% inhibition at 178 and 158 mg N/L, and resulted in lethal effects at 311 and 303 mg N/L, respectively. The stress of one-time ammonia concentrations up to 400 mg N/L could be reversible. Ammonia concentrations constantly above 219 mg N/L exerted irreversible stress. In the microcosms with ammonia concentrations above the 50% inhibition levels, plants played a minor role in nitrogen removal. Nitrogen removal performance was not affected considerably by ammonia stress. Orthophosphate removal was suppressed by ammonia stress due to less plant uptake. Design and operation of constructed wetlands should consider wastewater ammonia concentration so that the integrity of constructed wetland ecosystems can be maintained.

  16. Differential Decay of Wastewater Bacteria and Change of Microbial Communities in Beach Sand and Seawater Microcosms.

    PubMed

    Zhang, Qian; He, Xia; Yan, Tao

    2015-07-21

    Laboratory microcosm experiments were conducted to determine the decay kinetics of wastewater bacteria and the change of microbial communities in beach sand and seawater. Cultivation-based methods showed that common fecal indicator bacteria (FIBs; Escherichia coli, enterococci, and Clostridium perfringens) exhibited biphasic decay patterns in all microcosms. Enterococci and C. perfringens, but not E. coli, showed significantly smaller decay rates in beach sand than in seawater. Cultivation-independent qPCR quantification of 16S rRNA gene also showed significantly slower decrease of total bacterial densities in beach sand than in seawater. Microbial community analysis by next-generation sequencing (NGS) further illustrated that the decreasing relative abundance of wastewater bacteria was contrasted by the increase in indigenous beach sand and seawater microbiota, and the overall microbial community dynamics corresponded well with the decay of individual FIB populations. In summary, the differential decay of wastewater bacteria in beach sand and in seawater provides a kinetic explanation to the often-observed higher abundance of FIBs in beach sand, and the NGS-based microbial community analysis can provide valuable insights to understanding the fate of wastewater bacteria in the context of indigenous microbial communities in natural environments.

  17. Microbial culture dynamics and chromium (VI) removal in packed-column microcosm reactors.

    PubMed

    Molokwane, Pulane E; Nkhalambayausi-Chirwa, Evans M

    2009-01-01

    Microbial Cr(VI) reduction in groundwater aquifer media was investigated in microcosm reactors extracted from Cr(VI) contaminated sites in South Africa. The reactors were operated under an influent Cr(VI) concentration of 40 mg/L to simulate the current Cr(VI) level at the contaminated site. Near complete Cr(VI) removal was observed in microcosm reactors inoculated with Cr(VI) reducing bacteria from dried activated sludge collected from a treatment plant receiving periodic loadings of Cr(VI). The best performance was observed under low hydraulic loading (flow rate, Q=0.310 cm(3)/hr). Microbial culture characterisation results showed a change in culture composition after 17 days of reactor operation, indicating Bacillus and Lysinibacillus species as the most dominant organisms in reactors that reduced Cr(VI). The predominance of Bacillus and Lysinibacillus species was either due to resilience against toxicity or adaptation to the changing conditions in the reactor. This research was the initial step towards the development of an in situ bioremediation process to contain the spread of a Cr(VI) plume in a groundwater aquifer at contaminated site in Brits, South Africa. South Africa holds about 72% percent of the world's chromium resources, the majority of which is mined in the North Eastern region of the country formally known as Transvaal.

  18. Introduction of mercury resistant bacterial strains to Hg(II) amended soil microcosms increases the resilience of the natural microbial community to mercury stress

    SciTech Connect

    de Lipthay, Julia R.; Rasmussen, Lasse D.; Serensen, Soren J.

    2004-03-17

    Heavy metals are among the most important groups of pollutant compounds, and they are highly persistent in the soil environment. Techniques that can be used for the remediation of heavy metal contaminated environments thus need to be evolved. In the present study we evaluated the effect of introducing a Hg resistance plasmid in subsurface soil communities. This was done in microcosms with DOE subsurface soils amended with 5-10 ppm of HgCl2. Two microcosms were set up. In microcosm A we studied the effect of adding strain S03539 containing either the Hg resistance conjugative plasmid, pJORD 70, or the Hg resistance mobilizable plasmid, pPB117. In microcosm B we studied the effect of adding strain KT2442 with and without pJORD70. For both microcosms, the effect on the resilience of the indigenous bacterial community as well as the effect on the soil concentration of Hg was evaluated.

  19. Reflectance Spectra Comparison of Orbital Debris, Intact Spacecraft, and Intact Rocket Bodies in the GEO Regime

    NASA Astrophysics Data System (ADS)

    Albercromby, Kira J.; Abell, Paul; Barker, Ed

    2009-03-01

    A key objective of NASA's Orbital Debris program office at Johnson Space Center (JSC) is to characterize the debris environment by way of assessing the physical properties (type, mass, density, and size) of objects in orbit. Knowledge of the geosynchronous orbit (GEO) debris environment in particular can be used to determine the hazard probability at specific GEO altitudes and aid predictions of the future environment. To calculate an optical size from an intensity measurement of an object in the GEO regime, a 0.175 albedo is assumed currently. However, identification of specific material type or types could improve albedo accuracy and yield a more accurate size estimate for the debris piece. Using spectroscopy, it is possible to determine the surface materials of space objects. The study described herein used the NASA Infrared Telescope Facility (IRTF) to record spectral data in the ~ 0.65 to 2.5 micron regime on eight catalogued space objects. For comparison, all of the objects observed were in GEO or near-GEO. The eight objects consisted of two intact spacecraft, three rocket bodies, and three catalogued debris pieces. Two of the debris pieces stemmed from Titan 3C transtage breakup and the third is from COSMOS 2054. The reflectance spectra of the Titan 3C pieces share similar slopes (increasing with wavelength) and lack any strong absorption features. The COSMOS debris spectrum has a slight slope and has no absorption features. In contrast, the intact spacecraft show classic absorption features due to solar cells with a strong band gap feature near 1 micron. The two spacecraft were spin-stabilized objects and therefore have solar panels surrounding the outer surface. Two of the three rocket bodies are inertial upper stage (IUS) rocket bodies and have similar looking spectra. The slopes flatten out near 1.5 microns with absorption features in the near-infrared that are similar to that of white paint. The third rocket body has a similar flattening of slope but

  20. Reflectance Spectra Comparison of Orbital Debris, Intact Spacecraft, and Intact Rocket Bodies in the GEO Regime

    NASA Technical Reports Server (NTRS)

    Barker, Ed; Abercromby, Kira J.; Abell, Paul

    2009-01-01

    A key objective of NASA s Orbital Debris program office at Johnson Space Center (JSC) is to characterize the debris environment by way of assessing the physical properties (type, mass, density, and size) of objects in orbit. Knowledge of the geosynchronous orbit (GEO) debris environment in particular can be used to determine the hazard probability at specific GEO altitudes and aid predictions of the future environment. To calculate an optical size from an intensity measurement of an object in the GEO regime, a 0.175 albedo is assumed currently. However, identification of specific material type or types could improve albedo accuracy and yield a more accurate size estimate for the debris piece. Using spectroscopy, it is possible to determine the surface materials of space objects. The study described herein used the NASA Infrared Telescope Facility (IRTF) to record spectral data in the 0.6 to 2.5 micron regime on eight catalogued space objects. For comparison, all of the objects observed were in GEO or near-GEO. The eight objects consisted of two intact spacecraft, three rocket bodies, and three catalogued debris pieces. Two of the debris pieces stemmed from Titan 3C transtage breakup and the third is from COSMOS 2054. The reflectance spectra of the Titan 3C pieces share similar slopes (increasing with wavelength) and lack any strong absorption features. The COSMOS debris spectra is flat and has no absorption features. In contrast, the intact spacecraft show classic absorption features due to solar panels with a strong band gap feature near 1 micron. The two spacecraft are spin-stabilized objects and therefore have solar panels surrounding the outer surface. Two of the three rocket bodies are inertial upper stage (IUS) rocket bodies and have similar looking spectra. The slopes flatten out near 1.5 microns with absorption features in the near-infrared that are similar to that of white paint. The third rocket body has a similar flattening of slope but with fewer

  1. Treatment for burn blisters: debride or leave intact?

    PubMed

    Murphy, Faye; Amblum, Jeshi

    2014-05-01

    This article presents findings from a systematic literature review of whether blisters arising from minor burns should be de-roofed or left intact. It discusses the risks of infection, healing outcomes, discomfort, choice of dressings and costs associated with each method, and reveals that debriding blisters larger than the patient's little fingernail while leaving smaller ones intact is generally agreed to be the best option. The article also explains external factors that influence the choice of whether to debride or leave blisters intact, reviews policy at the trust where one of the authors works in the context of the research and makes recommendations for practice.

  2. Dental plaque microcosm biofilm behavior on calcium phosphate nanocomposite with quaternary ammonium

    PubMed Central

    Cheng, Lei; Weir, Michael D.; Zhang, Ke; Wu, Eric; Xu, Sarah M.; Zhou, Xuedong; Xu, Hockin H. K.

    2012-01-01

    Objectives Half of dental restorations fail in 10 years, with secondary caries as the main reason. Calcium phosphate composites could remineralize tooth lesions. The objectives of this study were to: (1) Impart antibacterial activity to a composite with nanoparticles of amorphous calcium phosphate (NACP); and (2) investigate the effect of quaternary ammonium dimethacrylate (QADM) on mechanical and dental plaque microcosm biofilm properties for the first time. Methods The NACP and glass particles were filled into a dental resin that contained bis(2-methacryloyloxy-ethyl) dimethyl-ammonium bromide, the QADM. NACP nanocomposites containing 0%, 7%, 14%, and 17.5% of QADM by mass, respectively, were photo-cured. A commercial composite with no antibacterial activity was used as control. Mechanical properties were measured in three-point flexure. A human saliva microcosm model was used to grow biofilms on composites. Live/dead assay, metabolic activity, colony-forming unit (CFU) counts, and lactic acid production of biofilms on the composites were measured. Results Increasing QADM mass fraction monotonically reduced the biofilm viability, CFU and lactic acid. Biofilms on NACP nanocomposite with 17.5% QADM had metabolic activity that was 30% that on a commercial composite control (p<0.05). Total microorganisms, total streptococci, and mutans streptococci CFU counts (mean±sd; n=6) on composite control was 6-fold those on NACP+17.5% QADM nanocomposite. Composite control had long strings of cells with normal short-rod shapes, while some cells on NACP-QADM nanocomposites disintegrated into pieces. Adding QADM to NACP did not decrease the strength and elastic modulus, which matched (p>0.1) those of a commercial composite without Ca-PO4 or antibacterial activity. Significance A dental plaque microcosm model was used to evaluate the novel NACP-QADM nanocomposite. The nanocomposite greatly reduced the biofilm viability, metabolic activity and lactic acid, while its mechanical

  3. 50 CFR 622.276 - Landing fish intact.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... ADMINISTRATION, DEPARTMENT OF COMMERCE FISHERIES OF THE CARIBBEAN, GULF OF MEXICO, AND SOUTH ATLANTIC Dolphin and Wahoo Fishery Off the Atlantic States § 622.276 Landing fish intact. (a) Dolphin and wahoo in or...

  4. 50 CFR 622.276 - Landing fish intact.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... ADMINISTRATION, DEPARTMENT OF COMMERCE FISHERIES OF THE CARIBBEAN, GULF OF MEXICO, AND SOUTH ATLANTIC Dolphin and Wahoo Fishery Off the Atlantic States § 622.276 Landing fish intact. (a) Dolphin and wahoo in or...

  5. 56. POWDER MAGAZINE, VIEW OF INTACT WOOD SHEATHING ON THE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    56. POWDER MAGAZINE, VIEW OF INTACT WOOD SHEATHING ON THE SOUTHWEST REAR VENTILATION PASSAGE. (SHEATHING HELP CONTROL HUMIDITY AND DECREASE DANGER OF MAETAL STRIKING STONE AND SPARKING.) - Fort Monroe, Fortress, Hampton, Hampton, VA

  6. 50 CFR 622.247 - Landing golden crab intact.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... ATLANTIC Golden Crab Fishery of the South Atlantic Region § 622.247 Landing golden crab intact. The... ashore. (a) A golden crab in or from the South Atlantic EEZ must be maintained in whole condition...

  7. 50 CFR 622.247 - Landing golden crab intact.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... ATLANTIC Golden Crab Fishery of the South Atlantic Region § 622.247 Landing golden crab intact. The... ashore. (a) A golden crab in or from the South Atlantic EEZ must be maintained in whole condition...

  8. Acoustic emissions during deformation of intact and jointed welded tuff

    NASA Astrophysics Data System (ADS)

    Holcomb, D. J.; Teufel, L. W.

    1982-07-01

    Monitoring of acoustic emissions (AE) has been widely used as a means of detecting failure in intact rock. For intact rock the technique is simple, because an increasing rate of AE is usually a sign of impending failure. However, most large rock masses contain numerous joints and the behavior of the joints controls the properties of the rock mass In particular, the failure mode often becomes stable or unstable slip (stick-slip) on a joint at stresses well below those required for failure of the intact rock. As an aid to understanding and monitoring the behavior of jointed rock masses, we have done a series of experiments on intact and artificially jointed samples of Grouse Canyon tuff. The tuff was selected because it is under consideration as a disposal medium for nuclear wastes. The samples were instrumented to measure axial and transverse displacements and AE rates.

  9. Preparation of Cardiac Extracellular Matrix from an Intact Porcine Heart

    PubMed Central

    Wainwright, John M.; Czajka, Caitlin A.; Patel, Urvi B.; Freytes, Donald O.; Tobita, Kimimasa; Gilbert, Thomas W.

    2010-01-01

    Whole organ engineering would benefit from a three-dimensional scaffold produced from intact organ-specific extracellular matrix (ECM). The microenvironment and architecture provided by such a scaffold would likely support site-appropriate cell differentiation and spatial organization. The methods to produce such scaffolds from intact organs require customized decellularization protocols. In the present study, intact adult porcine hearts were successfully decellularized in less than 10 h using pulsatile retrograde aortic perfusion. Serial perfusion of an enzymatic, nonionic detergent, ionic detergent, and acid solution with hypotonic and hypertonic rinses was used to systematically remove cellular content. The resultant cardiac ECM retained collagen, elastin, and glycosaminoglycans, and mechanical integrity. Cardiac ECM supported the formation of organized chicken cardiomyocyte sarcomere structure in vitro. The intact decellularized porcine heart provides a tissue engineering template that may be beneficial for future preclinical studies and eventual clinical applications. PMID:19702513

  10. Preparation of cardiac extracellular matrix from an intact porcine heart.

    PubMed

    Wainwright, John M; Czajka, Caitlin A; Patel, Urvi B; Freytes, Donald O; Tobita, Kimimasa; Gilbert, Thomas W; Badylak, Stephen F

    2010-06-01

    Whole organ engineering would benefit from a three-dimensional scaffold produced from intact organ-specific extracellular matrix (ECM). The microenvironment and architecture provided by such a scaffold would likely support site-appropriate cell differentiation and spatial organization. The methods to produce such scaffolds from intact organs require customized decellularization protocols. In the present study, intact adult porcine hearts were successfully decellularized in less than 10 h using pulsatile retrograde aortic perfusion. Serial perfusion of an enzymatic, nonionic detergent, ionic detergent, and acid solution with hypotonic and hypertonic rinses was used to systematically remove cellular content. The resultant cardiac ECM retained collagen, elastin, and glycosaminoglycans, and mechanical integrity. Cardiac ECM supported the formation of organized chicken cardiomyocyte sarcomere structure in vitro. The intact decellularized porcine heart provides a tissue engineering template that may be beneficial for future preclinical studies and eventual clinical applications.

  11. Hydrocarbon biodegradation by Arctic sea-ice and sub-ice microbial communities during microcosm experiments, Northwest Passage (Nunavut, Canada).

    PubMed

    Garneau, Marie-Ève; Michel, Christine; Meisterhans, Guillaume; Fortin, Nathalie; King, Thomas L; Greer, Charles W; Lee, Kenneth

    2016-10-01

    The increasing accessibility to navigation and offshore oil exploration brings risks of hydrocarbon releases in Arctic waters. Bioremediation of hydrocarbons is a promising mitigation strategy but challenges remain, particularly due to low microbial metabolic rates in cold, ice-covered seas. Hydrocarbon degradation potential of ice-associated microbes collected from the Northwest Passage was investigated. Microcosm incubations were run for 15 days at -1.7°C with and without oil to determine the effects of hydrocarbon exposure on microbial abundance, diversity and activity, and to estimate component-specific hydrocarbon loss. Diversity was assessed with automated ribosomal intergenic spacer analysis and Ion Torrent 16S rRNA gene sequencing. Bacterial activity was measured by (3)H-leucine uptake rates. After incubation, sub-ice and sea-ice communities degraded 94% and 48% of the initial hydrocarbons, respectively. Hydrocarbon exposure changed the composition of sea-ice and sub-ice communities; in sea-ice microcosms, Bacteroidetes (mainly Polaribacter) dominated whereas in sub-ice microcosms, the contribution of Epsilonproteobacteria increased, and that of Alphaproteobacteria and Bacteroidetes decreased. Sequencing data revealed a decline in diversity and increases in Colwellia and Moritella in oil-treated microcosms. Low concentration of dissolved organic matter (DOM) in sub-ice seawater may explain higher hydrocarbon degradation when compared to sea ice, where DOM was abundant and composed of labile exopolysaccharides.

  12. Evaluation of graphite for environmental toxicity using the standard aquatic microcosm. Technical report, June 1986-March 1987

    SciTech Connect

    Landis, W.G.; Chester, N.A.; Haley, M.V.; Johnson, D.W.; Tauber, R.M.

    1988-08-01

    The impact of a graphite dust on an aquatic ecosystem model, the Standard Aquatic microcosm (SAM), was investigated. Graphite dust produced effects that resembled eutrophication in that a diversity decreased, ammonia increased, and a photosynthesis/respiration ratio of less than one was observed in the highest concentration. Compared to brass dust, graphite has much less potential to adversely impact aquatic ecosystems.

  13. Near-Complete Genome Sequence of Thalassospira sp. Strain KO164 Isolated from a Lignin-Enriched Marine Sediment Microcosm

    PubMed Central

    Woo, Hannah L.; O’Dell, Kaela B.; Utturkar, Sagar; McBride, Kathryn R.; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Palaniappan, Krishnaveni; Varghese, Neha; Mikhailova, Natalia; Stamatis, Dimitrios; Reddy, T. B. K.; Ngan, Chew Yee; Daum, Chris; Shapiro, Nicole; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Woyke, Tanja; Brown, Steven D.

    2016-01-01

    Thalassospira sp. strain KO164 was isolated from eastern Mediterranean seawater and sediment laboratory microcosms enriched on insoluble organosolv lignin under oxic conditions. The near-complete genome sequence presented here will facilitate analyses into this deep-ocean bacterium’s ability to degrade recalcitrant organics such as lignin. PMID:27881538

  14. Near-Complete Genome Sequence of Thalassospira sp. Strain KO164 Isolated from a Lignin-Enriched Marine Sediment Microcosm.

    PubMed

    Woo, Hannah L; O'Dell, Kaela B; Utturkar, Sagar; McBride, Kathryn R; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Palaniappan, Krishnaveni; Varghese, Neha; Mikhailova, Natalia; Stamatis, Dimitrios; Reddy, T B K; Ngan, Chew Yee; Daum, Chris; Shapiro, Nicole; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Woyke, Tanja; Brown, Steven D; Hazen, Terry C

    2016-11-23

    Thalassospira sp. strain KO164 was isolated from eastern Mediterranean seawater and sediment laboratory microcosms enriched on insoluble organosolv lignin under oxic conditions. The near-complete genome sequence presented here will facilitate analyses into this deep-ocean bacterium's ability to degrade recalcitrant organics such as lignin.

  15. Use Of Statistical Tools To Evaluate The Reductive Dechlorination Of High Levels Of TCE In Microcosm Studies

    EPA Science Inventory

    A large, multi-laboratory microcosm study was performed to select amendments for supporting reductive dechlorination of high levels of trichloroethylene (TCE) found at an industrial site in the United Kingdom (UK) containing dense non-aqueous phase liquid (DNAPL) TCE. The study ...

  16. Litter quality indirectly influences community composition, reproductive mode and trophic structure of oribatid mite communities: a microcosm experiment.

    PubMed

    Gergócs, Veronika; Rétháti, Gabriella; Hufnagel, Levente

    2015-11-01

    Our knowledge of the assembly processes of species-rich oribatid mite communities is fairly limited. Also, very little information is available on the effects of habitat factors on these processes. In this paper, the role of litter quality in pattern formation was investigated in a microcosm experiment using the "home-field advantage" approach. Native (home) and foreign (away) types of microarthropod assemblages were extracted from three types of litter samples (Turkey oak, Scots pine and black locust tree), and transferred alive into 'home' and 'away' samples, which have been defaunated and reinoculated with microorganisms to form microcosms. Microarthropods were extracted from the microcosms after incubation for 3-12 months. In addition to species identification and abundance records, some chemical properties of the litter were measured. We hypothesized that oribatid mite communities deteriorate, the proportion of parthenogenetic individuals decreases and the proportion of omnivorous individuals increases in 'away' microcosms in contrast to 'home' systems. Pine and oak litter were favourable for all the three types of oribatid communities since their community traits in these types of litter were found to be similar to 'home' litter. Black locust litter was favourable only for its native oribatid community in the long run. The proportion of parthenogenetic individuals partly supported our hypothesis, mainly in black locust litter. The relative abundance of omnivorous individuals did not differ significantly between treatments. Litter quality is likely to influence oribatid mite assemblages only indirectly.

  17. Application of microcosmic system for assessment of insecticide effects on biomarker responses in ecologically different earthworm species.

    PubMed

    Velki, Mirna; Hackenberger, Branimir K; Lončarić, Zeljka; Hackenberger, Davorka K

    2014-06-01

    Earthworms from different ecological categories--epigeic Eisenia andrei and Lumbricus rubellus, endogeic Octolasion lacteum and anecic Lumbricus terrestris--were exposed in a microcosmic system to three commonly used insecticides. The effects of the insecticides were evaluated by measuring the following molecular biomarkers-the activities of AChE, CES, CAT, GST and the concentration of GSH. The results showed that environmentally relevant doses of organophosphates dimethoate and pirimiphos-methyl significantly affected the measured biomarkers, whereas pyrethroid deltamethrin did not affect the earthworms at the recommended agricultural dose. Considering the ecological category of earthworms, the results were inhomogeneous and species-specific differences in the biomarker responses were recorded. Since the biomarker responses of the investigated earthworm species were different after exposure to organophosphates in a microcosm compared to the exposure via standardized toxicity tests, two types of species sensitivity should be distinguished-physiological and environmental sensitivity. In addition, the hormetic effect of organophosphates on AChE and CES activities was recorded. The detection of hormesis in a microcosm is of great importance for future environmental research and soil biomonitoring, since in a realistic environment pollutants usually occur at low concentrations that could cause a hormetic effect. The results demonstrate the importance of the application of microcosmic systems in the assessment of the effects of environmental pollutants and the necessity of taking into account the possible differences between physiological and environmental species sensitivity.

  18. The effect of co-substrate activation on indigenous and bioaugmented PCB dechlorinating bacterial communities in sediment microcosms.

    PubMed

    Park, Joong-Wook; Krumins, Valdis; Kjellerup, Birthe V; Fennell, Donna E; Rodenburg, Lisa A; Sowers, Kevin R; Kerkhof, Lee J; Häggblom, Max M

    2011-03-01

    Microbial reductive dechlorination by members of the phylum Chloroflexi, including the genus Dehalococcoides, may play an important role in natural detoxification of highly chlorinated environmental pollutants, such as polychlorinated biphenyls (PCBs). Previously, we showed the increase of an indigenous bacterial population belonging to the Pinellas subgroup of Dehalococcoides spp. in Anacostia River sediment (Washington DC, USA) microcosms treated with halogenated co-substrates ("haloprimers"), tetrachlorobenzene (TeCB), or pentachloronitrobenzene (PCNB). The PCNB-amended microcosms exhibited enhanced dechlorination of weathered PCBs, while TeCB-amended microcosms did not. We therefore developed and used different phylogenetic approaches to discriminate the effect of the two different haloprimers. We also developed complementary approaches to monitor the effects of haloprimer treatments on 12 putative reductive dehalogenase (rdh) genes common to Dehalococcoides ethenogenes strain 195 and Dehalococcoides sp. strain CBDB1. Our results indicate that 16S rRNA gene-based phylogenetic analyses have a limit in their ability to distinguish the effects of two haloprimer treatments and that two of rdh genes were present in high abundance when microcosms were amended with PCNB, but not TeCB. rdh gene-based phylogenetic analysis supports that these two rdh genes originated from the Pinellas subgroup of Dehalococcoides spp., which corresponds to the 16S rRNA gene-based phylogenetic analysis.

  19. Molecular analysis of microbial community structures in pristine and contaminated aquifers--Field and laboratory microcosm experiments

    USGS Publications Warehouse

    Shi, Y.; Zwolinski, M.D.; Schreiber, M.E.; Bahr, J.M.; Sewell, G.W.; Hickey, W.J.

    1999-01-01

    Molecular Analysis of Microbial Community Structures in Pristine and Contaminated Aquifers: Field and Laboratory Microcosm Experimentsvar callbackToken='531E8ACDB6C8511'; var subCode='asmjournal_sub'; var OAS_sitepage = 'aem.asm.org'; This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminated (NC) and (ii) examine alterations in microbial community structures resulting from exposure to toluene and/or electron acceptor supplementation (nitrate). The latter objective was addressed by using the NC and FC aquifer materials for anaerobic microcosm studies in which phylogenetic probe analysis was complemented by microbial activity assays. Domain probe analysis of the aquifer samples showed that the communities were predominantlyBacteria; Eucarya and Archaea were not detectable. At the phylum and subclass levels, the FC and NC aquifer material had similar relative abundance distributions of 43 to 65% β- and γ-Proteobacteria (B+G), 31 to 35% α-Proteobacteria (ALF), 15 to 18% sulfate-reducing bacteria, and 5 to 10% high G+C gram positive bacteria. Compared to that of the NC region, the community structure of the FC material differed mainly in an increased abundance of B+G relative to that of ALF. The microcosm communities were like those of the field samples in that they were predominantly Bacteria (83 to 101%) and lacked detectable Archaea but differed in that a small fraction (2 to 8%) of Eucarya was detected regardless of the treatment applied. The latter result was hypothesized to reflect enrichment of anaerobic protozoa. Addition of nitrate and/or toluene stimulated microbial activity in the microcosms, but only supplementation of toluene alone significantly altered community structures. For the NC material, the dominant subclass shifted from B+G to ALF, while in the FC microcosms 55 to 65

  20. Unusual isotopic composition of C-CO2 from sterilized soil microcosms: a new way to separate intracellular from extracellular respiratory metabolisms.

    NASA Astrophysics Data System (ADS)

    Kéraval, Benoit; Alvarez, Gaël; Lehours, Anne Catherine; Amblard, Christian; Fontaine, Sebastien

    2015-04-01

    The mineralization of organic C requires two main steps. First, microorganisms secrete exoenzymes in soil in order to depolymerize plant and microbial cell walls and release soluble substrates for microbial assimilation. The second step of mineralization, during which C is released as CO2, implies the absorption and utilization of solubilized substrates by microbial cells with the aim to produce energy (ATP). In cells, soluble substrates are carried out by a cascade of respiratory enzymes, along which protons and electrons are transferred from a substrate to oxygen. Given the complexity of this oxidative metabolism and the typical fragility of respiratory enzymes, it is traditionally considered that respiration (second step of C mineralization process) is strictly an intracellular metabolism process. The recurrent observations of substantial CO2 emissions in soil microcosms where microbial cells have been reduced to extremely low levels challenges this paradigm. In a recent study where some respiratory enzymes have shown to function in an extracellular context in soils, Maire et al. (2013) suggested that an extracellular oxidative metabolism (EXOMET) substantially contributes to CO2 emission from soils. This idea is supported by the recent publication of Blankinship et al., 2014 who showed the presence of active enzymes involved in the Krebs cycle on soil particles. Many controversies subsist in the scientific community due to the presence of non-proliferating but morphologically intact cells after irradiation that could substantially contribute to those soil CO2 emissions. To test whether a purely extracellular oxidative metabolism contribute to soil CO2 emissions, we combined high doses of gamma irradiations to different time of soil autoclaving. The presence of active and non-active cells in soil was checked by DNA and RNA extraction and by electronic microscopy. None active cells (RNA-containing cells) were detectable after irradiation, but some morphological

  1. Decreases in ammonia volatilization in response to greater plant diversity in microcosms of constructed wetlands

    NASA Astrophysics Data System (ADS)

    Luo, Bin; Ge, Ying; Han, Wenjuan; Fan, Xing; Ren, Yuan; Du, Yuanyuan; Shi, Mengmeng; Chang, Jie

    2016-10-01

    Ammonia volatilization from wastewaters with a high concentration of ammonium is a serious environmental and health problem. Constructed wetlands (CWs) are widely used for treating wastewater, and plant diversity clearly improves some functions of ecosystem such as nitrogen removal. However, whether plant diversity can affect ammonia volatilization from wastewater is still unknown. In this study, we conducted a microcosm experiment with different plant diversity treatments using four plant species. Results showed that, (1) ammonia volatilization decreased with increasing plant species richness; (2) ammonia volatilization from systems containing Rumex japonicus was lower than other systems; and (3) ammonia volatilization was affected more by species composition than species richness. This paper is the first to report that ammonia volatilization is reduced by plant diversity, and that some plant species combinations are important to reduce ammonia volatilization from CWs when treating wastewater.

  2. Experimental approach to follow the spatiotemporal wood degradation in fungal microcosms.

    PubMed

    Hahn, Felix; Ullrich, René; Hofrichter, Martin; Liers, Christiane

    2013-01-01

    To investigate the spatiotemporal growth dynamics in fungal microcosms and to follow the spatial degradation effects of fungal lignocellulose fermentation, a new and flexible experimental setup was developed and tested. White and brown rot fungi were cultivated under solid-state conditions in beech wood-filled silicon tubes for 5 weeks. After inoculation of wood material at one end of the tube, the culture vessels were aerated and moistured by flushing air through alkaline and aqueous solutions. After incubation, the silicon tubes were harvested and segmented to follow different growth and degradation parameters. This new approach holds great potential since it allows the use of different growth substrates, variable aeration or moisturization conditions and is therefore a useful tool for diverse degradation studies, e.g. respiration/mineralization studies involving flow meters or carbon dioxide sensors or for molecular biological approaches.

  3. Competition between n-alkane-assimilating yeasts and bacteria during colonization of sandy soil microcosms.

    PubMed

    Schmitz, C; Goebel, I; Wagner, S; Vomberg, A; Klinner, U

    2000-07-01

    An n-alkane-assimilating strain of Candida tropicalis was selected in sandy soil inoculated with microorganisms from contaminated sites. Competition experiments with n-alkane utilizers from different strain collections confirmed that yeasts overgrow bacteria in sandy soil. Acidification of the soil is one of the colonization factors useful for the yeasts. It can be counteracted by addition of bentonite, a clay mineral with high ion exchange capacity, but not, however, by kaolin. Strains of different yeast species showed different levels of competitiveness. Strains of Arxula adeninivorans, Candida maltosa, and Yarrowia lipolytica overgrew strains of C. tropicalis, C. shehatae or Pichia stipitis. Two strains of C. maltosa and Y. lipolytica coexisted during several serial transfers under microcosm conditions.

  4. Recolonisation of mine tailing by meiofauna in mesocosm and microcosm experiments.

    PubMed

    Gwyther, David; Batterham, Grant J; Waworuntu, Jorina; Gultom, Tonny H; Prayogo, Windy; Susetiono; Karnan

    2009-06-01

    The Batu Hijau copper/gold mine in Sumbawa, Indonesia processes ore at approximately 130,000tpd and discharges tailing via a submarine pipeline to depths below 3000m at the base of a submarine canyon. The study investigated recolonisation of tailing by meiofauna and its dependence on subsequent accumulation of natural sediment. Microcosm and mesocosm scale experiments were carried out using two tailing and two control samples, the latter comprising defaunated and unaffected natural sediment. All test materials were similar in physical and chemical respects, except for the higher copper concentration in the tailing. The abundances of meiofauna colonising defaunated controls and both tailing samples increased from zero to levels statistically indistinguishable from natural unaffected controls after 97 and 203days. Colonisation was well established in tailing from freshly mined ore after 40days, and in oxidized tailing from stockpiled ore after 65days, and was not dependent on settled natural material.

  5. Application of electrical methods to measure microbial activity in soils: Preliminary microcosm results

    SciTech Connect

    Cox, B.L. Sweet, A.; Majer, E.

    1997-12-01

    The application of the geophysical technique known as self-potential to the measurement of microbial activity was tested on laboratory microcosms containing ferric iron and iron-reducing bacteria Shewanella alga BrY. Measurements of the electrical response of silver-coated copper electrodes distributed along a Teflon probe inserted into sterile and inoculated layers containing either ferric chloride, ferric citrate, or ferric oxide rich soil were recorded over hours or days. Strong electrical signals reached values more negative than {minus}400 mV for all types of inoculated ferric iron layers. Electric signals in sterile control layers, by contrast, rarely reached values more negative than {minus}150 mV. These preliminary experiments indicate that it may be possible to apply the self-potential geophysical method to monitor bioremediation in the field.

  6. Positive priming of terrestrially derived dissolved organic matter in a freshwater microcosm system

    NASA Astrophysics Data System (ADS)

    Bianchi, Thomas S.; Thornton, Daniel C. O.; Yvon-Lewis, Shari A.; King, Gary M.; Eglinton, Timothy I.; Shields, Michael R.; Ward, Nicholas D.; Curtis, Jason

    2015-07-01

    The role of priming processes in the remineralization of terrestrially derived dissolved organic carbon (TDOC) in aquatic systems has been overlooked. We provide evidence for TDOC priming using a lab-based microcosm experiment in which TDOC was primed by the addition of 13C-labeled algal dissolved organic carbon (ADOC) or a 13C-labeled disaccharide (trehalose). The rate of TDOC remineralization to carbon dioxide (CO2) occurred 4.1 ± 0.9 and 1.5 ± 0.3 times more rapidly with the addition of trehalose and ADOC, respectively, relative to experiments with TDOC as the sole carbon source over the course of a 301 h incubation period. Results from these controlled experiments provide fundamental evidence for the occurrence of priming of TDOC by ADOC and a simple disaccharide. We suggest that priming effects on TDOC should be considered in carbon budgets for large-river deltas, estuaries, lakes, hydroelectric reservoirs, and continental shelves.

  7. Effects of chemical additives on hydrocarbon disappearance and biodegradation in freshwater marsh microcosms.

    PubMed

    Nyman, J A; Klerks, P L; Bhattacharyya, S

    2007-09-01

    We determined how a cleaner and a dispersant affected hydrocarbon biodegradation in wetland soils dominated by the plant Panicum hemitomon, which occurs throughout North and South America. Microcosms received no hydrocarbons, South Louisiana crude, or diesel; and no additive, a dispersant, or a cleaner. We determined the concentration of four total petroleum hydrocarbon (TPH) measures and 43 target hydrocarbons in water and sediment fractions 1, 7, 31, and 186 days later. Disappearance was distinguished from biodegradation via hopane-normalization. After 186 days, TPH disappearance ranged from 24% to 97%. There was poor correlation among the four TPH measures, which indicated that each quantified a different suite of hydrocarbons. Hydrocarbon disappearance and biodegradation were unaltered by these additives under worse-case scenarios. Any use of these additives must generate benefits that outweigh the lack of effect on biodegradation demonstrated in this report, and the increase in toxicity that we reported earlier.

  8. Solder wetting behavior enhancement via laser-textured surface microcosmic topography

    NASA Astrophysics Data System (ADS)

    Chen, Haiyan; Peng, Jianke; Fu, Li; Wang, Xincheng; Xie, Yan

    2016-04-01

    In order to reduce or even replace the use of Sn-Pb solder in electronics industry, the laser-textured surface microstructures were used to enhance the wetting behavior of lead free solder during soldering. According to wetting theory and Sn-Ag-Cu lead free solder performance, we calculated and designed four microcosmic structures with the similar shape and different sizes to control the wetting behavior of lead free solder. The micro-structured surfaces with different dimensions were processed on copper plates by fiber femtosecond laser, and the effect of microstructures on wetting behavior was verified experimentally. The results showed that the wetting angle of Sn-Ag-Cu solder on the copper plate with microstructures decreased effectively compared with that on the smooth copper plate. The wetting angles had a sound fit with the theoretical values calculated by wetting model. The novel method provided a feasible route for adjusting the wetting behavior of solders and optimizing solders system.

  9. Biotic and abiotic interactions in aquatic microcosms determine fate and toxicity of Ag nanoparticles: part 2-toxicity and Ag speciation.

    PubMed

    Bone, Audrey J; Colman, Benjamin P; Gondikas, Andreas P; Newton, Kim M; Harrold, Katherine H; Cory, Rose M; Unrine, Jason M; Klaine, Stephen J; Matson, Cole W; Di Giulio, Richard T

    2012-07-03

    To study the effects of complex environmental media on silver nanoparticle (AgNP) toxicity, AgNPs were added to microcosms with freshwater sediments and two species of aquatic plants (Potamogeton diversifolius and Egeria densa), followed by toxicity testing with microcosm surface water. Microcosms were designed with four environmental matrices in order to determine the contribution of each environmental compartment to changes in toxicity: water only (W), water + sediment (WS), water + plants (WP), and water + plants + sediment (WPS). Silver treatments included AgNPs with two different coatings, gum arabic (GA-AgNPs) or polyvinylpyrollidone (PVP-AgNPs), as well as AgNO(3). Water samples taken from the microcosms at 24 h postdosing were used in acute toxicity tests with two standard model organisms, early life stage zebrafish (Danio rerio) and Daphnia magna. Speciation of Ag in these samples was analyzed using Ag L3-edge X-ray absorption near edge spectroscopy (XANES). Silver speciation patterns for the nanoparticle treatments varied significantly by coating type. While PVP-AgNPs were quite stable and resisted transformation across all matrices (>92.4% Ag(0)), GA-AgNP speciation patterns suggest significantly higher transformation rates, especially in treatments with plants (<69.2% and <58.8% Ag(0) in WP and WPS, respectively) and moderately increased transformation with sediments (<85.6% Ag(0)). Additionally, the presence of plants in the microcosms (with and without sediments) reduced both the concentration of Ag in the water column and toxicity for all Ag treatments. Reductions in toxicity may have been related to decreased water column concentrations as well as changes in the surface chemistry of the particles induced by organic substances released from the plants.

  10. The chemical and biological factors associated with ecosystem recovery from copper stress as exemplified by microcosms

    SciTech Connect

    Meador, J.P.

    1988-01-01

    The process of recovery from severe toxicant stress was examined in microcosms exposed to copper. The variables, algal and animal abundance, nutrient uptake, oxygen change, pH alkalinity, and the concentrations of total, dissolved, and ionic copper and dissolved organic carbon (DOC) were measured. Several process studies confirmed microcosm observations that algal metabolism was responsible for variation in pH and DOC concentration. It was demonstrated that these two parameters had a large influence on copper speciation and were responsible for ecosystem recovery. A complete three-factor, 48 hour bioassay was performed to assess the effects and interactions of DOC, pH and total copper on copper toxicity to Daphnia magma. A model using these 3 variables was developed which explained 84% of the variation in the determination of ionic copper. Mortality of Daphnia magma was modeled by using ionic copper as the dependent variable which explained 86% to 79% of the variation (at 24 and 48 hours). Variations in total copper concentration produced temporal variations in ecosystem recovery and the species dominance. Dissolved copper concentrations were correlated with pH values and consistently decreased to around 200 ppb (3:1 {mu}M) before algal recovery commenced. Dissolved copper concentrations were inadequate in explaining Daphnia magma toxicity when based on LC50 values. In this system, algal biomass, as an adsorbant, was shown to be insignificant in controlling copper toxicity. Alkalinity, which can be a major factor in copper speciation and toxicity, was also unimportant. It was determined that Daphnia magma populations were not inhibited when fed the copper-tolerant algal species, Oocystis pusilla, grown in a solution with a high copper concentration. Also, exposure to a high dissolved copper concentration did not confer resistance to copper toxicity in Daphnia magma.

  11. Evaluation of simulated acid precipitation effects on forest microcosms. Final report

    SciTech Connect

    Kelly, J.M.; Strickland, R.C.; Weatherford, F.P.; Noggle, J.C.

    1984-04-01

    Microcosms were treated for a 30-month period with simulated precipitation acidified to four pH levels (5.7, 4.5, 4.0, and 3.5) to evaluate the impact of acid precipitation on foliar leaching, plant nutrient content, soil leaching, soil nutrient content, and litter decomposition. Direct effects of acid precipitation on diameter growth, bud break, leaf senescence, chlorophyll content, stomatal size, stomatal density, photosynthesis, respiration, transpiration, and cuticle erosion were evaluated on tulip poplar, white oak, and Virginia pine seedlings growing as mixed stands in the microcosms. None of the plant physiological or morphological parameters evaluated responded in a statistically significant manner as a result of treatment. A significant treatment canopy interaction was observed in the form of a 60 percent increase in calcium input in throughfall in response to the pH 3.5 treatment. Foliar nutrient content did not change in response to treatment nor did field measurements of decomposer activity. Soil analysis indicated a significantly lower concentration of exchangeable calcium and magnesium in the top 3.5 cm of the mineral soil in association with the pH 3.5 treatment. Soil leachate concentrations exhibited significant increases at both the 25 and 50 cm depths. However, at the 100 cm depth no significant response in concentration or elemental loss from the system was observed. Laboratory respiration measurements indicated a small, but statistically significant reduction in decomposer activity in the lower litter (02) horizon. This reduction was masked in the field measurements of decomposer activity due to the relatively small contribution of the 02 to total soil respiration. 38 references, 12 figures, 18 tables.

  12. A soil microcosm to test the effects of pollutants on soil nematode and microarthropod communities

    SciTech Connect

    Parmelee, R.W.; Wentsel, R.S.; Checkai, R.T.; Phillips, C.T.; Bohlen, P.J.

    1995-12-31

    Previous studies have demonstrated that microcosms with field collected soil nematode and microarthropod communities are suitable model systems to detect effects of toxins on soil food web structure and function. The authors investigated the toxicity of copper, cadmium, malathion, and Aroclor 1254 to nematodes (total, bacterivores, fungivores, herbivores, omnivore-predators, hatchlings) and microarthropods (Prostigmata, Mesostigmata, Oribatida, Collembola, other arthropods). Nematodes were sensitive indicators of copper application, and total numbers were reduced at 100 {micro}g g{sup {minus}1}. Fungivore, bacterivore and omnivore-predators were the most susceptible trophic groups. Cadmium had no effects on either nematode or microarthropod communities. Microarthropods were more sensitive to malathion than nematodes, and total microarthropod abundance was lower than controls at 320 {micro}g g{sup {minus}1}. Prostigmatid mites and other arthropods were the most affected groups. Only the herbivore nematode trophic group was affected by malathion, and numbers did not decline until 1,280 {micro}g g{sup {minus}1}. Aroclor 1254 also had a greater negative impact on microarthropods than on nematodes. Total microarthropod abundance declined at 2,500 {micro}g g{sup {minus}1}, while there was no effect on nematodes. Prostigmatid and oribatid mites were the most susceptible groups to PCB application. Strong differential sensitivity between nematode and microarthropod communities indicates that both groups need to be examined to fully evaluate the impact of chemicals on soil systems. The authors conclude that microcosms with field-collected communities of soil microfauna offer high resolution of the ecotoxicological effects of chemicals in complex soil systems.

  13. Optimization of Differential Display of Prokaryotic mRNA: Application to Pure Culture and Soil Microcosms

    PubMed Central

    Fleming, James T.; Yao, Wen-Hsiang; Sayler, Gary S.

    1998-01-01

    The differential display (DD) technique, which is widely used almost exclusively for eukaryotic gene discovery, was optimized to detect differential mRNA transcription from both pure-culture and soil-derived bacterial RNA. A model system which included toluene induction of todC1 in Pseudomonas putida F1 was used to optimize the procedure. At 24-h tod induction was determined to be approximately 8 × 107 transcripts/μg or 0.08% of the total mRNA. The primer concentration, primer length, annealing temperature, and template, deoxynucleoside triphosphate, and MgCl2 concentrations were varied to optimize amplification of a todC1 fragment. The limit of detection of todC1 by DD was found to be 0.015 ng of total RNA template or approximately 103 transcripts. Once optimized, a todC1C2 gene fragment from P. putida F1 RNA was detected by using an arbitrary primer for the reverse transcriptase step in conjunction with the same arbitrary primer and a Shine-Dalgarno primer in the PCR. To verify the results, an arbitrary primer was used to detect recovery of a new salicylate-inducible naphthalene dioxygenase in Burkholderia cepacia JS150. The method was then used to detect mRNA induction in both inoculated and uninoculated toluene-induced soil microcosms. Several putative differentially expressed partial gene sequences obtained from the uninoculated microcosms were examined, and one novel fragment was found to be differentially expressed. PMID:9758787

  14. Soil microcosm for testing the effects of chemical pollutants on soil fauna communities and trophic structure

    SciTech Connect

    Parmelee, R.W. . Dept. of Entomology); Wentsel, R.S.; Phillips, C.T.; Checkai, R.T. ); Simini, M. )

    1993-08-01

    A microcosm technique is presented that uses community and trophic-level analysis of soil nematodes and microarthropods to determine the effects of chemicals on soil systems. Forest soil was treated with either copper, p-nitrophenol, or trinitrotoluene. Nematodes were sorted into bacterivore, fungivore, herbivore, and omnivore-predator trophic groups, and a hatchling category. Microarthropods were sorted to the acarine suborders Prostigmata, Mesostigmata, and Oribatida; the insectan order Collembola; and a miscellaneous group. Omnivore-predator nematodes and meso-stigmatid and oribatid mites were the groups most sensitive to copper and were significantly reduced at levels as low as 100 [mu]g g[sup [minus]1] copper. Total nematode and microarthropod numbers declined above 200 [mu]g g[sup [minus]1] copper. Trophic structure analysis suggested that high sensitivity of nematode predators to intermediate levels of copper reduced predation on herbivore nematodes and resulted in greater numbers of nematodes compared to controls. p-Nitrophenol was very toxic to the nematode community, and all trophic groups were significantly reduced above 20 [mu]g g[sup [minus]1]. However, there was no effect of p-nitrophenol on microarthropods. Trinitrotoluene had no significant negative effect on total abundance of either groups of soil fauna, but oribatids were significantly reduced at 200 [mu]g g[sup [minus]1]. The results demonstrated that soil nematodes and microarthropods were sensitive indicators of environmental contaminants and that trophic-structure and community analysis has the potential to detect more subtle indirect effects of chemicals on soil food-web structure. The authors conclude that microcosms with field communities of soil microfauna offer high resolution of the ecotoxicological effects of chemicals in complex soil systems.

  15. Liquid based formulations of bacteriophages for the management of waterborne bacterial pathogens in water microcosms.

    PubMed

    Ahiwale, Sangeeta; Tagunde, Sujata; Khopkar, Sushama; Karni, Mrudula; Gajbhiye, Milind; Kapadnis, Balasaheb

    2013-11-01

    Water resources are contaminated by life-threatening multidrug resistant pathogenic bacteria. Unfortunately, these pathogenic bacteria do not respond to the traditional water purification methods. Therefore, there is a need of environmentally friendly strategies to overcome the problems associated with the antimicrobial resistant bacterial pathogens. In the present study, highly potent lytic phages against multidrug-resistant Salmonella enterica serovar Paratyphi B, Pseudomonas aeruginosa and Klebsiella pneumoniae were isolated from the Pavana river water. They belonged to the Podoviridae and Siphoviridae families. These phages were purified and enriched in the laboratory. Monovalent formulations of phiSPB, BVPaP-3 and KPP phages were prepared in three different liquids viz., phage broth, saline and distilled water. The phages were stable for almost 8-10 months in the phage broth at 4 degrees C. The stability of the phages in saline and distilled water was 5-6 months at 4 degrees C. All of the phages were stable only for 4-6 months in the phage broth at 30 degrees C. The monovalent phage formulation of psiSPB was applied at MOI < 1, as disinfectant against an exponential and stationary phase cells of Salmonella enterica serovar Paratyphi B in various water microcosms. The results indicated that there was almost 80 % reduction in the log phase cells of Salmonella serovar Paratyphi B in 24 h. In stationary phase cells, the reduction was comparatively less within same period. At the same time, there was concomitant increase in the phage population by 80% in all the microcosms indicating that psiSPB phage is highly potent in killing pathogen in water. Results strongly support that the formulation of psiSPB in the phage broth in monovalent form could be used as an effective biological disinfectant for preventing transmission of water-borne bacterial pathogens, including antimicrobial resistant ones.

  16. Impact of acetochlor on ammonia-oxidizing bacteria in microcosm soils.

    PubMed

    Li, Xinyu; Zhang, Huiwen; Wu, Minna; Su, Zhencheng; Zhang, Chenggang

    2008-01-01

    Acetochlor is an increasingly used herbicide on corn in North China. Currently, the effect of acetochlor on soil ammonia-oxidizing bacteria (AOB) communities is not well documented. Here, we studied the diversity and community composition of AOB in soil amended with three concentrations of acetochlor (50, 150, 250 mg/kg) and the control (0 mg acetochlor/kg soil) in a microcosm experiment by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) and the phylogenetic analysis of excised DGGE bands. DGGE profiles showed that acetochlor had a stimulating effect on AOB at the early stage after acetochlor amended, and the order of intensity and duration is medium-acetochlor amended samples (AM) > low-acetochlor amended samples (AL) > high-acetochlor amended samples (AH). At the end of 60 d microcosm, acetochlor had a negative effect on the diversity of AOB. Cluster analysis of DGGE profiles showed that acetochlor had a greater effect on the community structure of AOB on day 60 than on day 1. The phylogenetic analysis revealed that all the sequences of excised DGGE bands were closely related to members of the genus Nitrosospira and formed two separate subclusters designated as subcluster 1 and subcluster 2 affiliated respectively with clusters 3 and 4 in Nitrosospira as defined by Stephen. Some dominant AOB had a change from subcluster 2 to subcluster 1 with the incubation. The results showed that acetochlor had an effect on the AOB on a long-term basis and the chronic effect of acetochlor should be paid more attention in future.

  17. Effect of amorphous calcium phosphate and silver nanocomposites on dental plaque microcosm biofilms

    PubMed Central

    Cheng, Lei; Weir, Michael D.; Xu, Hockin H. K.; Antonucci, Joseph M.; Lin, Nancy J.; Lin-Gibson, Sheng; Xu, Sarah M.; Zhou, Xuedong

    2012-01-01

    A dental composite containing amorphous calcium phosphate nanoparticles (NACP) was developed that released calcium (Ca) and phosphate (PO4) ions and possessed acid-neutralization capability. There has been little study on incorporation of antibacterial agents into calcium phosphate composites. The objective of this study was to investigate the effect of silver nanoparticle (NAg) mass fraction in NACP nanocomposite on mechanical properties and dental plaque microcosm biofilm for the first time. NACP nanoparticles of 116 nm were synthesized via a spray-drying technique. NAg nanoparticles were synthesized using Ag 2-ethylhexanoate and 2-(tert-butylamino)ethyl methacrylate, yielding NAg of particle size of 2.7 nm that were well-dispersed in the resin. Five NACP nanocomposites were fabricated with NAg mass fractions of 0, 0.028, 0.042, 0.088, and 0.175%, respectively. Mechanical properties of NACP nanocomposites containing 0–0.042% of NAg matched those of a commercial composite without antibacterial activity. Live/dead assay of dental plaque microcosm biofilms showed complete coverage with live bacteria on commercial composite. However, there were increasingly more dead bacteria with higher NAg content in the NACP nanocomposite. Colony-forming unit (CFU) counts for total microorganisms, total Streptococci, and mutans Streptococci for NACP nanocomposite with 0.042% NAg were about 1/4 those of commercial composite. Lactic acid production on NACP nanocomposite with 0.042% NAg was 1/3 that on commercial composite. In conclusion, novel NACP–NAg nanocomposites were developed which possessed good mechanical properties and potent antibacterial properties, with substantially reduced biofilm viability and lactic acid production. Hence, the NACP–NAg nanocomposites are promising for dental restorations with remineralizing and antibacterial capabilities. PMID:22566464

  18. Vulnerability of ecosystems to climate change moderated by habitat intactness.

    PubMed

    Eigenbrod, Felix; Gonzalez, Patrick; Dash, Jadunandan; Steyl, Ilse

    2015-01-01

    The combined effects of climate change and habitat loss represent a major threat to species and ecosystems around the world. Here, we analyse the vulnerability of ecosystems to climate change based on current levels of habitat intactness and vulnerability to biome shifts, using multiple measures of habitat intactness at two spatial scales. We show that the global extent of refugia depends highly on the definition of habitat intactness and spatial scale of the analysis of intactness. Globally, 28% of terrestrial vegetated area can be considered refugia if all natural vegetated land cover is considered. This, however, drops to 17% if only areas that are at least 50% wilderness at a scale of 48×48 km are considered and to 10% if only areas that are at least 50% wilderness at a scale of 4.8×4.8 km are considered. Our results suggest that, in regions where relatively large, intact wilderness areas remain (e.g. Africa, Australia, boreal regions, South America), conservation of the remaining large-scale refugia is the priority. In human-dominated landscapes, (e.g. most of Europe, much of North America and Southeast Asia), focusing on finer scale refugia is a priority because large-scale wilderness refugia simply no longer exist. Action to conserve such refugia is particularly urgent since only 1 to 2% of global terrestrial vegetated area is classified as refugia and at least 50% covered by the global protected area network.

  19. Structural and molecular interrogation of intact biological systems

    PubMed Central

    Chung, Kwanghun; Wallace, Jenelle; Kim, Sung-Yon; Kalyanasundaram, Sandhiya; Andalman, Aaron S.; Davidson, Thomas J.; Mirzabekov, Julie J.; Zalocusky, Kelly A.; Mattis, Joanna; Denisin, Aleksandra K.; Pak, Sally; Bernstein, Hannah; Ramakrishnan, Charu; Grosenick, Logan; Gradinaru, Viviana; Deisseroth, Karl

    2014-01-01

    Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Using mouse brains, we show intact-tissue imaging of long-range projections, local circuit wiring, cellular relationships, subcellular structures, protein complexes, nucleic acids and neurotransmitters. CLARITY also enables intact-tissue in situ hybridization, immunohistochemistry with multiple rounds of staining and de-staining in non-sectioned tissue, and antibody labelling throughout the intact adult mouse brain. Finally, we show that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease. PMID:23575631

  20. Tracking tagged molecules in single neurons in intact zebrafish.

    PubMed

    Armisen, Ricardo; Gleason, Michelle R; Fetcho, Joseph R; Mandel, Gail

    2007-08-01

    INTRODUCTIONThis protocol describes an approach for monitoring the movement of tagged molecules in single neurons in intact embryonic and larval zebrafish. The intact preparation provides a meaningful context for the physiological event being studied. Other advantages offered by the young zebrafish include direct in vivo imaging, the ability to produce large numbers of labeled embryos easily using microinjection, and the existence of identified sensory circuits that can be exploited to activate a particular cell type. One limitation of this system is the fragility of 2- to 3-d-old embryos, which demands delicate physical manipulation of the fish during all stages preceding and during the experiment. In contrast to brain slices or isolated cells, nearly all original neural connections and sensory components are maintained in the intact preparation, so the occurrence of a downstream event may be precluded (or its manifestation enhanced) by some complex interplay of biological processes that are not fully understood.

  1. A Retrievable Mineral Microcosm for Examining Microbial Colonization and Mineral Precipitation at Seafloor Hydrothermal Vents

    NASA Astrophysics Data System (ADS)

    Dunn, E. E.; Holloway, J. R.; Cary, S.; Voglesonger, K. M.; Ashbridge, D. A.; O'Day, P. A.

    2002-12-01

    Although seafloor hydrothermal vent environments are known to support thriving ecosystems, the microscale physical and chemical environment suitable for microbial colonization and the identity of pioneering organisms is unknown. Because of the fragility of young chimneys and their ephemeral nature, novel methods for sample retrieval and analysis are required. The mineral microcosm consists of four titanium mesh chambers containing crushed minerals mounted on a titanium base that allows for fluid flow through the chambers. The chambers can be filled with different minerals or mineral mixtures (or no minerals) to supply different substrates for microbial colonization and different local microenvironments as minerals react with the surrounding fluids. The device sets on top of an active hydrothermal vent for a period of days to weeks to allow colonization and mineral reaction. The mineral microcosm was deployed during the Atlantis/Alvin Extreme 2001 Cruise (Oct.- Nov.,2001) to 9° 50'N on the East Pacific Rise a total of three times, for ~ 24, ~ 96, and ~ 48 hours each. It was deployed in two different environments, twice in lower temperature (<300°C), diffuse-flow environments and once (for ~96 hours) in a higher temperature black smoker environment (>350°C).Seed minerals included sulfides, sulfates, magnetite, apatite, and quartz, both individually and in mixtures. In the first 24-hour deployment, dissolution of anhydrite but not sulfide minerals within the chambers indicated high temperatures in chamber interiors and rapid reaction rates. Temperatures measured on chamber exteriors before retrieval ranged from 4° -98°C. The 96-hour deployment on a hot vent (fluid ~370°C before deployment) resulted in extensive mineral precipitation and chimney growth inside the mineral chambers, on the outer surfaces of the chambers, and on the platform as a whole, creating micro-chimneys several centimeters tall. The young chimneys were mainly composed of pyrite with lesser

  2. In-situ Subaqueous Capping of Mercury-Contaminated Sediments in a Fresh-Water Aquatic System, Part I-Bench-Scale Microcosm Study to Assess Methylmercury Production

    EPA Science Inventory

    Bench-scale microcosm experiments were designed to provide a better understanding of the potential for Hg methylation in sediments from an aquatic environment. Experiments were conducted to examine the function of sulfate concentration, lactate concentration, the presence/absenc...

  3. Biodegradation of organic chemicals in soil/water microcosms system: Model development

    USGS Publications Warehouse

    Liu, L.; Tindall, J.A.; Friedel, M.J.; Zhang, W.

    2007-01-01

    The chemical interactions of hydrophobic organic contaminants with soils and sediments may result in strong binding and slow subsequent release rates that significantly affect remediation rates and endpoints. In order to illustrate the recalcitrance of chemical to degradation on sites, a sorption mechanism of intraparticle sequestration was postulated to operate on chemical remediation sites. Pseudo-first order sequestration kinetics is used in the study with the hypothesis that sequestration is an irreversibly surface-mediated process. A mathematical model based on mass balance equations was developed to describe the fate of chemical degradation in soil/water microcosm systems. In the model, diffusion was represented by Fick's second law, local sorption-desorption by a linear isotherm, irreversible sequestration by a pseudo-first order kinetics and biodegradation by Monod kinetics. Solutions were obtained to provide estimates of chemical concentrations. The mathematical model was applied to a benzene biodegradation batch test and simulated model responses correlated well compared to measurements of biodegradation of benzene in the batch soil/water microcosm system. A sensitivity analysis was performed to assess the effects of several parameters on model behavior. Overall chemical removal rate decreased and sequestration increased quickly with an increase in the sorption partition coefficient. When soil particle radius, a, was greater than 1 mm, an increase in radius produced a significant decrease in overall chemical removal rate as well as an increase in sequestration. However, when soil particle radius was less than 0.1 mm, an increase in radius resulted in small changes in the removal rate and sequestration. As pseudo-first order sequestration rate increased, both chemical removal rate and sequestration increased slightly. Model simulation results showed that desorption resistance played an important role in the bioavailability of organic chemicals in porous

  4. Capacity for Methane Oxidation in Landfill Cover Soils Measured in Laboratory-Scale Soil Microcosms

    PubMed Central

    Kightley, D.; Nedwell, D. B.; Cooper, M.

    1995-01-01

    Laboratory-scale soil microcosms containing different soils were permeated with CH(inf4) for up to 6 months to investigate their capacity to develop a methanotrophic community. Methane emissions were monitored continuously until steady states were established. The porous, coarse sand soil developed the greatest methanotrophic capacity (10.4 mol of CH(inf4) (middot) m(sup-2) (middot) day(sup-1)), the greatest yet reported in the literature. Vertical profiles of O(inf2), CH(inf4), and methanotrophic potential in the soils were determined at steady state. Methane oxidation potentials were greatest where the vertical profiles of O(inf2) and CH(inf4) overlapped. A significant increase in the organic matter content of the soil, presumably derived from methanotroph biomass, occurred where CH(inf4) oxidation was greatest. Methane oxidation kinetics showed that a soil community with a low methanotrophic capacity (V(infmax) of 258 nmol (middot) g of soil(sup-1) (middot) h(sup-1)) but relatively high affinity (k(infapp) of 1.6 (mu)M) remained in N(inf2)-purged control microcosms, even after 6 months without CH(inf4). We attribute this to a facultative, possibly mixotrophic, methanotrophic microbial community. When purged with CH(inf4), a different methanotrophic community developed which had a lower affinity (k(infapp) of 31.7 (mu)M) for CH(inf4) but a greater capacity (V(infmax) of 998 nmol (middot) g of soil(sup-1) (middot) h(sup-1)) for CH(inf4) oxidation, reflecting the enrichment of an active high-capacity methanotrophic community. Compared with the unamended control soil, amendment of the coarse sand with sewage sludge enhanced CH(inf4) oxidation capacity by 26%; K(inf2)HPO(inf4) amendment had no significant effect, while amendment with NH(inf4)NO(inf3) reduced the CH(inf4) oxidation capacity by 64%. In vitro experiments suggested that NH(inf4)NO(inf3) additions (10 and 71 (mu)mol (middot) g of soil(sup-1)) inhibited CH(inf4) oxidation by a nonspecific ionic effect

  5. The MICROBE (Microcosm Investigation of Carbonate Reef/Ocean Microbial Biogeochemistry & Ecology) Project

    NASA Astrophysics Data System (ADS)

    Hannides, A. K.; Gaidos, E. J.; Sansone, F. J.

    2003-12-01

    We present a methodology to manipulate carbonate reef sediments in order to study the geochemical and microbiological response of reef systems to perturbations. We specifically plan to study the effects of changes in the atmospheric partial pressure of CO2. Our laboratory set-up will consist of cores containing carbonate reef sediments and overlying water. These microcosms are designed to replicate the gross hydraulic and geochemical characteristics of sediments in a natural tropical reef patch. This is achieved by reproducing the advective transport of water and particulates in and out of the sediments induced by tides and surface waves. Seawater from nearby reefs is to be introduced into the cores with reversible peristaltic pumps. The pumps will vary the overlying water column and simulate the changes in hydrostatic head that accompany waves and tides. The parameters characterizing these oscillations will be set at values reflecting those at nearby natural settings. Sediment column characteristics will be determined non-destructively through openings at various depths down the sediment cores. These openings are fitted with rubber septa and shut-off valves, which allow gas-tight sampling of porewaters. An additional set of openings allows for the removal of small amounts of sediments using augers. Our porewater analyses will include dissolved O2, CO2, CH4 and alkalinity, ammonium, sulfide, and iron and manganese ions. Our solid phase analyses will include carbonate composition and framework structure, and iron and manganese abundances in the carbonate phases. We will measure microbial abundance in porewater and the sediment particles by DAPI cell counts and will assay community composition using Denaturing Gradient Gel Electrophoresis (DGGE). Our goal is to use this methodology to observe and record carbonate precipitation and dissolution by microbiota under varying carbon dioxide regimes. pCO2 concentrations will be manipulated by bubbling a N2/CO2 mixture

  6. Microcosm studies of subsurface PAH-degrading bacteria from a former manufactured gas plant

    NASA Astrophysics Data System (ADS)

    Durant, Neal D.; Wilson, Liza P.; Bouwer, Edward J.

    1995-01-01

    A study was conducted to evaluate the potential for natural in situ biodegradation of polycyclic aromatic hydrocarbons (PAH's) in the subsurface at the site of a former manufactured gas plant. Fifty-seven samples of unconsolidated subsurface sediments were aseptically obtained from five boreholes across the site. Bacteria capable of aerobically degrading PAH's without an acclimation period were detected throughout shallow (2.7 m) and deep (24.7 m) areas of the subsurface in both relatively clean (<20 μg L -1 naphthalene) and contaminated (4400 μg L -1 naphthalene) zones. Significant ( p < 0.05) quantities of naphthalene (8±3% to 43±7%) and/or phenanthrene (3±1% to 31±3%) were mineralized in sediment-groundwater microcosms during 4 weeks of aerobic incubation at 22°C. Three samples out of 11 were able to aerobically mineralize significant quantities of benzene (6±2% to 24±1%). Of 11 samples tested for anaerobic mineralization, naphthalene biodegradation (7±1% to 13±2%) in the presence of N03 was observed in two samples. Compound removals were first order with respect to substrate concentration during the first 10-15 days of incubation. Compound biodegradation plateaued in the later stages of incubation (15-40 days), most likely from diminishing bioavailability and nutrient and oxygen depletion. Population densities in the sediments were typically low, with viable aerobic counts ranging from 0 to 10 5 CFU gdw -1, viable anaerobic counts ranging from 0 to 104 CFU gdw -1, and total counts (AODC) usually 10-fold greater than viable counts. Total counts exhibited a strong ( p < 0.01) positive correlation with sample grain size. Viable aerobic and anaerobic populations commonly occurred in the same sample, suggesting the presence of facultative anaerobes. Bacteria were metabolically active in samples from groundwaters with low pH (3.7) and high naphthalene concentrations (11,000 μg L -1). Data from these enumeration and microcosm studies suggest that natural

  7. Microbial Community Phylogenetic and Functional Succession in Chromium-Reducing Aquifer-Derived Microcosms

    NASA Astrophysics Data System (ADS)

    Brodie, E. L.; Beller, H. R.; Goldfarb, K. C.; Han, R.; Santee, C. A.

    2009-12-01

    In situ reductive immobilization, whereby highly soluble Cr(VI) species are reduced to poorly soluble Cr(III) species, is a favored approach for remediating Cr-contaminated groundwater. How microbial populations respond phylogenetically and functionally to the injection of an organic electron donor to stimulate Cr(VI) reduction is unclear, as are the relative contributions of direct enzymatic Cr(VI) reduction versus indirect (e.g. sulfide-mediated) reduction. In this study, we inoculated anaerobic microcosms with groundwater from the Cr-contaminated Hanford 100H site (WA) and supplemented them with lactate and the electron acceptors nitrate, sulfate, and amorphous ferric oxyhydroxide. The microcosms progressed successively through nitrate-reducing, sulfate-reducing, and Fe(III)-reducing conditions, and after a second nitrate amendment, nitrate-dependent Fe(II)-oxidizing conditions. Cr(VI) reduction occurred during both the denitrification and the sulfate/iron reduction phases. DNA and RNA were harvested during each major biogeochemical phase and were subjected to PhyloChip analysis, qPCR, and transcript sequencing. Bacterial community succession followed a trajectory related to the sequential use of electron acceptors. During denitrification, bacterial communities were enriched in known denitrifiers within the Beta- and Gamma-proteobacteria and became phylogenetically clustered. Fermenters became enriched following nitrate reduction, preceding both iron and sulfate reduction. Iron reduction was stoichiometrically related to the formation of hydrogen sulfide and, although iron reducers were detected during this phase, their iron-reducing activity was not confirmed. Following the depletion of lactate and sulfate, iron reduction rates decreased and acetate and propionate concentrations stabilized, indicating a marginal contribution of acetate-coupled iron reduction. Rapid Fe(II) oxidation occurred following the nitrate amendment with a concomitant reduction of nitrate

  8. Microcosm investigations of stormwater pond sediment toxicity to embryonic and larval amphibians: variation in sensitivity among species.

    PubMed

    Snodgrass, Joel W; Casey, Ryan E; Joseph, Debra; Simon, Judith A

    2008-07-01

    Stormwater ponds have become common features of modern development and often represent significant amounts of open space in urbanized areas. Although stormwater ponds may provide habitat for wildlife, factors responsible for producing variation in wildlife use of ponds have received limited attention. To investigate the role of variation in species tolerances of pollutants in structuring pond-breeding amphibian assemblages, we exposed species tolerant (Bufo americanus) and not tolerant (Rana sylvatica) of urbanization to pond sediments in laboratory microcosms. Pond microcosms had elevated sediment metal levels and chloride water concentrations. Among R. sylvatica embryos, exposure to pond sediments resulted in 100% mortality. In contrast, B. americanus embryos and larvae experienced only sublethal effects (i.e., reduced size at metamorphosis) due to pond sediment exposure. Our results suggest variation in pollutant tolerance among early developmental stages of amphibians may act in concert with terrestrial habitat availability to structure amphibian assemblages associated with stormwater ponds.

  9. The effects of high-tannin leaf litter from transgenic poplars on microbial communities in microcosm soils

    PubMed Central

    Winder, Richard S.; Lamarche, Josyanne; Constabel, C. Peter; Hamelin, Richard C.

    2013-01-01

    The impacts of leaf litter from genetically modified hybrid poplar accumulating high levels of condensed tannins (proanthocyanidins) were examined in soil microcosms consisting of moss growing on sieved soil. Moss preferentially proliferated in microcosms with lower tannin content; DGGE (denaturing gradient gel electrophoresis) detected increased fungal diversity in microcosms with low-tannin litter. The proportion of cloned rDNA sequences from Actinobacteria decreased with litter addition while Bacteroidetes, Chloroflexi, Cyanobacteria, and α-Proteobacteria significantly increased. β-Proteobacteria were proportionally more numerous at high-tannin levels. Tannins had no significant impact on overall diversity of bacterial communities analyzed with various estimators. There was an increased proportion of N-fixing bacteria corresponding to the addition of litter with low-tannin levels. The addition of litter increased the proportion of Ascomycota/Basidiomycota. Dothideomycetes, Pucciniomycetes, and Tremellomycetes also increased and Agaricomycetes decreased. Agaricomycetes and Sordariomycetes were significantly more abundant in controls, whereas Pucciniomycetes increased in soil with litter from transformed trees (P = 0.051). Richness estimators and diversity indices revealed no significant difference in the composition of fungal communities; PCoA (principal coordinate analyses) partitioned the fungal communities into three groups: (i) those with higher amounts of added tannin from both transformed and untransformed treatments, (ii) those corresponding to soils without litter, and (iii) those corresponding to microcosms with litter added from trees transformed only with a β-glucuronidase control vector. While the litter from transformed poplars had significant effects on soil microbe communities, the observed impacts reflected known impacts on soil processes associated with tannins, and were similar to changes that would be expected from natural variation in

  10. Quorum sensing by N-acylhomoserine lactones is not required for Aeromonas hydrophila during growth with organic particles in lake water microcosms.

    PubMed

    Styp von Rekowski, Katharina; Hempel, Melanie; Philipp, Bodo

    2008-05-01

    It was investigated whether quorum sensing (QS) mediated by N-acylhomoserine lactones (AHLs) was important for heterotrophic bacteria from the littoral zone of the oligotrophic Lake Constance for growth with organic particles. More than 900 colonies from lake water microcosms with artificial organic aggregates consisting of autoclaved unicellular algae embedded in agarose beads were screened for AHL-production. AHL-producing bacteria of the genus Aeromonas enriched in the microcosms but AHLs could not be detected in any microcosm. To test for a potential function of AHL-mediated QS, growth experiments with the wild type and an AHL-deficient mutant of Aeromonas hydrophila in lake water microcosms were performed. Growth of both strains did not differ in single cultures and showed no mutual influence in co-cultures. In co-cultures with a competitor bacterium belonging to the Cytophaga-Flavobacterium group, growth of both A. hydrophila strains was reduced while growth of the competitor bacterium was not affected. Exogenous AHL-addition did not influence growth of the Aeromonas strains in any microcosm experiment. These results showed that AHL-mediated QS was not required for A. hydrophila during colonization and degradation of organic particles in lake water microcosms, suggesting that cell-cell signalling of heterotrophic bacteria in oligotrophic waters relies on novel signal molecules.

  11. Dynamic changes in microbial community structure and function in phenol-degrading microcosms inoculated with cells from a contaminated aquifer.

    PubMed

    Elliott, David R; Scholes, Julie D; Thornton, Steven F; Rizoulis, Athanasios; Banwart, Steven A; Rolfe, Stephen A

    2010-02-01

    Contamination of aquifers by organic pollutants threatens groundwater supplies and the environment. In situ biodegradation of organic pollutants by microbial communities is important for the remediation of contaminated sites, but our understanding of the relationship between microbial development and pollutant biodegradation is poor. A particular challenge is understanding the in situ status of microorganisms attached to solid surfaces, but not accessible via conventional sampling of groundwater. We have developed novel flow-through microcosms and examined dynamic changes in microbial community structure and function in a phenol-degrading system. Inoculation of these microcosms with a complex microbial community from a plume in a phenol-contaminated aquifer led to the initial establishment of a population dominated by a few species, most attached to the solid substratum. Initially, phenol biodegradation was incomplete, but as the microbial community structure became more complex, phenol biodegradation was more extensive and complete. These results were replicated between independent microcosms, indicating a deterministic succession of species. This work demonstrates the importance of examining community dynamics when assessing the potential for microbial biodegradation of organic pollutants. It provides a novel system in which such measurements can be made readily and reproducibly to study the temporal development and spatial succession of microbial communities during biodegradation of organic pollutants at interfaces within such environments.

  12. Impacts of loach bioturbation on the selective bioaccumulation of HBCDD diastereoisomers and enantiomers by mirror carp in a microcosm.

    PubMed

    Zhang, Yanwei; Wang, Lei; Sun, Hongwen; Yao, Tianqi; Zhu, Hongkai; Xu, Jiayao; Liu, Xiaowei

    2016-11-01

    To assess the impacts of bioturbation at the water-sediment interface on the bioaccumulation of hexabromocyclododecane diastereoisomers (HBCDDs) by pelagic organisms and the bioisomerization and enantioselectivity therein, we built microcosms containing water, mirror carp (Cyprinus carpio), and sediment. The microcosms were sorted into two groups, with or without loach (Misgurnus anguillicaudatus) living at the water-sediment interface. A 50-d accumulation test was conducted by spiking the microcosms with the three main HBCDD diastereoisomers (α-, β-, and γ-HBCDDs) separately. The HBCDDs were mainly associated with the sediment. The dissolved organic matter and suspended particulate matter content increased due to loach bioturbation, which promoted the release of sediment-associated HBCDDs and led to enhanced HBCDD bioaccumulation in the carp. Isomerization from β- and γ-HBCDD to α-HBCDD occurred in the carp, and the amounts of isomerization did not increase proportionally with increasing bioaccumulation. Moreover, the enantioselectivity of the HBCDD diastereoisomers showed species-specific differences between mirror carp and loach, and no significant change in the enantioselectivity in the carp was observed in the presence of loach.

  13. Determining the effects of pollutants on soil faunal communities and trophic structure using a refined microcosm system

    SciTech Connect

    Parmelee, R.W.; Phillips, C.T.; Checkai, R.T.; Bohlen, P.J.

    1997-06-01

    The authors used a refined microcosm technique to investigate the toxicity of copper, cadmium, malathion, and the polychlorinated biphenyl, to trophic groups of soil nematodes and to the microarthropod community. Comparisons of changes in nematode abundance in control soils through time indicated that day 7 was the most appropriate time to sample the microcosms after chemical application. Nematode abundance was reduced after exposure to copper at 100 {micro}g/g, with fungivore, bacterivore, and omnivore-predator nematodes being the most sensitive groups. Cadmium did not affect the nematode or microarthropod communities. Microarthropods were far more sensitive to malathion than were nematodes, and total microarthropod abundance was lower than controls at 400 {micro}g/g. Prostigmatid mites and other arthropods were the most affected groups. PCB also had a greater negative impact on microarthropods than on nematodes. Total microarthropod abundance declined at 2,500 {micro}g/g, with prostigmatid and oribatid mites exhibiting the highest susceptibility. Strong differential sensitivity between nematode and microarthropod communities indicates that both groups should be examined to fully evaluate the biological impact of chemicals on soils. The authors conclude that microcosms with field-collected soil microfaunal communities offer high resolution of the ecotoxicologic effects of chemicals in complex soil systems.

  14. Stimulation of anaerobic biodegradation of DDT and its metabolites in a muck soil: laboratory microcosm and mesocosm studies.

    PubMed

    Gohil, Hiral; Ogram, Andrew; Thomas, John

    2014-09-01

    The aim of this study was to evaluate the impact of selected electron donors and electron acceptors on the anaerobic biodegradation of DDT and its major metabolites in a muck soil with a long history of exposure to the pesticide. Loss of DDT was measured in anaerobic microcosms supplemented with H2, lactate, and acetate. The greatest loss of DDT (approximately 87 %) was observed in microcosms amended with lactate and no additional electron acceptor compared to the no additional electron donor or acceptor sets. An increase in measureable concentrations of DDx was observed in un-amended microcosms. In larger scale mesocosms, significant increases in dissolved organic carbon (DOC) corresponded with low redox potentials. Increases in DOC corresponded with sharp increases in measured concentrations of DDx, followed by a decrease in measured DDT concentrations in lactate-amended mesocosms. Our studies indicate that sorbed DDx is released upon anaerobic incubation, and that indigenous microorganisms capable of DDx degradation respond to lactate additions. Both the potential for release of sorbed DDx and the potential for biodegradation of DDx should be considered during remediation of DDx-contaminated organic soils at low redox potentials.

  15. Reduced growth of Listeria monocytogenes in two model cheese microcosms is not associated with individual microbial strains.

    PubMed

    Imran, Muhammad; Bré, Jean-Michel; Guéguen, Marielle; Vernoux, Jean-Paul; Desmasures, Nathalie

    2013-02-01

    Two model antilisterial microbial communities consisting of two yeasts, two Gram positive and two Gram negative bacteria, and originating from Livarot cheese smear were previously designed. They were used in the present study to analyse the impact of microbial population dynamics on growth of Listeria monocytogenes in cheese microcosm. Specific culture media and PCR primers were developed for simultaneous culture-dependent and real-time PCR quantification of strains belonging to Marinomonas sp., Paenibacillus sp., Staphylococcus equorum, Arthrobacter arilaitensis, Pseudomonas putida, Serratia liquefaciens, Candida natalensis, and Geotrichum candidum, in cheese microcosms. All strains were enumerated after 3, 5, 8 and 14 days at 15 °C. They established well at high counts in all cheese microcosms. Growth dynamics for all strains in presence of L. monocytogenes WSLC 1685 were compared to those of microbial communities obtained by omitting in turn one of the six members of the initial community. The growth of the microbial strains was neither markedly disturbed by Listeria presence nor by the removal of each strain in turn. Furthermore, these communities had a significant reducing effect on growth of L. monocytogenes independently of pH, as confirmed by mathematical modelling. A barrier effect was observed, that could be explained by specific competition for nutrients.

  16. Effects of Eichhornia crassipes and Ceratophyllum demersum on Soil and Water Environments and Nutrient Removal in Wetland Microcosms.

    PubMed

    Sung, Kijune; Lee, Geun-Joo; Munster, Clyde

    2015-01-01

    Wetland plants are important components that influence the biogeochemistry of wetland ecosystems. Therefore, remediation performance in wetlands can differ depending on the growth forms of plants. In this study, the effects of Eichhornia crassipes (floating plant) and Ceratophyllum demersum (submerged plant) on the wetland soil and water environments were investigated using a microcosm study with simulated hydrology of retention-type wetlands between rainfall events. The C. demersum microcosm (SP) showed the fastest recovery with a diel fluctuation pattern of dissolved oxygen, pH, and oxidation-reduction potential (ORP) from the impacts of nutrient inflow. Moreover, SP exhibited the lowest decrease in sediment ORP, the highest dehydrogenase activity, and more organic forms of nitrogen and phosphorus. E. crassipes microcosms exhibited the lowest water temperature, and efficiently controlled algae. In the presence of plants, the total nitrogen and phosphorus concentrations in water rapidly decreased, and the composition of organic and inorganic nutrient forms was altered along with a decrease in concentration. The results indicate that wetland plants help retain nutrients in the system, but the effects varied based on the wetland plant growth forms.

  17. Perceived parental control processes, parent-child relational qualities and psychological well-being of Chinese adolescents in intact and non-intact families in Hong Kong.

    PubMed

    Shek, Daniel T L; Lee, Tak Yan

    2007-01-01

    This paper examines whether Chinese adolescents' perceptions (N = 3,017) of parental behavioral control (parental knowledge, expectation, monitoring, discipline, and demandingness as well as parental control based on indigenous Chinese concepts), parental psychological control, parent-child relational qualities (perceived parental trust, child's trust of the parents, child's readiness to communicate with the parents, and child's satisfaction with parental control), and adolescent psychological well-being (hopelessness, mastery, life satisfaction and self-esteem) differed in intact and non-intact families. Results showed that relative to non-intact families, parental behavioral control processes were higher and parent-child relational qualities were better in intact families. In contrast, parental psychological control was higher in non-intact families than in intact families. Finally, the psychological well-being of adolescents in non-intact families was poorer than that of adolescents in intact families.

  18. Operative balloon dilatation for pulmonary atresia with intact ventricular septum.

    PubMed Central

    Hamilton, J R; Fonseka, S F; Wilson, N; Dickinson, D F; Walker, D R

    1987-01-01

    In six infants with pulmonary atresia and intact ventricular septum operative balloon dilatation was used to achieve continuity between the right ventricle and the main pulmonary artery as the initial procedure. Two of the six subsequently needed an aortico pulmonary shunt. All six are alive and well. Images Fig PMID:3676024

  19. Interleukin 6 in intact and injured mouse peripheral nerves.

    PubMed

    Reichert, F; Levitzky, R; Rotshenker, S

    1996-03-01

    The multifunctional cytokine interleukin 6 (IL-6) has direct growth, survival and differentiation effects on peripheral and central neurons. Furthermore, it can modulate the production by non-neuronal cells of other cytokines and growth factors, and thereby affect nerve cells indirectly. We have studied IL-6 expression and production in intact and injured peripheral nerves of C57/BL/6NHSD mice, which display the normal rapid progression of Wallerian degeneration. The IL-6 mRNA was detected in nerves degenerating in vitro or in vivo, but not in intact nerves. In vitro- and in vivo-degenerating nerve segments and neuroma nerve segments synthesized and secreted IL-6. The onset of IL-6 production was rapid and prolonged. It was detected as early as 2 h after injury and persisted for the entire period of 21 days tested after the injury. Of the non-neuronal cells that reside in intact and injured nerves, macrophages and fibroblasts were the major contributors to IL-6 production. We also studied IL-6 production in intact and injured nerves of mutant C57BL/6-WLD/OLA/NHSD mice, which display very slow progression of Wallerian degeneration. Injured nerves of C57BL/6-WLD/OLA/NHSD mice produced significantly lower amounts of IL-6 than did rapidly degenerating nerves of C57/BL/6NHSD mice.

  20. Fostering Activities of Daily Living by Intact Nursing Home Residents

    ERIC Educational Resources Information Center

    Blair, Charles E.; Glaister, Judy; Brown, Alston; Phillips, Carolyn

    2007-01-01

    We assessed effectiveness of four education programs in providing nursing assistants with ability to produce a therapeutic milieu supportive of intact residents' activities of daily living, positive self-esteem and mood: (1) a combination of Orem's Systems of Nursing Care and Skinner's Applied Behavioral Analysis, (2) Applied Behavioral Analysis,…

  1. Phosphorylation of intact erythrocytes in human muscular dystrophy

    SciTech Connect

    Johnson, R.M.; Nigro, M.

    1986-04-01

    The uptake of exogenous /sup 32/Pi into the membrane proteins of intact erythrocytes was measured in 8 patients with Duchenne muscular dystrophy. No abnormalities were noted after autoradiographic analysis. This contrasts with earlier results obtained when isolated membranes were phosphorylated with gamma-(/sup 32/P)ATP, and suggests a possible reinterpretation of those experiments.

  2. Diverse Reductive Dehalogenases Are Associated with Clostridiales-Enriched Microcosms Dechlorinating 1,2-Dichloroethane

    PubMed Central

    Merlino, Giuseppe; Balloi, Annalisa; Marzorati, Massimo; Mapelli, Francesca; Rizzi, Aurora; Lavazza, Davide; de Ferra, Francesca; Carpani, Giovanna; Daffonchio, Daniele

    2015-01-01

    The achievement of successful biostimulation of active microbiomes for the cleanup of a polluted site is strictly dependent on the knowledge of the key microorganisms equipped with the relevant catabolic genes responsible for the degradation process. In this work, we present the characterization of the bacterial community developed in anaerobic microcosms after biostimulation with the electron donor lactate of groundwater polluted with 1,2-dichloroethane (1,2-DCA). Through a multilevel analysis, we have assessed (i) the structural analysis of the bacterial community; (ii) the identification of putative dehalorespiring bacteria; (iii) the characterization of functional genes encoding for putative 1,2-DCA reductive dehalogenases (RDs). Following the biostimulation treatment, the structure of the bacterial community underwent a notable change of the main phylotypes, with the enrichment of representatives of the order Clostridiales. Through PCR targeting conserved regions within known RD genes, four novel variants of RDs previously associated with the reductive dechlorination of 1,2-DCA were identified in the metagenome of the Clostridiales-dominated bacterial community. PMID:26273600

  3. Temperature Responses of Ammonia-Oxidizing Prokaryotes in Freshwater Sediment Microcosms

    PubMed Central

    Yu, Zhongbo; Huang, Rui; Wu, Qinglong L.

    2014-01-01

    In order to investigate the effects of temperature on the abundances and community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB), lake microcosms were constructed and incubated at 15°C, 25°C and 35°C for 40 days, respectively. Temperature exhibited different effects on the abundance and diversity of archaeal and bacterial amoA gene. The elevated temperature increased the abundance of archaeal amoA gene, whereas the abundance of bacterial amoA gene decreased. The highest diversity of bacterial amoA gene was found in the 25°C treatment sample. However, the 25°C treatment sample maintained the lowest diversity of archaeal amoA gene. Most of the archaeal amoA sequences obtained in this study affiliated with the Nitrosopumilus cluster. Two sequences obtained from the 15°C treatment samples were affiliated with the Nitrosotalea cluster. N. oligotropha lineage was the most dominant bacterial amoA gene group. Several sequences affiliated to Nitrosospira and undefined N. europaea/NC. mobilis like lineage were found in the pre-incubation and 25°C treatment groups. PMID:24959960

  4. Microcosm assays and Taguchi experimental design for treatment of oil sludge containing high concentration of hydrocarbons.

    PubMed

    Castorena-Cortés, G; Roldán-Carrillo, T; Zapata-Peñasco, I; Reyes-Avila, J; Quej-Aké, L; Marín-Cruz, J; Olguín-Lora, P

    2009-12-01

    Microcosm assays and Taguchi experimental design was used to assess the biodegradation of an oil sludge produced by a gas processing unit. The study showed that the biodegradation of the sludge sample is feasible despite the high level of pollutants and complexity involved in the sludge. The physicochemical and microbiological characterization of the sludge revealed a high concentration of hydrocarbons (334,766+/-7001 mg kg(-1) dry matter, d.m.) containing a variety of compounds between 6 and 73 carbon atoms in their structure, whereas the concentration of Fe was 60,000 mg kg(-1) d.m. and 26,800 mg kg(-1) d.m. of sulfide. A Taguchi L(9) experimental design comprising 4 variables and 3 levels moisture, nitrogen source, surfactant concentration and oxidant agent was performed, proving that moisture and nitrogen source are the major variables that affect CO(2) production and total petroleum hydrocarbons (TPH) degradation. The best experimental treatment yielded a TPH removal of 56,092 mg kg(-1) d.m. The treatment was carried out under the following conditions: 70% moisture, no oxidant agent, 0.5% of surfactant and NH(4)Cl as nitrogen source.

  5. Predation effect of three fish species and a shrimp on macrobenthos and meiobenthos in microcosms

    NASA Astrophysics Data System (ADS)

    Service, Susan K.; Feller, Robert J.; Coull, Bruce C.; Woods, Roberta

    1992-03-01

    The responses of macrofaunal and meiofaunal benthic communities to predation by three fish species and a penaeid shrimp were examined to evaluate the potential for epibenthic predators to reduce abundance of benthos. Experiments conducted in 1987 analysed only the macrofaunal community and indicated capitellid polychaete abundance was significantly reduced in the presence of white shrimp [ Penaeus setiferus (Linneaus)], while mummichogs [ Fundulus heteroclitus (Linneaus)] had no significant effect on any macrobenthic taxon. Experiments in 1988 using mullet ( Mugil cephalus Linneaus) as predators resulted in significantly decreased abundances of total meiofauna and the copepod Enhydrosoma propinquum (Brady), while abundances of macrofaunal prey were not significantly reduced. Abundances of the polychaete Streblospio benedicti Webster, total macrofauna and total copepods were significantly reduced by spot ( Leiostomus xanthurus Lacépéde) predation. While these experiments were designed with sufficient power to demonstrate that epibenthic predators are possibly capable of causing significant reductions in the populations of macrofaunal and meiofaunal prey, a general paucity of significant impacts indicates that these predators may be but one of many factors influencing benthic abundance in the field. The microcosm experiment approach must incorporate multifactorial designs in the future.

  6. Area V5—a microcosm of the visual brain

    PubMed Central

    Zeki, Semir

    2015-01-01

    Area V5 of the visual brain, first identified anatomically in 1969 as a separate visual area, is critical for the perception of visual motion. As one of the most intensively studied parts of the visual brain, it has yielded many insights into how the visual brain operates. Among these are: the diversity of signals that determine the functional capacities of a visual area; the relationship between single cell activity in a specialized visual area and perception of, and preference for, attributes of a visual stimulus; the multiple asynchronous inputs into, and outputs from, an area as well as the multiple operations that it undertakes asynchronously; the relationship between activity at given, specialized, areas of the visual brain and conscious awareness; and the mechanisms used to “bind” signals from one area with those from another, with a different specialization, to give us our unitary perception of the visual world. Hence V5 is, in a sense, a microcosm of the visual world and its study gives important insights into how the whole visual brain is organized—anatomically, functionally and perceptually. PMID:25883556

  7. Fatigue characteristics and microcosmic mechanism of Al-Si-Mg alloys under multiaxial proportional loadings

    NASA Astrophysics Data System (ADS)

    Jiang, Xiao-Song; He, Guo-Qiu; Liu, Bing; Zhu, Zheng-Yu; Zhang, Wei-Hua

    2011-08-01

    With the increasing use of Al-Si-Mg alloys in the automotive industry, the fatigue performance of Al-Si-Mg alloy has become a major concern with regard to their reliability. The fatigue characteristics and microcosmic mechanism of an Al-Si-Mg alloy under multiaxial proportional loadings were investigated in this research. As low cycle fatigue life and material strengthening behavior are closely related, the effect of equivalent strain amplitude on the multiaxial fatigue properties was analyzed. Fatigue tests were conducted to determine the influence of equivalent strain amplitude on the multiaxial proportional fatigue properties. The fatigue life exhibits a stable behavior under multiaxial proportional loadings. The dislocation structures of the Al-Si-Mg alloy were observed by transmission electron microscopy (TEM). The dislocation structure evolution of the Al-Si-Mg alloy under multiaxial proportional loadings during low cycle fatigue develops step by step by increasing fatigue cycles. Simultaneously, the dislocation structure changes with the change in equivalent strain amplitude under multiaxial proportional loadings. The experimental evidence indicates that the multiaxial fatigue behavior and life are strongly dependent on the microstructure of the material, which is caused by multiaxial proportional loadings.

  8. Final Technical Report. Origins of subsurface microorganisms: Relating laboratory microcosm studies to a geologic time scale

    SciTech Connect

    Kieft, Thomas; Amy, Penny S.; Phillips, Fred M.

    1998-12-01

    This project was conducted as part of the Department of Energy's Deep Subsurface Science Program. It was part of a larger effort to determine the origins of subsurface microorganisms. Two hypotheses have been suggested for the origins of subsurface microorganisms: (1) microorganisms were deposited at the time of (or shortly after) geologic deposition of rocks and sediments (the in situ survival hypothesis), and (2) microorganisms have been transported from surface environments to subsurface rocks and sediments since the time of geologic deposition (transport hypothesis). These two hypotheses are not mutually exclusive. Depending on the geological setting, either one or both of these hypotheses may best explain microbial origins. Our project focused on the in situ survival hypothesis. We tested the hypothesis that microorganisms (individuals populations and communities) can survive long-term sequestration within subsurface sediments. Other objectives were to identify geologic conditions that favor long-term survival, identify physiological traits of microorganisms that favor long-term survival, and determine which groups of microorganisms are most likely to survive long-term sequestration in subsurface sediments. We tested this hypothesis using a combination of pure culture techniques in laboratory microcosms under controlled conditions and field experiments with buried subsurface sediments.

  9. Temporal succession in carbon incorporation from macromolecules by particle-attached bacteria in marine microcosms.

    PubMed

    Mayali, Xavier; Stewart, Benjamin; Mabery, Shalini; Weber, Peter K

    2016-02-01

    We investigated bacterial carbon assimilation from stable isotope-labelled macromolecular substrates (proteins; lipids; and two types of polysaccharides, starch and cellobiose) while attached to killed diatom detrital particles during laboratory microcosms incubated for 17 days. Using Chip-SIP (secondary ion mass spectrometry analysis of RNA microarrays), we identified generalist operational taxonomic units (OTUs) from the Gammaproteobacteria, belonging to the genera Colwellia, Glaciecola, Pseudoalteromonas and Rheinheimera, and from the Bacteroidetes, genera Owenweeksia and Maribacter, that incorporated the four tested substrates throughout the incubation period. Many of these OTUs exhibited the highest isotope incorporation relative to the others, indicating that they were likely the most active. Additional OTUs from the Gammaproteobacteria, Bacteroidetes and Alphaproteobacteria exhibited generally (but not always) lower activity and did not incorporate all tested substrates at all times, showing species succession in organic carbon incorporation. We also found evidence to suggest that both generalist and specialist OTUs changed their relative substrate incorporation over time, presumably in response to changing substrate availability as the particles aged. This pattern was demonstrated by temporal succession from relatively higher starch incorporation early in the incubations, eventually switching to higher cellobiose incorporation after 2 weeks.

  10. High Pb concentration stress on Typha latifolia growth and Pb removal in microcosm wetlands.

    PubMed

    Han, Jianqiu; Chen, Fengzhen; Zhou, Yumei; Wang, Chaohua

    2015-01-01

    When constructed wetlands are used to treat high-Pb wastewater, Pb may become a stress to wetland plants, which subsequently reduces treatment performance and the other ecosystem services. To facilitate the design and operation of constructed wetlands for treatment of Pb-rich wastewater, we investigated the irreversible inhibitory level of Pb for Typha latifolia through experiments in microcosm wetlands. Seven horizontal subsurface flow constructed wetlands were built with rectangular plastic tanks and packed with marble chips and sand. All wetlands were transplanted with nine stems of Typha latifolia each. The wetlands were batch operated in a greenhouse with artificial wastewater (10 L each) for 12 days. Influent to the seven wetlands had different concentrations of Pb: 0 mg/L, 10 mg/L, 25 mg/L, 50 mg/L, 100 mg/L, 200 mg/L, and 500 mg/L, respectively. The results suggested that leaf chlorophyll relative content, relative growth rate, photosynthetic characteristics, activities of superoxide dismutase, peroxidase, and content of malondialdehyde were not affected when initial Pb concentration was at 100 mg/L and below. But when initial Pb concentration was above 100 mg/L, all of them were seriously affected. We conclude that high Pb concentrations wastewater could inhibit the growth of Typha latifolia and decrease the removal rate of wetlands.

  11. Hydrologic variability affects invertebrate grazing on phototrophic biofilms in stream microcosms.

    PubMed

    Ceola, Serena; Hödl, Iris; Adlboller, Martina; Singer, Gabriel; Bertuzzo, Enrico; Mari, Lorenzo; Botter, Gianluca; Waringer, Johann; Battin, Tom J; Rinaldo, Andrea

    2013-01-01

    The temporal variability of streamflow is known to be a key feature structuring and controlling fluvial ecological communities and ecosystem processes. Although alterations of streamflow regime due to habitat fragmentation or other anthropogenic factors are ubiquitous, a quantitative understanding of their implications on ecosystem structure and function is far from complete. Here, by experimenting with two contrasting flow regimes in stream microcosms, we provide a novel mechanistic explanation for how fluctuating flow regimes may affect grazing of phototrophic biofilms (i.e., periphyton) by an invertebrate species (Ecdyonurus sp.). In both flow regimes light availability was manipulated as a control on autotroph biofilm productivity and grazer activity, thereby allowing the test of flow regime effects across various ratios of biofilm biomass to grazing activity. Average grazing rates were significantly enhanced under variable flow conditions and this effect was highest at intermediate light availability. Our results suggest that stochastic flow regimes, characterised by suitable fluctuations and temporal persistence, may offer increased windows of opportunity for grazing under favourable shear stress conditions. This bears important implications for the development of comprehensive schemes for water resources management and for the understanding of trophic carbon transfer in stream food webs.

  12. Meiofaunal and bacterial community response to diesel additions in a microcosm study.

    PubMed

    Lindgren, J Fredrik; Hassellöv, Ida-Maja; Dahllöf, Ingela

    2012-03-01

    Effects of low PAH-containing diesel were studied in a 60-day microcosm experiment at PAH concentrations 130, 1300 and 13,000μg/kg sediment. Nutrient fluxes, potential nitrification and meiofaunal community composition were analysed at three time points. Changed ∑NOx-fluxes indicated reduced sediment nitrification in Medium and High with time, in agreement with lowered potential nitrification rates in all treatments. Reduction in silicate and phosphate fluxes over time suggested severe effects on activity of meiofauna. Reduced activity increased the anoxic sediment layer, which could have contributed to the changed ∑NOx-fluxes. There were significant differences in meiofaunal community composition after 30 and 60days in Medium and High. Changes were due to increasing numbers of harpacticoids and the foraminiferan group Rotaliina, as well as decreasing numbers of Nematodes and the foraminiferan group Reophax. In spite of the low PAH-level, small additions of this diesel can still have pronounced effects on meiofaunal and bacterial communities.

  13. Hydrologic Variability Affects Invertebrate Grazing on Phototrophic Biofilms in Stream Microcosms

    PubMed Central

    Ceola, Serena; Hödl, Iris; Adlboller, Martina; Singer, Gabriel; Bertuzzo, Enrico; Mari, Lorenzo; Botter, Gianluca; Waringer, Johann; Battin, Tom J.; Rinaldo, Andrea

    2013-01-01

    The temporal variability of streamflow is known to be a key feature structuring and controlling fluvial ecological communities and ecosystem processes. Although alterations of streamflow regime due to habitat fragmentation or other anthropogenic factors are ubiquitous, a quantitative understanding of their implications on ecosystem structure and function is far from complete. Here, by experimenting with two contrasting flow regimes in stream microcosms, we provide a novel mechanistic explanation for how fluctuating flow regimes may affect grazing of phototrophic biofilms (i.e., periphyton) by an invertebrate species (Ecdyonurus sp.). In both flow regimes light availability was manipulated as a control on autotroph biofilm productivity and grazer activity, thereby allowing the test of flow regime effects across various ratios of biofilm biomass to grazing activity. Average grazing rates were significantly enhanced under variable flow conditions and this effect was highest at intermediate light availability. Our results suggest that stochastic flow regimes, characterised by suitable fluctuations and temporal persistence, may offer increased windows of opportunity for grazing under favourable shear stress conditions. This bears important implications for the development of comprehensive schemes for water resources management and for the understanding of trophic carbon transfer in stream food webs. PMID:23613735

  14. Effects of Current on Microcosmic Properties of Catalyst and Reforming of Bio-oil

    NASA Astrophysics Data System (ADS)

    Yuan, Li-xia; Ye, Tong-qi; Gong, Fei-yan; Li, Quan-xin

    2009-02-01

    Highly effective production of hydrogen from bio-oil was achieved by using a low-temperature electrochemical catalytic reforming approach over the conventional Ni-based reforming catalyst (NiO-Al2O3), where an AC electronic current passed through the catalyst bed. The promoting effects of current on the bio-oil reforming were studied. It was found that the performance of the bio-oil reforming was remarkably enhanced by the current which passed through the catalyst. The effects of currents on the microcosmic properties of the catalyst, including the Brunauer-Emmett-Teller (BET) surface area, pore diameter, pore volume, the size of the crystallites and the reduction level of NiO into Ni, were carefully characterized by BET, X-ray diffraction, X-ray photoelectron spectroscopy, and scanning electron microscope. The desorption of the thermal electrons from the electrified catalyst was directly observed by the TOF (time of flight) measurements. The mechanism of the electrochemical catalytic reforming of bio-oil is discussed based on the above investigation.

  15. Fate of Viable but Non-culturable Listeria monocytogenes in Pig Manure Microcosms

    PubMed Central

    Desneux, Jérémy; Biscuit, Audrey; Picard, Sylvie; Pourcher, Anne-Marie

    2016-01-01

    The fate of two strains of Listeria monocytogenes and their ability to become viable but non-culturable (VBNC) was investigated in microcosms containing piggery effluents (two raw manures and two biologically treated manures) stored for 2 months at 8 and 20°C. Levels of L. monocytogenes were estimated using the culture method, qPCR, and propidium monoazide treatment combined with qPCR (qPCRPMA). The chemical composition and the microbial community structure of the manures were also analyzed. The strains showed similar decline rates and persisted up to 63 days. At day zero, the percentage of VBNC cells among viable cells was higher in raw manures (81.5–94.8%) than in treated manures (67.8–79.2%). The changes in their proportion over time depended on the temperature and on the type of effluent: the biggest increase was observed in treated manures at 20°C and the smallest increase in raw manures at 8°C. The chemical parameters had no influence on the behavior of the strains, but decrease of the persistence of viable cells was associated with an increase in the microbial richness of the manures. This study demonstrated that storing manure altered the culturability of L. monocytogenes, which rapidly entered the VBNC state, and underlines the importance of including VBNC cells when estimating the persistence of the pathogens in farm effluents. PMID:26973623

  16. Temperature responses of ammonia-oxidizing prokaryotes in freshwater sediment microcosms.

    PubMed

    Zeng, Jin; Zhao, Dayong; Yu, Zhongbo; Huang, Rui; Wu, Qinglong L

    2014-01-01

    In order to investigate the effects of temperature on the abundances and community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB), lake microcosms were constructed and incubated at 15°C, 25°C and 35°C for 40 days, respectively. Temperature exhibited different effects on the abundance and diversity of archaeal and bacterial amoA gene. The elevated temperature increased the abundance of archaeal amoA gene, whereas the abundance of bacterial amoA gene decreased. The highest diversity of bacterial amoA gene was found in the 25°C treatment sample. However, the 25°C treatment sample maintained the lowest diversity of archaeal amoA gene. Most of the archaeal amoA sequences obtained in this study affiliated with the Nitrosopumilus cluster. Two sequences obtained from the 15°C treatment samples were affiliated with the Nitrosotalea cluster. N. oligotropha lineage was the most dominant bacterial amoA gene group. Several sequences affiliated to Nitrosospira and undefined N. europaea/NC. mobilis like lineage were found in the pre-incubation and 25°C treatment groups.

  17. Impact of polymer-coated silver nanoparticles on marine microbial communities: a microcosm study.

    PubMed

    Doiron, K; Pelletier, E; Lemarchand, K

    2012-11-15

    The use of silver nanoparticles (AgNPs) in consumer products is increasing drastically and their potential environmental impacts on aquatic organisms from bacterial communities to vertebrates are not well understood. This study reports on changes in marine bacterial richness using denaturing gradient gel electrophoresis (DGGE), and overall community abundance determined by flow cytometry in marine microcosms exposed to polymer-coated AgNPs (20±5 nm) and ionic silver (Ag(+)). Our study clearly demonstrated that at low concentrations (5 and 50 μg L(-1) total silver), un-aggregated polymer-coated AgNPs and dissolved Ag(+) contamination produced similar effects: a longer lag phase suggesting an adaptation period for microorganisms. As richness decreased in the treated samples, this longer lag phase could correspond to the selection of a fraction of the initial community that is insensitive to silver contamination. Polymer-coated AgNPs preserved their bactericidal properties even under the high ionic strength of estuarine waters.

  18. Resource niche overlap promotes stability of bacterial community metabolism in experimental microcosms

    PubMed Central

    Hunting, Ellard R.; Vijver, Martina G.; van der Geest, Harm G.; Mulder, Christian; Kraak, Michiel H. S.; Breure, Anton M.; Admiraal, Wim

    2015-01-01

    Decomposition of organic matter is an important ecosystem process governed in part by bacteria. The process of decomposition is expected to benefit from interspecific bacterial interactions such as resource partitioning and facilitation. However, the relative importance of resource niche breadth (metabolic diversity) and resource niche overlap (functional redundancy) on decomposition and the temporal stability of ecosystem processes received little scientific attention. Therefore, this study aims to evaluate the effect of an increase in bacterial community resemblance on both decomposition and the stability of bacterial metabolism in aquatic sediments. To this end, we performed laboratory microcosm experiments in which we examined the influence of bacterial consortia differing in number and composition of species on bacterial activity (Electron Transport System Activity, ETSA), dissolved organic carbon production and wavelet transformed measurements of redox potential (Eh). Single substrate affinities of the individual bacterial species were determined in order to calculate the metabolic diversity of the microbial community. Results presented here indicate that bacterial activity and organic matter decomposition increase with widening of the resource niche breadth, and that metabolic stability increases with increasing overlap in bacterial resource niches, hinting that resource niche overlap can promote the stability of bacterial community metabolism. PMID:25759686

  19. The effects of plant diversity on nitrous oxide emissions in hydroponic microcosms

    NASA Astrophysics Data System (ADS)

    Sun, Hongying; Zhang, Chongbang; Song, Changchun; Chang, Scott X.; Gu, Baojing; Chen, Zhengxin; Peng, Changhui; Chang, Jie; Ge, Ying

    2013-10-01

    Previous studies have shown that plant diversity can improve the wastewater purification efficiency of constructed wetlands (CWs), but its effect on the nitrous oxide (N2O) emission in CWs has been unknown. To investigate the effect of plant diversity on the N2O emission, we established four plant species richness levels (each level containing 1, 2, 3 and 4 species, respectively) by using 96 hydroponic microcosms. Results showed that plant species richness enhanced the N2O emission, ranging from 27.1 to 115.4 μg N2O m-2 d-1, and improved nitrate removal (P < 0.001). The presence of Phalaris arundinacea within a given plant community increased the N2O emission (P < 0.001). The presence of Rumex japonicas had no influence on the N2O emissions (P > 0.05), but improved nitrogen removal (P < 0.001). Hence, our study highlights the importance of both plant species richness and species identity in mediating the N2O emission and nitrogen removal in CWs.

  20. Changes in Arctic and Antarctic Sea Ice as a Microcosm of Global Climate Change

    NASA Technical Reports Server (NTRS)

    Parkinson, Claire L.

    2014-01-01

    Polar sea ice is a key element of the climate system and has now been monitored through satellite observations for over three and a half decades. The satellite observations reveal considerable information about polar ice and its changes since the late 1970s, including a prominent downward trend in Arctic sea ice coverage and a much lesser upward trend in Antarctic sea ice coverage, illustrative of the important fact that climate change entails spatial contrasts. The decreasing ice coverage in the Arctic corresponds well with contemporaneous Arctic warming and exhibits particularly large decreases in the summers of 2007 and 2012, influenced by both preconditioning and atmospheric conditions. The increasing ice coverage in the Antarctic is not as readily explained, but spatial differences in the Antarctic trends suggest a possible connection with atmospheric circulation changes that have perhaps been influenced by the Antarctic ozone hole. The changes in the polar ice covers and the issues surrounding those changes have many commonalities with broader climate changes and their surrounding issues, allowing the sea ice changes to be viewed in some important ways as a microcosm of global climate change.

  1. Response of bacteria and meiofauna to iron oxide colloids in sediments of freshwater microcosms.

    PubMed

    Höss, Sebastian; Frank-Fahle, Béatrice; Lueders, Tillmann; Traunspurger, Walter

    2015-11-01

    The use of colloidal iron oxide (FeOx) in the bioremediation of groundwater contamination implies its increasing release into the environment and requires an assessment of its ecotoxicological risk. Therefore, microcosm experiments were carried out to investigate the impact of ferrihydrite colloids on the bacterial and meiofaunal communities of pristine freshwater sediments. The effects of ferrihydrite colloids were compared with those of ferrihydrite macroaggregates to discriminate between colloid-specific and general FeOx impacts. The influence of ferrihydrite colloids on the toxicity of sediment-bound fluoranthene was also considered. At high concentrations (496 mg Fe kg(-1) sediment dry wt), ferrihydrite colloids had a significant, but transient impact on bacterial and meiofaunal communities. Although bacterial community composition specifically responded to ferrihydrite colloids, a more general FeOx effect was observed for meiofauna. Bacterial activity responded most sensitively (already at 55 mg Fe kg(-1) dry wt) without the potential of recovery. Ferrihydrite colloids did not influence the toxicity of sediment-bound fluoranthene. Significant correlations between bacterial activity and meiofaunal abundances were indicative of trophic interactions between bacteria and meiofauna and therefore of the contribution of indirect food web effects to the observed impacts. The results suggest that the application of ferrihydrite colloids for remediation purposes in the field poses no risk for benthic communities, given that, with the exception of generic bacterial activity, any negative effects on communities were reversible.

  2. Applicability of Hydrogen Peroxide in Brown Tide Control – Culture and Microcosm Studies

    PubMed Central

    Randhawa, Varunpreet; Thakkar, Megha; Wei, Liping

    2012-01-01

    Brown tide algal blooms, caused by the excessive growth of Aureococcus anophagefferens, recur in several northeastern US coastal bays. Direct bloom control could alleviate the ecological and economic damage associated with bloom outbreak. This paper explored the effectiveness and safety of natural chemical biocide hydrogen peroxide (H2O2) for brown tide bloom control. Culture studies showed that H2O2 at 1.6 mg L−1 effectively eradicated high density A. anophagefferens within 24-hr, but caused no significant growth inhibition in the diatoms, prymnesiophytes, green algae and dinoflagellates of >2–3 μm cell sizes among 12 phytoplankton species tested over 1-week observation. When applied to brown tide bloom prone natural seawater in a microcosm study, this treatment effectively removed the developing brown tide bloom, while the rest of phytoplankton assemblage (quantified via HPLC based marker pigment analyses), particularly the diatoms and green algae, experienced only transient suppression then recovered with total chlorophyll a exceeding that in the controls within 72-hr; cyanobacteria was not eradicated but was still reduced about 50% at 72-hr, as compared to the controls. The action of H2O2 against phytoplankton as a function of cell size and cell wall structure, and a realistic scenario of H2O2 application were discussed. PMID:23082223

  3. Frontiers of the food-energy-water trilemma: Sri Lanka as a microcosm of tradeoffs

    NASA Astrophysics Data System (ADS)

    Perrone, Debra; Hornberger, George

    2016-01-01

    Food, energy, and water are three critical resources for humanity. As climate variability, population growth, and lifestyle changes amplify the stress placed on each of the resources, the interrelationships among food, energy, and water systems become more pronounced. Political conflict, social and cultural norms, and spatial and temporal distribution of the resources add additional layers of complexity. It is in this context that the significance of understanding the impacts of water scarcity on the decisions around food and energy productions has emerged. Our work establishes tradeoff frontiers (TFs) as a method useful in illustrating the system-level tradeoffs between allocating water for food and water for energy. This paper illustrates how TFs can be used to (1) show how scarcity in water resources affects the tradeoffs between food and energy and (2) explore the political and social constraints that can move production away from what is feasible technically. We use Sri Lanka, a country where water resources are variable both in space and time and a country with relatively self-contained energy and agricultural sectors, as a microcosm of the food security, energy security, and water security trilemma. Nevertheless, our application of tradeoff frontiers is applicable widely to other systems.

  4. Impact of lime, nitrogen and plant species on bacterial community structure in grassland microcosms.

    PubMed

    Kennedy, Nabla; Brodie, Eoin; Connolly, John; Clipson, Nicholas

    2004-10-01

    A microcosm-based approach was used to study impacts of plant and chemical factors on the bacterial community structure of an upland acidic grassland soil. Seven perennial plant species typical of both natural, unimproved (Nardus stricta, Agrostis capillaris, Festuca ovina and F. rubra) and fertilized, improved (Holcus lanatus, Lolium perenne and Trifolium repens) grasslands were either left unamended or treated with lime, nitrogen, or lime plus nitrogen in a 75-day glasshouse experiment. Lime and nitrogen amendment were shown to have a greater effect on microbial activity, biomass and bacterial ribotype number than plant species. Liming increased soil pH, microbial activity and biomass, while decreasing ribotype number. Nitrogen addition decreased soil pH, microbial activity and ribotype number. Addition of lime plus nitrogen had intermediate effects, which appeared to be driven more by lime than nitrogen. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed that lime and nitrogen addition altered soil bacterial community structure, while plant species had little effect. These results were further confirmed by multivariate redundancy analysis, and suggest that soil lime and nitrogen status are more important controllers of bacterial community structure than plant rhizosphere effects.

  5. The corrosion of carbon steel in rock microcosms containing native Yucca Mountain microorganisms

    SciTech Connect

    Castro, P.R.; Amy, P.S.; Crossen, H.V.; Jones, D.A.; Southam, G.; Donald, R.; Ringelberg, D.B.

    1998-12-31

    Microorganisms implicated in microbially-influenced corrosion were isolated from the deep subsurface at Yucca Mountain, and include iron-oxidizing (FeOx), sulfate-reducing (SRB), and exopolysaccharide (EPS)-producing bacterial species. Various combinations of these microorganisms were inoculated into a test system composed of a 1020 carbon steel coupon immersed in a mixture of sterile rock and soft R2A agar prepared with simulated groundwater. A 1% KC1 bridge was used to connect the test system to a calomel reference electrode. A platinum counter electrode was used to apply a potential and the corrosion rate was measured by polarization resistance. Prior studies at ambient and elevated (50 C) temperatures demonstrated that these microorganisms were capable of corroding carbon steel. The current research investigated whether the presence of a rock surface enhanced the ability of the test microorganisms to survive elevated temperature and corrode carbon steel. Uninoculated electrochemical cells were prepared to monitor abiotic corrosion. Initial and weekly corrosion rates were obtained for the duration of the experiment. Upon completion of the experiment, the test system was dismantled and the coupons prepared for phospholipid fatty acid and microscopic analyses, to assess microbial biomass and biofilm formation, respectively. Increased biomass and higher corrosion rates were observed in the rock/agar microcosms.

  6. Persistence of pentolite (PETN and TNT) in soil microcosms and microbial enrichment cultures.

    PubMed

    Arbeli, Ziv; Garcia-Bonilla, Erika; Pardo, Cindy; Hidalgo, Kelly; Velásquez, Trigal; Peña, Luis; C, Eliana Ramos; Avila-Arias, Helena; Molano-Gonzalez, Nicolás; Brandão, Pedro F B; Roldan, Fabio

    2016-05-01

    Pentolite is a mixture (1:1) of 2,4,6-trinitrotoluene (TNT) and pentaerythritol tetranitrate (PETN), and little is known about its fate in the environment. This study was aimed to determine the dissipation of pentolite in soils under laboratory conditions. Microcosm experiments conducted with two soils demonstrated that dissipation rate of PETN was significantly slower than that of TNT. Interestingly, the dissipation of PETN was enhanced by the presence of TNT, while PETN did not enhanced the dissipation of TNT. Pentolite dissipation rate was significantly faster under biostimulation treatment (addition of carbon source) in soil from the artificial wetland, while no such stimulation was observed in soil from detonation field. In addition, the dissipation rate of TNT and PETN in soil from artificial wetland under biostimulation was significantly faster than the equivalent abiotic control, although it seems that non-biological processes might also be important for the dissipation of TNT and PETN. Transformation of PETN was also slower during establishment of enrichment culture using pentolite as the sole nitrogen source. In addition, transformation of these explosives was gradually reduced and practically stopped after the forth cultures transfer (80 days). DGGE analysis of bacterial communities from these cultures indicates that all consortia were dominated by bacteria from the order Burkholderiales and Rhodanobacter. In conclusion, our results suggest that PETN might be more persistent than TNT.

  7. Effects of drain-fill cycling on chlorpyrifos mineralization in wetland sediment-water microcosms.

    PubMed

    Gebremariam, Seyoum Yami; Beutel, Marc W

    2010-03-01

    Constructed treatment wetlands are efficient at retaining a range of pesticides, however the ultimate fate of many of these compound is not well understood. This study evaluated the effect of drain-fill cycling on the mineralization of chlorpyrifos, a commonly used organophosphate insecticide, in wetland sediment-water microcosms. Monitoring of the fate of (14)C ring-labeled chlorpyrifos showed that drain-fill cycling resulted in significantly lower mineralization rates relative to permanently flooded conditions. The reduction in mineralization was linked to enhanced partitioning of the pesticide to the sediment phase, which could potentially inhibit chlorpyrifos hydrolysis and mineralization. Over the nearly two-month experiment, less than 2.5% of the added compound was mineralized. While rates of mineralization in this experiment were higher than those reported for other soils and sediments, their low magnitude underscores how persistent chlorpyrifos and its metabolites are in aquatic environments, and suggests that management strategies and ecological risk assessment should focus more on ultimate mineralization rather than the simple disappearance of the parent compound.

  8. Herbicide mitigation in microcosms simulating stormwater basins subject to polluted water inputs.

    PubMed

    Bois, P; Huguenot, D; Jézéquel, K; Lollier, M; Cornu, J Y; Lebeau, T

    2013-03-01

    Non-point source pollution as a result of wine-growing activity is of high concern. Stormwater basins (SWB) found downstream of vineyard watersheds could show a potential for the mitigation of runoff water containing herbicides. In this study, mitigation of vinery-used herbicides was studied in microcosms with a very similar functioning to that recorded in SWB. Mitigation efficiency of glyphosate, diuron and 3,4-dichloroaniline (3,4-DCA) was investigated by taking into account hydraulic flow rate, mitigation duration, bioaugmentation and plant addition. Mitigation efficiency measured in water ranged from 63.0% for diuron to 84.2% for 3,4-DCA and to 99.8% for glyphosate. Water-storage duration in the SWB and time between water supplies were shown to be the most influential factors on the mitigation efficiency. Six hours water-storage duration allowed an efficient sorption of herbicides and their degradation by indigenous microorganisms in 5 weeks. Neither bioaugmentation nor plant addition had a significant effect on herbicide mitigation. Our results show that this type of SWB are potentially relevant for the mitigation of these herbicides stemming from wine-growing activity, providing a long enough hydraulic retention time.

  9. Applicability of hydrogen peroxide in brown tide control - culture and microcosm studies.

    PubMed

    Randhawa, Varunpreet; Thakkar, Megha; Wei, Liping

    2012-01-01

    Brown tide algal blooms, caused by the excessive growth of Aureococcus anophagefferens, recur in several northeastern US coastal bays. Direct bloom control could alleviate the ecological and economic damage associated with bloom outbreak. This paper explored the effectiveness and safety of natural chemical biocide hydrogen peroxide (H(2)O(2)) for brown tide bloom control. Culture studies showed that H(2)O(2) at 1.6 mg L(-1) effectively eradicated high density A. anophagefferens within 24-hr, but caused no significant growth inhibition in the diatoms, prymnesiophytes, green algae and dinoflagellates of >2-3 μm cell sizes among 12 phytoplankton species tested over 1-week observation. When applied to brown tide bloom prone natural seawater in a microcosm study, this treatment effectively removed the developing brown tide bloom, while the rest of phytoplankton assemblage (quantified via HPLC based marker pigment analyses), particularly the diatoms and green algae, experienced only transient suppression then recovered with total chlorophyll a exceeding that in the controls within 72-hr; cyanobacteria was not eradicated but was still reduced about 50% at 72-hr, as compared to the controls. The action of H(2)O(2) against phytoplankton as a function of cell size and cell wall structure, and a realistic scenario of H(2)O(2) application were discussed.

  10. Spatial heterogeneity and functional response: an experiment in microcosms with varying obstacle densities.

    PubMed

    Hauzy, Céline; Tully, Thomas; Spataro, Thierry; Paul, Grégory; Arditi, Roger

    2010-07-01

    Spatial heterogeneity of the environment has long been recognized as a major factor in ecological dynamics. Its role in predator-prey systems has been of particular interest, where it can affect interactions in two qualitatively different ways: by providing (1) refuges for the prey or (2) obstacles that interfere with the movements of both prey and predators. There have been relatively fewer studies of obstacles than refuges, especially studies on their effect on functional responses. By analogy with reaction-diffusion models for chemical systems in heterogeneous environments, we predict that obstacles are likely to reduce the encounter rate between individuals, leading to a lower attack rate (predator-prey encounters) and a lower interference rate (predator-predator encounters). Here, we test these predictions under controlled conditions using collembolans (springtails) as prey and mites as predators in microcosms. The effect of obstacle density on the functional response was investigated at the scales of individual behavior and of the population. As expected, we found that increasing obstacle density reduces the attack rate and predator interference. Our results show that obstacles, like refuges, can reduce the predation rate because obstacles decrease the attack rate. However, while refuges can increase predator dependence, we suggest that obstacles can decrease it by reducing the rate of encounters between predators. Because of their opposite effect on predator dependence, obstacles and refuges could modify in different ways the stability of predator-prey communities.

  11. Evaluation of aquatic plants for removing polar microcontaminants: a microcosm experiment.

    PubMed

    Matamoros, Víctor; Nguyen, Loc Xuan; Arias, Carlos A; Salvadó, Victòria; Brix, Hans

    2012-08-01

    Microcosm wetland systems (5 L containers) planted with Salvinia molesta, Lemna minor, Ceratophyllum demersum, and Elodea canadensis were investigated for the removal of diclofenac, triclosan, naproxen, ibuprofen, caffeine, clofibric acid and MCPA. After 38 days of incubation, 40-99% of triclosan, diclofenac, and naproxen were removed from the planted and unplanted reactors. In covered control reactors no removal was observed. Caffeine and ibuprofen were removed from 40% to 80% in planted reactors whereas removals in control reactors were much lower (2-30%). Removal of clofibric acid and MCPA were negligible in both planted and unplanted reactors. The findings suggested that triclosan, diclofenac, and naproxen were removed predominantly by photodegradation, whereas caffeine and naproxen were removed by biodegradation and/or plant uptake. Pseudo-first-order removal rate constants estimated from nonlinear regressions of time series concentration data were used to describe the contaminant removals. Removal rate constants ranged from 0.003 to 0.299 d(-1), with half-lives from 2 to 248 days. The formation of two major degradation products from ibuprofen, carboxy-ibuprofen and hydroxy-ibuprofen, and a photodegradation product from diclofenac, 1-(8-Chlorocarbazolyl)acetic acid, were followed as a function of time. This study emphasizes that plants contribute to the elimination capacity of microcontaminants in wetlands systems through biodegradation and uptake processes.

  12. Threats to intact tropical peatlands and opportunities for their conservation.

    PubMed

    Roucoux, K H; Lawson, I T; Baker, T R; Del Castillo Torres, D; Draper, F C; Lähteenoja, O; Gilmore, M P; Honorio Coronado, E N; Kelly, T J; Mitchard, E T A; Vriesendorp, C

    2017-03-08

    Large, intact areas of tropical peatland are highly threatened at a global scale by the expansion of commercial agriculture and other forms of economic development. Conserving peatlands on a landscape scale, with their hydrology intact, is of international conservation importance to preserve their distinctive biodiversity and ecosystem services, and maintain their resilience to future environmental change. Here, we explore the threats and opportunities for conserving remaining intact tropical peatlands. Our focus therefore largely excludes the peatlands of Indonesia and Malaysia, where extensive deforestation, drainage and conversion to plantation of peat swamp forests over the last few decades means that conservation efforts in this region are reduced to protecting small fragments of the original ecosystem, attempting to restore drained peatlands, or dissuading companies from expanding existing plantations. In contrast, here we focus on a case study, the Pastaza-Marañón Foreland Basin (PMFB) in Peru, which is among the largest known intact tropical peatland landscapes in the world and representative of their vulnerability. Maintenance of the hydrological conditions critical for carbon storage and ecosystem function of peatlands is, in the PMFB, primarily threatened by expansion of commercial agriculture linked to new transport infrastructure that is facilitating access to remote areas. In contrast to Indonesia and Malaysia, there remain opportunities in the PMFB and elsewhere to develop alternative, more sustainable land-use practices. Although some of the peatlands in the PMFB fall within existing legally protected areas, this protection is patchy, weak and not focused on protecting the most carbon-dense areas. New carbon-based conservation funding, developing markets for sustainable peatland products, transferring land title to local communities, and expanding protected areas offer pathways to increased protection for intact tropical peatlands in Amazonia and

  13. Effects of sediment-spiked lufenuron on benthic macroinvertebrates in outdoor microcosms and single-species toxicity tests.

    PubMed

    Brock, T C M; Bas, D A; Belgers, J D M; Bibbe, L; Boerwinkel, M-C; Crum, S J H; Diepens, N J; Kraak, M H S; Vonk, J A; Roessink, I

    2016-08-01

    Sediment ecotoxicity studies were conducted with lufenuron to (i) complement the results of a water-spiked mesocosm experiment with this lipophilic benzoylurea insecticide, (ii) to explore the predictive value of laboratory single-species tests for population and community-level responses of benthic macroinvertebrates, and (iii) to calibrate the tier-1 effect assessment procedure for sediment organisms. For this purpose the concentration-response relationships for macroinvertebrates between sediment-spiked microcosms and those of 28-d sediment-spiked single-species toxicity tests with Chironomus riparius, Hyalella azteca and Lumbriculus variegatus were compared. Lufenuron persisted in the sediment of the microcosms. On average, 87.7% of the initial lufenuron concentration could still be detected in the sediment after 12 weeks. Overall, benthic insects and crustaceans showed treatment-related declines and oligochaetes treatment-related increases. The lowest population-level NOEC in the microcosms was 0.79μg lufenuron/g organic carbon in dry sediment (μg a.s./g OC) for Tanytarsini, Chironomini and Dero sp. Multivariate analysis of the responses of benthic macroinvertebrates revealed a community-level NOEC of 0.79μg a.s./g OC. The treatment-related responses observed in the microcosms are in accordance with the results of the 28-d laboratory toxicity tests. These tests showed that the insect C. riparius and the crustacean H. azteca were approximately two orders of magnitude more sensitive than the oligochaete L. variegatus. In our laboratory tests, using field-collected sediment, the lowest 28-d EC10 (0.49μg a.s./g OC) was observed for C. riparius (endpoint survival), while for the standard OECD test with this species, using artificial sediment, a NOEC of 2.35μg a.s./g OC (endpoint emergence) is reported. In this particular case, the sediment tier-1 effect assessment using the chronic EC10 (field-collected sediment) or chronic NOEC (artificial sediment) of C

  14. Crude oil degradation efficiency of a recombinant Acinetobacter baumannii strain and its survival in crude oil-contaminated soil microcosm.

    PubMed

    Mishra, Sanjeet; Sarma, Priyangshu M; Lal, Banwari

    2004-06-15

    A hydrocarbon degrading Acinetobacter baumannii S30 strain, isolated from crude oil-contaminated soil, was inserted with the lux gene from the luciferase gene cassette luxCDABE. Soil microcosms were designed to study the degradation efficacy for total petroleum hydrocarbon (TPH) of crude oil by lux-tagged A. baumannii S30 pJES. Bioaugmentation of a TPH-contaminated microcosm with A baumannii S30 pJES showed that TPH levels were reduced from 89.3 to 53.9 g/kg soil in 90 days. Biodegradation of TPH by A baumannii S30 pJES was also monitored in shake flask conditions, which showed a reduction of initial TPH levels by over 50% at the end of 120 h. A lux-PCR-based approach along with the standard dilution plating with selective antibiotics was successfully utilized to monitor the survivability of the lux-tagged strain A. baumannii S30 pJES in soil microcosms and stability of the lux insert in the host strain A. baumannii S30. The selective plating technique indicated the population of A. baumannii S30 pJES to be 6.5+/-0.13 x 10(8) CFU/g at day zero (just after bioaugmentation) and 2.09+/-0.08 x 10(8) CFU/g of soil after 90 days of incubation. lux-PCR confirmed the stability of the insert in all the randomly selected colonies of A. baumannii strains from the antibiotic plates. The lux insert was stable after 50 generations in Luria Bertini broth and storage at -70 degrees C as glycerol stocks for over a year. These results revealed that the lux insert was stable and lux-tagged A. baumannii S30 strain could survive in a TPH-contaminated soil microcosm and could degrade TPH in the soil microcosm conditions. It can be used as an effective marker to monitor the survival of augmented strains at a bioremediation site.

  15. The Multilevel Mixed Intact Group Analysis: A Mixed Method to Seek, Detect, Describe, and Explain Differences Among Intact Groups

    ERIC Educational Resources Information Center

    Schoonenboom, Judith

    2016-01-01

    Educational innovations often involve intact subgroups, such as school classes or university departments. In small-scale educational evaluation research, typically involving 1 to 20 subgroups, differences among these subgroups are often neglected. This article presents a mixed method from a qualitative perspective, in which differences among…

  16. Use of potassium tellurite for testing the survival and viability of Pseudomonas pseudoalcaligenes KF707 in soil microcosms contaminated with polychlorinated biphenyls.

    PubMed

    Zanaroli, Giulio; Fedi, Stefano; Carnevali, Monica; Fava, Fabio; Zannoni, Davide

    2002-01-01

    This study shows that the oxyanion tellurite TeO3(2-) can be used as a tool to detect and quantify the release in soil microcosms of Pseudomonas pseudoalcaligenes KF707, a strain spontaneously resistant to tellurite with a minimal inhibitory concentration (MIC) of 150 microg ml(-1). KF707 cells which carry the genes for degradation of a wide range of polychlorinated biphenyl congeners (PCBs) were used for inoculation of laboratory microcosms prepared with two different PCB-contaminated soils (Ci/s and Di/s) in the presence or absence of biphenyl as carbon source. In all microcosms supplemented with biphenyl, significant survival of strain KF707 was noted over a time period of 35 days; conversely, in microcosms containing Ci/s soil without biphenyl addition a rapid decrease in KF707 inoculated cells was observed. By comparing the number of inoculated KF707 cells with the number of indigenous bacteria growing on biphenyl (IBGB) of both Ci/s and Di/s microcosms, it could be concluded that the KF707/IBGB ratio is a relevant parameter in determining the fate of the added strain. The efficacy of potassium tellurite as a selective marker to monitor strain KF707 in laboratory microcosms was confirmed by ARDRA analyses of the 16S rDNA, while the isolated indigenous bacteria growing on biphenyl were identified as members of three different species of the genus Pseudomonas. We also report that in microcosms inoculated with KF707 cells in the absence of biphenyl, only low chlorinated biphenyls were degraded.

  17. Microcosm Approach to Understanding Methane-oxidizing Communities and the Role of Nitrogen Sources

    NASA Astrophysics Data System (ADS)

    Chistoserdova, L.; Hernandez, M. E.; Oshkin, I.

    2014-12-01

    We will report our observations on the dynamics of bacterial communities in response to methane and nitrate stimuli in laboratory microcosm incubations prepared with Lake Washington sediment samples. The experiments were designed to test our hypothesis of methane oxidation as a communal function, with the specific contents of the communities being determined by environmental factors such as oxygen concentration and the nature of the nitrogen source. We first measure taxonomic compositions of long-term oxygenated enrichment cultures and determine that, while dominated by Methylococcaceae bacteria, these cultures also contain accompanying types belonging to a limited number of bacterial taxa, both methylotrophs and non-methylotrophs. We then follow with the short-term community dynamics, under different oxygen tension regimens ('high' to 'low'), different nitrogen source regimens (added nitrate versus no nitrate) and different temperature ranges (10 to 30 oC). We observe rapid loss of species diversity in all incubations, but the composition of the communities depends on the specific environmental factors. Methylobacter represents the major methane-oxidizing partner in the communities incubated at low temperatures while Methylomonas and Methylocystis are more competitive at higher temperatures. All methanotrophs respond positively to nitrate. The non-methanotroph members of the communities reveal different trajectories in response to different oxygen tensions over time, with Methylotenera species persisting under 'low' and Methylophilus species persisting under 'high' oxygen tensions. Metagenomic sequencing reveals successions of different types of the major methane-oxidizing species as well as accompanying species. These types differ in their physiological details such as central carbon meand nitrate metabolism. A broad range of denitrifying capabilities in the organisms forming these stable methane-oxidizing communities is evident from genomic analysis. Our results

  18. Ecological impact and environmental fate of perfluorooctane sulfonate on the zooplankton community in indoor microcosms.

    PubMed

    Sanderson, Hans; Boudreau, Timothy M; Mabury, Scott A; Cheong, Woo-Jay; Solomon, Keith R

    2002-07-01

    There is presently a substantial amount of information being gathered concerning the environmental risk associated with the perfluorooctane sulfonate (PFOS) compound. The U.S. Environmental Protection Agency (U.S. EPA) is requiring that more research be completed before making definitive decisions concerning the regulatory issues covered in the significant new use rule (18/10-2000) under the Toxic Substance Control Act. However, there are no risk assessment requirements under seminatural conditions in microcosms. The PFOS can enter, and has been found in, the aquatic environment through different pathways, including spills associated with use of fire-fighting foams containing PFOS, leaching from washing Scotchgard-treated clothes with the wastewater, leaching from various coatings, discharges as residual waste from fluorochemical production, or volatilization and transportation atmospherically. The biota is the sink of PFOS rather than the sediment or soil. The aim of this article is to determine a 35-d community no-observable-effect concentration (NOECcommunity) for freshwater zooplankton and the fate of PFOS during the course of study. The PFOS persisted in the water phase with only slight reductions over the study; only the decrease from 33.9 mg/L at day 1 to 29.8 mg/L at day 35 was significant. A 90 to 100% reduction (p < 0.01) of the total zooplankton population was found after one week of exposure to 30 mg PFOS/L and a similar reduction after two weeks at 10 mg PFOS/L. The Daphnia magna 21-d NOECsurvival of 12 mg/L has previously been found in a standard laboratory bioassay by 3M. The rank order of susceptibility for the test community was Copepoda > Cladocera > Rotifera, assuming all adverse direct effects.

  19. Biogeochemical modeling of CO2 and CH4 production in anoxic Arctic soil microcosms

    NASA Astrophysics Data System (ADS)

    Tang, Guoping; Zheng, Jianqiu; Xu, Xiaofeng; Yang, Ziming; Graham, David E.; Gu, Baohua; Painter, Scott L.; Thornton, Peter E.

    2016-09-01

    Soil organic carbon turnover to CO2 and CH4 is sensitive to soil redox potential and pH conditions. However, land surface models do not consider redox and pH in the aqueous phase explicitly, thereby limiting their use for making predictions in anoxic environments. Using recent data from incubations of Arctic soils, we extend the Community Land Model with coupled carbon and nitrogen (CLM-CN) decomposition cascade to include simple organic substrate turnover, fermentation, Fe(III) reduction, and methanogenesis reactions, and assess the efficacy of various temperature and pH response functions. Incorporating the Windermere Humic Aqueous Model (WHAM) enables us to approximately describe the observed pH evolution without additional parameterization. Although Fe(III) reduction is normally assumed to compete with methanogenesis, the model predicts that Fe(III) reduction raises the pH from acidic to neutral, thereby reducing environmental stress to methanogens and accelerating methane production when substrates are not limiting. The equilibrium speciation predicts a substantial increase in CO2 solubility as pH increases, and taking into account CO2 adsorption to surface sites of metal oxides further decreases the predicted headspace gas-phase fraction at low pH. Without adequate representation of these speciation reactions, as well as the impacts of pH, temperature, and pressure, the CO2 production from closed microcosms can be substantially underestimated based on headspace CO2 measurements only. Our results demonstrate the efficacy of geochemical models for simulating soil biogeochemistry and provide predictive understanding and mechanistic representations that can be incorporated into land surface models to improve climate predictions.

  20. Effect of a simulated oil spill on natural assemblages of marine phytoplankton enclosed in microcosms

    NASA Astrophysics Data System (ADS)

    González, J.; Figueiras, F. G.; Aranguren-Gassis, M.; Crespo, B. G.; Fernández, E.; Morán, X. A. G.; Nieto-Cid, M.

    2009-07-01

    Two microcosm experiments were carried out to simulate the effect of sporadic oil spills derived from tanker accidents on oceanic and coastal marine phytoplankton assemblages. Treatments were designed to reproduce the spill from the Prestige, which took place in Galician coastal waters (NW Iberia) in November 2002. Two different concentrations of the water soluble fraction of oil were used: low (8.6 ± 0.7 μg l -1 of chrysene equivalents) and high (23 ± 5 μg l -1 of chrysene equivalents l -1). Photosynthetic activity and chlorophyll a concentration decreased in both assemblages after 24-72 h of exposure to the two oil concentrations, even though the effect was more severe on the oceanic assemblage. These variables progressively recovered up to values close or higher than those in the controls, but the short-term negative effect of oil, which was generally stronger at the high concentration, also induced changes in the structure of the plankton community. While the biomass of nanoflagellates increased in both assemblages, oceanic picophytoplankton was drastically reduced by the addition of oil. Effects on diatoms were also observed, particularly in the coastal assemblage. The response of coastal diatoms to oil addition showed a clear dependence on size. Small diatoms (<20 μm) were apparently stimulated by oil, whereas diatoms >20 μm were only negatively affected by the high oil concentration. These differences, which could be partially due to indirect trophic interactions, might also be related to different sensitivity of species to PAHs. These results, in agreement with previous observations, additionally show that the negative effect of the water soluble fraction of oil on oceanic phytoplankton was stronger than on coastal phytoplankton.

  1. Assessing the Response of Nematode Communities to Climate Change-Driven Warming: A Microcosm Experiment

    PubMed Central

    Gingold, Ruth; Moens, Tom; Rocha-Olivares, Axayácatl

    2013-01-01

    Biodiversity has diminished over the past decades with climate change being among the main responsible factors. One consequence of climate change is the increase in sea surface temperature, which, together with long exposure periods in intertidal areas, may exceed the tolerance level of benthic organisms. Benthic communities may suffer structural changes due to the loss of species or functional groups, putting ecological services at risk. In sandy beaches, free-living marine nematodes usually are the most abundant and diverse group of intertidal meiofauna, playing an important role in the benthic food web. While apparently many functionally similar nematode species co-exist temporally and spatially, experimental results on selected bacterivore species suggest no functional overlap, but rather an idiosyncratic contribution to ecosystem functioning. However, we hypothesize that functional redundancy is more likely to observe when taking into account the entire diversity of natural assemblages. We conducted a microcosm experiment with two natural communities to assess their stress response to elevated temperature. The two communities differed in diversity (high [HD] vs. low [LD]) and environmental origin (harsh vs. moderate conditions). We assessed their stress resistance to the experimental treatment in terms of species and diversity changes, and their function in terms of abundance, biomass, and trophic diversity. According to the Insurance Hypothesis, we hypothesized that the HD community would cope better with the stressful treatment due to species functional overlap, whereas the LD community functioning would benefit from species better adapted to harsh conditions. Our results indicate no evidence of functional redundancy in the studied nematofaunal communities. The species loss was more prominent and size specific in the HD; large predators and omnivores were lost, which may have important consequences for the benthic food web. Yet, we found evidence for

  2. Assessing local planning to control groundwater depletion: California as a microcosm of global issues

    NASA Astrophysics Data System (ADS)

    Nelson, Rebecca L.

    2012-01-01

    Groundwater pumping has caused excessive groundwater depletion around the world, yet regulating pumping remains a profound challenge. California uses more groundwater than any other U.S. state, and serves as a microcosm of the adverse effects of pumping felt worldwide—land subsidence, impaired water quality, and damaged ecosystems, all against the looming threat of climate change. The state largely entrusts the control of depletion to the local level. This study uses internationally accepted water resources planning theories systematically to investigate three key aspects of controlling groundwater depletion in California, with an emphasis on local-level action: (a) making decisions and engaging stakeholders; (b) monitoring groundwater; and (c) using mandatory, fee-based and voluntary approaches to control groundwater depletion (e.g., pumping restrictions, pumping fees, and education about water conservation, respectively). The methodology used is the social science-derived technique of content analysis, which involves using a coding scheme to record these three elements in local rules and plans, and State legislation, then analyzing patterns and trends. The study finds that Californian local groundwater managers rarely use, or plan to use, mandatory and fee-based measures to control groundwater depletion. Most use only voluntary approaches or infrastructure to attempt to reduce depletion, regardless of whether they have more severe groundwater problems, or problems which are more likely to have irreversible adverse effects. The study suggests legal reforms to the local groundwater planning system, drawing upon its empirical findings. Considering the content of these recommendations may also benefit other jurisdictions that use a local groundwater management planning paradigm.

  3. Manure biochar influence upon soil properties, phosphorus distribution and phosphatase activities: A microcosm incubation study.

    PubMed

    Jin, Yi; Liang, Xinqiang; He, Miaomiao; Liu, Yu; Tian, Guangming; Shi, Jiyan

    2016-01-01

    Using manure-derived-biochar as an alternative phosphorus (P) source has bright future prospects to improve soil P status. A 98-day microcosm incubation experiment was set up for two soils which were amended with manure biochar at proportions of 0, 0.5% and 1.5%. Swine manure samples were air-dried and manure biochar was prepared by pyrolysis at 400 °C for 4 h. As determined by P-31 nuclear magnetic resonance ((31)P NMR) spectroscopy, manure biochar mainly increased the contents and fractions of orthophosphate and pyrophosphate in two soils, while decreased those of monoesters (P<0.05). At the end of incubation, 1.5% of manure biochar raised soil pH by 0.5 and 0.6 units, cation exchange capacity by 16.9% and 32.2%, and soil total P by 82.1% and 81.1% for silt loam and clay loam soils, respectively, as compared with those soils without biochar. Simultaneously, 1.5% of manure biochar decreased acid phosphomonoesterase activities by 18.6% and 34.0% for clay loam and silt loam, respectively; while it increased alkaline phosphomonoesterase activities by 28.5% and 95.1% for clay loam and silt loam, respectively. The enhancement of soil P availability after manure biochar addition was firstly due to the orthophosphate and pyrophosphate as the major P species in manure biochar which directly increased contents of soil inorganic P, and also attributed to the decomposition of some organic P like monoesters by enhanced alkaline phosphomonoesterase activities from manure biochar addition.

  4. Evaluation of the biodegradation of Alaska North Slope oil in microcosms using the biodegradation model BIOB.

    PubMed

    Torlapati, Jagadish; Boufadel, Michel C

    2014-01-01

    We present the details of a numerical model, BIOB that is capable of simulating the biodegradation of oil entrapped in the sediment. The model uses Monod kinetics to simulate the growth of bacteria in the presence of nutrients and the subsequent consumption of hydrocarbons. The model was used to simulate experimental results of Exxon Valdez oil biodegradation in laboratory columns (Venosa et al., 2010). In that study, samples were collected from three different islands: Eleanor Island (EL107), Knight Island (KN114A), and Smith Island (SM006B), and placed in laboratory microcosms for a duration of 168 days to investigate oil bioremediation through natural attenuation and nutrient amendment. The kinetic parameters of the BIOB model were estimated by fitting to the experimental data using a parameter estimation tool based on Genetic Algorithms (GA). The parameter values of EL107 and KN114A were similar whereas those of SM006B were different from the two other sites; in particular biomass growth at SM006B was four times slower than at the other two islands. Grain size analysis from each site revealed that the specific surface area per unit mass of sediment was considerably lower at SM006B, which suggest that the surface area of sediments is a key control parameter for microbial growth in sediments. Comparison of the BIOB results with exponential decay curves fitted to the data indicated that BIOB provided better fit for KN114A and SM006B in nutrient amended treatments, and for EL107 and KN114A in natural attenuation. In particular, BIOB was able to capture the initial slow biodegradation due to the lag phase in microbial growth. Sensitivity analyses revealed that oil biodegradation at all three locations were sensitive to nutrient concentration whereas SM006B was sensitive to initial biomass concentration due to its slow growth rate. Analyses were also performed to compare the half-lives of individual compounds with that of the overall polycyclic aromatic hydrocarbons

  5. Streambed sediment controls on hyporheic greenhouse gas production - a microcosm experiment

    NASA Astrophysics Data System (ADS)

    Romeijn, P.; Comer, S.; Krause, S.; Hannah, D. M.; Gooddy, D.

    2015-12-01

    Hyporheic zones, as the interfaces between groundwater and surface water, can contribute significantly to whole stream carbon respiration. The drivers and controls of rates and magnitude of hyporheic greenhouse gas (GHG) production remain poorly understood. Recent research has hypothesised that nitrous oxide emissions resulting from incomplete denitrification in nutrient rich agricultural streams may contribute substantially to GHG emissions. This paper reports on a controlled microcosm incubation experiment that has been set up to quantify the sensitivity of hyporheic zone GHG production to temperature and nutrient concentrations. Experiments were conducted with sediment from two contrasting UK lowland rivers (sandstone and chalk). Adopting a gradient approach, sediments with different organic matter and carbon content were analysed from both rivers. Our analytical approach integrated several novel methods, such as push-pull application of the Resazurin/Resorufin smart tracer system for estimation of sediment microbial metabolic activity, high-resolution gas sampling and analysis of methane, carbon dioxide and nitrous oxide by gas chromatography with mass spectrometry, coupled with and high precision in-situ dissolved oxygen measurements. Our results indicate strong temperature controls of GHG production rates, overlapping with the observed impacts of different sediment types. Experimental findings indicate that increased hyporheic temperatures during increasing baseflow and drought conditions may enhance substantially sediment respiration and thus, GHG emissions from the streambed interface. The presented results integrated with field experiments of respiration and GHG emission rates under different treatments. This research advances understanding of scale dependent drivers and controls of whole stream carbon and nitrogen budgets and the role of streambed interfaces in GHG emissions.

  6. Streambed sediment controls on hyporheic greenhouse gas production - a microcosm experiment

    NASA Astrophysics Data System (ADS)

    Romejn, Paul; Comer, Sophie; Gooddy, Daren; Ullah, Sami; Hannah, David; Krause, Stefan

    2016-04-01

    Hyporheic zones, as the interfaces between groundwater and surface water, can contribute significantly to whole stream carbon respiration. The drivers and controls of rates and magnitude of hyporheic greenhouse gas (GHG) production remain poorly understood. Recent research has hypothesised that nitrous oxide emissions resulting from incomplete denitrification in nutrient rich agricultural streams may contribute substantially to GHG emissions. This paper reports on a controlled microcosm incubation experiment that has been set up to quantify the sensitivity of hyporheic zone GHG production to temperature and nutrient concentrations. Experiments were conducted with sediment from two contrasting UK lowland rivers (sandstone and chalk). Adopting a gradient approach, sediments with different organic matter and carbon content were analysed from both rivers. Our analytical approach integrated several novel methods, such as push-pull application of the Resazurin/Resorufin smart tracer system for estimation of sediment microbial metabolic activity, high-resolution gas sampling and analysis of methane, carbon dioxide and nitrous oxide by gas chromatography with mass spectrometry, coupled with and high precision in-situ dissolved oxygen measurements. Our results indicate strong temperature controls of GHG production rates, overlapping with the observed impacts of different sediment types. Experimental findings indicate that increased hyporheic temperatures during increasing baseflow and drought conditions may enhance substantially sediment respiration and thus, GHG emissions from the streambed interface. The presented results integrated with field experiments of respiration and GHG emission rates under different treatments. This research advances understanding of scale dependent drivers and controls of whole stream carbon and nitrogen budgets and the role of streambed interfaces in GHG emissions.

  7. Indirect Evidence Link PCB Dehalogenation with Geobacteraceae in Anaerobic Sediment-Free Microcosms

    PubMed Central

    Praveckova, Martina; Brennerova, Maria V.; Holliger, Christof; De Alencastro, Felippe; Rossi, Pierre

    2016-01-01

    Although polychlorinated biphenyls (PCBs) production was brought to a halt 30 years ago, recalcitrance to degradation makes them a major environmental pollutant at a global scale. Previous studies confirmed that organohalide-respiring bacteria (OHRB) were capable of utilizing chlorinated congeners as electron acceptor. OHRB belonging to the Phyla Chloroflexi and Firmicutes are nowadays considered as the main PCB-dechlorinating organisms. In this study, we aimed at exploring the involvement of other taxa in PCB dechlorination using sediment-free microcosms (SFMs) and the Delor PCB mixture. High rates of congener dehalogenation (up to 96%) were attained in long-term incubations of up to 692 days. Bacterial communities were dominated by Chloroflexi, Proteobacteria, and Firmicutes, among strictly simplified community structures composed of 12 major phyla only. In a first batch of SFMs, Dehalococcoides mccartyi closely affiliated with strains CG4 and CBDB1 was considered as the main actor associated with congener dehalogenation. Addition of 2-bromoethanesulfonate (BES), a known inhibitor of methanogenic activity in a second batch of SFMs had an adverse effect on the abundance of Dehalococcoides sp. Only two sequences affiliated to this Genus could be detected in two (out of six) BES-treated SFMs, contributing to a mere 0.04% of the communities. BES-treated SFMs showed very different community structures, especially in the contributions of organisms involved in fermentation and syntrophic activities. Indirect evidence provided by both statistical and phylogenetic analysis validated the implication of a new cluster of actors, distantly affiliated with the Family Geobacteraceae (Phylum δ-Proteobacteria), in the dehalogenation of low chlorinated PCB congeners. Members of this Family are known already for their dehalogenation capacity of chlorinated solvents. As a result, the present study widens the knowledge for the phylogenetic reservoir of indigenous PCB dechlorinating

  8. Linking stoichiometric homeostasis of microorganisms with soil phosphorus dynamics in wetlands subjected to microcosm warming.

    PubMed

    Wang, Hang; Li, Hongyi; Zhang, Zhijian; Muehlbauer, Jeffrey D; He, Qiang; Xu, Xinhua; Yue, Chunlei; Jiang, Daqian

    2014-01-01

    Soil biogeochemical processes and the ecological stability of wetland ecosystems under global warming scenarios have gained increasing attention worldwide. Changes in the capacity of microorganisms to maintain stoichiometric homeostasis, or relatively stable internal concentrations of elements, may serve as an indicator of alterations to soil biogeochemical processes and their associated ecological feedbacks. In this study, an outdoor computerized microcosm was set up to simulate a warmed (+5°C) climate scenario, using novel, minute-scale temperature manipulation technology. The principle of stoichiometric homeostasis was adopted to illustrate phosphorus (P) biogeochemical cycling coupled with carbon (C) dynamics within the soil-microorganism complex. We hypothesized that enhancing the flux of P from soil to water under warming scenarios is tightly coupled with a decrease in homeostatic regulation ability in wetland ecosystems. Results indicate that experimental warming impaired the ability of stoichiometric homeostasis (H) to regulate biogeochemical processes, enhancing the ecological role of wetland soil as an ecological source for both P and C. The potential P flux from soil to water ranged from 0.11 to 34.51 mg m(-2) d(-1) in the control and 0.07 to 61.26 mg m(-2) d(-1) in the warmed treatment. The synergistic function of C-P acquisition is an important mechanism underlying C∶P stoichiometric balance for soil microorganisms under warming. For both treatment groups, strongly significant (p<0.001) relationships fitting a negative allometric power model with a fractional exponent were found between n-HC∶P (the specialized homeostatic regulation ability as a ratio of soil highly labile organic carbon to dissolved reactive phosphorus in porewater) and potential P flux. Although many factors may affect soil P dynamics, the n-HC∶P term fundamentally reflects the stoichiometric balance or interactions between the energy landscape (i.e., C) and flow of resources

  9. Biogeochemical modeling of CO2 and CH4 production in anoxic Arctic soil microcosms

    DOE PAGES

    Tang, Guoping; Zheng, Jianqiu; Xu, Xiaofeng; ...

    2016-09-12

    Soil organic carbon turnover to CO2 and CH4 is sensitive to soil redox potential and pH conditions. However, land surface models do not consider redox and pH in the aqueous phase explicitly, thereby limiting their use for making predictions in anoxic environments. Using recent data from incubations of Arctic soils, we extend the Community Land Model with coupled carbon and nitrogen (CLM-CN) decomposition cascade to include simple organic substrate turnover, fermentation, Fe(III) reduction, and methanogenesis reactions, and assess the efficacy of various temperature and pH response functions. Incorporating the Windermere Humic Aqueous Model (WHAM) enables us to approximately describe themore » observed pH evolution without additional parameterization. Although Fe(III) reduction is normally assumed to compete with methanogenesis, the model predicts that Fe(III) reduction raises the pH from acidic to neutral, thereby reducing environmental stress to methanogens and accelerating methane production when substrates are not limiting. The equilibrium speciation predicts a substantial increase in CO2 solubility as pH increases, and taking into account CO2 adsorption to surface sites of metal oxides further decreases the predicted headspace gas-phase fraction at low pH. Without adequate representation of these speciation reactions, as well as the impacts of pH, temperature, and pressure, the CO2 production from closed microcosms can be substantially underestimated based on headspace CO2 measurements only. Our results demonstrate the efficacy of geochemical models for simulating soil biogeochemistry and provide predictive understanding and mechanistic representations that can be incorporated into land surface models to improve climate predictions.« less

  10. The effect of lead contamination on bioturbation by Lumbriculus variegatus in a freshwater microcosm.

    PubMed

    Blankson, Emmanuel R; Deb Adhikary, Nihar R; Klerks, Paul L

    2017-01-01

    The present study investigated the effect of lead (Pb) on bioturbation by the oligochaete worm Lumbriculus variegatus, using freshwater microcosms. The experiment used lead at "0", 140, 700, and 3500 μg/g in sediment, and used two different laboratory populations of L. variegatus. A molecular genetic analysis and bioassays were conducted to determine if the two populations differed genetically and whether they differed in Pb-sensitivity. The bioturbation of L. variegatus was estimated using luminophores placed at the sediment-water interface at the beginning of the experiment. After the 14 d experiment the luminophore profiles in sediment were used to estimate the biodiffusion and bioadvection coefficients, using the diffusion-advection model. The results showed that the biodiffusion and bioadvection coefficients were generally negatively related to the Pb concentrations in the sediment. Lead at 700 and 3500 μg/g reduced both coefficients, while Pb at 140 μg/g did not. Luminophore profiles in the "0" and 140 μg/g treatments were indicative of a non-local transport, while a diffusive transport was observed at the higher Pb levels. The two laboratory populations of L. variegatus used in the experiment differed in their sensitivity to Pb when mortality was used as the endpoint, but they did not differ in sediment bioturbation or the Pb-sensitivity of this process. Moreover, the genetic analysis did not detect any genetic differences between the populations. This study demonstrated that elevated levels of Pb can impact ecosystem functioning by decreasing the bioturbation activity of benthic organisms such as L. variegatus.

  11. Comparative metagenomic analysis of microcosm structures and lignocellulolytic enzyme systems of symbiotic biomass-degrading consortia.

    PubMed

    Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Mhuantong, Wuttichai; Tangphatsornruang, Sithichoke; Eurwilaichitr, Lily; Igarashi, Yasuo; Champreda, Verawat

    2013-10-01

    Decomposition of lignocelluloses by cooperative microbial actions is an essential process of carbon cycling in nature and provides a basis for biomass conversion to fuels and chemicals in biorefineries. In this study, structurally stable symbiotic aero-tolerant lignocellulose-degrading microbial consortia were obtained from biodiversified microflora present in industrial sugarcane bagasse pile (BGC-1), cow rumen fluid (CRC-1), and pulp mill activated sludge (ASC-1) by successive subcultivation on rice straw under facultative anoxic conditions. Tagged 16S rRNA gene pyrosequencing revealed that all isolated consortia originated from highly diverse environmental microflora shared similar composite phylum profiles comprising mainly Firmicutes, reflecting convergent adaptation of microcosm structures, however, with substantial differences at refined genus level. BGC-1 comprising cellulolytic Clostridium and Acetanaerobacterium in stable coexistence with ligninolytic Ureibacillus showed the highest capability on degradation of agricultural residues and industrial pulp waste with CMCase, xylanase, and β-glucanase activities in the supernatant. Shotgun pyrosequencing of the BGC-1 metagenome indicated a markedly high relative abundance of genes encoding for glycosyl hydrolases, particularly for lignocellulytic enzymes in 26 families. The enzyme system comprised a unique composition of main-chain degrading and side-chain processing hydrolases, dominated by GH2, 3, 5, 9, 10, and 43, reflecting adaptation of enzyme profiles to the specific substrate. Gene mapping showed metabolic potential of BGC-1 for conversion of biomass sugars to various fermentation products of industrial importance. The symbiotic consortium is a promising simplified model for study of multispecies mechanisms on consolidated bioprocessing and a platform for discovering efficient synergistic enzyme systems for biotechnological application.

  12. Radioactive satellites - Intact reentry and breakup by debris impact

    NASA Technical Reports Server (NTRS)

    Anz-Meador, P. D.; Potter, A. E., Jr.

    1991-01-01

    There is a substantial mass of radioactive material in nuclear reactors or radioisotope thermal generators (RTGs) in orbit about the earth. This paper examines the reentry of intact nuclear fuel cores and RTGs and the fragmentation and subsequent radioactive debris cloud deposition and evolution resulting from the impact of orbital debris upon an orbiting reactor, fuel core, or RTG. To assess the intact reentry, decay rates and a predicted decay date using historical and projected orbital decay data, are estimated. The current NASA debris environment model is utilized to estimate impact rates and debris cloud evolution of a fragmentation event. Results of these analyses are compared and concepts are tendered which would tend to minimize the radiological debris hazard to personnel and structures both on the earth's surface and in low earth orbit.

  13. On the sensitivity of intact cells to perturbation by ethanol

    SciTech Connect

    Hitzemann, R.; Whitaker-Azmitia, P. ); Dains, K.; Lin, J. )

    1989-01-01

    A comparison was made of ethanol's effects on the order of plasma membranes in intact cells and some isolated membrane preparations. Order was assessed by steady-state fluorescence polarization techniques using the non-permeant probe, TMA-DPH. The data show that two cultured cells, rat neonatal astroglial and N2A neuroblastoma, were sensitive to significant ethanol-induced disordering within the anesthetically relevant range. Human erythrocytes, cultured fibroblasts and homogenized astroglial cells required higher ethanol concentrations to produce a similar effect. Intact erythrocytes were approximately twice as sensitive as erythrocyte ghost membranes to ethanol induced perturbation. The neonatal glial and N2A cells were approximately five times more sensitive than synaptic membranes to ethanol effects. DMPC and DMPC + cholesterol liposomes and myelin membranes were insensitive to ethanol's effects. The incorporation of 10 mole % ganglioside GM{sub 1} sensitized the liposomes to ethanol-induced perturbation.

  14. Intrathecal application of cyproheptadine impairs locomotion in intact rats.

    PubMed

    Majczyński, Henryk; Cabaj, Anna; Górska, Teresa

    In intact adult rats, cyproheptadine, a 5-HT2 antagonist, administered intrathecally at the midlumbar segments was found to impair hindlimb locomotor movements during overground locomotion. These effects were dose-dependent; they varied from transient complete hindlimb paraplegia seen at doses of 300 microg/20 microl, to short-lasting trunk instability at doses of 100 microg/20 microl. After the return of overground locomotion, transient abduction of one of the hindlimbs was observed in some animals. These findings demonstrate that the blockade of 5-HT2 receptors affects locomotion in intact rats. Our results provide support for the hypothesis of serotonergic involvement in rat locomotion, which, so far, has been based mainly on the effects of 5-HT2 agonists on the recovery of locomotion in spinal rats.

  15. Spelling-stress regularity effects are intact in developmental dyslexia.

    PubMed

    Mundy, Ian R; Carroll, Julia M

    2013-01-01

    The current experiment investigated conflicting predictions regarding the effects of spelling-stress regularity on the lexical decision performance of skilled adult readers and adults with developmental dyslexia. In both reading groups, lexical decision responses were significantly faster and significantly more accurate when the orthographic structure of a word ending was a reliable as opposed to an unreliable predictor of lexical stress assignment. Furthermore, the magnitude of this spelling-stress regularity effect was found to be equivalent across reading groups. These findings are consistent with intact phoneme-level regularity effects also observed in dyslexia. The paper discusses how findings of intact spelling-sound regularity effects at both prosodic and phonemic levels, as well as other similar results, can be reconciled with the obvious difficulties that people with dyslexia experience in other domains of phonological processing.

  16. Structural determination of intact proteins using mass spectrometry

    DOEpatents

    Kruppa, Gary; Schoeniger, Joseph S.; Young, Malin M.

    2008-05-06

    The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

  17. Binding of Clostridium botulinum C3 exoenzyme to intact cells.

    PubMed

    Rohrbeck, Astrid; von Elsner, Leonie; Hagemann, Sandra; Just, Ingo

    2014-06-01

    C3 from Clostridium botulinum (C3) specifically modifies Rho GTPases RhoA, RhoB, and RhoC by mono-ADP-ribosylation. The confined substrate profile of C3 is the basis for its use as pharmacological tool in cell biology to study cellular functions of Rho GTPases. Although C3 exoenzyme does not possess a cell-binding/-translocation domain, C3 is taken up by intact cells via an unknown mechanism. In the present work, binding of C3 to the hippocampus-derived HT22 cells and J774A.1 macrophages was characterized. C3 bound concentration-dependent to HT22 and J774A.1 cells. Pronase treatment of intact cells significantly reduced both C3 binding and C3 cell entry. Removal of sugar residues by glycosidase F treatment resulted in an increased binding of C3, but a reduced cell entry. To explore the involvement of phosphorylation in the binding process of C3, intact HT22 and J774A.1 cells were pre-treated with vanadate prior to incubation with C3. Inhibition of de-phosphorylation by vanadate resulted in an increased binding of C3. To differentiate between intracellular and extracellular phosphorylation, intact cells were treated with CIP (calf intestine phosphatase) to remove extracellular phosphate residues. The removal of phosphate residues resulted in a strong reduction in binding of C3 to cells. In sum, the C3 membranous binding partner is proteinaceous, and the glycosylation as well as the phosphorylation state is critical for efficient binding of C3.

  18. Dental abscess in a tooth with intact dens evaginatus.

    PubMed

    Cho, S Y

    2006-03-01

    This article reports a case of dental abscess in a mandibular premolar with intact dens evaginatus. Dentists are advised to critically evaluate those teeth with dens evaginatus, both clinically and radiographically, before attempting prophylactic treatments. This is particularly important medicolegally in case the tooth develops symptoms shortly after the prophylactic treatment. Dentists practising in Western countries should also be aware of this dental anomaly because of the increasing global migration of people from Asia.

  19. Crisscross heart with dextrocardia and intact interventricular septum.

    PubMed

    Muneer, P Kader; Kalathingathodika, Sajeer; Chakanalil, Govindan Sajeev; Sony, Manuel M

    2014-01-01

    Crisscross heart is a rare congenital heart disease characterized by a twisted atrioventricular connection, as a result of rotation of the ventricular mass along its long axis. We report an asymptomatic 48-year-old woman referred to us for evaluation of a cardiac murmur. Further evaluation showed situs solitus, dextrocardia with normal atrioventricular and ventriculoarterial connection, and a crisscross relation of the atrioventricular valves. Unlike the usual case of crisscross heart, our patient had an intact ventricular septum.

  20. Acoustic emissions during deformation of intact and jointed welded tuff

    SciTech Connect

    Holcomb, D.J.; Teufel, L.W.

    1982-07-01

    Monitoring of acoustic emissions (AE) has been widely used as a means of detecting failure in intact rock. For intact rock the technique is simple, because an increasing rate of AE is usually a sign of impending failure. However, most large rock masses contain numerous joints and the behavior of the joints controls the properties of the rock mass. In particular, the failure mode often becomes stable or unstable slip (stick-slip) on a joint at stresses well below those required for failure of the intact rock. As an aid to understanding and monitoring the behavior of jointed rock masses, we have done a series of experiments on intact and artificially jointed samples of Grouse Canyon tuff. The tuff was selected because it is under consideration as a disposal medium for nuclear wastes. The samples were instrumented to measure axial and transverse displacements and AE rates. Testing was done in a servo-controlled machine at axial displacement rates of 5 x 10{sup -5} cm/sec, and confining pressures ranging from 10 to 40 MPa. For the jointed samples four modes of slip were identified. First, stable sliding accompanied by a steady rate of AE. Second, stick-slip with a sharp drop in load, large displacements but no premonitory AE or slip. Third, stick-slip, as in mode 2, but with premonitory AE and slip. Fourth, slow stick-slip where the load dropped and the displacements increased but the process was slow and culminated in stable sliding. Mode 4 exhibited premonitory AE and slip and after the event, a steady rate of AE during sliding. There seemed to be no way to predict which mode would occur at a given point in the test. In all cases where stable or unstable slip occurred there was a corresponding occurrence of AE. This indicates that slip is related to damage to the joint surfaces and adjacent material. Monitoring AE would be a useful method of detecting slip.

  1. Posttranslational protein modification by polyamines in intact and regenerating nerves.

    PubMed

    Chakraborty, G; Leach, T; Zanakis, M F; Sturman, J A; Ingoglia, N A

    1987-03-01

    A 150,000-g supernatant from axoplasm of the giant axon of the stellate nerve of the squid and from rat sciatic and goldfish optic nerves was found to be able to incorporate covalently [3H]putrescine and [3H]spermidine into an exogenous protein (N,N'-dimethylcasein). Incorporation of radioactivity was inhibited by CuSO4, a specific inhibitor of transglutaminases, the enzymes mediating these reactions in other tissues. Analysis of pH and temperature range and enzyme kinetics displayed characteristics predicted for transglutaminase-mediated reactions. Transglutaminase activity increased during regeneration of both vertebrate nerves, but greater activity was found in segments of nerve containing no intact axons than in either intact segments or in segments containing regenerating axons. Polyacrylamide gel electrophoresis of endogenous modified proteins (in the absence of N,N'-dimethylcasein) showed labeling of 18-, 46- and 200-kilodalton proteins by both [3H]putrescine and [3H]spermidine. Analysis of the protein-bound radioactivity from intact and regenerating rat sciatic nerves demonstrated it to be predominantly in the form of the parent radioactive polyamine. These experiments demonstrate the covalent modification of proteins by polyamines at low levels in squid axoplasm and at relatively higher levels in rat sciatic and goldfish optic nerves. In the latter two cases, the activity of these modification reactions may be due in part to the modification of axonal proteins, but the majority of the activity occurs in nonneuronal cells of the nerve.

  2. Vehicle influence on permeation through intact and compromised skin.

    PubMed

    Gujjar, Meera; Banga, Ajay K

    2014-09-10

    The purpose of this study was to compare the transdermal permeation of a model compound, diclofenac diethylamine, from a hydrophilic and lipophilic vehicle across in vitro models simulating compromised skin. Mineral oil served as a lipophilic vehicle while 10mM phosphate buffered saline served as a hydrophilic vehicle. Compromised skin was simulated by tape stripping, delipidization, or microneedle application and compared with intact skin as a control. Transepidermal water loss was measured to assess barrier function. Skin compromised with tape stripping and delipidization significantly (p<0.05) increased permeation of diclofenac diethylamine compared to intact and microneedle treated skin with phosphate buffered saline vehicle. A similar trend in permeation was observed with mineral oil as the vehicle. For both vehicles, permeation across skin increased in the same order and correlated with degree of barrier impairment as indicated by transepidermal water loss values: intact

  3. Microcosm Studies to Evaluate Aerobic Cometabolism of Low Concentrations of 1,4-Dioxane by Isobutane-utilizing Microorganisms in the Presence of Chlorinated Solvent Co-contaminants

    NASA Astrophysics Data System (ADS)

    Rolston, H. M.; Azizian, M.; Hyman, M. R.; Semprini, L.

    2015-12-01

    Due to its use as a stabilizer for chlorinated solvents, 1,4-dioxane (1,4D), a probable human carcinogen, is a common co-contaminant in solvent spills at industrial and military sites and landfills. Its persistence in large groundwater plumes at low concentrations makes it a relevant candidate for in-situ bioremediation via cometabolism. Microcosm studies are being performed to evaluate the capability of aerobic microorganisms to cometabolize mixtures of 1,4D and chlorinated solvents, such as trichloroethylene (TCE), 1,1,1-trichloroethane (1,1,1TCA), and 1,1-dichloroethene (1,1DCE), with isobutane as the primary substrate. Microcosms were constructed using aquifer solids from Fort Carson, Colorado, a site contaminated with 1,4D and TCE, to assess the isobutane uptake and transformation of 1,4D and chlorinated solvents by microorganisms native to the site. Additional microcosms were augmented with Rhodococcus rhodochrous, a bacterium shown to cometabolize 1,4D and chlorinated solvents. Results indicate that native microcosms cometabolized 1,4D upon stimulation with isobutane after a lag period of about 15 days. TCE was also transformed, but at significantly slower rates. The presence of 1,4D and TCE at 500 and 300 ppb, respectively, did not inhibit the growth of native microorganisms on isobutane, with isobutane uptake and 1,4D transformation occurring simultaneously. Bioaugmented microcosms transformed 1,4D immediately after inoculation with R. rhodochrous. Tests in bioaugmented microorganisms indicated that the presence of TCE at low concentrations inhibits but does not block the transformation of 1,4D. Results from the microcosms will be used to design field tests to be performed at Fort Carson. Additional microcosm studies will compare the stimulation of native and bioaugmented microcosms and the transformation of mixtures of 1,4D, 1,1,1TCA and 1,1DCE. Molecular methods will analyze the monoxygenase enzymes expressed in the native and bioaugmented microcosms.

  4. Solid lipid nanoparticles affect microbial colonization and enzymatic activity throughout the decomposition of alder leaves in freshwater microcosms.

    PubMed

    Sampaio, A C; Mendes, R J; Castro, P G; Silva, A M

    2017-01-01

    Solid lipid nanoparticles (SLNs) are used as carriers for drug delivery, and are high biocompatible and designed to endure in the host organism. Despite its current industrial production is low, many of these substances are available on the market, and much more are in the production pipeline. As a result, many of them will end in aquatic systems raising the question whether they can pose a risk to aquatic biota and the associated ecological processes. Microbial decomposers of plant litter, play a key role in forested streams being responsible for the energy flow between terrestrial and aquatic environments. Here, we investigated the effects of SLNs on alder leaf litter decomposition by aquatic microbes. Alder leaves were immersed in a stream of Northeast Portugal to allow microbial colonization before being exposed in microcosms of two types of SLNs at two concentrations for 42 days. Results showed that rates of leaf decomposition decreased with exposure to SLNs. Bacterial biomass was not inhibited by SLNs, and cultivable fungi densities remained constant (SLN-A) or increased (SLN-C) compared with control microcosms. The type and concentration of SLNs influenced differently the leaf colonization by fungi as well as fungal sporulation rate. These effects were accompanied by changes in the community extraenzymatic profile: the activities of alkaline phosphatase, acidic phosphatase, Naphthol-AS-BI-phosphohydrolase (P cycle) and lipases increased in the SLNs microcosms. This study provided the first evidence of the adverse effects of the release of SLNs to streams on leaf litter decomposition. Those effects seem to depend on the composition and concentration of SLNs, as well on the microbial target group, or enzyme. Thus, prior to massive industrial production of these nanomaterials, some measures should be taken to avoid environmental impact affecting the microbial communities responsible for detritus decomposition.

  5. From a microcosm to the catchment scale: studying the fate of organic runoff pollutants in aquatic ecosystems

    NASA Astrophysics Data System (ADS)

    Böttcher, T.; Schroll, R.

    2009-04-01

    Spray-drift, drainage, erosion and runoff events are the major causes responsible for deportation of agrochemicals as micropollutants to aquatic non-target sites. These processes can lead to the contamination of nearby freshwater ecosystems with considerably high concentrations of xenobiotics. Thus, it is important to unravel the fate of these pollutants and to evaluate their ecological effects. A novel approach to address this goal was established by the development of a microcosm with multiple sampling abilities enabling quantitative assessment of organic volatilisation, mineralization, metabolization and distribution within the aquatic ecosystem. This microcosm system was designed to support modelling approaches of the catchment scale and gain insights into the fate of pesticides simulating a large scale water body. The potential of this microcosm was exemplified for Isoproturon (IPU), a phenylurea derived systemic herbicide, which is frequently found as contaminant in water samples and with the free-floating macrophyte Lemna minor as non-target species, that is common to occur in rural water bodies. During 21 days exposure time, only a small amount of 14C labeled IPU was removed from the aquatic medium. The major portion (about 5%) was accumulated by Lemna minor resulting in a BCF of 15.8. IPU-volatilisation was very low with 0.13% of the initially applied herbicide. Only a minor amount of IPU was completely metabolized, presumably by rhizosphere microorganisms and released as 14CO2. The novel experimental system allowed to quantitatively investigate the fate of IPU and showed a high reproducibility with a mean average 14C-recovery rate of 97.1

  6. Hydrocarbon Specificity During Aerobic oil Biodegradation Revealed in Marine Microcosms With the use of Comprehensive, Two-Dimensional Gas Chromatography.

    NASA Astrophysics Data System (ADS)

    Wardlaw, G. D.; Reddy, C. M.; Nelson, R. K.; Valentine, D. L.

    2008-12-01

    In 2003 the National Research Council reported more than 380 million gallons of oil is emitted into the ocean each year from natural seepage and as a result of anthropogenic activities. Many of the hydrocarbons making up this oil are persistent and toxic to marine life. Petroleum emitted into biologically sensitive areas can lead to environmental stress and ecosystem collapse. As a result many studies and a substantial amount of resources have been devoted to creating efficient and effective remediation tools and developing a better understanding of natural hydrocarbon weathering processes occurring in marine environments. The goal of this study is to elucidate patterns and extent of aerobic hydrocarbon degradation in marine sediments. In order to assess the specific molecular transformations occurring in petroleum emitted into oxic marine environments, we prepared microcosm experiments using sediments and seawater collected from the natural oil seeps offshore Coal Oil Point, California. Petroleum recovered from Platform Holly in the Santa Barbara Channel, was added to a sediment-seawater mixture and the microcosm bottles were allowed to incubate under aerobic conditions for slightly more than 100 days. Comprehensive, two-dimensional gas chromatography was employed in this study to quantify changes in the concentrations of individual hydrocarbon compounds because of the increased resolution and resolving power provided with this robust analytical method. We show significant hydrocarbon mass loss due to aerobic biodegradation for hundreds of tracked compounds in the microcosm bottles. The results shown here provide quantitative evidence for broad-scale metabolic specificity during aerobic hydrocarbon degradation in surface and shallow subsurface marine sediments.

  7. Effect of quaternary ammonium and silver nanoparticle-containing adhesives on dentin bond strength and dental plaque microcosm biofilms

    PubMed Central

    Zhang, Ke; Melo, Mary Anne S.; Cheng, Lei; Weir, Michael D.; Bai, Yuxing; Xu, Hockin H. K.

    2012-01-01

    Objectives Antibacterial bonding agents are promising to hinder the residual and invading bacteria at the tooth-restoration interfaces. The objectives of this study were to develop an antibacterial bonding agent by incorporation of quaternary ammonium dimethacrylate (QADM) and nanoparticles of silver (NAg), and to investigate the effect of QADM-NAg adhesive and primer on dentin bond strength and plaque microcosm biofilm response for the first time. Methods Scotchbond Multi-Purpose adhesive and primer were used as control. Experimental adhesive and primer were made by adding QADM and NAg into control adhesive and primer. Human dentin shear bond strengths were measured (n = 10). A dental plaque microcosm biofilm model with human saliva as inoculum was used to investigate biofilm metabolic activity, colony-forming unit (CFU) counts, lactic acid production, and live/dead staining assay (n = 6). Results Adding QADM and NAg into adhesive and primer did not compromise the dentin shear bond strength which ranged from 30 to 35 MPa (p > 0.1). Scanning electron microscopy (SEM) examinations revealed numerous resin tags, which were similar for the control and the QADM and NAg groups. Adding QADM or NAg markedly reduced the biofilm viability, compared to adhesive control. QADM and NAg together in the adhesive had a much stronger antibacterial effect than using each agent alone (p < 0.05). Adding QADM and NAg in both adhesive and primer had the strongest antibacterial activity, reducing metabolic activity, CFU, and lactic acid by an order of magnitude, compared to control. Significance Without compromising dentin bond strength and resin tag formation, the QADM and NAg containing adhesive and primer achieved strong antibacterial effects against microcosm biofilms for the first time. QADM-NAg adhesive and primer are promising to combat residual bacteria in tooth cavity and invading bacteria at the margins, thereby to inhibit secondary caries. QADM and NAg incorporation may have a

  8. Naturally occurring heavy radioactive elements in the geothermal microcosm of the Los Azufres (Mexico) volcanic complex.

    PubMed

    Abuhani, W A; Dasgupta-Schubert, N; Villaseñor, L M; García Avila, D; Suárez, L; Johnston, C; Borjas, S E; Alexander, S A; Landsberger, S; Suárez, M C

    2015-01-01

    The Los Azufres geothermal complex of central Mexico is characterized by fumaroles and boiling hot-springs. The fumaroles form habitats for extremophilic mosses and ferns. Physico-chemical measurements of two relatively pristine fumarolic microcosms point to their resemblance with the paleo-environment of earth during the Ordovician and Devonian periods. These geothermal habitats were analysed for the distribution of elemental mass fractions in the rhizospheric soil (RS), the native volcanic substrate (VS) and the sediments (S), using the new high-sensitivity technique of polarized x-ray energy dispersive fluorescence spectrometry (PEDXRF) as well as instrumental neutron activation analysis (INAA) for selected elements. This work presents the results for the naturally occurring heavy radioactive elements (NOHRE) Bi, Th and U but principally the latter two. For the RS, the density was found to be the least and the total organic matter content the most. Bi was found to be negligibly present in all substrate types. The average Th and U mass fractions in the RS were higher than in the VS and about equal to their average mass fractions in the S. The VS mass fraction of Th was higher, and of U lower, than the mass fractions in the earth's crust. In fact for the fumaroles of one site, the average RS mass fractions of these elements were higher than the averaged values for S (without considering the statistical dispersion). The immobilization of the NOHRE in the RS is brought about by the bio-geochemical processes specific to these extremophiles. Its effectiveness is such that despite the small masses of these plants, it compares with, or may sometimes exceed, the immobilization of the NOHRE in the S by the abiotic and aggressive chemical action of the hot-springs. These results indicate that the fumarolic plants are able to transform the volcanic substrate to soil and to affect the NOHRE mass fractions even though these elements are not plant nutrients. Mirrored back to

  9. Evaluation of the biodegradation of Alaska North Slope oil in microcosms using the biodegradation model BIOB

    PubMed Central

    Torlapati, Jagadish; Boufadel, Michel C.

    2014-01-01

    We present the details of a numerical model, BIOB that is capable of simulating the biodegradation of oil entrapped in the sediment. The model uses Monod kinetics to simulate the growth of bacteria in the presence of nutrients and the subsequent consumption of hydrocarbons. The model was used to simulate experimental results of Exxon Valdez oil biodegradation in laboratory columns (Venosa et al., 2010). In that study, samples were collected from three different islands: Eleanor Island (EL107), Knight Island (KN114A), and Smith Island (SM006B), and placed in laboratory microcosms for a duration of 168 days to investigate oil bioremediation through natural attenuation and nutrient amendment. The kinetic parameters of the BIOB model were estimated by fitting to the experimental data using a parameter estimation tool based on Genetic Algorithms (GA). The parameter values of EL107 and KN114A were similar whereas those of SM006B were different from the two other sites; in particular biomass growth at SM006B was four times slower than at the other two islands. Grain size analysis from each site revealed that the specific surface area per unit mass of sediment was considerably lower at SM006B, which suggest that the surface area of sediments is a key control parameter for microbial growth in sediments. Comparison of the BIOB results with exponential decay curves fitted to the data indicated that BIOB provided better fit for KN114A and SM006B in nutrient amended treatments, and for EL107 and KN114A in natural attenuation. In particular, BIOB was able to capture the initial slow biodegradation due to the lag phase in microbial growth. Sensitivity analyses revealed that oil biodegradation at all three locations were sensitive to nutrient concentration whereas SM006B was sensitive to initial biomass concentration due to its slow growth rate. Analyses were also performed to compare the half-lives of individual compounds with that of the overall polycyclic aromatic hydrocarbons

  10. Shifts in Microbial Community Structure with Changes in Cathodic Potential in Marine Sediment Microcosms

    NASA Astrophysics Data System (ADS)

    Lam, B. R.; Rowe, A. R.; Nealson, K. H.

    2014-12-01

    Microorganisms comprise more than 90% of the biomass of the ocean. Their ability to thrive and survive in a wide range of environments from oligotrophic waters to the deep subsurface stems from the great metabolic versatility that exists among them. This metabolic versatility has further expanded with the discovery of extracellular electron transport (EET). EET is the capability of microorganisms to transfer electrons to and from insoluble substrates outside of the cell. Much of what is known about EET comes from studies of model metal reducing microorganisms in the groups Shewanellaceae and Geobacteraceae. However, EET is not limited to these metal reducing microorganisms, and may play a large role in the biogeochemical cycling of several elements. We have developed an electrochemical culturing technique designed to target microorganisms with EET ability and tested these methods in marine sediments. The use of electrodes allows for greater control and quantification of electrons flowing to insoluble substrates as opposed to insoluble substrates such as minerals that are often difficult to measure. We have recently shown that poising electrodes at different redox potentials will enrich for different microbial groups and thus possible metabolisms. In marine sediment microcosms, triplicate electrodes were poised at different cathodic (electron donating) potentials (-300, -400, -500 and -600 mV) and incubated for eight weeks. Community analysis of the 16S rRNA revealed that at lower negative potentials (-500 and -600 mV), more sulfate reducing bacteria in the class Deltaproteobacteria were enriched in comparison to the communities at -300 and -400 mV being dominated by microorganisms within Alphaproteobacteria, Gammaproteobacteria, and Clostridia. This can be explained by sulfate (abundant in seawater) becoming a more energetically favorable electron acceptor with lower applied potentials. In addition, communities at higher potentials showed greater enrichment of the

  11. Linking variations in sea spray aerosol particle hygroscopicity to composition during two microcosm experiments

    NASA Astrophysics Data System (ADS)

    Forestieri, Sara D.; Cornwell, Gavin C.; Helgestad, Taylor M.; Moore, Kathryn A.; Lee, Christopher; Novak, Gordon A.; Sultana, Camille M.; Wang, Xiaofei; Bertram, Timothy H.; Prather, Kimberly A.; Cappa, Christopher D.

    2016-07-01

    The extent to which water uptake influences the light scattering ability of marine sea spray aerosol (SSA) particles depends critically on SSA chemical composition. The organic fraction of SSA can increase during phytoplankton blooms, decreasing the salt content and therefore the hygroscopicity of the particles. In this study, subsaturated hygroscopic growth factors at 85 % relative humidity (GF(85 %)) of predominately submicron SSA particles were quantified during two induced phytoplankton blooms in marine aerosol reference tanks (MARTs). One MART was illuminated with fluorescent lights and the other was illuminated with sunlight, referred to as the "indoor" and "outdoor" MARTs, respectively. Optically weighted GF(85 %) values for SSA particles were derived from measurements of light scattering and particle size distributions. The mean optically weighted SSA diameters were 530 and 570 nm for the indoor and outdoor MARTs, respectively. The GF(85 %) measurements were made concurrently with online particle composition measurements, including bulk composition (using an Aerodyne high-resolution aerosol mass spectrometer) and single particle (using an aerosol time-of-flight mass spectrometer) measurement, and a variety of water-composition measurements. During both microcosm experiments, the observed optically weighted GF(85 %) values were depressed substantially relative to pure inorganic sea salt by 5 to 15 %. There was also a time lag between GF(85 %) depression and the peak chlorophyll a (Chl a) concentrations by either 1 (indoor MART) or 3-to-6 (outdoor MART) days. The fraction of organic matter in the SSA particles generally increased after the Chl a peaked, also with a time lag, and ranged from about 0.25 to 0.5 by volume. The observed depression in the GF(85 %) values (relative to pure sea salt) is consistent with the large observed volume fractions of non-refractory organic matter (NR-OM) comprising the SSA. The GF(85 %) values exhibited a reasonable negative

  12. Linking Stoichiometric Homeostasis of Microorganisms with Soil Phosphorus Dynamics in Wetlands Subjected to Microcosm Warming

    PubMed Central

    Wang, Hang; Li, HongYi; Zhang, ZhiJian; Muehlbauer, Jeffrey D.; He, Qiang; Xu, XinHua; Yue, ChunLei; Jiang, DaQian

    2014-01-01

    Soil biogeochemical processes and the ecological stability of wetland ecosystems under global warming scenarios have gained increasing attention worldwide. Changes in the capacity of microorganisms to maintain stoichiometric homeostasis, or relatively stable internal concentrations of elements, may serve as an indicator of alterations to soil biogeochemical processes and their associated ecological feedbacks. In this study, an outdoor computerized microcosm was set up to simulate a warmed (+5°C) climate scenario, using novel, minute-scale temperature manipulation technology. The principle of stoichiometric homeostasis was adopted to illustrate phosphorus (P) biogeochemical cycling coupled with carbon (C) dynamics within the soil-microorganism complex. We hypothesized that enhancing the flux of P from soil to water under warming scenarios is tightly coupled with a decrease in homeostatic regulation ability in wetland ecosystems. Results indicate that experimental warming impaired the ability of stoichiometric homeostasis (H) to regulate biogeochemical processes, enhancing the ecological role of wetland soil as an ecological source for both P and C. The potential P flux from soil to water ranged from 0.11 to 34.51 mg m−2 d−1 in the control and 0.07 to 61.26 mg m−2 d−1 in the warmed treatment. The synergistic function of C-P acquisition is an important mechanism underlying C∶P stoichiometric balance for soil microorganisms under warming. For both treatment groups, strongly significant (p<0.001) relationships fitting a negative allometric power model with a fractional exponent were found between n-HC∶P (the specialized homeostatic regulation ability as a ratio of soil highly labile organic carbon to dissolved reactive phosphorus in porewater) and potential P flux. Although many factors may affect soil P dynamics, the n-HC∶P term fundamentally reflects the stoichiometric balance or interactions between the energy landscape (i.e., C) and flow of resources

  13. Feasible pickup from intact ossicular chain with floating piezoelectric microphone

    PubMed Central

    2012-01-01

    Objectives Many microphones have been developed to meet with the implantable requirement of totally implantable cochlear implant (TICI). However, a biocompatible one without destroying the intactness of the ossicular chain still remains under investigation. Such an implantable floating piezoelectric microphone (FPM) has been manufactured and shows an efficient electroacoustic performance in vitro test at our lab. We examined whether it pick up sensitively from the intact ossicular chain and postulated whether it be an optimal implantable one. Methods Animal controlled experiment: five adult cats (eight ears) were sacrificed as the model to test the electroacoustic performance of the FPM. Three groups were studied: (1) the experiment group (on malleus): the FPM glued onto the handle of the malleus of the intact ossicular chains; (2) negative control group (in vivo): the FPM only hung into the tympanic cavity; (3) positive control group (Hy-M30): a HiFi commercial microphone placed close to the site of the experiment ear. The testing speaker played pure tones orderly ranged from 0.25 to 8.0 kHz. The FPM inside the ear and the HiFi microphone simultaneously picked up acoustic vibration which recorded as .wav files to analyze. Results The FPM transformed acoustic vibration sensitively and flatly as did the in vitro test across the frequencies above 2.0 kHz, whereas inefficiently below 1.0 kHz for its overloading mass. Although the HiFi microphone presented more efficiently than the FPM did, there was no significant difference at 3.0 kHz and 8.0 kHz. Conclusions It is feasible to develop such an implantable FPM for future TICIs and TIHAs system on condition that the improvement of Micro Electromechanical System and piezoelectric ceramic material technology would be applied to reduce its weight and minimize its size. PMID:22353161

  14. An integrated workflow for characterizing intact phosphoproteins from complex mixtures

    PubMed Central

    Wu, Si; Yang, Feng; Zhao, Rui; Tolić, Nikola; Robinson, Errol W.; Camp, David; Smith, Richard D.; Paša-Tolić, Ljiljana

    2014-01-01

    The phosphorylation of any site on a given protein can affect its activity, degradation rate, ability to dock with other proteins or bind divalent cations, and/or its localization. These effects can operate within the same protein; in fact, multisite phosphorylation is a key mechanism for achieving signal integration in cells. Hence, knowing the overall phosphorylation signature of a protein is essential for understanding the "state" of a cell. However, current technologies to monitor the phosphorylation status of proteins are inefficient at determining the relative stoichiometries of phosphorylation at multiple sites. Here we report a new capability for comprehensive liquid chromatography mass spectrometry (LC/MS) analysis of intact phosphoproteins. The technology platform built upon integrated bottom-up and top-down approach that is facilitated by intact protein reversed-phase (RP)LC concurrently coupled with Fourier transform ion cyclotron resonance (FTICR) MS and fraction collection. As the use of conventional RPLC systems for phosphopeptide identification has proven challenging due to the formation of metal ion complexes at various metal surfaces during LC/MS and ESI-MS analysis, we have developed a “metal-free” RPLC-ESI-MS platform for phosphoprotein characterization. This platform demonstrated a significant sensitivity enhancement for phosphorylated casein proteins enriched from a standard protein mixture and revealed the presence of over 20 casein isoforms arising from genetic variants with varying numbers of phosphorylation sites. The integrated workflow was also applied to an enriched yeast phosphoproteome to evaluate the feasibility of this strategy for characterizing complex biological systems, and revealed ~16% of the detected yeast proteins to have multiple phosphorylation isoforms. Intact protein LC/MS platform for characterization of combinatorial posttranslational modifications (PTMs), with special emphasis on multisite phosphorylation, holds

  15. Comparison of Microcosm Tests and a Field Demonstration of Cometabolic Air Sparging With Propane for the Bioremediation of Trichloroethylene and cis-Dichloroethylene

    NASA Astrophysics Data System (ADS)

    Timmins, B.; Dolan, M. E.; Tovannabootr, A.; Azizian, M.; Semprini, L.; Magar, V. S.; Leeson, A.

    2001-12-01

    Cometabolic air sparging (CAS) is an innovative form of conventional air sparging, and is designed to degrade or remove chlorinated aliphatic hydrocarbon compounds (CAHs) in groundwater and to potentially treat these contaminants in the vadose zone. A CAS demonstration was conducted at McClellan AFB, California, for removal of chloroethenes (TCE, cis-DCE) from groundwater using propane as the cometabolic substrate. In support of this field demonstration both groundwater and vadose zone microcosm studies were performed. The microcosms were created with groundwater and aquifer materials from the demonstration site. Concentrations of compounds in the microcosms were created to mimic conditions where the demonstration was performed. The microcosms were used to test the potential of the propane-utilizers to transform the CAHs of interest, and determine their nutrient requirements while transforming these compounds. Results from the first season of field-testing showed propane-utilizers could be effectively stimulated in the saturated zone with repeated intermediate sparging of propane and air. The lag time for effective propane utilization to be observed in the field was about 30 to 40 days, while in laboratory microcosms the lag period was about 12 days. Consistent with the field tests the groundwater microcosms showed cis-DCE was more rapidly transformed than TCE. Microcosm tests also indicated that propane inhibited the transformation of cis-DCE and TCE, and as observed in the field, most of the transformation of these compounds occurred after propane was reduced to low concentrations. In the field demonstration propane utilization rates and rates of CAH removal slowed after three to four months of repeated propane additions, which coincided with the depletion of nitrogen (as nitrate) in the treatment zone. Similar results were obtained with repeated additions of propane to the microcosms. In the field test ammonia was added to the propane/air mixture to provide a

  16. Controlled therapy by imaging of functional structures of intact liver

    NASA Astrophysics Data System (ADS)

    Wang, W.; Zhuang, Feng Y.; Ruan, G.; Kakihana, Yasuyuki; Krug, A.; Kessler, Manfred D.

    2000-04-01

    Ligustrazine, a Chinese herb medicine has been used to treat the diseases of cardiovascular and cerebral vascular diseases in China by Chinese traditional physicians or many years. Recently, results showed that ligustrazine is a powerful hepatic vasodilator. It can greatly change the blood supply of the tissues. Due to micro-optical tissue sensor developed recently it became possible to image functional structures of tissue on the level of intact blood capillaries. In our experiment we used the Oxyscan in order to study the effect of Ligustrazine on the oxygen supply of rat liver.

  17. Fast Imaging of Intact and Shattered Cryogenic Neon Pellets

    SciTech Connect

    Wang, Zhehui; Combs, Stephen Kirk; Baylor, Larry R; Foust, Charles R; Lyttle, Mark S; Meitner, Steven J; Rasmussen, David A

    2014-01-01

    Compact condensed-matter injection technologies are increasingly used in magnetic fusion. One recent application is in disruption mitigation. An imaging system with less-than-100- m- and sub- s-resolution is described and used to characterize intact and shattered cryogenic neon pellets. Shattered pellets contain fine particles ranging from tens of m to about 7 mm. Time-of-flight analyses indicate that pellets could slow down if hitting the wall of the guide tube. Fast high-resolution imaging systems are thus useful to neon and other condensed-matter injector development.

  18. Fast imaging of intact and shattered cryogenic neon pellets

    SciTech Connect

    Wang, Zhehui; Combs, S. K.; Baylor, L. R.; Foust, C. R.; Lyttle, M. S.; Meitner, S. J.; Rasmussen, D. A.

    2014-11-15

    Compact condensed-matter injection technologies are increasingly used in magnetic fusion. One recent application is in disruption mitigation. An imaging system with less-than-100-µm- and sub-µs-resolution is described and used to characterize intact and shattered cryogenic neon pellets. Shattered pellets contain fine particles ranging from tens of µm to about 7 mm. Time-of-flight analyses indicate that pellets could slow down if hitting the wall of the guide tube. Fast high-resolution imaging systems are thus useful to neon and other condensed-matter injector development.

  19. Imaging of Intact Tissue Sections: Moving beyond the Microscope*

    PubMed Central

    Seeley, Erin H.; Schwamborn, Kristina; Caprioli, Richard M.

    2011-01-01

    MALDI-imaging MS is a new molecular imaging technology for direct in situ analysis of thin tissue sections. Multiple analytes can be monitored simultaneously without prior knowledge of their identities and without the need for target-specific reagents such as antibodies. Imaging MS provides important insights into biological processes because the native distributions of molecules are minimally disturbed, and histological features remain intact throughout the analysis. A wide variety of molecules can be imaged, including proteins, peptides, lipids, drugs, and metabolites. Several specific examples are presented to highlight the utility of the technology. PMID:21632549

  20. Physiological characterization of motor unit properties in intact cats.

    PubMed

    O'Donovan, M J; Hoffer, J A; Loeb, G E

    1983-02-01

    Single motor units were isolated in intact cats, by microstimulation through chronically implanted microwires in the L5 ventral roots. Motor unit axonal and mechanical properties were obtained by stimulus-triggered averaging the signals from an implanted femoral nerve recording cuff and patellar tendon force transducer. All unit types were sampled with this technique, and it was also possible to stimulate in isolation an axon whose ventral root spike was recorded during treadmill locomotion. A new technique was described, spike-triggered microstimulation, for verifying the identity of a stimulated and a recorded axon.

  1. Fast imaging of intact and shattered cryogenic neon pellets.

    PubMed

    Wang, Zhehui; Combs, S K; Baylor, L R; Foust, C R; Lyttle, M S; Meitner, S J; Rasmussen, D A

    2014-11-01

    Compact condensed-matter injection technologies are increasingly used in magnetic fusion. One recent application is in disruption mitigation. An imaging system with less-than-100-µm- and sub-µs-resolution is described and used to characterize intact and shattered cryogenic neon pellets. Shattered pellets contain fine particles ranging from tens of µm to about 7 mm. Time-of-flight analyses indicate that pellets could slow down if hitting the wall of the guide tube. Fast high-resolution imaging systems are thus useful to neon and other condensed-matter injector development.

  2. Multivariate analysis of the impacts of the turbine fuel JP-4 in a microcosm toxicity test with implications for the evaluation of ecosystem dynamics and risk assessment.

    PubMed

    Landis, W G; Matthews, R A; Markiewicz, A J; Matthews, G B

    1993-12-01

    Turbine fuels are often the only aviation fuel available in most of the world. Turbine fuels consist of numerous constituents with varying water solubilities, volatilities and toxicities. This study investigates the toxicity of the water soluble fraction (WSF) of JP-4 using the Standard Aquatic Microcosm (SAM). Multivariate analysis of the complex data, including the relatively new method of nonmetric clustering, was used and compared to more traditional analyses. Particular emphasis is placed on ecosystem dynamics in multivariate space.The WSF is prepared by vigorously mixing the fuel and the SAM microcosm media in a separatory funnel. The water phase, which contains the water-soluble fraction of JP-4 is then collected. The SAM experiment was conducted using concentrations of 0.0, 1.5 and 15% WSF. The WSF is added on day 7 of the experiments by removing 450 ml from each microcosm including the controls, then adding the appropriate amount of toxicant solution and finally bringing the final volume to 3 L with microcosm media. Analysis of the WSF was performed by purge and trap gas chromatography. The organic constituents of the WSF were not recoverable from the water column within several days of the addition of the toxicant. However, the impact of the WSF on the microcosm was apparent. In the highest initial concentration treatment group an algal bloom ensued, generated by the apparent toxicity of the WSF of JP-4 to the daphnids. As the daphnid populations recovered the algal populations decreased to control values. Multivariate methods clearly demonstrated this initial impact along with an additional oscillation seperating the four treatment groups in the latter segment of the experiment. Apparent recovery may be an artifact of the projections used to describe the multivariate data. The variables that were most important in distinguishing the four groups shifted during the course of the 63 day experiment. Even this simple microcosm exhibited a variety of dynamics

  3. 46 CFR 178.325 - Intact stability requirements for a sailing vessel.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...) Commanding Officer, Marine Safety Center, may prescribe additional or different stability requirements for a... 46 Shipping 7 2010-10-01 2010-10-01 false Intact stability requirements for a sailing vessel. 178... VESSELS (UNDER 100 GROSS TONS) INTACT STABILITY AND SEAWORTHINESS Intact Stability Standards §...

  4. 46 CFR 178.325 - Intact stability requirements-monohull sailing vessels.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... protected waters or partially protected waters. (d) The Commanding Officer, Marine Safety Center, may... 46 Shipping 7 2014-10-01 2014-10-01 false Intact stability requirements-monohull sailing vessels... PASSENGER VESSELS (UNDER 100 GROSS TONS) INTACT STABILITY AND SEAWORTHINESS Intact Stability Standards §...

  5. Microcosm experiments to control anaerobic redox conditions when studying the fate of organic micropollutants in aquifer material

    NASA Astrophysics Data System (ADS)

    Barbieri, Manuela; Carrera, Jesús; Sanchez-Vila, Xavier; Ayora, Carlos; Cama, Jordi; Köck-Schulmeyer, Marianne; López de Alda, Miren; Barceló, Damià; Tobella Brunet, Joana; Hernández García, Marta

    2011-11-01

    The natural processes occurring in subsurface environments have proven to effectively remove a number of organic pollutants from water. The predominant redox conditions revealed to be one of the controlling factors. However, in the case of organic micropollutants the knowledge on this potential redox-dependent behavior is still limited. Motivated by managed aquifer recharge practices microcosm experiments involving aquifer material, settings potentially feasible in field applications, and organic micropollutants at environmental concentrations were carried out. Different anaerobic redox conditions were promoted and sustained in each set of microcosms by adding adequate quantities of electron donors and acceptors. Whereas denitrification and sulfate-reducing conditions are easily achieved and maintained, Fe- and Mn-reduction are strongly constrained by the slower dissolution of the solid phases commonly present in aquifers. The thorough description and numerical modeling of the evolution of the experiments, including major and trace solutes and dissolution/precipitation of solid phases, have been proven necessary to the understanding of the processes and closing the mass balance. As an example of micropollutant results, the ubiquitous beta-blocker atenolol is completely removed in the experiments, the removal occurring faster under more advanced redox conditions. This suggests that aquifers constitute a potentially efficient alternative water treatment for atenolol, especially if adequate redox conditions are promoted during recharge and long enough residence times are ensured.

  6. Decomposition of leaves of the metallophyte Arabidopsis halleri in soil microcosms: fate of Zn and Cd from plant residues.

    PubMed

    Boucher, Uriel; Lamy, Isabelle; Cambier, Philippe; Balabane, May

    2005-05-01

    In order to better understand the fate of metals during the biodegradation of organic matter in soils, an in vitro incubation experiment was conducted with metal-rich and metal-free leaves of Arabidopsis halleri introduced in a non-contaminated soil. During incubation of these microcosms, we followed the partitioning of Zn and Cd between the solution and their solid components, by determining the metal contents of six soil fractions and dissolved metals after granulo-densimetric separations at selected times. Microbial biomass and exchangeable metals in K(2)SO(4) solutions were also determined at the same times, and two main stages were identified. The first one takes place after a fast abiotic transfer of Zn and Cd from readily soluble plant tissues onto fine soil constituents, keeping metals away from the liquid phase: during about 14 days, microbial biomass increased as well as metal contents of some soil fractions, particularly those rich in particulate organic matter. During the second stage, between 14 and 60 days and for the metal-rich microcosms, Zn and Cd contents in solution increased, while microbial biomass decreased instead of staying constant as in control. A change of Zn and Cd speciation is assumed, from non-toxic adsorbed forms to more toxic species in solution. Remaining metal-rich plant residues seem to create a stable organic C compartment in the soil.

  7. Biotic and abiotic interactions in aquatic microcosms determine fate and toxicity of Ag nanoparticles. Part 1. Aggregation and dissolution.

    PubMed

    Unrine, Jason M; Colman, Benjamin P; Bone, Audrey J; Gondikas, Andreas P; Matson, Cole W

    2012-07-03

    To better understand their fate and toxicity in aquatic environments, we compared the aggregation and dissolution behavior of gum arabic (GA) and polyvinylpyrrolidone (PVP) coated Ag nanoparticles (NPs) in aquatic microcosms. There were four microcosm types: surface water; water and sediment; water and aquatic plants; or water, sediment, and aquatic plants. Dissolution and aggregation behavior of AgNPs were examined using ultracentrifugation, ultrafiltration, and asymmetrical flow field flow fractionation coupled to ultraviolet-visible spectroscopy, dynamic and static laser light scattering, and inductively coupled plasma mass spectrometry. Plants released dissolved organic matter (DOM) into the water column either through active or passive processes in response to Ag exposure. This organic matter fraction readily bound Ag ions. The plant-derived DOM had the effect of stabilizing PVP-AgNPs as primary particles, but caused GA-AgNPs to be removed from the water column, likely by dissolution and binding of released Ag ions on sediment and plant surfaces. The destabilization of the GA-AgNPs also corresponded with X-ray absorption near edge spectroscopy results which suggest that 22-28% of the particulate Ag was associated with thiols and 5-14% was present as oxides. The results highlight the potential complexities of nanomaterial behavior in response to biotic and abiotic modifications in ecosystems, and may help to explain differences in toxicity of Ag observed in realistic exposure media compared to simplified laboratory exposures.

  8. Bioaugmentation of copper polluted soil microcosms with Amycolatopsis tucumanensis to diminish phytoavailable copper for Zea mays plants.

    PubMed

    Albarracín, Virginia Helena; Amoroso, María Julia; Abate, Carlos Mauricio

    2010-03-01

    Amycolatopsis tucumanensis DSM 45259, the strain of a recently recognized novel species of the genus Amycolatopsis with remarkable copper resistance, was used to bioaugment soil microcosms experimentally polluted with copper and for studying the ability of this strain to effectively diminish phytoavailable copper from soils. Our results demonstrated that A. tucumanensis was capable of profusely colonizing both, copper polluted and non-polluted soil. Copper bioimmobilization ability of A. tucumanensis on soil was assessed measuring the bioavailable copper in the soil solution extracted from polluted soil by using chemical and physical methods and, in this way, 31% lower amounts of the metal were found in soil solution as compared to non-bioaugmented soil. The results obtained when using Zea mays as bioindicator correlated well with the values obtained by the chemical and physical procedures: 20% and 17% lower tissue contents of copper were measured in roots and leaves, respectively. These data confirmed the efficiency of the bioremediation process using A. tucumanensis and at the same time proved that chemical, physical and biological methods for assessing copper bioavailability in soils were correlated. These results suggest a potential use of this strain at large scale in copper soil bioremediation strategies. To our knowledge, this work is the first to apply and to probe the colonization ability of an Amycolatopsis strain in soil microcosms and constitutes the first application of an Amycolatopsis strain on bioremediation of polluted soils.

  9. Influence of salinity and organic nutrient concentration on survival and growth of Vibrio cholerae in aquatic microcosms.

    PubMed Central

    Singleton, F L; Attwell, R W; Jangi, M S; Colwell, R R

    1982-01-01

    Laboratory microcosms were employed to evaluate the influence of selected environmental parameters, organic nutrient concentration, and salinity on the growth and survival of a toxigenic strain of Vibrio cholerae LA4808. Over the range conditions tested, this strain of V. cholerae showed maximum response as determined by increased plate counts and direct microscopic counts in microcosms prepared with a chemically defined sea salts solution at a salinity of 25%, but with lower or higher salinity levels, the maximum population size declined. When added organic concentrations of less than 1,000 micrograms/liter were present, a marked salinity effect on the growth of V. cholerae was detected. However, at or above an organic nutrient concentration of 1,000 micrograms/liter, the need for an optimum salinity level was spared. From the results of this study, it is concluded that V. cholerae can grow under conditions of organic nutrient concentration and salinity typical of estuaries. Results obtained support the hypothesis that V. cholerae is an autochthonous member of the estuarine microbial community. PMID:6896621

  10. Speedy speciation in a bacterial microcosm: new species can arise as frequently as adaptations within a species

    PubMed Central

    Koeppel, Alexander F; Wertheim, Joel O; Barone, Laura; Gentile, Nicole; Krizanc, Danny; Cohan, Frederick M

    2013-01-01

    Microbiologists are challenged to explain the origins of enormous numbers of bacterial species worldwide. Contributing to this extreme diversity may be a simpler process of speciation in bacteria than in animals and plants, requiring neither sexual nor geographical isolation between nascent species. Here, we propose and test a novel hypothesis for the extreme diversity of bacterial species—that splitting of one population into multiple ecologically distinct populations (cladogenesis) may be as frequent as adaptive improvements within a single population's lineage (anagenesis). We employed a set of experimental microcosms to address the relative rates of adaptive cladogenesis and anagenesis among the descendants of a Bacillus subtilis clone, in the absence of competing species. Analysis of the evolutionary trajectories of genetic markers indicated that in at least 7 of 10 replicate microcosm communities, the original population founded one or more new, ecologically distinct populations (ecotypes) before a single anagenetic event occurred within the original population. We were able to support this inference by identifying putative ecotypes formed in these communities through differences in genetic marker association, colony morphology and microhabitat association; we then confirmed the ecological distinctness of these putative ecotypes in competition experiments. Adaptive mutations leading to new ecotypes appeared to be about as common as those improving fitness within an existing ecotype. These results suggest near parity of anagenesis and cladogenesis rates in natural populations that are depauperate of bacterial diversity. PMID:23364353

  11. Evaluating macroinvertebrate population and community level effects in outdoor microcosms: Use of in situ bioassays and multivariate analysis

    SciTech Connect

    Shaw, J.L.; Manning, J.P.

    1996-05-01

    Evaluating toxicant effects on aquatic communities is difficult due to the ecological complexity at higher levels of organization. Two methods were assessed to improve the understanding of effects on macroinvertebrate communities in aquatic model ecosystems. First, in situ bioassay population effects were used to interpret effects at a higher organization level. Second, canonical discriminant analysis was used to investigate effects on community structure. In situ bioassays were conducted on six occasions in 17-m{sup 3} microcosms treated with copper sulfate. Macroinvertebrates occurring naturally in the microcosms were monitored. Epibenthic in situ bioassays were conducted using Caenis sp. (Ephemeroptera) and Hyalella azteca (Amphipoda) and a water column bioassay was conducted using Notonectidae (Hemiptera). Survival and growth were assessed after 3 d. Effects of copper on both notonectidae and Caenis were observed following application. However, the final Caenis epibenthic bioassays indicated that potential for recovery and survival was {ge}95%. Potential for recovery was less distinct in the water column bioassays. Copper effects also occurred on epibenthic macroinvertebrate populations and communities. Only four taxa, including Caenis, distinguished community differences among copper treatments soon after application. Later, communities showed similarities to the pretreatment bioassay. However, actual recovery was less apparent than the potential for recovery indicated by the bioassays, and community differences due to Caenis persisted.

  12. Detection by denaturing gradient gel electrophoresis of ammonia-oxidizing bacteria in microcosms of crude oil-contaminated mangrove sediments.

    PubMed

    dos Santos, A C F; Marques, E L S; Gross, E; Souza, S S; Dias, J C T; Brendel, M; Rezende, R P

    2012-01-27

    Currently, the effect of crude oil on ammonia-oxidizing bacterium communities from mangrove sediments is little understood. We studied the diversity of ammonia-oxidizing bacteria in mangrove microcosm experiments using mangrove sediments contaminated with 0.1, 0.5, 1, 2, and 5% crude oil as well as non-contaminated control and landfarm soil from near an oil refinery in Camamu Bay in Bahia, Brazil. The evolution of CO(2) production in all crude oil-contaminated microcosms showed potential for mineralization. Cluster analysis of denaturing gradient gel electrophoresis-derived samples generated with primers for gene amoA, which encodes the functional enzyme ammonia monooxygenase, showed differences in the sample contaminated with 5% compared to the other samples. Principal component analysis showed divergence of the non-contaminated samples from the 5% crude oil-contaminated sediment. A Venn diagram generated from the banding pattern of PCR-denaturing gradient gel electrophoresis was used to look for operational taxonomic units (OTUs) in common. Eight OTUs were found in non-contaminated sediments and in samples contaminated with 0.5, 1, or 2% crude oil. A Jaccard similarity index of 50% was found for samples contaminated with 0.1, 0.5, 1, and 2% crude oil. This is the first study that focuses on the impact of crude oil on the ammonia-oxidizing bacterium community in mangrove sediments from Camamu Bay.

  13. Degradation of 1,1,2,2-tetrachloroethane and accumulation of vinyl chloride in wetland sediment microcosms and in situ porewater: Biogeochemical controls and associations with microbial communities

    USGS Publications Warehouse

    Lorah, M.M.; Voytek, M.A.

    2004-01-01

    The biodegradation pathways of 1,1,2,2-tetrachloroethane (TeCA) and 1,1,2-trichloroethane (112TCA) and the associated microbial communities in anaerobic wetland sediments were evaluated using concurrent geochemical and genetic analyses over time in laboratory microcosm experiments. Experimental results were compared to in situ porewater data in the wetland to better understand the factors controlling daughter product distributions in a chlorinated solvent plume discharging to a freshwater tidal wetland at Aberdeen Proving Ground, Maryland. Microcosms constructed with wetland sediment from two sites showed little difference in the initial degradation steps of TeCA, which included simultaneous hydrogenolysis to 112TCA and dichloroelimination to 1,2-dichloroethene (12DCE). The microcosms from the two sites showed a substantial difference, however, in the relative dominance of subsequent dichloroelimination of 112TCA. A greater dominance of 112TCA dichloroelimination in microcosms constructed with sediment that was initially iron-reducing and subsequently simultaneously iron-reducing and methanogenic caused approximately twice as much vinyl chloride (VC) production as microcosms constructed with sediment that was methanogenic only throughout the incubation. The microcosms with higher VC production also showed substantially more rapid VC degradation. Field measurements of redox-sensitive constituents, TeCA, and its anaerobic degradation products along flowpaths in the wetland porewater also showed greater production and degradation of VC with concurrent methanogenesis and iron reduction. Molecular fingerprinting indicated that bacterial species [represented by a peak at a fragment size of 198 base pairs (bp) by MnlI digest] are associated with VC production from 112TCA dichloroelimination, whereas methanogens (190 and 307 bp) from the Methanococcales or Methanobacteriales family are associated with VC production from 12DCE hydrogenolysis. Acetate-utilizing methanogens

  14. Degradation of 1,1,2,2-tetrachloroethane and accumulation of vinyl chloride in wetland sediment microcosms and in situ porewater: biogeochemical controls and associations with microbial communities

    USGS Publications Warehouse

    Lorah, Michelle M.; Voytek, Mary A.

    2004-01-01

    The biodegradation pathways of 1,1,2,2-tetrachloroethane (TeCA) and 1,1,2-trichloroethane (112TCA) and the associated microbial communities in anaerobic wetland sediments were evaluated using concurrent geochemical and genetic analyses over time in laboratory microcosm experiments. Experimental results were compared to in situ porewater data in the wetland to better understand the factors controlling daughter product distributions in a chlorinated solvent plume discharging to a freshwater tidal wetland at Aberdeen Proving Ground, Maryland. Microcosms constructed with wetland sediment from two sites showed little difference in the initial degradation steps of TeCA, which included simultaneous hydrogenolysis to 112TCA and dichloroelimination to 1,2-dichloroethene (12DCE). The microcosms from the two sites showed a substantial difference, however, in the relative dominance of subsequent dichloroelimination of 112TCA. A greater dominance of 112TCA dichloroelimination in microcosms constructed with sediment that was initially iron-reducing and subsequently simultaneously iron-reducing and methanogenic caused approximately twice as much vinyl chloride (VC) production as microcosms constructed with sediment that was methanogenic only throughout the incubation. The microcosms with higher VC production also showed substantially more rapid VC degradation. Field measurements of redox-sensitive constituents, TeCA, and its anaerobic degradation products along flowpaths in the wetland porewater also showed greater production and degradation of VC with concurrent methanogenesis and iron reduction.Molecular fingerprinting indicated that bacterial species [represented by a peak at a fragment size of 198 base pairs (bp) by MnlI digest] are associated with VC production from 112TCA dichloroelimination, whereas methanogens (190 and 307 bp) from the Methanococcales or Methanobacteriales family are associated with VC production from 12DCE hydrogenolysis. Acetate-utilizing methanogens

  15. Final Technical Report: Optimization and Directed, Natural Evolution of Biologically-Mediated Chromate Reduction in Subsurface Soil Microcosms

    SciTech Connect

    Thompson, Dorothea K; Wickham, Gene S; Layton, Alice C

    2012-07-27

    The U.S. Department of Energy (DOE) is faced with the complex challenge of remediating or containing the various mixed wastes present in the subsurface environments of numerous DOE sites. The development of scientifically grounded strategies for the effective management and reclamation of these contaminated sites requires fundamental knowledge on the composition, dynamics, and metabolic potential of indigenous microbial communities, which are of primary importance in the fate and transport of heavy metals and radionuclides in subsurface environments. To date, the complex effect of environmental (both geochemical and biological) parameters on the bioremediative potential of subsurface microbial populations is only partially understood; this is primarily because the majority of microbial ecological studies have focused only on a qualitative analysis of subsurface microbial diversity, while the impact of quantitative changes in microbial communities as a function of environmental factors has been ignored. The project described here directly addresses the need for a more comprehensive, molecular understanding of how microbial growth and activity quantitatively relate to mineral and contaminant biotransformation (Science Element: Subsurface Microbial Ecology and Community, Notice DE-FG02-06ER06-12). The proposed study uses a truly novel combination of standard molecular phylogenetic analyses, rRNA-targeted fluorescence in situ hybridization, and mass spectrometry (MS)-based proteomics to investigate the biological response to experimentally controlled conditions and the concomitant effect on chromate reduction in situ. This response will be characterized in terms of microbial community structure (principally, population number and spatial distribution) and community proteome dynamics. Towards this overarching goal, we will (1) set up aerobic and anaerobic laboratory microcosms derived from subsurface soil collected from a chromate [Cr(VI)]-contaminated DOE site, and

  16. Selective ion changes during spontaneous mitochondrial transients in intact astrocytes.

    PubMed

    Azarias, Guillaume; Chatton, Jean-Yves

    2011-01-01

    The bioenergetic status of cells is tightly regulated by the activity of cytosolic enzymes and mitochondrial ATP production. To adapt their metabolism to cellular energy needs, mitochondria have been shown to exhibit changes in their ionic composition as the result of changes in cytosolic ion concentrations. Individual mitochondria also exhibit spontaneous changes in their electrical potential without altering those of neighboring mitochondria. We recently reported that individual mitochondria of intact astrocytes exhibit spontaneous transient increases in their Na(+) concentration. Here, we investigated whether the concentration of other ionic species were involved during mitochondrial transients. By combining fluorescence imaging methods, we performed a multiparameter study of spontaneous mitochondrial transients in intact resting astrocytes. We show that mitochondria exhibit coincident changes in their Na(+) concentration, electrical potential, matrix pH and mitochondrial reactive oxygen species production during a mitochondrial transient without involving detectable changes in their Ca(2+) concentration. Using widefield and total internal reflection fluorescence imaging, we found evidence for localized transient decreases in the free Mg(2+) concentration accompanying mitochondrial Na(+) spikes that could indicate an associated local and transient enrichment in the ATP concentration. Therefore, we propose a sequential model for mitochondrial transients involving a localized ATP microdomain that triggers a Na(+)-mediated mitochondrial depolarization, transiently enhancing the activity of the mitochondrial respiratory chain. Our work provides a model describing ionic changes that could support a bidirectional cytosol-to-mitochondria ionic communication.

  17. Bacterial clearance in the intact and regenerating liver

    SciTech Connect

    Gross, K.; Katz, S.; Dunn, S.P.; Cikrit, D.; Rosenthal, R.; Grosfeld, J.L.

    1985-08-01

    The Kupffer cells in the liver play an important role in reticuloendothelial system (RES) function by clearing particulate matter and bacteria from the blood stream. While hepatocyte regeneration and function have been extensively studied following partial hepatectomy, little information is available concerning RES function in the regenerating liver. This study investigates hepatic RES function by evaluating bacterial clearance (live E. coli) in the intact and regenerating liver. Thirty-four young male Sprague Dawley rats were studied. Twenty-two animals underwent a standard 70% partial hepatectomy using ligature technique and 12 had a sham operation. Both groups of rats received 10(9) organism of TVS labeled E coli, intravenously at 24 hours, 72 hours, 2 1/2 weeks, and 6 weeks postoperatively. Rats were killed 10 minutes following injection and liver, lung, spleen, and kidney harvested, fixed, and radioactivity was determined using a scintillation spectrometer interfaced with a micro-computer counting the TVS radiolabel. The total organ count of trapped bacteria in liver in partially hepatectomized rats was lower than intact controls at 24 hours, but was similar at 72 hours, 2 1/2 weeks, and 6 weeks. Partial hepatectomy increased the amount of bacterial trapping in the lung at 24 hours and 72 hours and returned to normal at 2 1/2 weeks and 6 weeks. Splenic activity was increased following hepatectomy at 2 1/2 weeks. Renal clearance was increased at 72 hours and 2 1/2 weeks.

  18. Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution.

    PubMed

    Sylwestrak, Emily Lauren; Rajasethupathy, Priyamvada; Wright, Matthew Arnot; Jaffe, Anna; Deisseroth, Karl

    2016-02-11

    In recently developed approaches for high-resolution imaging within intact tissue, molecular characterization over large volumes has been largely restricted to labeling of proteins. But volumetric nucleic acid labeling may represent a far greater scientific and clinical opportunity, enabling detection of not only diverse coding RNA variants but also non-coding RNAs. Moreover, scaling immunohistochemical detection to large tissue volumes has limitations due to high cost, limited renewability/availability, and restricted multiplexing capability of antibody labels. With the goal of versatile, high-content, and scalable molecular phenotyping of intact tissues, we developed a method using carbodiimide-based chemistry to stably retain RNAs in clarified tissue, coupled with amplification tools for multiplexed detection. The resulting technology enables robust measurement of activity-dependent transcriptional signatures, cell-identity markers, and diverse non-coding RNAs in rodent and human tissue volumes. The growing set of validated probes is deposited in an online resource for nucleating related developments from across the scientific community.

  19. STREPTOMYCIN FORMATION BY INTACT MYCELIUM OF STREPTOMYCES GRISEUS

    PubMed Central

    Nomi, Ryosaku

    1963-01-01

    Nomi, Ryosaku (Rutgers, The State University, New Brunswick, N.J.). Streptomycin formation by intact mycelium of Streptomyces griseus. J. Bacteriol. 86:1220–1230. 1963.—A study was made of streptomycin formation by intact mycelium of Streptomyces griseus 107 grown in glucose-yeast extract medium. When mycelium harvested after 24, 48, and 72 hr was compared, the earliest growth showed the highest activity in producing streptomycin from glucose. The concentration of streptomycin in the mycelium was higher in the older growth. Calcium chloride had a remarkable effect in increasing streptomycin production from the precursors in the mycelium, especially when the mycelium was grown for 48 hr or longer. The effect of calcium chloride cannot be attributed to the precipitation of an excess of inorganic phosphate in the medium. Glucose, fructose, glycerol, lactic acid, glucosamine, streptidine, and inositol stimulated streptomycin formation, whereas gluconic acid, glucuronic acid, streptamine, and strepturea did not. When 24-hr-old mycelium was suspended and shaken in 0.5% glucose solution, the antibiotic precursors necessary to produce streptomycin were found mainly in the supernatant of the culture rather than in the mycelium. The supernatant included some substance which had a weak antibiotic activity. This substance was less basic than streptomycin and was transformed to streptomycin with a remarkable increase in antibiotic activity. PMID:14086093

  20. Microarray Noninvasive Neuronal Seizure Recordings from Intact Larval Zebrafish

    PubMed Central

    Meyer, Michaela; Dhamne, Sameer C.; LaCoursiere, Christopher M.; Tambunan, Dimira; Poduri, Annapurna; Rotenberg, Alexander

    2016-01-01

    Zebrafish epilepsy models are emerging tools in experimental epilepsy. Zebrafish larvae, in particular, are advantageous because they can be easily genetically altered and used for developmental and drug studies since agents applied to the bath penetrate the organism easily. Methods for electrophysiological recordings in zebrafish are new and evolving. We present a novel multi-electrode array method to non-invasively record electrical activity from up to 61 locations of an intact larval zebrafish head. This method enables transcranial noninvasive recording of extracellular field potentials (which include multi-unit activity and EEG) to identify epileptic seizures. To record from the brains of zebrafish larvae, the dorsum of the head of an intact larva was secured onto a multi-electrode array. We recorded from individual electrodes for at least three hours and quantified neuronal firing frequency, spike patterns (continuous or bursting), and synchrony of neuronal firing. Following 15 mM potassium chloride- or pentylenetetrazole-infusion into the bath, spike and burst rate increased significantly. Additionally, synchrony of neuronal firing across channels, a hallmark of epileptic seizures, also increased. Notably, the fish survived the experiment. This non-invasive method complements present invasive zebrafish neurophysiological techniques: it affords the advantages of high spatial and temporal resolution, a capacity to measure multiregional activity and neuronal synchrony in seizures, and fish survival for future experiments, such as studies of epileptogenesis and development. PMID:27281339

  1. Analytical strategies for the global quantification of intact proteins.

    PubMed

    Collier, Timothy S; Muddiman, David Charles

    2012-09-01

    The quantification of intact proteins is a relatively recent development in proteomics. In eukaryotic organisms, proteins are present as multiple isoforms as the result of variations in genetic code, alternative splicing, post-translational modification and other processing events. Understanding the identities and biological functions of these isoforms and how their concentrations vary across different states is the central goal of proteomics. To date, the bulk of proteomics research utilizes a "bottom-up" approach, digesting proteins into their more manageable constitutive peptides, but sacrificing information about the specific isoform and combinations of post-translational modifications present on the protein. Very specific strategies for protein quantification such as the enzyme-linked immunosorbent assay and Western blot are commonplace in laboratories and clinics, but impractical for the study of global biological changes. Herein, we describe strategies for the quantification of intact proteins, their distinct advantages, and challenges to their employment. Techniques contained in this review include the more traditional and widely employed methodology of differential gel electrophoresis and more recently developed mass spectrometry-based techniques including metabolic labeling, chemical labeling, and label-free methodologies.

  2. Nickel in plants: I. Uptake kinetics using intact soybean seedlings.

    PubMed

    Cataldo, D A; Garland, T R; Wildung, R E

    1978-10-01

    The absorption of Ni(2+) by 21-day-old soybean plants (Glycine max cv. Williams) was investigated with respect to its concentration dependence, transport kinetics, and interactions with various nutrient cations. Nickel absorption, measured as a function of concentration (0.02 to 100 mum), demonstrated the presence of multiple absorption isotherms. Each of the three isotherms conforms to Michaelis-Menten kinetics; kinetic constants are reported for uptake by the intact plant and for transfer from root to shoot tissues. The absorption of Ni(2+) by the intact plant and its transfer from root to shoot were inhibited by the presence of Cu(2+), Zn(2+), Fe(2+), and Co(2+). Competition kinetic studies showed Cu(2+) and Zn(2+) to inhibit Ni(2+) absorption competitively, suggesting that Ni(2+), Cu(2+), and Zn(2+) are absorbed using the same carrier site. Calculated K(m) and K(i) constants for Ni(2+) in the presence and absence of Cu(2+) were 6.1 and 9.2 mum, respectively, whereas K(m) and K(i) constants were calculated to be 6.7 and 24.4 mum, respectively, for Ni(2+) in the presence and absence of Zn(2+). The mechanism of inhibition of Ni(2+) in the presence of Fe(2+) and Co(2+) was not resolved by classical kinetic relationships.

  3. Effects of Triclocarban on Intact Immature Male Rat

    PubMed Central

    Duleba, Antoni J.; Ahmed, Mohamed I.; Sun, Meng; Gao, Allen C.; Villanueva, Jesus; Conley, Alan J.; Turgeon, Judith L.; Benirschke, Kurt; Gee, Nancy A.; Chen, Jiangang; Green, Peter G.; Lasley, Bill L.

    2011-01-01

    Triclocarban (TCC; 3,4,4′-trichlorocarbanilide) is an antimicrobial agent used widely in various personal hygiene products including soaps. Recently, TCC has been shown to enhance testosterone-induced effects in vitro and to enlarge accessory sex organs in castrated male rats. This study was designed to evaluate the effects of TCC on intact age-matched male rats and on human prostate LNCaP and C4–2B cells. Seven-week-old male Sprague-Dawley rats received either a normal diet or a diet supplemented with TCC (0.25% in diet) for 10 days. Triclocarban induced hyperplasia of accessory sex organs in the absence of significant qualitative histological changes. Serum luteinizing hormone (LH) and testosterone were not significantly altered by TCC treatment. In prostate cancer-derived LNCaP and C4–2B cells, TCC potentiated androgen actions via androgen receptor-dependent actions. In conclusion, TCC significantly affects intact male reproductive organs and potentiates androgen effects in prostate cancer cells. PMID:20889956

  4. The phosphorylation of coated membrane proteins in intact neurons

    PubMed Central

    1986-01-01

    To complement studies that have demonstrated the prominent phosphorylation of a 50-kD coated vesicle polypeptide in vitro, we have evaluated the phosphorylation of coated membrane proteins in intact cells. A co-assembly assay has been devised in which extracts of cultured rat sympathetic neurons labeled with [32P]-Pi were combined with unlabeled carrier bovine brain coat proteins and reassembled coat structures were isolated by gradient centrifugation. Two groups of phosphorylated polypeptides, of 100-110 kD (pp100-110) and 155 kD (pp155) apparent molecular mass, were incorporated into reassembled coats. The neuronal pp100-110 are structurally and functionally related to the 100-110-kD component of the bovine brain assembly protein (AP), a protein complex that also contains 50-kD and 16.5-kD components and is characterized by its ability to promote the reassembly of clathrin coat structures under physiological conditions of pH and ionic strength (Zaremba, S. and J. H. Keen, 1983, J. Cell Biol., 97:1337-1348). The neuronal pp155 detected in reassembled coat structures was readily observable in total extracts of [32P]-Pi-labeled neurons dissolved in SDS-containing buffer. A bovine brain counterpart to the neuronal pp155 was also observed when brain coated vesicles were subjected to two- dimensional gel electrophoresis. Phosphoserine was the predominant phosphoaminoacid found in both the pp100 and pp155. A structural and functional counterpart to the 50-kD brain assembly polypeptide (AP50) was also identified in these neurons. Although the brain AP50 is prominently phosphorylated by an endogenous protein kinase in isolated coated vesicle preparations, the neuronal AP50 was not detectably phosphorylated in intact cells as assessed by two-dimensional non- equilibrium pH gradient gel electrophoresis of labeled cells dissolved directly in SDS-containing buffers. These results demonstrate that the bovine brain assembly polypeptides of 50 kD and 100-110 kD that we have

  5. Intact Conceptual Priming in the Absence of Declarative Memory

    PubMed Central

    Levy, D.A.; Stark, C.E.L.; Squire, L.R.

    2009-01-01

    Priming is an unconscious (nondeclarative) form of memory whereby identification or production of an item is improved by an earlier encounter. It has been proposed that declarative memory and priming might be related—for example, that conceptual priming results in more fluent processing, thereby providing a basis for familiarity judgments. In two experiments, we assessed conceptual priming and recognition memory across a 5-min interval in 5 memory-impaired patients. All patients exhibited fully intact priming in tests of both free association (study tent; at test, provide an association to canvas) and category verification (study lemon; at test, decide: Is lemon a type of fruit?). Yet the 2 most severely amnesic patients performed at chance on matched tests of recognition memory. These findings count against the notion that conceptual priming provides feelings of familiarity that can support accurate recognition judgments. We suggest that priming is inaccessible to conscious awareness and does not influence declarative memory. PMID:15447639

  6. Bursty gene expression in the intact mammalian liver

    PubMed Central

    Halpern, Keren Bahar; Tanami, Sivan; Landen, Shanie; Chapal, Michal; Szlak, Liran; Hutzler, Anat; Nizhberg, Anna; Itzkovitz, Shalev

    2015-01-01

    Summary Bursts of nascent mRNA have been shown to lead to substantial cell-cell variation in unicellular organisms, facilitating diverse responses to environmental challenges. It is unknown whether similar bursts and gene-expression noise occur in mammalian tissues. To address this, we combine single molecule transcript counting with dual-color labeling and quantification of nascent mRNA to characterize promoter states, transcription rates and transcript lifetimes in the intact mouse liver. We find that liver gene expression is highly bursty, with promoters stochastically switching between transcriptionally active and inactive states. Promoters of genes with short mRNA lifetimes are active longer, facilitating rapid response while reducing burst-associated noise. Moreover, polyploid hepatocytes exhibit less noise than diploid hepatocytes, suggesting a possible benefit to liver polyploidy. Thus temporal averaging and liver polyploidy dampen the intrinsic variability associated with transcriptional bursts. Our approach can be used to study transcriptional bursting in diverse mammalian tissues. PMID:25728770

  7. Rhesus monkey brain imaging through intact skull with thermoacoustic tomography.

    PubMed

    Xu, Yuan; Wang, Lihong V

    2006-03-01

    Two-dimensional microwave-induced thermoacoustic tomography (TAT) is applied to imaging the Rhesus monkey brain through the intact skull. To reduce the wavefront distortion caused by the skull, only the low-frequency components of the thermoacoustic signals (< 1 MHz) are used to reconstruct the TAT images. The methods of signal processing and image reconstruction are validated by imaging a lamb kidney. The resolution of the system is found to be 4 mm when we image a 1-month-old monkey head containing inserted needles. We also image the coronal and axial sections of a 7-month-old monkey head. Brain features that are 3 cm deep in the head are imaged clearly. Our results demonstrate that TAT has potential for use in portable, cost-effective imagers for pediatric brains.

  8. Calcium Activation Profile In Electrically Stimulated Intact Rat Heart Cells

    NASA Astrophysics Data System (ADS)

    Geerts, Hugo; Nuydens, Rony; Ver Donck, Luc; Nuyens, Roger; De Brabander, Marc; Borgers, Marcel

    1988-06-01

    Recent advances in fluorescent probe technology and image processing equipment have made available the measurement of calcium in living systems on a real-time basis. We present the use of the calcium indicator Fura-2 in intact normally stimulated rat heart cells for the spatial and dynamic measurement of the calcium excitation profile. After electric stimulation (1 Hz), the activation proceeds from the center of the myocyte toward the periphery. Within two frame times (80 ms), the whole cell is activated. The activation is slightly faster in the center of the cell than in the periphery. The mean recovery time is 200-400 ms. There is no difference along the cell's long axis. The effect of a beta-agonist and of a calcium antagonist is described.

  9. Temperature dependence of the zeta potential in intact natural carbonates

    NASA Astrophysics Data System (ADS)

    Al Mahrouqi, Dawoud; Vinogradov, Jan; Jackson, Matthew D.

    2016-11-01

    The zeta potential is a measure of the electrical charge on mineral surfaces and is an important control on subsurface geophysical monitoring, adsorption of polar species in aquifers, and rock wettability. We report the first measurements of zeta potential in intact, water-saturated, natural carbonate samples at temperatures up to 120°C. The zeta potential is negative and decreases in magnitude with increasing temperature at low ionic strength (0.01 M NaCl, comparable to potable water) but is independent of temperature at high ionic strength (0.5 M NaCl, comparable to seawater). The equilibrium calcium concentration resulting from carbonate dissolution also increases with increasing temperature at low ionic strength but is independent of temperature at high ionic strength. The temperature dependence of the zeta potential is correlated with the temperature dependence of the equilibrium calcium concentration and shows a Nernstian linear relationship. Our findings are applicable to many subsurface carbonate rocks at elevated temperature.

  10. Citrate synthesis in intact rat-liver mitochondria is irreversible.

    PubMed

    Greksák, M; Lopes-Cardozo, M; van den Bergh, S G

    1982-02-01

    Rat-liver mitochondria were incubated with [1,5-14C]citrate in the presence of fluorocitrate to block its oxidation in the Krebs cycle. The reaction products were analysed enzymatically and by anion-exchange chromatography. Incorporation of 14C into acetyl-L-carnitine or ketone bodies via a backward action of citrate synthase was not observed. The optimal rate of citrate synthesis from pyruvate and malate in the presence of fluorocitrate was 15 nmol . mg-1 min-1. In the absence of fluorocitrate, but in the presence of malonate, citrate was oxidized to succinate at a rate of 4 nmol . mg-1 . min-1. We conclude that the synthesis of citrate by intact rat liver mitochondria is an irreversible process. The possible mechanism underlying this phenomenon and the consequence for metabolic regulation are discussed.

  11. Probing Metabolism in the Intact Retina Using Stable Isotope Tracers.

    PubMed

    Du, Jianhai; Linton, Jonathan D; Hurley, James B

    2015-01-01

    Vertebrate retinas have several characteristics that make them particularly interesting from a metabolic perspective. The retinas have a highly laminated structure, high energy demands, and they share several metabolic features with tumors, such as a strong Warburg effect and abundant pyruvate kinase M2 isoform expression. The energy demands of retinas are both qualitatively and quantitatively different in light and darkness and metabolic dysfunction could cause retinal degeneration. Stable isotope-based metabolic analysis with mass spectrometry is a powerful tool to trace the dynamic metabolic reactions and reveal novel metabolic pathways within cells and between cells in retina. Here, we describe methods to quantify retinal metabolism in intact retinas and discuss applications of these methods to the understanding of neuron-glia interaction, light and dark adaptation, and retinal degenerative diseases.

  12. Perforation of Meckel's diverticulum by an intact fish bone

    PubMed Central

    Mouawad, Nicolas J; Hammond, Stephen; Kaoutzanis, Christodoulos

    2013-01-01

    Meckel's diverticulum is the most common congenital anomaly of the gastrointestinal tract, with an overall incidence of approximately 2.2%. It is generally noted incidentally during laparotomy for management of other abdominal pathology. Complications are infrequent, developing in 4% of individuals with this abnormality, and are usually seen in childhood. Herein, we discuss the case of a 52-year-old Caucasian man presenting with a 1-day history of worsening central and right-sided abdominal pain. Initial evaluation posed a broad differential however, following conservative measures and unremarkable plain films, the patient developed peritoneal signs necessitating operative intervention. During diagnostic laparoscopy, a Meckel's diverticulum was noted to be inflamed and perforated by an intact fish bone. The patient was treated successfully with a segmental resection and primary anastomosis, and had an uneventful postoperative recovery. PMID:23429021

  13. Effects of fumigants on microbial diversity and persistence of E. coli O15:H7 in contrasting soil microcosms.

    PubMed

    Ibekwe, A Mark; Ma, J

    2011-09-01

    Persistence of E. coli O157 in the environment is a serious public health concern. However, little is known about the persistence of this pathogen after exposure to chemical compounds like fumigants in the environment. In this study, the persistence behavior of pathogenic E. coli O157:H7 was investigated after fumigation with methyl bromide (MeBr; CH(3)Br) and methyl iodide (MeI, iodomethane; CH(3)I) in soil microcosms under laboratory conditions. Our goal was to assess changes in soil microbial community structure and persistence of E. coli O157:H7 in microcosm soils after fumigation. PCR was used to amplify 16S rRNA genes from total bacterial community composition, and the products were subjected to denaturing gradient gel electrophoresis (DGGE). Microbial diversity as determined by DGGE was significantly higher in clay soil than sandy soil. Real-time PCR and plate counts were used to quantify the survival of E. coli O157:H7 in the two soils after fumigation with MeBr and MeI. The survival of the pathogen was higher in the non fumigated controls than the fumigated treatments when determined using plate counts. These results were confirmed by real time PCR analysis targeting the stx1, stx2, and the eae genes. E. coli O157:H7 survived for about 35 days when determined using the plate count method but continued to be detected at about the detection limit of 10(2) by real time PCR for more than 86 days. Our results showed that there was a fast inactivation of the pathogen during the first 35 days. After this period, a small proportion of the pathogen continued to survive in the soil microcosms. Subsequent enrichment of soil samples and immunomagnetic separation revealed the continuous presence of viable cells after 86 days of incubation. The data presented contribute to a better understanding of the behavior of E. coli O157:H7 in soil, and showed the need for more investigation of the role of dormant cells in soil that may be a source for recontamination of the

  14. Zeta Potential in Intact Natural Carbonates at Elevated Temperatures

    NASA Astrophysics Data System (ADS)

    Al-Mahrouqi, D.; Vinogradov, J.; Jackson, M.

    2015-12-01

    Measurements of zeta potential have been used to monitor subsurface flows in many natural brine systems. Numerous studies report zeta potentials in carbonates using crushed samples at low ionic strength and laboratory temperatures. However, natural brines have much higher salinity; moreover, temperatures are considerably higher in many subsurface settings. The variation of zeta potentials with temperature has not been examined in natural carbonates. We report zeta potential values interpreted from streaming potential measurements in two intact carbonate rock samples, saturated with artificial brines at elevated temperatures. We measure streaming potential using an experimental set-up that incorporates in-situ measurements of saturated rock conductivity, brine temperature, brine pH, brine electrical conductivity, pressure difference and voltage at temperatures up to 120oC. The streaming potential measurements are complemented with brine effluent studies. We find that the interpreted zeta potential is negative and decreases in magnitude with increasing temperature at low ionic strength (0.01M) and independent of temperature at high ionic strength (0.5M); consistent with published zeta potential in intact natural sandstones. The concentration of Ca2+ (main potential determining ion) also decreases with temperature at low ionic strength, but remains constant at high ionic strength. The temperature dependence of the zeta potential is consistent between two different natural carbonate samples and can be explained by the temperature dependence of pCa2+. We suggest that zeta potential of carbonate is independent of temperature or pH when pCa2+ remains constant. A linear variation of pH vs. pCa2+ is exhibited, at ambient and elevated temperatures, when pCa2+ is allowed to change with pH. This linear variation explains the numerous published data that shows apparent relationship between zeta potential of carbonates and pH.

  15. Isolation of intact sub-dermal secretory cavities from Eucalyptus

    PubMed Central

    2010-01-01

    Background The biosynthesis of plant natural products in sub-dermal secretory cavities is poorly understood at the molecular level, largely due to the difficulty of physically isolating these structures for study. Our aim was to develop a protocol for isolating live and intact sub-dermal secretory cavities, and to do this, we used leaves from three species of Eucalyptus with cavities that are relatively large and rich in essential oils. Results Leaves were digested using a variety of commercially available enzymes. A pectinase from Aspergillus niger was found to allow isolation of intact cavities after a relatively short incubation (12 h), with no visible artifacts from digestion and no loss of cellular integrity or cavity contents. Several measurements indicated the potential of the isolated cavities for further functional studies. First, the cavities were found to consume oxygen at a rate that is comparable to that estimated from leaf respiratory rates. Second, mRNA was extracted from cavities, and it was used to amplify a cDNA fragment with high similarity to that of a monoterpene synthase. Third, the contents of the cavity lumen were extracted, showing an unexpectedly low abundance of volatile essential oils and a sizeable amount of non-volatile material, which is contrary to the widely accepted role of secretory cavities as predominantly essential oil repositories. Conclusions The protocol described herein is likely to be adaptable to a range of Eucalyptus species with sub-dermal secretory cavities, and should find wide application in studies of the developmental and functional biology of these structures, and the biosynthesis of the plant natural products they contain. PMID:20807444

  16. Survival and alteration of the plasmid-containing microorganism Escherichia coli Z905/pPHL7 introduced into manmade closed aquatic microcosms

    NASA Astrophysics Data System (ADS)

    Boyandin, A. N.; Lobova, T. I.; Popova, L. Yu.; Pechurkin, N. S.

    It has been demonstrated that the transgenic microorganism Escherichia coli Z905/pPHL7 (Ap rLux +) can exist for a long time at an elevated concentration of mineral salts. The microorganism was introduced into microcosms with sterile brackish water (salinity variable from 21 to 22 gl -1) taken from Lake Shira (Khakasia, Russia). The survival of the microorganism was estimated both by measuring the growth of the colonies on solid nutrient media and by the bioluminescence exhibited by the transgenic strain in samples from the microcosms and in the enrichment culture with the added selective factor - ampicillin (50 μg/ml). In the enrichment culture, the bioluminescent signal was registered through the 160-day experiment. It has been shown that in the closed microcosms with brackish water the E. coli strain becomes heterogeneous in its ampicillin resistance. The populations of the transgenic strain were mainly represented by isolates able to persist in the medium containing 50 μg/ml, but there were also the cells (about 10%) with the threshold of ampicillin resistance not more than 0.05 μg/ml. Thus, it was shown that in the microcosms with brackish water and in the absence of the selective factor the transgenic strain survives and retails the recombinant plasmid.

  17. Biodegradation of high concentrations of mixed polycyclic aromatic hydrocarbons by indigenous bacteria from a river sediment: a microcosm study and bacterial community analysis.

    PubMed

    Muangchinda, Chanokporn; Yamazoe, Atsushi; Polrit, Duangporn; Thoetkiattikul, Honglada; Mhuantong, Wuttichai; Champreda, Verawat; Pinyakong, Onruthai

    2017-02-01

    This study assessed the biodegradation of mixtures of polycyclic aromatic hydrocarbons (PAHs) by indigenous bacteria in river sediment. Microcosms were constructed from sediment from the Chao Phraya River (the main river in Thailand) by supplementation with high concentrations of fluorene, phenanthrene, pyrene (300 mg kg(-1) of each PAH), and acenaphthene (600 mg kg(-1)). Fluorene and phenanthrene were completely degraded, whereas 50% of the pyrene and acenaphthene were removed at the end of the incubation period (70 days). Community analyses revealed the dynamics of the bacterial profiles in the PAH-degrading microcosms after PAH exposure. Actinobacteria predominated and became significantly more abundant in the microcosms after 14 days of incubation at room temperature under aerobic conditions. Furthermore, the remaining PAHs and alpha diversity were positively correlated. The sequencing of clone libraries of the PAH-RHDα genes also revealed that the dioxygenase genes of Mycobacterium sp. comprised 100% of the PAH-RHDα library at the end of the microcosm setup. Moreover, two PAH-degrading Actinobacteria (Arthrobacter sp. and Rhodococcus ruber) were isolated from the original sediment sample and showed high activity in the degradation of phenanthrene and fluorene in liquid cultivation. This study reveals that indigenous bacteria had the ability to degrade high concentrations of mixed PAHs and provide clear evidence that Actinobacteria may be potential candidates to play a major role in PAH degradation in the river sediment.

  18. Dynamic changes in the structure of microbial communities in Baltic Sea coastal seawater microcosms modified by crude oil, shale oil or diesel fuel.

    PubMed

    Viggor, Signe; Juhanson, Jaanis; Jõesaar, Merike; Mitt, Mario; Truu, Jaak; Vedler, Eve; Heinaru, Ain

    2013-08-25

    The coastal waters of the Baltic Sea are constantly threatened by oil spills, due to the extensive transportation of oil products across the sea. To characterise the hydrocarbon-degrading bacterial community of this marine area, microcosm experiments on diesel fuel, crude oil and shale oil were performed. Analysis of these microcosms, using alkane monooxygenase (alkB) and 16S rRNA marker genes in PCR-DGGE experiments, demonstrated that substrate type and concentration strongly influence species composition and the occurrence of alkB genes in respective oil degrading bacterial communities. Gammaproteobacteria (particularly the genus Pseudomonas) and Alphaproteobacteria were dominant in all microcosms treated with oils. All alkB genes carried by bacterial isolates (40 strains), and 8 of the 11 major DGGE bands from the microcosms, had more than 95% sequence identity with the alkB genes of Pseudomonas fluorescens. However, the closest relatives of the majority of sequences (54 sequences from 79) of the alkB gene library from initially collected seawater DNA were Actinobacteria. alkB gene expression, induced by hexadecane, was recorded in isolated bacterial strains. Thus, complementary culture dependent and independent methods provided a more accurate picture about the complex seawater microbial communities of the Baltic Sea.

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

    NASA Astrophysics Data System (ADS)

    Mautner, Michael N.

    2002-03-01

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

  20. CHANGES IN ENANTIOMERIC FRACTIONS DURING MICROBIAL REDUCTIVE DECHLORINATION OF PCB132, PCB149, AND AROCLOR 1254 IN LAKE HARTWELL SEDIMENT MICROCOSMS

    EPA Science Inventory

    Enantioselectivity of microbial reductive dechlorination of chiral PCBs in sediments from Lake Hartwell, SC, was determined by microcosm studies and enantiomer-specific GC analysis. Sediments from two locations in the vicinity of the highest levels of PCB contamination were used...

  1. Draft Genome Sequence of Clostridium sp. Strain W14A Isolated from a Cellulose-Degrading Biofilm in a Landfill Leachate Microcosm

    PubMed Central

    2016-01-01

    Here, we report the draft genome of Clostridium sp. strain W14A, isolated from the anaerobic, cellulolytic biofilm of a cotton string sample incubated in a landfill leachate microcosm. The draft genome comprises 131 contigs, 3,823,510 bp, 51.5% G+C content, and 4,119 predicted coding domain sequences. PMID:27660778

  2. Survival, growth, and body residues of Hyalella azteca (Saussure) exposed to fipronil contaminated sediments from non-vegetated and vegetated microcosms

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We assessed chronic effects of fipronil and metabolite contaminated sediments from non-vegetated and Thallia dealbata vegetated wetland microcosms on Hyalella azteca during wet and dry exposures. Mean sediment concentrations (ng g-1) ranged from 0.72-1.26, 0.01-0.69, 0.07-0.23, and 0.49-7.87 for fip...

  3. The relative impacts of spills of two alternative fuels on the microalgae of a sandy site: a microcosm study.

    PubMed

    Suderman, Keith; Thistle, David

    2004-09-01

    Electric power generation in the United States uses substantial amounts of fuel oil #6. Orimulsion, an emulsion of bitumen, water, and a surfactant, is an alternative. A portion of the information that managers need to compare the two fuels is their relative environmental impacts. Both fuels are shipped by sea, so the impact of spills on the marine benthos is a concern. We used microcosms to assess the relative impacts of simulated spills of these fuels on the microalgae of shallow subtidal sandy bottoms. Response variables included microalgal abundance, primary productivity, ratio of chlorophyll a to phaeophytin, and ratio of primary production to chlorophyll a. During our 88-day experiment, we found no significant differences between the fuels for any variable. We suggest that weathering before the spill reaches the shore removes the most toxic components, rendering the fuels essentially equal in their impact on benthic microalgae.

  4. Effects of reclamation on macrobenthic assemblages in the coastline of the Arabian Gulf: a microcosm experimental approach.

    PubMed

    Naser, Humood A

    2011-03-01

    Coastal reclamation and modifications are extensively carried out in Bahrain, which may physically smother the coastal and subtidal habitats resulting in changes to abundance and distribution of macrobenthic assemblages. A microcosm laboratory experiment using three common macrobenthic invertebrates from a proposed reclaimed coastal area was preformed to examine their responses to mud burial using marine sediment collected from a designated borrow area. Significant difference in numbers of survived organisms between control and experimental treatments with a survival percentage of 41.8% for all of the selected species was observed. The polychaete Perinereis nuntia showed the highest percentage of survival (57.1%) followed by the bivalve Tellinavaltonis (42.3%) and the gastropod Cerithidea cingulata (24.0%). Quantifying species responses to sediment burial resulted from dredging and reclamation will aid in predicting the expected ecological impacts associated with coastal developments and subsequently minimizing these impacts and maintaining a sustainable use of coastal and marine ecosystems in the Arabian Gulf.

  5. Metagenomic data of the bacterial community in coastal Gulf of Mexico sediment microcosms following exposure to Macondo oil (MC252)

    PubMed Central

    Koo, Hyunmin; Bej, Asim K.

    2015-01-01

    The data in this article includes the sequences of bacterial 16S rRNA gene from metagenome of Macondo oil (MC252)-treated and non-oil-treated sediment microcosms, collected from coastal Gulf of Mexico and Bayou La Batre, USA. Metacommunity DNA was PCR amplified with 341F and 907R oligonucleotide primers, targeting V3–V5 regions of the 16S rRNA gene. Data were generated by using bacterial tag-encoded FLX-amplicon pyrosequencing (bTEFAP) methodology and then processed using bioinformatics tools such as QIIME. The data information is deposited to NCBI׳s BioProject and BioSample and raw sequence files are available via NCBI׳s Sequence Read Archive (SRA) database. PMID:26858973

  6. Metagenomic data of the bacterial community in coastal Gulf of Mexico sediment microcosms following exposure to Macondo oil (MC252).

    PubMed

    Koo, Hyunmin; Bej, Asim K

    2016-03-01

    The data in this article includes the sequences of bacterial 16S rRNA gene from metagenome of Macondo oil (MC252)-treated and non-oil-treated sediment microcosms, collected from coastal Gulf of Mexico and Bayou La Batre, USA. Metacommunity DNA was PCR amplified with 341F and 907R oligonucleotide primers, targeting V3-V5 regions of the 16S rRNA gene. Data were generated by using bacterial tag-encoded FLX-amplicon pyrosequencing (bTEFAP) methodology and then processed using bioinformatics tools such as QIIME. The data information is deposited to NCBI׳s BioProject and BioSample and raw sequence files are available via NCBI׳s Sequence Read Archive (SRA) database.

  7. Use of Fixed-Film Bioreactors, in Situ Microcosms, and Molecular Biological Analyses to Evaluate Bioremediation of Chlorinated Benzenes By Indigenous Bacteria and a Bioaugmented Dechlorinating Consortium

    NASA Astrophysics Data System (ADS)

    Lorah, M. M.; Teunis, J. A.

    2014-12-01

    Evaluation of bioremediation is complicated by contaminant mixtures, high concentrations, variable site conditions, and multiple possible degradation pathways. In this study, fixed-film bioreactor experiments, in situ microcosms, and microbial analyses were utilized to evaluate both anaerobic and aerobic biodegradation processes for tri- and dichlorobenzene isomers, monochlorobenzene, and benzene in a wetland. Biofilm-based bioreactors provide a robust assessment tool because of their typically high degree of stability, even with major and repeated perturbations. Two bioreactor units seeded with an anaerobic dechlorinating consortium (WBC-2) and one unit seeded only with bacteria indigenous to the site were operated under flow-through conditions to compare biougmentation and natural attenuation. Electron donor levels were varied to fluctuate between anaerobic and aerobic conditions, and inflow concentrations of total chlorobenzenes were transitioned from 1-10 mg/L to 50-100 mg/L. Biodegradation resulted in removal efficiencies of 80 to 99 percent for the different compounds and inflow concentrations. Degradation efficiency in the native bioreactor was not impacted by cycling between anaerobic and aerobic conditions, although removal rates for monochlorobenzene and benzene increased under aerobic conditions. In situ microcosms were incubated below the wetland surface in sets of 3 treatments—unamended, biostimulated (lactate addition), and bioaugmented (WBC-2 and lactate). Additional treatment sets contained 13C-labeled contaminants to monitor for production of 13C-containing carbon dioxide and cellular material. Microcosm results verified that WBC-2 bioaugmentation can enhance biodegradation, with complete mineralization of chlorobenzene and benzene in bioaugmented and native treatments. Microbial analyses using QuantArrayTM for functional and taxonomic genes indicated potential for co-occurrence of anaerobic and aerobic biodegradation. Compared to the unamended

  8. Microbial community characterization and functional gene quantification in RDX-degrading microcosms derived from sediment and groundwater at two naval sites.

    PubMed

    Wilson, Fernanda Paes; Cupples, Alison M

    2016-08-01

    The explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has long been recognized as a problematic environmental pollutant, and efforts to remediate contaminated soils, sediments, and groundwater have been going on for decades. In recent years, much interest has focused on using bioremediation to clean up these sites. The current study investigated the microorganisms (16S rRNA genes, Illumina) and functional genes (xenA, xenB, and xplA) linked to RDX biodegradation in microcosms composed of sediment or groundwater from two Navy sites. For this, experiments included sediment samples from three depths (5 to 30 ft) from two wells located in one Navy site. In addition, the groundwater upstream and downstream of an emulsified oil biobarrier was examined from another Navy site. Further, for the groundwater experiments, the effect of glucose addition was explored. For the sediment experiments, the most enriched phylotypes during RDX degradation varied over time, by depth and well locations. However, several trends were noted, including the enrichment of Pseudomonas, Rhodococcus, Arthrobacter, and Sporolactobacillus in the sediment microcosms. For the groundwater-based experiments, Pseudomonas, unclassified Rhodocyclaceae, Sphingomonas, and Rhodococcus were also highly abundant during RDX degradation. The abundance of both xplA and xenA significantly increased during RDX degradation compared to the control microcosms for many treatments (both groundwater and sediment microcosms). In a limited number of microcosms, the copy number of the xenB gene increased. Phylotype data were correlated with functional gene data to highlight potentially important biomarkers for RDX biodegradation at these two Navy sites.

  9. Responses of the Anaerobic Bacterial Community to Addition of Organic C in Chromium(VI)- and Iron(III)-Amended Microcosms

    PubMed Central

    Kourtev, Peter S.; Nakatsu, Cindy H.; Konopka, Allan

    2006-01-01

    Chromium (VI) is toxic to microorganisms and can inhibit the biodegradation of organic pollutants in contaminated soils. We used microcosms amended with either glucose or protein (to drive bacterial community change) and Fe(III) (to stimulate iron-reducing bacteria) to study the effect of various concentrations of Cr(VI) on anaerobic bacterial communities. Microcosms were destructively sampled based on microbial activity (measured as evolution of CO2) and analyzed for the following: (i) dominant bacterial community by PCR-denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene; (ii) culturable Cr-resistant bacteria; and (iii) enrichment of iron-reducing bacteria of the Geobacteraceae family by real-time PCR. The addition of organic C stimulated the activities of anaerobic communities. Cr(VI) amendment resulted in lower rates of CO2 production in glucose microcosms and a slow mineralization phase in protein-amended microcosms. Glucose and protein amendments selected for different bacterial communities. This selection was modified by the addition of Cr(VI), since some DGGE bands were intensified and new bands appeared in Cr(VI)-amended microcosms. A second dose of Cr(VI), added after the onset of activity, had a strong inhibitory effect when higher levels of Cr were added, indicating that the developing Cr-resistant communities had a relatively low tolerance threshold. Most of the isolated Cr-resistant bacteria were closely related to previously studied Cr-resistant anaerobes, such as Pantoea, Pseudomonas, and Enterobacter species. Geobacteraceae were not enriched during the incubation. The studied Cr(VI)-contaminated soil contained a viable anaerobic bacterial community; however, Cr(VI) altered its composition, which could affect the soil biodegradation potential. PMID:16391100

  10. Decay rates of faecal indicator bacteria from sewage and ovine faeces in brackish and freshwater microcosms with contrasting suspended particulate matter concentrations.

    PubMed

    Perkins, Tracy L; Perrow, Karen; Rajko-Nenow, Paulina; Jago, Colin F; Jones, Davey L; Malham, Shelagh K; McDonald, James E

    2016-12-01

    To safeguard human health, legislative measures require the monitoring of faecal indicator bacteria (FIB) concentrations in recreational and shellfish waters. Consequently, numerous studies have focussed on FIB survival in the water column and more recently in estuarine sediments. However, there is a paucity of information regarding the influence of contrasting suspended particulate matter (SPM) concentrations on the survival of FIB in the water column of estuaries. Here, microcosms containing freshwater or brackish water with low, high and extreme SPM concentrations were inoculated with sewage and ovine faeces and the decay rate of Escherichia coli, coliforms and enterococci were determined by enumeration over five consecutive days. E. coli derived from ovine faeces proliferated and persisted at high levels in both freshwater and brackish microcosms (no decay), whereas ovine enterococci demonstrated a net decay over the duration of the experiment. Furthermore, SPM concentration had a significant effect on the decay rates of both E. coli and enterococci from ovine faeces in brackish microcosms, but decay rate was greater at low SPM concentrations for E. coli, whereas the opposite was observed for enterococci, whose decay rates increased as SPM concentration increased. E. coli, enterococci and coliforms derived from wastewater demonstrated a net decay in both freshwater and brackish microcosms, with contrasting effects of SPM concentration on decay rate. In addition, some FIB groups demonstrated contrasting responses (decay or proliferation) in the first 24h following inoculation into freshwater versus brackish microcosms. Overall, SPM concentrations influenced the proliferation and decay rates of FIB in brackish waters, but had minimal influence in freshwater. These results demonstrate that the survival rates of FIB in aquatic environments are system specific, species and source dependent, and influenced by SPM concentration. This study has important implications

  11. Hindrance of 1,4-dioxane biodegradation in microcosms biostimulated with inducing or non-inducing auxiliary substrates.

    PubMed

    Li, Mengyan; Liu, Yuanyuan; He, Ya; Mathieu, Jacques; Hatton, James; DiGuiseppi, William; Alvarez, Pedro J J

    2017-04-01

    A microcosm study was conducted to assess two biostimulation strategies (relative to natural attenuation) to bioremediate 1,4-dioxane contamination at a site in west Texas. Dioxane concentrations were relatively low (<300 μg/L), which represents a potential challenge to sustain and induce specific degraders. Thus, biostimulation was attempted with an auxiliary substrate known to induce dioxane-degrading monooxygenases (i.e., tetrahydrohyran [THF]) or with a non-inducing growth substrate (1-butanol [1-BuOH]). Amendment of 1-BuOH (100 mg/L) to microcosms that were not oxygen-limited temporarily enhanced dioxane biodegradation by the indigenous microorganisms. However, this stimulatory effect was not sustained by repeated amendments, which might be attributed to i) the inability of 1-BuOH to induce dioxane-degrading enzymes, ii) curing of catabolic plasmids, iii) metabolic flux dilution and catabolite repression, and iv) increased competition by commensal bacteria that do not degrade dioxane. Experiments with the archetype dioxane degrader Pseudonocardia dioxanivorans CB1190 repeatedly amended with 1-BuOH (500 mg/L added weekly for 4 weeks) corroborated the partial curing of catabolic plasmids (9.5 ± 7.4% was the plasmid retention ratio) and proliferation of derivative segregants that lost their ability to degrade dioxane. Addition of THF (300 μg/L) also had limited benefit due to competitive inhibition; significant dioxane degradation occurred only when the THF concentration decreased below approximately 160 μg/L. Overall, these results illustrate the importance of considering the possibility of unintentional hindrance of catabolism associated with the addition of auxiliary carbon sources to bioremediate aquifers impacted with trace concentrations of dioxane.

  12. Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms.

    PubMed

    Hausmann, Bela; Knorr, Klaus-Holger; Schreck, Katharina; Tringe, Susannah G; Glavina Del Rio, Tijana; Loy, Alexander; Pester, Michael

    2016-10-01

    Dissimilatory sulfate reduction in peatlands is sustained by a cryptic sulfur cycle and effectively competes with methanogenic degradation pathways. In a series of peat soil microcosms incubated over 50 days, we identified bacterial consortia that responded to small, periodic additions of individual fermentation products (formate, acetate, propionate, lactate or butyrate) in the presence or absence of sulfate. Under sulfate supplementation, net sulfate turnover (ST) steadily increased to 16-174 nmol cm(-3) per day and almost completely blocked methanogenesis. 16S rRNA gene and cDNA amplicon sequencing identified microorganisms whose increases in ribosome numbers strongly correlated to ST. Natively abundant (⩾0.1% estimated genome abundance) species-level operational taxonomic units (OTUs) showed no significant response to sulfate. In contrast, low-abundance OTUs responded significantly to sulfate in incubations with propionate, lactate and butyrate. These OTUs included members of recognized sulfate-reducing taxa (Desulfosporosinus, Desulfopila, Desulfomonile, Desulfovibrio) and also members of taxa that are either yet unknown sulfate reducers or metabolic interaction partners thereof. Most responsive OTUs markedly increased their ribosome content but only weakly increased in abundance. Responsive Desulfosporosinus OTUs even maintained a constantly low population size throughout 50 days, which suggests a novel strategy of rare biosphere members to display activity. Interestingly, two OTUs of the non-sulfate-reducing genus Telmatospirillum (Alphaproteobacteria) showed strongly contrasting preferences towards sulfate in butyrate-amended microcosms, corroborating that closely related microorganisms are not necessarily ecologically coherent. We show that diverse consortia of low-abundance microorganisms can perform peat soil sulfate reduction, a process that exerts control on methane production in these climate-relevant ecosystems.

  13. Disturbance Promotes Non-Indigenous Bacterial Invasion in Soil Microcosms: Analysis of the Roles of Resource Availability and Community Structure

    PubMed Central

    Liu, Manqiang; Bjørnlund, Lisa; Rønn, Regin; Christensen, Søren; Ekelund, Flemming

    2012-01-01

    Background Invasion-biology is largely based on non-experimental observation of larger organisms. Here, we apply an experimental approach to the subject. By using microbial-based microcosm-experiments, invasion-biology can be placed on firmer experimental, and hence, less anecdotal ground. A better understanding of the mechanisms that govern invasion-success of bacteria in soil communities will provide knowledge on the factors that hinder successful establishment of bacteria artificially inoculated into soil, e.g. for remediation purposes. Further, it will yield valuable information on general principles of invasion biology in other domains of life. Methodology/Principal Findings Here, we studied invasion and establishment success of GFP-tagged Pseudomonas fluorescens DSM 50090 in laboratory microcosms during a 42-day period. We used soil heating to create a disturbance gradient, and hypothesized that increased disturbance would facilitate invasion; our experiments confirmed this hypothesis. We suggest that the key factors associated with the heating disturbance that explain the enhanced invasion success are increased carbon substrate availability and reduced diversity, and thus, competition- and predation-release. In a second experiment we therefore separated the effects of increased carbon availability and decreased diversity. Here, we demonstrated that the effect of the indigenous soil community on bacterial invasion was stronger than that of resource availability. In particular, introduced bacteria established better in a long term perspective at lower diversity and predation pressure. Conclusion We propose increased use of microbial systems, for experimental study of invasion scenarios. They offer a simple and cost-efficient way to study and understand biological invasion. Consequently such systems can help us to better predict the mechanisms controlling changes in stability of communities and ecosystems. This is becoming increasingly relevant since

  14. Response of Deep Subsurface Microbial Community to Different Carbon Sources and Electron Acceptors during ∼2 months Incubation in Microcosms

    PubMed Central

    Purkamo, Lotta; Bomberg, Malin; Nyyssönen, Mari; Ahonen, Lasse; Kukkonen, Ilmo; Itävaara, Merja

    2017-01-01

    Acetate plays a key role as electron donor and acceptor and serves as carbon source in oligotrophic deep subsurface environments. It can be produced from inorganic carbon by acetogenic microbes or through breakdown of more complex organic matter. Acetate is an important molecule for sulfate reducers that are substantially present in several deep bedrock environments. Aceticlastic methanogens use acetate as an electron donor and/or a carbon source. The goal of this study was to shed light on carbon cycling and competition in microbial communities in fracture fluids of Finnish crystalline bedrock groundwater system. Fracture fluid was anaerobically collected from a fracture zone at 967 m depth of the Outokumpu Deep Drill Hole and amended with acetate, acetate + sulfate, sulfate only or left unamended as a control and incubated up to 68 days. The headspace atmosphere of microcosms consisted of 80% hydrogen and 20% CO2. We studied the changes in the microbial communities with community fingerprinting technique as well as high-throughput 16S rRNA gene amplicon sequencing. The amended microcosms hosted more diverse bacterial communities compared to the intrinsic fracture zone community and the control treatment without amendments. The majority of the bacterial populations enriched with acetate belonged to clostridial hydrogenotrophic thiosulfate reducers and Alphaproteobacteria affiliating with groups earlier found from subsurface and groundwater environments. We detected a slight increase in the number of sulfate reducers after the 68 days of incubation. The microbial community changed significantly during the experiment, but increase in specifically acetate-cycling microbial groups was not observed. PMID:28265265

  15. Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms

    SciTech Connect

    Hausmann, Bela; Knorr, Klaus-Holger; Schreck, Katharina; Tringe, Susannah G.; Glavina del Rio, Tijana; Loy, Alexander; Pester, Michael

    2016-03-25

    A cryptic sulfur cycle and effectively competes with methanogenic degradation pathways sustains dissimilatory sulfate reduction in peatlands. In a series of peat soil microcosms incubated over 50 days, we identified bacterial consortia that responded to small, periodic additions of individual fermentation products (formate, acetate, propionate, lactate or butyrate) in the presence or absence of sulfate. Under sulfate supplementation, net sulfate turnover (ST) steadily increased to 16–174 nmol cm–3 per day and almost completely blocked methanogenesis. 16S rRNA gene and cDNA amplicon sequencing identified microorganisms whose increases in ribosome numbers strongly correlated to ST. Natively abundant (greater than or equal to0.1% estimated genome abundance) species-level operational taxonomic units (OTUs) showed no significant response to sulfate. In contrast, low-abundance OTUs responded significantly to sulfate in incubations with propionate, lactate and butyrate. These OTUs included members of recognized sulfate-reducing taxa (Desulfosporosinus, Desulfopila, Desulfomonile, Desulfovibrio) and also members of taxa that are either yet unknown sulfate reducers or metabolic interaction partners thereof. The most responsive OTUs markedly increased their ribosome content but only weakly increased in abundance. Responsive Desulfosporosinus OTUs even maintained a constantly low population size throughout 50 days, which suggests a novel strategy of rare biosphere members to display activity. Interestingly, two OTUs of the non-sulfate-reducing genus Telmatospirillum (Alphaproteobacteria) showed strongly contrasting preferences towards sulfate in butyrate-amended microcosms, corroborating that closely related microorganisms are not necessarily ecologically coherent. We show that diverse consortia of low-abundance microorganisms can perform peat soil sulfate reduction, a process that exerts control on methane production in these climate-relevant ecosystems.

  16. Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms

    DOE PAGES

    Hausmann, Bela; Knorr, Klaus-Holger; Schreck, Katharina; ...

    2016-03-25

    A cryptic sulfur cycle and effectively competes with methanogenic degradation pathways sustains dissimilatory sulfate reduction in peatlands. In a series of peat soil microcosms incubated over 50 days, we identified bacterial consortia that responded to small, periodic additions of individual fermentation products (formate, acetate, propionate, lactate or butyrate) in the presence or absence of sulfate. Under sulfate supplementation, net sulfate turnover (ST) steadily increased to 16–174 nmol cm–3 per day and almost completely blocked methanogenesis. 16S rRNA gene and cDNA amplicon sequencing identified microorganisms whose increases in ribosome numbers strongly correlated to ST. Natively abundant (greater than or equal to0.1%more » estimated genome abundance) species-level operational taxonomic units (OTUs) showed no significant response to sulfate. In contrast, low-abundance OTUs responded significantly to sulfate in incubations with propionate, lactate and butyrate. These OTUs included members of recognized sulfate-reducing taxa (Desulfosporosinus, Desulfopila, Desulfomonile, Desulfovibrio) and also members of taxa that are either yet unknown sulfate reducers or metabolic interaction partners thereof. The most responsive OTUs markedly increased their ribosome content but only weakly increased in abundance. Responsive Desulfosporosinus OTUs even maintained a constantly low population size throughout 50 days, which suggests a novel strategy of rare biosphere members to display activity. Interestingly, two OTUs of the non-sulfate-reducing genus Telmatospirillum (Alphaproteobacteria) showed strongly contrasting preferences towards sulfate in butyrate-amended microcosms, corroborating that closely related microorganisms are not necessarily ecologically coherent. We show that diverse consortia of low-abundance microorganisms can perform peat soil sulfate reduction, a process that exerts control on methane production in these climate-relevant ecosystems.« less

  17. Decomposition in soil microcosms of leaves of the metallophyte Arabidopsis halleri: effect of leaf-associated heavy metals on biodegradation.

    PubMed

    Boucher, Uriel; Balabane, May; Lamy, Isabelle; Cambier, Philippe

    2005-05-01

    More knowledge is needed concerning the disturbance of soil organic matter cycling due to heavy metal pollution. The present study deals with the impact of heavy metal pollution on litter breakdown. Our aim was to assess whether heavy metals initially present in the leaves of the metallophyte Arabidopsis halleri: (i) slow down the rate of C mineralization, in relation to metal toxicity towards microflora, and/or (ii) increase the amount of organic C resistant to biodegradation, in relation to an intrinsic resistance of metallophyte residues to biodegradation. We incubated uncontaminated soil samples with either metal-free or metal-rich plant material. Metal-free material was grown in a greenhouse, and metal-rich material was collected in situ. During the 2-month period of incubation, we measured evolved CO(2)-C and residual plant C in the coarse organic fraction. Our results of CO(2)-C evolution showed a similar mineralization from the microcosms amended with highly metal-rich leaves of A. halleri and the microcosms amended with the metal-free but otherwise similar plant material. Measuring residual plant C in its input size-fraction gave a more precise insight. Our results suggest that only the large pool of easily decomposable C mineralized similarly from metal-free and from metal-rich plant residues. The pool of less decomposable C seemed on the contrary to be preferentially preserved in the case of metal-rich material. These results support the hypothesis of an annual extra-accumulation in situ of such a slowly decomposable fraction of plant residues which could account to some extent for the observed accumulation of metallophyte litter on the surface of highly metal-polluted soils.

  18. Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data.

    PubMed

    Bargiela, Rafael; Gertler, Christoph; Magagnini, Mirko; Mapelli, Francesca; Chen, Jianwei; Daffonchio, Daniele; Golyshin, Peter N; Ferrer, Manuel

    2015-01-01

    Biostimulation with different nitrogen sources is often regarded as a strategy of choice in combating oil spills in marine environments. Such environments are typically depleted in nitrogen, therefore limiting the balanced microbial utilization of carbon-rich petroleum constituents. It is fundamental, yet only scarcely accounted for, to analyze the catabolic consequences of application of biostimulants. Here, we examined such alterations in enrichment microcosms using sediments from chronically crude oil-contaminated marine sediment at Ancona harbor (Italy) amended with natural fertilizer, uric acid (UA), or ammonium (AMM). We applied the web-based AromaDeg resource using as query Illumina HiSeq meta-sequences (UA: 27,893 open reading frames; AMM: 32,180) to identify potential catabolic differences. A total of 45 (for UA) and 65 (AMM) gene sequences encoding key catabolic enzymes matched AromaDeg, and their participation in aromatic degradation reactions could be unambiguously suggested. Genomic signatures for the degradation of aromatics such as 2-chlorobenzoate, indole-3-acetate, biphenyl, gentisate, quinoline and phenanthrene were common for both microcosms. However, those for the degradation of orcinol, ibuprofen, phenylpropionate, homoprotocatechuate and benzene (in UA) and 4-aminobenzene-sulfonate, p-cumate, dibenzofuran and phthalate (in AMM), were selectively enriched. Experimental validation was conducted and good agreement with predictions was observed. This suggests certain discrepancies in action of these biostimulants on the genomic content of the initial microbial community for the catabolism of petroleum constituents or aromatics pollutants. In both cases, the emerging microbial communities were phylogenetically highly similar and were composed by very same proteobacterial families. However, examination of taxonomic assignments further revealed different catabolic pathway organization at the organismal level, which should be considered for designing

  19. Silver nanoparticle toxicity to Atlantic killifish (Fundulus heteroclitus) and Caenorhabditis elegans: a comparison of mesocosm, microcosm, and conventional laboratory studies.

    PubMed

    Bone, Audrey J; Matson, Cole W; Colman, Benjamin P; Yang, Xinyu; Meyer, Joel N; Di Giulio, Richard T

    2015-02-01

    The use of silver nanoparticles (AgNPs) in consumer products and industrial applications, as well as their recent detection in waste streams, has created concern about potential impacts on aquatic ecosystems. The effect of complex environmental media on AgNP toxicity was investigated using wetland mesocosms and smaller scale microcosms. Mesocosms were dosed with 2.5 mg Ag/L as gum arabic (GA)-coated AgNPs, polyvinylpyrrolidone (PVP)-coated AgNPs, or AgNO3. Water samples were taken from mesocosms 24 h after dosing for acute toxicity tests with embryos and larvae of Atlantic killifish (Fundulus heteroclitus) and the nematode Caenorhabditis elegans. Acute toxicity tests were also performed on Atlantic killifish with AgNO3, GA AgNPs, and PVP AgNPs prepared in the laboratory with similar water. For killifish embryos, mesocosm samples were much less toxic than laboratory samples for all types of silver. For larvae, in contrast, all 3 silver mesocosm treatments exhibited toxicity. Interestingly, mesocosm samples of AgNO3 were less toxic than laboratory samples; samples containing GA AgNPs were similar in toxicity, and samples containing PVP AgNPs were more toxic. For C. elegans, results were similar to killifish larvae. Results obtained from the mesocosms were not replicated on the smaller scale of the microcosms. These results indicate that environmental factors unique to the mesocosms acted differentially on AgNO3 to reduce its toxicity in a manner that does not translate to AgNPs for larval fish.

  20. Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms

    PubMed Central

    Hausmann, Bela; Knorr, Klaus-Holger; Schreck, Katharina; Tringe, Susannah G; Glavina del Rio, Tijana; Loy, Alexander; Pester, Michael

    2016-01-01

    Dissimilatory sulfate reduction in peatlands is sustained by a cryptic sulfur cycle and effectively competes with methanogenic degradation pathways. In a series of peat soil microcosms incubated over 50 days, we identified bacterial consortia that responded to small, periodic additions of individual fermentation products (formate, acetate, propionate, lactate or butyrate) in the presence or absence of sulfate. Under sulfate supplementation, net sulfate turnover (ST) steadily increased to 16–174 nmol cm–3 per day and almost completely blocked methanogenesis. 16S rRNA gene and cDNA amplicon sequencing identified microorganisms whose increases in ribosome numbers strongly correlated to ST. Natively abundant (⩾0.1% estimated genome abundance) species-level operational taxonomic units (OTUs) showed no significant response to sulfate. In contrast, low-abundance OTUs responded significantly to sulfate in incubations with propionate, lactate and butyrate. These OTUs included members of recognized sulfate-reducing taxa (Desulfosporosinus, Desulfopila, Desulfomonile, Desulfovibrio) and also members of taxa that are either yet unknown sulfate reducers or metabolic interaction partners thereof. Most responsive OTUs markedly increased their ribosome content but only weakly increased in abundance. Responsive Desulfosporosinus OTUs even maintained a constantly low population size throughout 50 days, which suggests a novel strategy of rare biosphere members to display activity. Interestingly, two OTUs of the non-sulfate-reducing genus Telmatospirillum (Alphaproteobacteria) showed strongly contrasting preferences towards sulfate in butyrate-amended microcosms, corroborating that closely related microorganisms are not necessarily ecologically coherent. We show that diverse consortia of low-abundance microorganisms can perform peat soil sulfate reduction, a process that exerts control on methane production in these climate-relevant ecosystems. PMID:27015005

  1. Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data

    PubMed Central

    Bargiela, Rafael; Gertler, Christoph; Magagnini, Mirko; Mapelli, Francesca; Chen, Jianwei; Daffonchio, Daniele; Golyshin, Peter N.; Ferrer, Manuel

    2015-01-01

    Biostimulation with different nitrogen sources is often regarded as a strategy of choice in combating oil spills in marine environments. Such environments are typically depleted in nitrogen, therefore limiting the balanced microbial utilization of carbon-rich petroleum constituents. It is fundamental, yet only scarcely accounted for, to analyze the catabolic consequences of application of biostimulants. Here, we examined such alterations in enrichment microcosms using sediments from chronically crude oil-contaminated marine sediment at Ancona harbor (Italy) amended with natural fertilizer, uric acid (UA), or ammonium (AMM). We applied the web-based AromaDeg resource using as query Illumina HiSeq meta-sequences (UA: 27,893 open reading frames; AMM: 32,180) to identify potential catabolic differences. A total of 45 (for UA) and 65 (AMM) gene sequences encoding key catabolic enzymes matched AromaDeg, and their participation in aromatic degradation reactions could be unambiguously suggested. Genomic signatures for the degradation of aromatics such as 2-chlorobenzoate, indole-3-acetate, biphenyl, gentisate, quinoline and phenanthrene were common for both microcosms. However, those for the degradation of orcinol, ibuprofen, phenylpropionate, homoprotocatechuate and benzene (in UA) and 4-aminobenzene-sulfonate, p-cumate, dibenzofuran and phthalate (in AMM), were selectively enriched. Experimental validation was conducted and good agreement with predictions was observed. This suggests certain discrepancies in action of these biostimulants on the genomic content of the initial microbial community for the catabolism of petroleum constituents or aromatics pollutants. In both cases, the emerging microbial communities were phylogenetically highly similar and were composed by very same proteobacterial families. However, examination of taxonomic assignments further revealed different catabolic pathway organization at the organismal level, which should be considered for designing

  2. Distribution and composition of polycyclic aromatic hydrocarbons within experimental microcosms treated with creosote-impregnated Douglas fir pilings

    SciTech Connect

    Bestari, K.T.J.; Solomon, K.R.; Steele, T.S.; Sibley, P.K.; Robinson, R.D.; Day, K.E.

    1998-12-01

    Temporal changes in the concentration and relative composition of 15 priority polycyclic aromatic hydrocarbons (PAHs) in water, sediment, and polyvinylchloride (PVC) strips were assessed to evaluate the fate of creosote leached from impregnated wood pilings in aquatic environments. The study consisted of single microcosms containing one of 0.5, 1, 2, 3, 4, or 6 creosote-impregnated pilings and two microcosms containing untreated pilings. Quantitative analyses of PAHs were performed using high-performance liquid chromatography equipped with a fluorescence detector. For each treatment, total PAHs ({Sigma} PAH) in water increased rapidly up to 7 d posttreatment yielding a clear dose-dependant concentration gradient ranging from 7.3 to 97.2 {micro}g/L. Total PAHs declined exponentially after 7 d and was reduced close to background concentrations by the end of the study. No increase in {Sigma} PAH was observed in sediments at any treatment, nor was there any relationship between sediment PAHs and distance from each piling cluster. However, a slight increase in PAHs was observed on PVC liner strips that exhibited a concentration gradient similar to that in water. The PVC-bound {Sigma} PAH ranged from 0.3 to 2.4 {micro}g/cm{sup 2} and 0.2 to 2.2 {micro}g/cm{sup 2} at 31 and 58 d posttreatment, respectively. Based on these data, the authors estimated a rate loss of creosote from the pilings of approximately 50 {micro}g/cm{sup 2}/d. The low concentration of PAHs on the PVC, along with the absence of accumulation of PAHs in sediments, suggests that creosote was lost primarily from water via degradative pathways such as photolysis and microbial decomposition and adsorption onto PVC. The rapid loss of creosote from water in conjunction with the slow rate of leaching from the pilings suggests that risks associated with the use of creosote-impregnated pilings in aquatic environments may be minimal.

  3. Cell proliferation in type C gastritis affecting the intact stomach

    PubMed Central

    Mac, D; Willis, P; Prescott, R; Lamonby, S; Lynch, D

    2000-01-01

    Aims—Type C gastritis caused by bile reflux has a characteristic appearance, similar to that seen in other forms of chemical gastritis, such as those associated with NSAIDs or alcohol. An increase in mucosal cell proliferation increases the likelihood of a neoplastic clone of epithelial cells emerging, particularly where there is chronic epithelial injury associated with bile reflux. It has been shown previously that type C gastritis is associated with increased cell proliferation in the postsurgical stomach. The aim of this study was to determine cell proliferation in type C gastritis caused by bile reflux affecting the intact stomach. Methods—Specimens from 15 patients with a histological diagnosis of type C gastritis on antral biopsy were obtained from the pathology archives between 1994 and 1997. A control group of nine normal antral biopsies was also selected and all underwent MIB-1 immunostaining. The gastric glands were divided into three zones (zone 1, gastric pit; zone 2, isthmus; and zone 3, gland base) and the numbers of positively staining nuclei for 500 epithelial cell nuclei were counted in each zone to determine the percentage labelling index (LI%). Results—Cell proliferation was significantly higher in all three zones of the gastric glands with type C gastritis compared with controls as follows: zone 1, median LI% in type C gastritis 64.7 (range, 7.8–99.2), controls 4.7 (range, 2.0–11.3); zone 2, median LI% in type C gastritis 94.7 (range, 28.8–98.7), controls 40.2 (range, 23.1–70.3); and zone 3, median LI% in type C gastritis 20.0 (range, 1.3–96.0), controls 2.6 (range, 0.9–8.7). Conclusions—Bile reflux is thought to act as a promoter of gastric carcinogenesis in the postsurgical stomach. The same may be true in the intact stomach. Key Words: cell proliferation • epithelial kinetics • chemical gastritis PMID:11064674

  4. Optimized Planning Target Volume for Intact Cervical Cancer

    SciTech Connect

    Khan, Alvin; Jensen, Lindsay G.; Sun Shuai; Song, William Y.; Yashar, Catheryn M.; Mundt, Arno J.; Zhang Fuquan; Jiang, Steve B.; Mell, Loren K.

    2012-08-01

    Purpose: To model interfraction clinical target volume (CTV) variation in patients with intact cervical cancer and design a planning target volume (PTV) that minimizes normal tissue dose while maximizing CTV coverage. Methods and Materials: We analyzed 50 patients undergoing external-beam radiotherapy for intact cervical cancer using daily online cone-beam computed tomography (CBCT). The CBCTs (n = 972) for each patient were rigidly registered to the planning CT. The CTV was delineated on the planning CT (CTV{sub 0}) and the set of CBCTs ({l_brace}CTV{sub 1}-CTV{sub 25}{r_brace}). Manual (n = 98) and automated (n = 668) landmarks were placed over the surface of CTV{sub 0} with reference to defined anatomic structures. Normal vectors were extended from each landmark, and the minimum length required for a given probability of encompassing CTV{sub 1}-CTV{sub 25} was computed. The resulting expansions were used to generate an optimized PTV. Results: The mean (SD; range) normal vector length to ensure 95% coverage was 4.3 mm (2.7 mm; 1-16 mm). The uniform expansion required to ensure 95% probability of CTV coverage was 13 mm. An anisotropic margin of 20 mm anteriorly and posteriorly and 10 mm superiorly, inferiorly, and laterally also would have ensured a 95% probability of CTV coverage. The volume of the 95% optimized PTV (1470 cm{sup 3}) was significantly lower than both the anisotropic PTV (2220 cm{sup 3}) and the uniformly expanded PTV (2110 cm{sup 3}) (p < 0.001). For a 95% probability of CTV coverage, normal lengths of 1-3 mm were found along the superior and lateral regions of CTV{sub 0}, 5-10 mm along the interfaces of CTV{sub 0} with the bladder and rectum, and 10-14 mm along the anterior surface of CTV{sub 0} at the level of the uterus. Conclusion: Optimizing PTV definition according to surface landmarking resulted in a high probability of CTV coverage with reduced PTV volumes. Our results provide data justifying planning margins to use in practice and

  5. Mechanisms of the Frank-Starling phenomena studied in intact hearts.

    PubMed

    Burkhoff, D; Stennett, R A; Ogino, K

    1995-01-01

    The impact of ventricular volume on the relationship between intracellular calcium and ventricular pressure under steady-state conditions was determined in intact ferret hearts. The results reveal major quantitative differences and minor qualitative differences between these relations and those previously measured in isolated intact and skinned cardiac muscle. The importance of these differences is discussed within the context of developing a comprehensive mechanistic theory to describe load-dependence of the intact ventricle.

  6. Spontaneous NA+ transients in individual mitochondria of intact astrocytes.

    PubMed

    Azarias, Guillaume; Van de Ville, Dimitri; Unser, Michael; Chatton, Jean-Yves

    2008-02-01

    Mitochondria in intact cells maintain low Na(+) levels despite the large electrochemical gradient favoring cation influx into the matrix. In addition, they display individual spontaneous transient depolarizations. The authors report here that individual mitochondria in living astrocytes exhibit spontaneous increases in their Na(+) concentration (Na(mit)(+) spiking), as measured using the mitochondrial probe CoroNa Red. In a field of view with approximately 30 astrocytes, up to 1,400 transients per minute were typically detected under resting conditions. Na(mit)(+) spiking was also observed in neurons, but was scarce in two nonneural cell types tested. Astrocytic Na(mit)(+) spikes averaged 12.2 +/- 0.8 s in duration and 35.5 +/- 3.2 mM in amplitude and coincided with brief mitochondrial depolarizations; they were impaired by mitochondrial depolarization and ruthenium red pointing to the involvement of a cation uniporter. Na(mit)(+) spiking activity was significantly inhibited by mitochondrial Na(+)/H(+) exchanger inhibition and sensitive to cellular pH and Na(+) concentration. Ca(2+) played a permissive role on Na(mit)(+) spiking activity. Finally, the authors present evidence suggesting that Na(mit)(+) spiking frequency was correlated with cellular ATP levels. This study shows that, under physiological conditions, individual mitochondria in living astrocytes exhibit fast Na(+) exchange across their inner membrane, which reveals a new form of highly dynamic and localized functional regulation.

  7. Activation and deactivation of vibronic channels in intact phycocyanin rods.

    PubMed

    Nganou, C; David, L; Meinke, R; Adir, N; Maultzsch, J; Mkandawire, M; Pouhè, D; Thomsen, C

    2014-02-28

    We investigated the excitation modes of the light-harvesting protein phycocyanin (PC) from Thermosynechococcus vulcanus in the crystalline state using UV and near-infrared Raman spectroscopy. The spectra revealed the absence of a hydrogen out-of-plane wagging (HOOP) mode in the PC trimer, which suggests that the HOOP mode is activated in the intact PC rod, while it is not active in the PC trimer. Furthermore, in the PC trimer an intense mode at 984 cm(-1) is assigned to the C-C stretching vibration while the mode at 454 cm(-1) is likely due to ethyl group torsion. In contrast, in the similar chromophore phytochromobilin the C5,10,15-D wag mode at 622 cm(-1) does not come from a downshift of the HOOP. Additionally, the absence of modes between 1200 and 1300 cm(-1) rules out functional monomerization. A correlation between phycocyanobilin (PCB) and phycoerythrobilin (PEB) suggests that the PCB cofactors of the PC trimer appear in a conformation similar to that of PEB. The conformation of the PC rod is consistent with that of the allophycocyanin (APC) trimer, and thus excitonic flow is facilitated between these two independent light-harvesting compounds. This excitonic flow from the PC rod to APC appears to be modulated by the vibration channels during HOOP wagging, C = C stretching, and the N-H rocking in-plan vibration.

  8. Management of Relocation in Cognitively Intact Older Adults.

    PubMed

    Hertz, Judith E; Koren, Mary Elaine; Rossetti, Jeanette; Tibbits, Kathryn

    2016-11-01

    Relocation, a major life transition that can affect health positively and negatively, is moving from one permanent home to another. Many older adults will relocate at some time during their life. Relocation is also a complex process that requires careful consideration and planning before the move (i.e., pre-location) and adjustment to the new home after the move (i.e., post-relocation). The current article is a summary of content based on a comprehensive evidence-based practice guideline focused on management of relocation in cognitively intact older adults. The guideline was designed to be used across diverse settings by nurses and other providers. Pre-relocation guidelines include assessment for the need for relocation, interventions prior to moving, and outcomes for evaluation of the pre-relocation process. For post-relocation, content focuses on assessment of risks for not adjusting after the move as well as intervention guidelines to promote adjustment and outcomes for evaluation. Implications include advocacy for older adults by using the guideline, disseminating it, and conducting future research. [Journal of Gerontological Nursing, 42(11), 14-23.].

  9. Basic Timing Abilities Stay Intact in Patients with Musician's Dystonia

    PubMed Central

    van der Steen, M. C.; van Vugt, Floris T.; Keller, Peter E.; Altenmüller, Eckart

    2014-01-01

    Task-specific focal dystonia is a movement disorder that is characterized by the loss of voluntary motor control in extensively trained movements. Musician's dystonia is a type of task-specific dystonia that is elicited in professional musicians during instrumental playing. The disorder has been associated with deficits in timing. In order to test the hypothesis that basic timing abilities are affected by musician's dystonia, we investigated a group of patients (N = 15) and a matched control group (N = 15) on a battery of sensory and sensorimotor synchronization tasks. Results did not show any deficits in auditory-motor processing for patients relative to controls. Both groups benefited from a pacing sequence that adapted to their timing (in a sensorimotor synchronization task at a stable tempo). In a purely perceptual task, both groups were able to detect a misaligned metronome when it was late rather than early relative to a musical beat. Overall, the results suggest that basic timing abilities stay intact in patients with musician's dystonia. This supports the idea that musician's dystonia is a highly task-specific movement disorder in which patients are mostly impaired in tasks closely related to the demands of actually playing their instrument. PMID:24667273

  10. Stress dependence of permeability of intact and fractured shale cores.

    NASA Astrophysics Data System (ADS)

    van Noort, Reinier; Yarushina, Viktoriya

    2016-04-01

    Whether a shale acts as a caprock, source rock, or reservoir, understanding fluid flow through shale is of major importance for understanding fluid flow in geological systems. Because of the low permeability of shale, flow is thought to be largely confined to fractures and similar features. In fracking operations, fractures are induced specifically to allow for hydrocarbon exploration. We have constructed an experimental setup to measure core permeabilities, using constant flow or a transient pulse. In this setup, we have measured the permeability of intact and fractured shale core samples, using either water or supercritical CO2 as the transporting fluid. Our measurements show decreasing permeability with increasing confining pressure, mainly due to time-dependent creep. Furthermore, our measurements show that for a simple splitting fracture, time-dependent creep will also eliminate any significant effect of this fracture on permeability. This effect of confinement on fracture permeability can have important implications regarding the effects of fracturing on shale permeability, and hence for operations depending on that.

  11. Compensatory mechanisms underlie intact task-switching performance in schizophrenia.

    PubMed

    Jamadar, S; Michie, P; Karayanidis, F

    2010-04-01

    Individuals with schizophrenia tend to perform poorly on many measures of cognitive control. However, recent task-switching studies suggest that they show intact task-switching performance, despite the fact that the regions involved in task-switching are known to be structurally and functionally impaired in the disorder. Behavioral, event-related potential (ERP) and functional magnetic resonance imaging (fMRI) measures were used to compare the temporal and spatial dynamics of task-switching performance in individuals with schizophrenia and controls. Consistent with previous studies, reaction time (RT) switch cost and its reduction with anticipatory preparation did not differ between groups. There were also no group differences on cue-locked ERP components associated with anticipatory preparation processes. However, both stimulus- and response-locked ERPs were significantly disrupted in schizophrenia, suggesting difficulty with task-set implementation. fMRI analyses indicated that individuals with schizophrenia showed hyperactivity in the dorsolateral prefrontal cortex and posterior parietal cortex. RT-fMRI and ERP-fMRI associations suggested that individuals with schizophrenia employ compensatory mechanisms to overcome difficulties in task-set implementation and thereby achieve the same behavioral outcomes as controls.

  12. Action Perception Is Intact in Autism Spectrum Disorder

    PubMed Central

    Williams, Justin H.G.; Neri, Peter

    2015-01-01

    Autistic traits span a wide spectrum of behavioral departures from typical function. Despite the heterogeneous nature of autism spectrum disorder (ASD), there have been attempts at formulating unified theoretical accounts of the associated impairments in social cognition. A class of prominent theories capitalizes on the link between social interaction and visual perception: effective interaction with others often relies on discrimination of subtle nonverbal cues. It has been proposed that individuals with ASD may rely on poorer perceptual representations of other people's actions as returned by dysfunctional visual circuitry and that this, in turn, may lead to less effective interpretation of those actions for social behavior. It remains unclear whether such perceptual deficits exist in ASD: the evidence currently available is limited to specific aspects of action recognition, and the reported deficits are often attributable to cognitive factors that may not be strictly visual (e.g., attention). We present results from an exhaustive set of measurements spanning the entire action processing hierarchy, from motion detection to action interpretation, designed to factor out effects that are not selectively relevant to this function. Our results demonstrate that the ASD perceptual system returns functionally intact signals for interpreting other people's actions adequately; these signals can be accessed effectively when autistic individuals are prompted and motivated to do so under controlled conditions. However, they may fail to exploit them adequately during real-life social interactions. PMID:25653346

  13. Structure of the intact ATM/Tel1 kinase

    NASA Astrophysics Data System (ADS)

    Wang, Xuejuan; Chu, Huanyu; Lv, Mengjuan; Zhang, Zhihui; Qiu, Shuwan; Liu, Haiyan; Shen, Xuetong; Wang, Weiwu; Cai, Gang

    2016-05-01

    The ataxia-telangiectasia mutated (ATM) protein is an apical kinase that orchestrates the multifaceted DNA-damage response. Normally, ATM kinase is in an inactive, homodimer form and is transformed into monomers upon activation. Besides a conserved kinase domain at the C terminus, ATM contains three other structural modules, referred to as FAT, FATC and N-terminal helical solenoid. Here we report the first cryo-EM structure of ATM kinase, which is an intact homodimeric ATM/Tel1 from Schizosaccharomyces pombe. We show that two monomers directly contact head-to-head through the FAT and kinase domains. The tandem N-terminal helical solenoid tightly packs against the FAT and kinase domains. The structure suggests that ATM/Tel1 dimer interface and the consecutive HEAT repeats inhibit the binding of kinase substrates and regulators by steric hindrance. Our study provides a structural framework for understanding the mechanisms of ATM/Tel1 regulation as well as the development of new therapeutic agents.

  14. True navigation in migrating gulls requires intact olfactory nerves

    PubMed Central

    Wikelski, Martin; Arriero, Elena; Gagliardo, Anna; Holland, Richard A.; Huttunen, Markku J.; Juvaste, Risto; Mueller, Inge; Tertitski, Grigori; Thorup, Kasper; Wild, Martin; Alanko, Markku; Bairlein, Franz; Cherenkov, Alexander; Cameron, Alison; Flatz, Reinhard; Hannila, Juhani; Hüppop, Ommo; Kangasniemi, Markku; Kranstauber, Bart; Penttinen, Maija-Liisa; Safi, Kamran; Semashko, Vladimir; Schmid, Heidi; Wistbacka, Ralf

    2015-01-01

    During migratory journeys, birds may become displaced from their normal migratory route. Experimental evidence has shown that adult birds can correct for such displacements and return to their goal. However, the nature of the cues used by migratory birds to perform long distance navigation is still debated. In this experiment we subjected adult lesser black-backed gulls migrating from their Finnish/Russian breeding grounds (from >60°N) to Africa (to < 5°N) to sensory manipulation, to determine the sensory systems required for navigation. We translocated birds westward (1080 km) or eastward (885 km) to simulate natural navigational challenges. When translocated westwards and outside their migratory corridor birds with olfactory nerve section kept a clear directional preference (southerly) but were unable to compensate for the displacement, while intact birds and gulls with the ophthalmic branch of the trigeminal nerve sectioned oriented towards their population-specific migratory corridor. Thus, air-borne olfactory information seems to be important for migrating gulls to navigate successfully in some circumstances. PMID:26597351

  15. Activation and deactivation of vibronic channels in intact phycocyanin rods

    NASA Astrophysics Data System (ADS)

    Nganou, C.; David, L.; Meinke, R.; Adir, N.; Maultzsch, J.; Mkandawire, M.; Pouhè, D.; Thomsen, C.

    2014-02-01

    We investigated the excitation modes of the light-harvesting protein phycocyanin (PC) from Thermosynechococcus vulcanus in the crystalline state using UV and near-infrared Raman spectroscopy. The spectra revealed the absence of a hydrogen out-of-plane wagging (HOOP) mode in the PC trimer, which suggests that the HOOP mode is activated in the intact PC rod, while it is not active in the PC trimer. Furthermore, in the PC trimer an intense mode at 984 cm-1 is assigned to the C-C stretching vibration while the mode at 454 cm-1 is likely due to ethyl group torsion. In contrast, in the similar chromophore phytochromobilin the C5,10,15-D wag mode at 622 cm-1 does not come from a downshift of the HOOP. Additionally, the absence of modes between 1200 and 1300 cm-1 rules out functional monomerization. A correlation between phycocyanobilin (PCB) and phycoerythrobilin (PEB) suggests that the PCB cofactors of the PC trimer appear in a conformation similar to that of PEB. The conformation of the PC rod is consistent with that of the allophycocyanin (APC) trimer, and thus excitonic flow is facilitated between these two independent light-harvesting compounds. This excitonic flow from the PC rod to APC appears to be modulated by the vibration channels during HOOP wagging, C = C stretching, and the N-H rocking in-plan vibration.

  16. Covert spatial attention is functionally intact in amblyopic human adults

    PubMed Central

    Roberts, Mariel; Cymerman, Rachel; Smith, R. Theodore; Kiorpes, Lynne; Carrasco, Marisa

    2016-01-01

    Certain abnormalities in behavioral performance and neural signaling have been attributed to a deficit of visual attention in amblyopia, a neurodevelopmental disorder characterized by a diverse array of visual deficits following abnormal binocular childhood experience. Critically, most have inferred attention's role in their task without explicitly manipulating and measuring its effects against a baseline condition. Here, we directly investigate whether human amblyopic adults benefit from covert spatial attention—the selective processing of visual information in the absence of eye movements—to the same degree as neurotypical observers. We manipulated both involuntary (Experiment 1) and voluntary (Experiment 2) attention during an orientation discrimination task for which the effects of covert spatial attention have been well established in neurotypical and special populations. In both experiments, attention significantly improved accuracy and decreased reaction times to a similar extent (a) between the eyes of the amblyopic adults and (b) between the amblyopes and their age- and gender-matched controls. Moreover, deployment of voluntary attention away from the target location significantly impaired task performance (Experiment 2). The magnitudes of the involuntary and voluntary attention benefits did not correlate with amblyopic depth or severity. Both groups of observers showed canonical performance fields (better performance along the horizontal than vertical meridian and at the lower than upper vertical meridian) and similar effects of attention across locations. Despite their characteristic low-level vision impairments, covert spatial attention remains functionally intact in human amblyopic adults. PMID:28033433

  17. Amniotic Fluid Infection in Preterm Pregnancies with Intact Membranes

    PubMed Central

    Rahkonen, Leena; Nupponen, Irmeli; Pätäri-Sampo, Anu; Tikkanen, Minna; Sorsa, Timo; Juhila, Juuso; Andersson, Sture; Paavonen, Jorma; Stefanovic, Vedran

    2017-01-01

    Introduction. Intra-amniotic infection (IAI) is a major cause of preterm labor and adverse neonatal outcome. We evaluated amniotic fluid (AF) proteolytic cascade forming biomarkers in relation to microbial invasion of the amniotic cavity (MIAC) and IAI in preterm pregnancies with intact membranes. Material and Methods. Amniocentesis was made to 73 women with singleton pregnancies; 27 with suspected IAI; and 46 controls. AF biomarkers were divided into three cascades: Cascade 1: matrix metalloproteinase-8 (MMP-8), MMP-9, myeloperoxidase (MPO), and interleukin-6; Cascade 2: neutrophil elastase (HNE), elafin, and MMP-9; Cascade 3: MMP-2, tissue inhibitor of matrix metalloproteinases-1 (TIMP-1), MMP-8/TIMP-1 molar ratio, and C-reactive protein (CRP). MMP-8 was measured by an immunoenzymometric assay and the others were measured by ELISA. Standard biochemical methods, molecular microbiology, and culture techniques were used. Results. MMP-8, MMP-9, MPO, elafin, and TIMP-1 concentrations were higher in IAI suspected cases compared to controls and also in IAI suspected cases with MIAC compared to those without MIAC when adjusted by gestational age at amniocentesis. All biomarkers except elafin and MMP-2 had the sensitivity of 100% with thresholds based on ROC-curve. Odd ratios of biomarkers for MIAC were 1.2-38 and 95% confidential intervals 1.0-353.6. Conclusions. Neutrophil based AF biomarkers were associated with IAI and MIAC. PMID:28167848

  18. Rapid isolation of intact, viable fetal cartilage models

    SciTech Connect

    Schmidt, R.R.; Chepenik, K.P.; Paynton, B.V.; Cotler, J.M.

    1982-04-01

    A rapid procedure is described for the isolation of viable, intact, femoral cartilage models (humeri and femora) obtained from pregnant rats on the 18th day of gestation. Viability of these models is demonstrated in an in vitro system where the incorporation of /sup 35/S-sulfate was linear with time of incubation and with numbers of cartilage models utilized. Treatment of cartilage models with ice-cold trichloroacetic acid and a boiling water bath prior to incubation with radiolabel, reduced the amount of radioactivity incorporated to 1.3% of that observed for models incubated by routine procedures. Furthermore, digestion of cartilage model homogenates with protease yielded a supernatant from which 51% to 57% of the radioactivity was precipitated as GAG. This method may also be used to isolate fetal cartilage models as early as the 16th day of gestation. with this system, specific biochemical parameters of mammalian fetal chondrogenesis may be surveyed in normally and abnormally developing fetal cartilage free of surrounding soft tissue.

  19. Right ventricular outflow obstruction with intact ventricular septum in adults.

    PubMed Central

    Werner, A M; Darrell, J C; Pallegrini, R V; Woelfel, G F; Grant, K; Marrangoni, A G

    1997-01-01

    Cardiothoracic surgeons whose practice is limited to adults rarely see patients with right ventricular outflow obstruction and an intact ventricular septum. Of more than 10,000 open-heart procedures performed at our institution from 1983 to 1993 (in patients 18 to 75 years old), only 5 procedures were for correction of this problem. Both the pulmonary valve and the subvalvular area were abnormal in these 5 patients, and 4 of the 5 had subvalvular stenosis. The gradient across the right ventricular outflow tract was measured by cardiac catheterization before repair in all patients and averaged 118 mmHg. Various surgical approaches were used for repair. In the 2 patients whose pressures were measured postoperatively, the gradients were 25 mmHg and 45 mmHg, respectively. There were no operative deaths. At follow-up (range, 2 months to 5 years after surgery), all patients were in New York Heart Association functional class I and all had murmurs. Those who underwent echocardiography were found to have minimal gradients across the right ventricular outflow tract. Images PMID:9205983

  20. Measurement of the Mechanical Properties of Intact Collagen Fibrils

    NASA Astrophysics Data System (ADS)

    Mercedes, H.; Heim, A.; Matthews, W. G.; Koob, T.

    2006-03-01

    Motivated by the genetic disorder Ehlers-Danlos syndrome (EDS), in which proper collagen synthesis is interrupted, we are investigating the structural and mechanical properties of collagen fibrils. The fibrous glycoprotein collagen is the most abundant protein found in the human body and plays a key role in the extracellular matrix of the connective tissue, the properties of which are altered in EDS. We have selected as our model system the collagen fibrils of the sea cucumber dermis, a naturally mutable tissue. This system allows us to work with native fibrils which have their proteoglycan complement intact, something that is not possible with reconstituted mammalian collagen fibrils. Using atomic force microscopy, we measure, as a function of the concentration of divalent cations, the fibril diameter, its response to force loading, and the changes in its rigidity. Through these experiments, we will shed light on the mechanisms which control the properties of the sea cucumber dermis and hope to help explain the altered connective tissue extracellular matrix properties associated with EDS.

  1. Structure of the intact ATM/Tel1 kinase.

    PubMed

    Wang, Xuejuan; Chu, Huanyu; Lv, Mengjuan; Zhang, Zhihui; Qiu, Shuwan; Liu, Haiyan; Shen, Xuetong; Wang, Weiwu; Cai, Gang

    2016-05-27

    The ataxia-telangiectasia mutated (ATM) protein is an apical kinase that orchestrates the multifaceted DNA-damage response. Normally, ATM kinase is in an inactive, homodimer form and is transformed into monomers upon activation. Besides a conserved kinase domain at the C terminus, ATM contains three other structural modules, referred to as FAT, FATC and N-terminal helical solenoid. Here we report the first cryo-EM structure of ATM kinase, which is an intact homodimeric ATM/Tel1 from Schizosaccharomyces pombe. We show that two monomers directly contact head-to-head through the FAT and kinase domains. The tandem N-terminal helical solenoid tightly packs against the FAT and kinase domains. The structure suggests that ATM/Tel1 dimer interface and the consecutive HEAT repeats inhibit the binding of kinase substrates and regulators by steric hindrance. Our study provides a structural framework for understanding the mechanisms of ATM/Tel1 regulation as well as the development of new therapeutic agents.

  2. Structure of the intact ATM/Tel1 kinase

    PubMed Central

    Wang, Xuejuan; Chu, Huanyu; Lv, Mengjuan; Zhang, Zhihui; Qiu, Shuwan; Liu, Haiyan; Shen, Xuetong; Wang, Weiwu; Cai, Gang

    2016-01-01

    The ataxia-telangiectasia mutated (ATM) protein is an apical kinase that orchestrates the multifaceted DNA-damage response. Normally, ATM kinase is in an inactive, homodimer form and is transformed into monomers upon activation. Besides a conserved kinase domain at the C terminus, ATM contains three other structural modules, referred to as FAT, FATC and N-terminal helical solenoid. Here we report the first cryo-EM structure of ATM kinase, which is an intact homodimeric ATM/Tel1 from Schizosaccharomyces pombe. We show that two monomers directly contact head-to-head through the FAT and kinase domains. The tandem N-terminal helical solenoid tightly packs against the FAT and kinase domains. The structure suggests that ATM/Tel1 dimer interface and the consecutive HEAT repeats inhibit the binding of kinase substrates and regulators by steric hindrance. Our study provides a structural framework for understanding the mechanisms of ATM/Tel1 regulation as well as the development of new therapeutic agents. PMID:27229179

  3. The intact capture of hypervelocity dust particles using underdense foams

    NASA Technical Reports Server (NTRS)

    Maag, Carl R.; Borg, J.; Tanner, William G.; Stevenson, T. J.; Bibring, J.-P.

    1994-01-01

    probability of survival for the impacting particle. The primary objectives of the experiment are to (1) Examine the morphology of primary and secondary hypervelocity impact craters. Primary attention will be paid to craters caused by ejecta during hypervelocity impacts of different substrates. (2) Determine the size distribution of ejecta by means of witness plates and collect fragments of ejecta from craters by means of momentum-sensitive mcropore foam. (3) Assess the directionality of the flux by means of penetration-hole alignment of thin films placed above the cells. (4) Capture intact the particles that perforated the thin film and entered the cell. Capture media consisted of both previously flight-tested micropore foams and aerogel. The foams had different latent heats of fusion and, accordingly, will capture particles over a range of momenta. Aerogel was incorporated into the cells to determine the minimum diameter than can be captured intact.

  4. The intact capture of hypervelocity dust particles using underdense foams

    NASA Astrophysics Data System (ADS)

    Maag, Carl R.; Borg, J.; Tanner, William G.; Stevenson, T. J.; Bibring, J.-P.

    probability of survival for the impacting particle. The primary objectives of the experiment are to (1) Examine the morphology of primary and secondary hypervelocity impact craters. Primary attention will be paid to craters caused by ejecta during hypervelocity impacts of different substrates. (2) Determine the size distribution of ejecta by means of witness plates and collect fragments of ejecta from craters by means of momentum-sensitive mcropore foam. (3) Assess the directionality of the flux by means of penetration-hole alignment of thin films placed above the cells. (4) Capture intact the particles that perforated the thin film and entered the cell. Capture media consisted of both previously flight-tested micropore foams and aerogel. The foams had different latent heats of fusion and, accordingly, will capture particles over a range of momenta. intact.

  5. Dead or Alive? Probing Microbial Ecosystems With Intact Polar Lipids.

    NASA Astrophysics Data System (ADS)

    Sturt, H. F.; Smith, K. J.; Xu, L.; Molyneaux, S. J.; Teske, A.; Orphan, V. J.; Summons, R. E.; Hinrichs, K.

    2002-12-01

    Multi-proxy approaches consisting of isotopic information derived from diagnostic lipid biomarkers together with phylogenetic techniques have advanced our understanding of naturally occurring microbial communities. Examples include the significant advances in our understanding of the ecology of archaeal methanotrophs and planktonic crenarchaeota. However, this approach has to be modified for application to microbial ecosystems in the deep subsurface in order to distinguish live matter from dead. Polar lipids, i.e., phospho- and glycolipids, fulfill that requirement and potentially provide information on the structure, size and function of the microbial community. We utilized a high-performance-liquid-chromatograph coupled to a mass-spectrometer (HPLC-MS) to examine the distribution of intact polar lipids from microbial isolates and surface sediments that are relevant for the study of deep subsurface biospheres. Structural features of bacterial and archaeal-derived polar lipids are identified on the basis of their sequential fragmentation in an ion-trap mass spectrometer upon electrospray ionization. Additional details are obtained from a series of chemical degradations designed to release alkyl units of the polar lipids rendering them analyzable by conventional gas-chromatography-mass-spectrometry (GC-MS). Fingerprints of polar lipids from microbial isolates allow distinction of taxonomically closely related prokaryotes. Moreover, sediments from seep environments in Eel River Basin and Guaymas Basin that host anaerobic methanotrophic communities are both dominated by similar types of glycosyl biphytanyl tetraethers suggestive of a predominant low-diversity archaeal assemblage. First applications of this technique to sediments from the deep subsurface will be presented.

  6. Intact reading in patients with profound early visual dysfunction

    PubMed Central

    Yong, Keir X.X.; Warren, Jason D.; Warrington, Elizabeth K.; Crutch, Sebastian J.

    2013-01-01

    Despite substantial neuroscientific evidence for a region of visual cortex dedicated to the processing of written words, many studies continue to reject explanations of letter-by-letter (LBL) reading in terms of impaired word form representations or parallel letter processing in favour of more general deficits of visual function. In the current paper, we demonstrate that whilst LBL reading is often associated with general visual deficits, these deficits are not necessarily sufficient to cause reading impairment and have led to accounts of LBL reading which are based largely on evidence of association rather than causation. We describe two patients with posterior cortical atrophy (PCA) who exhibit remarkably preserved whole word and letter reading despite profound visual dysfunction. Relative to controls, both patients demonstrated impaired performance on tests of early visual, visuoperceptual and visuospatial processing; visual acuity was the only skill preserved in both individuals. By contrast, both patients were able to read aloud words with perfect to near-perfect accuracy. Reading performance was also rapid with no overall significant difference in response latencies relative to age- and education-matched controls. Furthermore, the patients violated a key prediction of general visual accounts of LBL reading – that pre-lexical impairments should result in prominent word length effects; in the two reported patients, evidence for abnormal word length effects was equivocal or absent, and certainly an order of magnitude different to that reported for LBL readers. We argue that general visual accounts cannot explain the pattern of reading data reported, and attribute the preserved reading performance to preserved direct access to intact word form representations and/or parallel letter processing mechanisms. The current data emphasise the need for much clearer evidence of causality when attempting to draw connections between specific aspects of visual processing

  7. Pointing in visual periphery: is DF's dorsal stream intact?

    PubMed

    Hesse, Constanze; Ball, Keira; Schenk, Thomas

    2014-01-01

    Observations of the visual form agnosic patient DF have been highly influential in establishing the hypothesis that separate processing streams deal with vision for perception (ventral stream) and vision for action (dorsal stream). In this context, DF's preserved ability to perform visually-guided actions has been contrasted with the selective impairment of visuomotor performance in optic ataxia patients suffering from damage to dorsal stream areas. However, the recent finding that DF shows a thinning of the grey matter in the dorsal stream regions of both hemispheres in combination with the observation that her right-handed movements are impaired when they are performed in visual periphery has opened up the possibility that patient DF may potentially also be suffering from optic ataxia. If lesions to the posterior parietal cortex (dorsal stream) are bilateral, pointing and reaching deficits should be observed in both visual hemifields and for both hands when targets are viewed in visual periphery. Here, we tested DF's visuomotor performance when pointing with her left and her right hand toward targets presented in the left and the right visual field at three different visual eccentricities. Our results indicate that DF shows large and consistent impairments in all conditions. These findings imply that DF's dorsal stream atrophies are functionally relevant and hence challenge the idea that patient DF's seemingly normal visuomotor behaviour can be attributed to her intact dorsal stream. Instead, DF seems to be a patient who suffers from combined ventral and dorsal stream damage meaning that a new account is needed to explain why she shows such remarkably normal visuomotor behaviour in a number of tasks and conditions.

  8. Intact reading in patients with profound early visual dysfunction.

    PubMed

    Yong, Keir X X; Warren, Jason D; Warrington, Elizabeth K; Crutch, Sebastian J

    2013-10-01

    Despite substantial neuroscientific evidence for a region of visual cortex dedicated to the processing of written words, many studies continue to reject explanations of letter-by-letter (LBL) reading in terms of impaired word form representations or parallel letter processing in favour of more general deficits of visual function. In the current paper, we demonstrate that whilst LBL reading is often associated with general visual deficits, these deficits are not necessarily sufficient to cause reading impairment and have led to accounts of LBL reading which are based largely on evidence of association rather than causation. We describe two patients with posterior cortical atrophy (PCA) who exhibit remarkably preserved whole word and letter reading despite profound visual dysfunction. Relative to controls, both patients demonstrated impaired performance on tests of early visual, visuoperceptual and visuospatial processing; visual acuity was the only skill preserved in both individuals. By contrast, both patients were able to read aloud words with perfect to near-perfect accuracy. Reading performance was also rapid with no overall significant difference in response latencies relative to age- and education-matched controls. Furthermore, the patients violated a key prediction of general visual accounts of LBL reading - that pre-lexical impairments should result in prominent word length effects; in the two reported patients, evidence for abnormal word length effects was equivocal or absent, and certainly an order of magnitude different to that reported for LBL readers. We argue that general visual accounts cannot explain the pattern of reading data reported, and attribute the preserved reading performance to preserved direct access to intact word form representations and/or parallel letter processing mechanisms. The current data emphasise the need for much clearer evidence of causality when attempting to draw connections between specific aspects of visual processing and

  9. Raman mapping of intact biofilms on stainless steel surfaces

    NASA Astrophysics Data System (ADS)

    Nguyen, Julie K.; Heighton, Lynne; Xu, Yunfeng; Nou, Xiangwu; Schmidt, Walter F.

    2016-05-01

    Many issues occur when microbial bacteria contaminates human food or water; it can be dangerous to the public. Determining how the microbial are growing, it can help experts determine how to prevent the outbreaks. Biofilms are a tightly group of microbial cells that grow on living surfaces or surrounding themselves. Though biofilms are not necessarily uniform; when there are more than one type of microbial bacteria that are grown, Raman mapping is performed to determine the growth patterns. Depending on the type of microbial bacteria, they can grow in various patterns such as symmetrical or scattered on the surface. The biofilms need to be intact in order to preclude and potentially figuring out the relative intensity of different components in a biofilm mixture. In addition, it is important to determine whether one biofilms is a substrate for another biofilm to be detected. For example, it is possible if layer B appears above layer A, but layer A doesn't appear above layer B. In this case, three types of biofilms that are grown includes Listeria(L), Ralstonia(R), and a mixture of the two (LR). Since microbe deposits on metal surfaces are quite suitable, biofilms were grown on stainless steel surface slides. Each slide was viewed under a Raman Microscope at 100X and using a 532nm laser to provide great results and sharp peaks. The mapping of the laser helps determine how the bacteria growth, at which intensity the bacteria appeared in order to identify specific microbes to signature markers on biofilms.

  10. Optical properties of intact leaves for estimating chlorophyll concentration.

    PubMed

    Carter, Gregory A; Spiering, Bruce A

    2002-01-01

    Changes in leaf chlorophyll content can serve as relative indicators of plant vigor and environmental quality. This study identified reflectance, transmittance, and absorptance wavebands and band ratios within the 400- to 850-nm range for intact leaves that could be used to estimate extracted leaf chlorophyll per unit leaf area (areal concentration) with minimal error. Leaf optical properties along with chlorophyll a, b, and a + b concentrations were measured for the planar-leaved sweetgum (Liquidambar styraciflua L.), red maple (Acer rubrum L.), wild grape (Vitis rotundifolia Michx.), and switchcane [Arundinaria gigantea (Walter) Muhl.], and for needles of longleaf pine (Pinus palustris Miller). Generally, reflectance, transmittance, and absorptance corresponded most precisely with chlorophyll concentrations at wavelengths near 700 nm, although regressions were also strong in the 550- to 625-nm range. A power function was superior to a simple linear function in yielding low standard deviations of the estimate (s). When data were combined among the planar-leaved species, s values were low at approximately 50 mumol/m2 out of a 940 mumol/m2 range in chlorophyll a + b at best-fit wavelengths of 707 to 709 nm. Minimal s values for chlorophyll a + b ranged from 32 to 62 mumol/m2 across species when band ratios having numerator wavelengths of 693 to 720 nm were used with the application of a power function. Optimal denominator wavelengths for the band ratios were 850 nm for reflectance and transmittance and 400 nm for absorptance. This information can be applied in designing field portable chlorophyll meters and in the landscape-scale remote sensing of plant responses to the environment.

  11. Optical properties of intact leaves for estimating chlorophyll concentration

    NASA Technical Reports Server (NTRS)

    Carter, Gregory A.; Spiering, Bruce A.

    2002-01-01

    Changes in leaf chlorophyll content can serve as relative indicators of plant vigor and environmental quality. This study identified reflectance, transmittance, and absorptance wavebands and band ratios within the 400- to 850-nm range for intact leaves that could be used to estimate extracted leaf chlorophyll per unit leaf area (areal concentration) with minimal error. Leaf optical properties along with chlorophyll a, b, and a + b concentrations were measured for the planar-leaved sweetgum (Liquidambar styraciflua L.), red maple (Acer rubrum L.), wild grape (Vitis rotundifolia Michx.), and switchcane [Arundinaria gigantea (Walter) Muhl.], and for needles of longleaf pine (Pinus palustris Miller). Generally, reflectance, transmittance, and absorptance corresponded most precisely with chlorophyll concentrations at wavelengths near 700 nm, although regressions were also strong in the 550- to 625-nm range. A power function was superior to a simple linear function in yielding low standard deviations of the estimate (s). When data were combined among the planar-leaved species, s values were low at approximately 50 mumol/m2 out of a 940 mumol/m2 range in chlorophyll a + b at best-fit wavelengths of 707 to 709 nm. Minimal s values for chlorophyll a + b ranged from 32 to 62 mumol/m2 across species when band ratios having numerator wavelengths of 693 to 720 nm were used with the application of a power function. Optimal denominator wavelengths for the band ratios were 850 nm for reflectance and transmittance and 400 nm for absorptance. This information can be applied in designing field portable chlorophyll meters and in the landscape-scale remote sensing of plant responses to the environment.

  12. Multipurpose Dissociation Cell for Enhanced ETD of Intact Protein Species

    PubMed Central

    Rose, Christopher M.; Russell, Jason D.; Ledvina, Aaron R.; McAlister, Graeme C.; Westphall, Michael S.; Griep-Raming, Jens; Schwartz, Jae C.; Coon, Joshua J.; Syka, John E.P.

    2013-01-01

    We describe and characterize an improved implementation of ETD on a modified hybrid linear ion trap-Orbitrap instrument. Instead of performing ETD in the mass-analyzing quadrupole linear ion trap (A-QLT), the instrument collision cell was modified to enable ETD. We partitioned the collision cell into a multi-section RF ion storage and transfer device to enable injection and simultaneous separate storage of precursor and reagent ions. Application of a secondary (axial) confinement voltage to the cell end lens electrodes enables charge-sign independent trapping for ion-ion reactions. The approximately two-fold higher quadrupole field frequency of this cell relative to that of the A-QLT, enables higher reagent ion densities and correspondingly faster ETD reactions, and, with the collision cell’s longer axial dimensions, larger populations of precursor ions may be reacted. The higher ion capacity of the collision cell permits the accumulation and reaction of multiple full loads of precursor ions from the A-QLT followed by FT Orbitrap m/z analysis of the ETD product ions. This extends the intra-scan dynamic range by increasing the maximum number of product ions in a single MS/MS event. For analyses of large peptide/small protein precursor cations, this reduces or eliminates the need for spectral averaging to achieve acceptable ETD product ion signal-to-noise levels. Using larger ion populations, we demonstrate improvements in protein sequence coverage and aggregate protein identifications in LC-MS/MS analysis of intact protein species as compared to the standard ETD implementation. PMID:23609185

  13. Multipurpose dissociation cell for enhanced ETD of intact protein species.

    PubMed

    Rose, Christopher M; Russell, Jason D; Ledvina, Aaron R; McAlister, Graeme C; Westphall, Michael S; Griep-Raming, Jens; Schwartz, Jae C; Coon, Joshua J; Syka, John E P

    2013-06-01

    We describe and characterize an improved implementation of ETD on a modified hybrid linear ion trap-Orbitrap instrument. Instead of performing ETD in the mass-analyzing quadrupole linear ion trap (A-QLT), the instrument collision cell was modified to enable ETD. We partitioned the collision cell into a multi-section rf ion storage and transfer device to enable injection and simultaneous separate storage of precursor and reagent ions. Application of a secondary (axial) confinement voltage to the cell end lens electrodes enables charge-sign independent trapping for ion-ion reactions. The approximately 2-fold higher quadrupole field frequency of this cell relative to that of the A-QLT enables higher reagent ion densities and correspondingly faster ETD reactions, and, with the collision cell's longer axial dimensions, larger populations of precursor ions may be reacted. The higher ion capacity of the collision cell permits the accumulation and reaction of multiple full loads of precursor ions from the A-QLT followed by FT Orbitrap m/z analysis of the ETD product ions. This extends the intra-scan dynamic range by increasing the maximum number of product ions in a single MS/MS event. For analyses of large peptide/small protein precursor cations, this reduces or eliminates the need for spectral averaging to achieve acceptable ETD product ion signal-to-noise levels. Using larger ion populations, we demonstrate improvements in protein sequence coverage and aggregate protein identifications in LC-MS/MS analysis of intact protein species as compared to the standard ETD implementation.

  14. Secretion of acid and base equivalents by intact distal airways.

    PubMed

    Inglis, S K; Wilson, S M; Olver, R E

    2003-05-01

    Secretion of HCO(3)(-) by airway submucosal glands is essential for normal liquid and mucus secretion. Because the liquid bathing the airway surface (ASL) is acidic, it has been proposed that the surface epithelium may acidify HCO(3)(-)-rich glandular fluid. The aim of this study was to investigate the mechanisms by which intact distal bronchi, which contain both surface and glandular epithelium, modify pH of luminal fluid. Distal bronchi were isolated from pig lungs, cannulated in a bath containing HCO(3)(-)-buffered solution, and perfused continually with an aliquot of similar, lightly buffered solution (LBS) in which NaCl replaced NaHCO(3)(-) (pH 7 with NaOH). The pH of this circulating LBS initially acidified (by 0.053 +/- 0.0053 pH units) and transepithelial potential difference (PD) depolarized. The magnitude of acidification was increased when pH(LBS) was higher. This acidification was unaffected by luminal dimethylamiloride (DMA, 100 microM) but was inhibited by 100 nM bafilomycin A(1) (by 76 +/- 13%), suggesting involvement of vacuolar-H(+) ATPase. Addition of ACh (10 microM) evoked alkalinization of luminal LBS and hyperpolarization of transepithelial PD. The alkalinization was inhibited in HCO(3)(-)-free solutions containing acetazolamide (1 mM) and by DMA and was enhanced by bumetanide (100 microM), an inhibitor of Cl(-) secretion. The hyperpolarization was unaffected by these maneuvers. The anion channel blocker 5-nitro-2-(3-phenylpropylamino)benzoate (300 microM) and combined treatment with DMA and bumetanide blocked both the alkalinization and hyperpolarization responses to ACh. These results are consistent with earlier studies showing that ACh evokes glandular secretion of HCO(3)(-) and Cl(-). Isolated distal airways thus secrete both acid and base equivalents.

  15. Uptake of intact nucleoside monophosphates by Bdellovibrio bacteriovorus 109J.

    PubMed Central

    Ruby, E G; McCabe, J B; Barke, J I

    1985-01-01

    The degraded nucleic acids and ribosomes of its prey cell provide Bdellovibrio bacteriovorus 109J with a source of ribonucleoside monophosphates and deoxyribonucleoside monophosphates for biosynthesis and respiration. We demonstrate that bdellovibrios, in contrast to almost all other bacteria, take up these nucleoside monophosphates into the cell in an intact, phosphorylated form. In this way they are able to assimilate more effectively the cellular contents of their prey. Studies with UMP and dTMP demonstrate that they are transported and accumulated against a concentration gradient, achieving internal levels at least 10 times the external levels. Treatment of the bdellovibrios with azide or carbonyl cyanide m-chlorophenylhydrazone eliminates their ability to either transport or maintain accumulated UMP and suggests the presence of a freely reversible exchange mechanism. There are at least two separate classes of transport systems for nucleoside monophosphates, each exhibiting partial specificity for either ribonucleoside monophosphates or deoxyribonucleoside monophosphates. Kinetic analyses of UMP transport in different developmental stages of strain 109J indicate that each stage expresses a single, saturable uptake system with a distinct apparent substrate affinity constant (Kt) of 104 microM in attack phase cells and 35 microM in prematurely released growth phase filaments. The capacity for transport of UMP by the growth phase filaments was 2.4 times that of the attack phase cells. These data, in addition to the apparent lack of environmental control of UMP transport capacity in attack phase cells, suggest that there are two transport systems for UMP in bdellovibrios and that the high-affinity, high-capacity growth phase system is developmentally regulated. PMID:4030692

  16. Polyacrylamide gel electrophoresis of intact bacteriophage T4D particles.

    PubMed Central

    Childs, J D; Birnboim, H C

    1975-01-01

    A method for the electrophoresis of intact bacteriophage T4D particles through polyacrylamide gels has been developed. It was found that phage particles will migrate through dilute polyacrylamide gels (less than 2.1%) in the presence of a low concentration of MgCl2. As few as 5 x 10(9) phage particles can be seen directly as a light-scattering band during the course of electrophoresis. The band can also be detected by scanning gels at 260 to 265 nm or by eluting viable phage particles from gel slices. A new mutant (eph1) has been identified on the basis of its decreased electrophoretic mobility compared with that of the wild type; mutant particles migrated 14% slower than the wild type particles at pH 8.3 and 35% slower at pH 5.0. The isoelectric points of both the wild type and eph1 mutant were found to be between pH 4.0 and 5.0. Particles of T4 with different head lengths were also studied. Petite particles (heads 20% shorter than normal) migrated at the same rate as normal-size particles. Giant particles, heterogenous with respect to head length (two to nine times normal), migrated faster than normal-size particles as a diffuse band. This diffuseness was due to separation within the band of particles having mobilities ranging from 8 to 35% faster than those of normal-size particles. These observations extend the useful range of polyacrylamide gel electrophoresis to include much larger particles than have previously been studied, including most viruses. Images PMID:240037

  17. Ultrastructure of the intact skeleton of the human erythrocyte membrane.

    PubMed

    Shen, B W; Josephs, R; Steck, T L

    1986-03-01

    Filamentous skeletons were liberated from isolated human erythrocyte membranes in Triton X-100, spread on fenestrated carbon films, negatively stained, and viewed intact and unfixed in the transmission electron microscope. Two forms of the skeleton were examined: (a) basic skeletons, stripped of accessory proteins with 1.5 M NaCl so that they contain predominantly polypeptide bands 1, 2, 4.1, and 5; and (b) unstripped skeletons, which also bore accessory proteins such as ankyrin and band 3 and small plaques of residual lipid. Freshly prepared skeletons were highly condensed. Incubation at low ionic strength and in the presence of dithiothreitol for an hour or more caused an expansion of the skeletons, which greatly increased the visibility of their elements. The expansion may reflect the opening of spectrin from a compact to an elongated disposition. Expanded skeletons appeared to be organized as networks of short actin filaments joined by multiple (5-8) spectrin tetramers. In unstripped preparations, globular masses were observed near the centers of the spectrin filaments, probably corresponding to complexes of ankyrin with band 3 oligomers. Some of these globules linked pairs of spectrin filaments. Skeletons prepared with a minimum of perturbation had thickened actin protofilaments, presumably reflecting the presence of accessory proteins. The length of these actin filaments was highly uniform, averaging 33 +/- 5 nm. This is the length of nonmuscle tropomyosin. Since there is almost enough tropomyosin present to saturate the F-actin, our data support the hypothesis that tropomyosin may determine the length of actin protofilaments in the red cell membrane.

  18. Effects of N and P fertilisation on greenhouse gas (GHG) production in floodplain fen peat: A microcosm fertilisation experiment.

    NASA Astrophysics Data System (ADS)

    Stanley, Kieran; Heppell, Catherine; Belyea, Lisa; Baird, Andrew

    2016-04-01

    Biogeochemical and hydrological cycles are being significantly perturbed by anthropic activities altering atmospheric mole fractions of greenhouse gases (GHG) and increasing global temperatures. With the intensification of the hydrological cycle, lowland areas, such as floodplain fens, may be inundated more frequently. Rivers in agricultural catchments have the potential to pollute floodplain fens with significant amounts of nitrogen (N) and phosphorus (P); however, the effects of short-term (< 15 days) N and P fertilisation via fluvial inundation on GHG emissions from floodplain fens are poorly understood. The aim of this research was to determine how N (51 mg L-1 NO3-N) and P (1.4 mg L-1 PO43--P) additions may alter GHG (CO2, CH4, and N2O) production in floodplain fens of contrasting nutrient status under anaerobic conditions. A five-level (control, glucose (G), N+G, P+G, and N+P+G), fully-factorial microcosm experiment was designed and undertaken in Spring 2013 with peat from two floodplain fens under conservation management with similar vegetation (from Norfolk, United Kingdom). One site receives a higher nutrient load than the other and has a historical legacy of higher N and P contents within the peat. Results from the experiment showed no significant difference in CO2 production between the control and fertilised treatments from 0 to 96 hours, but a significant difference between treatments (ANCOVA, between factors: treatment and site; covariate: time; F4,419 = 11.844, p < 0.001) and site (F1,149 = 5.721, p = 0.017) from 96 hours to in the end of the experiment due to fermentation. N2O production only occurred in samples fertilised with N (N+G and N+P+G) due to denitrification. Rates of N2O production were significantly greater in samples from the lower-nutrient site in comparison to the nutrient-rich site (t12= 6.539, p < 0.001 and t12= 7.273, p < 0.001 for N+G and N+P+G fertilised samples, respectively). Fertilisation with N and P had different effects on

  19. Relationship between Size of Broken and Intact Families and Academic Achievement.

    ERIC Educational Resources Information Center

    Cherian, Varghese I.

    1991-01-01

    Compares relationship between family size and academic achievement of children from broken and intact families among Black African Xhosa-speaking children between the ages of 13 and 17. Results indicate a negative relationship between family size and academic achievement, regardless of broken or intact families. (Author/NL)

  20. 46 CFR 28.545 - Intact stability when using lifting gear.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 1 2012-10-01 2012-10-01 false Intact stability when using lifting gear. 28.545 Section... COMMERCIAL FISHING INDUSTRY VESSELS Stability § 28.545 Intact stability when using lifting gear. (a) Each vessel which lifts a weight over the side, or that uses fishing gear that can impose an...

  1. 46 CFR 28.545 - Intact stability when using lifting gear.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 1 2011-10-01 2011-10-01 false Intact stability when using lifting gear. 28.545 Section... COMMERCIAL FISHING INDUSTRY VESSELS Stability § 28.545 Intact stability when using lifting gear. (a) Each vessel which lifts a weight over the side, or that uses fishing gear that can impose an...

  2. Impact of Deepwater Horizon Oil Contamination on the Aqueous Geochemistry of Salt Marsh Sediment/Seawater Microcosms

    NASA Astrophysics Data System (ADS)

    Rentschler, E. K.; Donahoe, R. J.

    2011-12-01

    On April 20th, 2010, the Deepwater Horizon oil drilling rig, located in the Gulf of Mexico about 41 miles off the Louisiana coast, exploded, burned for two days, and sank. Approximately 4.9 million gallons of crude oil were released and traveled with ocean currents to reach the coasts of Louisiana, Mississippi, Alabama, and Florida. Previous studies have primarily considered the direct impact of oil and dispersant contamination on coastal ecosystems, but have not examined the potential impact of the accident on the inorganic geochemistry of coastal waters and sediments. In this study, microcosm experiments were conducted to determine how oil contamination will affect the concentration and distribution of trace elements in a salt marsh environment. Uncontaminated sediment and seawater, collected from a salt marsh at Bayou la Batre, Alabama, were measured into jars and spiked with 500 ppm MC-252 oil. Twenty jars, including duplicates and both sterile and non-sterile controls, were placed on a shaker table at 100 rpm. The jars were sacrificed at predetermined time intervals (0 h, 6 h, 12 h, 24 h, 48 h, 7 d, and 14 d), and the aqueous samples prepared for analysis by ICP-OES and IC. The pH for the water in the time series experiment ranged from 7.16 to 8.06. Seawater alkalinity was measured at 83.07 mg CaCO3/L. ICP-OES data show variations in aqueous element concentrations over the 14 day microcosm experiment. Significant positive correlations (>0.75) were found for the following pairs of elements: calcium and magnesium, calcium and sodium, magnesium and sodium, silica and boron, beryllium and boron, iron and silica, manganese and silica, boron and manganese, arsenic and nickel, beryllium and selenium, beryllium and zinc, copper and chloride, bromide and sulfate. Aqueous iron concentrations were highly correlated with solution pH. The presence of iron oxide and clays in the sediment indicates a potential for adsorption of trace elements sourced from the environment and

  3. Local knowledge, environmental politics, and the founding of ecology in the United States. Stephen Forbes and "The Lake as a Microcosm" (1887).

    PubMed

    Schneider, D W

    2000-12-01

    Stephen Forbes's "The Lake as a Microcosm" is one of the founding documents of the science of ecology in the United States. By tracing the connections between scientists and local fishermen underlying the research on floodplain lakes presented in "The Lake as a Microcosm," this essay shows how the birth of ecology was tied to local knowledge and the local politics of environmental transformation. Forbes and the other scientists of the Illinois Natural History Survey relied on fishermen for manual labor, expertise in catching fish, and knowledge of the natural history of the fishes. As Forbes and his colleagues worked in close contact with fishermen, they also adopted many of their political concerns over the privatization of the floodplain and became politically active in supporting their interests. The close connection between scientists and local knowledge forced the ecologists to reframe the boundaries of ecology as objective or political, pure or applied, local or scientific.

  4. After rotator cuff tears, the remaining (intact) tendons are mechanically altered.

    PubMed

    Perry, Stephanie M; Getz, Charles L; Soslowsky, Louis J

    2009-01-01

    Although presumed, damage in the remaining (intact) rotator cuff tendons in the presence of an isolated supraspinatus tendon tear or multiple tendon tear has not been well studied. This study used an animal model of multiple rotator cuff tendon tears to investigate alterations in the remaining (intact) tendon mechanical properties at 4 and 8 weeks after injury. Twenty-four rats served as uninjured controls, whereas 72 were divided among 3 tendon detachment groups: supraspinatus tendon detachment, supraspinatus + infraspinatus tendon detachment, and supraspinatus + subscapularis tendon detachment. The remaining (intact) rotator cuff tendons had decreased mechanical properties in the presence of rotator cuff tears. The remaining (intact) subscapularis and infraspinatus tendon cross-sectional areas increased, whereas tendon modulus decreased after tears of both 1 and 2 tendons. The remaining (intact) tendon cross-sectional areas continued to increase with time after injury. These alterations could potentially lead to further tendon damage and tear progression.

  5. Planetary Bioresources and Astroecology. 1. Planetary Microcosm Bioassays of Martian and Carbonaceous Chondrite Materials: Nutrients, Electrolyte Solutions, and Algal and Plant Responses

    NASA Astrophysics Data System (ADS)

    Mautner, Michael N.

    2002-07-01

    The biological fertilities of planetary materials can be assessed using microcosms based on meteorites. This study applies microcosm tests to martian meteorites and analogues and to carbonaceous chondrites. The biological fertilities of these materials are rated based on the soluble electrolyte nutrients, the growth of mesophile and cold-tolerant algae, and plant tissue cultures. The results show that the meteorites, in particular the Murchison CM2 carbonaceous chondrite and DaG 476 martian shergottite, contain high levels of water-extractable Ca, Mg, and SO 4-S. The martian meteorites DaG 476 and EETA 79001 also contain higher levels of extractable essential nutrients NO 3-N (0.013-0.017 g kg -1) and PO 4-P (0.019-0.046 g kg -1) than the terrestrial analogues. The yields of most of the water-extractable electrolytes vary only by factors of 2-3 under a wide range of planetary conditions. However, the long-term extractable phosphate increases significantly under a CO 2 atmosphere. The biological yields of algae and plant tissue cultures correlate with extractable NO 3-N and PO 4-P, identifying these as the limiting nutrients. Mesophilic algae and Asparagus officinalis cultures are identified as useful bioassay agents. A fertility rating system based on microcosm tests is proposed. The results rate the fertilities in the order martian basalts > terrestrial basalt, agricultural soil > carbonaceous chondrites, lava ash > cumulate igneous rock. The results demonstrate the application of planetary microcosms in experimental astroecology to rate planetary materials as targets for astrobiology exploration and as potential space bioresources. For example, the extractable materials in Murchison suggest that concentrated internal solutions in carbonaceous asteroids (3.8 mol L -1 electrolytes and 10 g L -1 organics) can support and disperse microorganisms introduced by natural or directed panspermia in early solar systems. The results also suggest that carbonaceous asteroids

  6. Molecular- and cultivation-based analyses of microbial communities in oil field water and in microcosms amended with nitrate to control H2S production.

    PubMed

    Kumaraswamy, Raji; Ebert, Sara; Gray, Murray R; Fedorak, Phillip M; Foght, Julia M

    2011-03-01

    Nitrate injection into oil fields is an alternative to biocide addition for controlling sulfide production ('souring') caused by sulfate-reducing bacteria (SRB). This study examined the suitability of several cultivation-dependent and cultivation-independent methods to assess potential microbial activities (sulfidogenesis and nitrate reduction) and the impact of nitrate amendment on oil field microbiota. Microcosms containing produced waters from two Western Canadian oil fields exhibited sulfidogenesis that was inhibited by nitrate amendment. Most probable number (MPN) and fluorescent in situ hybridization (FISH) analyses of uncultivated produced waters showed low cell numbers (≤10(3) MPN/ml) dominated by SRB (>95% relative abundance). MPN analysis also detected nitrate-reducing sulfide-oxidizing bacteria (NRSOB) and heterotrophic nitrate-reducing bacteria (HNRB) at numbers too low to be detected by FISH or denaturing gradient gel electrophoresis (DGGE). In microcosms containing produced water fortified with sulfate, near-stoichiometric concentrations of sulfide were produced. FISH analyses of the microcosms after 55 days of incubation revealed that Gammaproteobacteria increased from undetectable levels to 5-20% abundance, resulting in a decreased proportion of Deltaproteobacteria (50-60% abundance). DGGE analysis confirmed the presence of Delta- and Gammaproteobacteria and also detected Bacteroidetes. When sulfate-fortified produced waters were amended with nitrate, sulfidogenesis was inhibited and Deltaproteobacteria decreased to levels undetectable by FISH, with a concomitant increase in Gammaproteobacteria from below detection to 50-60% abundance. DGGE analysis of these microcosms yielded sequences of Gamma- and Epsilonproteobacteria related to presumptive HNRB and NRSOB (Halomonas, Marinobacterium, Marinobacter, Pseudomonas and Arcobacter), thus supporting chemical data indicating that nitrate-reducing bacteria out-compete SRB when nitrate is added.

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

    PubMed

    Mautner, Michael N

    2002-01-01

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

  8. Detection and quantification of a mycorrhization helper bacterium and a mycorrhizal fungus in plant-soil microcosms at different levels of complexity

    PubMed Central

    2013-01-01

    Background Host plant roots, mycorrhizal mycelium and microbes are important and potentially interacting factors shaping the performance of mycorrhization helper bacteria (MHB). We investigated the impact of a soil microbial community on the interaction between the extraradical mycelium of the ectomycorrhizal fungus Piloderma croceum and the MHB Streptomyces sp. AcH 505 in both the presence and the absence of pedunculate oak microcuttings. Results Specific primers were designed to target the internal transcribed spacer of the rDNA and an intergenic region between two protein encoding genes of P. croceum and the intergenic region between the gyrA and gyrB genes of AcH 505. These primers were used to perform real-time PCR with DNA extracted from soil samples. With a sensitivity of 10 genome copies and a linear range of 6 orders of magnitude, these real-time PCR assays enabled the quantification of purified DNA from P. croceum and AcH 505, respectively. In soil microcosms, the fungal PCR signal was not affected by AcH 505 in the absence of the host plant. However, the fungal signal became weaker in the presence of the plant. This decrease was only observed in microbial filtrate amended microcosms. In contrast, the PCR signal of AcH 505 increased in the presence of P. croceum. The increase was not significant in sterile microcosms that contained plant roots. Conclusions Real-time quantitative PCR assays provide a method for directly detecting and quantifying MHB and mycorrhizal fungi in plant microcosms. Our study indicates that the presence of microorganisms and plant roots can both affect the nature of MHB-fungus interactions, and that mycorrhizal fungi may enhance MHB growth. PMID:24025151

  9. Field and microcosm experiments to evaluate the effects of agricultural Cu treatment on the density and genetic structure of microbial communities in two different soils.

    PubMed

    Ranjard, Lionel; Echairi, Abdelwahad; Nowak, Virginie; Lejon, David P H; Nouaïm, Rachida; Chaussod, Rémi

    2006-11-01

    The effects of Cu amendment on indigenous soil microorganisms were investigated in two soils, a calcareous silty clay (Ep) and a sandy soil (Au), by means of a 1-year field experiment and a two-month microcosm incubation. Cu was added as 'Bordeaux mixture' [CuSO(4), Ca(OH)(2)] at the standard rate used in viticulture (B1=16 kg Cu kg(-1) soil) and at a higher level of contamination (B3=48 kg Cu ha(-1) soil). More extractable Cu was observed in sandy soil (Au) than in silty soil (Ep). Furthermore, total Cu and Cu-EDTA declined with time in Au soil, whereas they remained stable in Ep soil. Quantitative modifications of the microflora were assessed by C-biomass measurements and qualitative modifications were assessed by the characterization of the genetic structure of bacterial and fungal communities from DNA directly extracted from the soil, using B- and F-ARISA (bacterial and fungal automated ribosomal intergenic spacer analysis). In the field study, no significant modifications were observed in C-biomass whereas microcosm incubation showed a decrease in B3 contamination only. ARISA fingerprinting showed slight but significant modifications of bacterial and fungal communities in field and microcosm incubation. These modifications were transient in all cases, suggesting a short-term effect of Cu stress. Microcosm experiments detected the microbial community modifications with greater precision in the short-term, while field experiments showed that the biological effects of Cu contamination may be overcome or hidden by pedo-climatic variations.

  10. Preparation and Characterization of the Activated Carbon-Nylon Beads: Novel Material for In Situ Microbe Sampler and Microcosm Experiment in Groundwater Environment

    NASA Astrophysics Data System (ADS)

    Liu, J.; Liu, H.

    2015-12-01

    The organic pollution of groundwater is a widespread problem in the word. It is significant to study the microbial community especially related to organic contaminant biodegradation and their variation with groundwater environment parameters, so as to evaluate the biodegradability of the organic contaminants and then make a right decision for bioremediation. One of good ways for this study is to build a microcosm in groundwater containing target contaminant, where microbes especially relating to biodegradation will grow in the microcosm and be collected for analysis. This research aims to prepare a novel material for in situ microbe sampler and microcosm experiment in groundwater environment. The novel material, namely, the activated carbon-nylon (AC-N) beads, was prepared using activated carbon and nylon as main raw materials. The material consists of 3-4mm diameter spherical beads (Fig.1A and Fig.2 A) which have an internal surface area greater than 500 m2 g-1. FT-IR spectra (Fig.3) indicated the composition of activated carbon and nylon due to the variation of the peaks at the near 1627 cm-1and 1558 -1538 cm-1 before and after complex reaction. The equilibrium adsorption capacity of benzene on the beads was 16.76 mg/g at the initial concentration of 100 mg/L. The adsorption kinetics was found to follow the pseudo-second-order kinetic model (Fig.4). The mechanism of the adsorption process was determined from the intraparticle diffusion model. Camera and SEM images (Fig.1 B and Fig.2 A and B) showed that the beads had an open and channel pore structures, the microbes might enter into and grow up in the beads (Fig.1 C and Fig.2 C). All these results showed that the AC-N beads could form the in situ microcosm of organic pollutants and microbes, which provided a promising prospect for assessing the biodegradability of the organic pollutants by intrinsic microbes in the groundwater.

  11. Inoculation of PAH-degrading strains of Fusarium solani and Arthrobacter oxydans in rhizospheric sand and soil microcosms: microbial interactions and PAH dissipation.

    PubMed

    Thion, Cécile; Cébron, Aurélie; Beguiristain, Thierry; Leyval, Corinne

    2013-07-01

    Very little is known about the influence of bacterial-fungal ecological interactions on polycyclic aromatic hydrocarbon (PAH) dissipation in soils. Fusarium solani MM1 and Arthrobacter oxydans MsHM11 can dissipate PAHs in vitro. We investigated their interactions and their effect on the dissipation of three PAHs-phenanthrene (PHE), pyrene (PYR) and dibenz(a,h)anthracene (DBA)-in planted microcosms, in sterile sand or non-sterile soil. In sterile sand microcosms planted with alfalfa, the two microbes survived and grew, without any significant effect of co-inoculation. Co-inoculation led to the dissipation of 46 % of PHE after 21 days. In soil microcosms, whether planted with alfalfa or not, both strains persisted throughout the 46 days of the experiment, without any effect of co-inoculation or of alfalfa, as assessed by real-time PCR targeting taxon-level indicators, i.e. Actinobacteria 16S rDNA and the intergenic transcribed spacer specific to the genus Fusarium. The microbial community was analyzed by temporal temperature gradient electrophoresis and real-time PCR targeting bacterial and fungal rDNA and PAH-ring hydroxylating dioxygenase genes. These communities were modified by PAH pollution, which selected PAH-degrading bacteria, by the presence of alfalfa and, concerning the bacterial community, by inoculation. PHE and PYR concentrations significantly decreased (91 and 46 %, respectively) whatever the treatment, but DBA concentration significantly decreased (30 %) in planted and co-inoculated microcosms only.

  12. Calcium Sparks in Intact Skeletal Muscle Fibers of the Frog

    PubMed Central

    Hollingworth, S.; Peet, J.; Chandler, W.K; Baylor, S.M.

    2001-01-01

    Calcium sparks were studied in frog intact skeletal muscle fibers using a home-built confocal scanner whose point-spread function was estimated to be ∼0.21 μm in x and y and ∼0.51 μm in z. Observations were made at 17–20°C on fibers from Rana pipiens and Rana temporaria. Fibers were studied in two external solutions: normal Ringer's ([K+] = 2.5 mM; estimated membrane potential, −80 to −90 mV) and elevated [K+] Ringer's (most frequently, [K+] = 13 mM; estimated membrane potential, −60 to −65 mV). The frequency of sparks was 0.04–0.05 sarcomere−1 s−1 in normal Ringer's; the frequency increased approximately tenfold in 13 mM [K+] Ringer's. Spark properties in each solution were similar for the two species; they were also similar when scanned in the x and the y directions. From fits of standard functional forms to the temporal and spatial profiles of the sparks, the following mean values were estimated for the morphological parameters: rise time, ∼4 ms; peak amplitude, ∼1 ΔF/F (change in fluorescence divided by resting fluorescence); decay time constant, ∼5 ms; full duration at half maximum (FDHM), ∼6 ms; late offset, ∼0.01 ΔF/F; full width at half maximum (FWHM), ∼1.0 μm; mass (calculated as amplitude × 1.206 × FWHM3), 1.3–1.9 μm3. Although the rise time is similar to that measured previously in frog cut fibers (5–6 ms; 17–23°C), cut fiber sparks have a longer duration (FDHM, 9–15 ms), a wider extent (FWHM, 1.3–2.3 μm), and a strikingly larger mass (by 3–10-fold). Possible explanations for the increase in mass in cut fibers are a reduction in the Ca2+ buffering power of myoplasm in cut fibers and an increase in the flux of Ca2+ during release. PMID:11723160

  13. Measurements and interpretations of light scattering from intact biological cells

    NASA Astrophysics Data System (ADS)

    Wilson, Jeremy D.

    Visible light interacts with biological cells primarily through elastic scattering. The details of how cells scatter light depend on their morphology and their substructures. In this thesis we first present a series of experiments and models to discern the specific contributions of certain sub-cellular constituents to whole-cell scattering. Exploiting the findings of those studies, we report on experiments within model systems of cell death that demonstrate the potential of light scattering measurements as a tool in modern biology. Instrumentation capable of exploiting the findings of this thesis from a biology-relevant microscopy platform is designed and developed. A Mie theory based interpretation of light scattering signals originating from a collection of particles with a broad size distribution is developed. Upon applying this model to scattering data from intact cells, we find that it robustly extracts the size scale of dominant light scattering particles, suggests that scattering measurements are sensitive primarily to mitochondrial and lysosomal morphology, and unites conflicting results in the literature. Using this model as a basis, we present a collection of studies in which we use various strategies of photodynamic therapy (PDT) as a biophysical tool to perturb mitochondria and lysosomes, and observe the effects of these perturbations on whole-cell scattering. Through these experiments, we are able to discern the individual contributions of mitochondria and lysosomes to whole-cell light scattering, and demonstrate that mitochondria are responsible for roughly 80% of the scattering signal. Results of experiments aimed at demonstrating the potential role that light scattering measurements have to play in future studies of cell death biology are presented. We first show that mitochondrial-PDT-induced morphology changes measured with light scattering map into the cell killing efficacy of the therapy. We next demonstrate that mitochondrial

  14. Use of acetate, propionate and butyrate for reduction of nitrate and sulfate and methanogenesis in microcosms and bioreactors simulating an oil reservoir.

    PubMed

    Chen, Chuan; Shen, Yin; An, Dongshan; Voordouw, Gerrit

    2017-01-27

    Acetate, propionate and butyrate (volatile fatty acids, VFA) occur in oil field waters and are frequently used for microbial growth of oil field consortia. We determined the kinetics of use of these VFA components (3 mM of each) by an anaerobic oil field consortium in microcosms containing 2 mM sulfate and either 0, 4, 6, 8 or 13 mM of nitrate. Nitrate was reduced first with preference for acetate and propionate. Sulfate reduction then proceeded with propionate (not butyrate) as the electron donor, whereas the fermentation of butyrate (not propionate) was associated with methanogenesis. Microbial community analyses indicated Paracoccus-Thauera, Desulfobulbus and Syntrophomonas-Methanobacterium as the dominant taxa catalyzing these three processes. Most probable number assays showed the presence of up to 10(7)/ml of propionate-oxidizing SRB in waters from the Medicine Hat Glauconitic C field. Bioreactors with the same concentrations of sulfate and VFA responded similarly to increasing concentrations of injected nitrate as observed in the microcosms: sulfide formation was prevented by adding approximately 80% of the nitrate dose needed to completely oxidize VFA to CO2 in both. Thus this work has demonstrated that simple time-dependent observations of the use of acetate, propionate and butyrate for nitrate reduction, sulfate reduction and methanogenesis in microcosms are a good proxy for these processes in bioreactors of which monitoring is more complex.

  15. Microbial-Catalyzed Reductive Dechlorination of Polychlorinated Biphenyls in Hudson and Grasse River Sediment Microcosms: Determination of Dechlorination Preferences and Identification of Rare Ortho Removal Pathways.

    PubMed

    Xu, Yan; Gregory, Kelvin B; VanBriesen, Jeanne M

    2016-12-06

    Biodegradation of polychlorinated biphenyls (PCBs) is an important transformation and detoxification route in the environment. To better understand the influence of PCB congener compositions on dechlorination, sediments from two rivers, Hudson and Grasse, and two PCB mixtures (PCB 5/12, 64/71, 105/114, and 149/153/170 in Mixture 1 and PCB 5/12, 64/71, 82/97/99, and 144/170 in Mixture 2) were used for this microcosm study. The Grasse River sediment microcosms exhibited more extensive dechlorination than the Hudson River sediment microcosms. The extent of dechlorination was predominantly controlled by sediment itself, not by the PCB compositions. Rare ortho dechlorination, targeting mono-ortho PCB congeners was observed in Grasse sediment, indicating a potential for full dechlorination of some PCBs in this sediment. The identified ortho dechlorination pathways were PCB 28 (24-4-CB) to PCB 15 (4-4-CB) and PCB 25 (24-3-CB) to PCB 13(3-4-CB). The relative abundances of Dehalococcoides were much higher in both sediments spiked with PCBs. An apparent increase of Dehalococcoides 16S rRNA genes coincided with the commencement of dechlorination. The dechlorination preferences were identified using a modified data analysis approach focusing on chlorine neighboring conditions. In both sediments, the overall dechlorination preferred meta > para > ortho. Specially, ortho-/double-flanked meta-chlorines were primarily targeted followed by single-/double-flanked para-chlorines.

  16. Evaluation of ethyl tert-butyl ether biodegradation in a contaminated aquifer by compound-specific isotope analysis and in situ microcosms.

    PubMed

    Bombach, Petra; Nägele, Norbert; Rosell, Mònica; Richnow, Hans H; Fischer, Anko

    2015-04-09

    Ethyl tert-butyl ether (ETBE) is an upcoming groundwater pollutant in Europe whose environmental fate has been less investigated, thus far. In the present study, we investigated the in situ biodegradation of ETBE in a fuel-contaminated aquifer using compound-specific stable isotope analysis (CSIA), and in situ microcosms in combination with total lipid fatty acid (TLFA)-stable isotope probing (SIP). In a first field investigation, CSIA revealed insignificant carbon isotope fractionation, but low hydrogen isotope fractionation of up to +14‰ along the prevailing anoxic ETBE plume suggesting biodegradation of ETBE. Ten months later, oxygen injection was conducted to enhance the biodegradation of petroleum hydrocarbons (PH) at the field site. Within the framework of this remediation measure, in situ microcosms loaded with [(13)C6]-ETBE (BACTRAP(®)s) were exposed for 119 days in selected groundwater wells to assess the biodegradation of ETBE by TLFA-SIP under the following conditions: (i) ETBE as main contaminant; (ii) ETBE as main contaminant subjected to oxygen injection; (iii) ETBE plus other PH; (iv) ETBE plus other PH subjected to oxygen injection. Under all conditions investigated, significant (13)C-incorporation into microbial total lipid fatty acids extracted from the in situ microcosms was found, providing clear evidence of ETBE biodegradation.

  17. Brackish Eutrophic Water Treatment by Iris pseudacorus L.-Planted Microcosms: Physiological Responses of Iris pseudacorus L. to Salinity.

    PubMed

    Zhao, Huilin; Wang, Fen; Ji, Min

    2015-01-01

    Iris pseudacorus L. has been widely used in aquatic ecosystem to remove nutrient and has achieved positive effects. However, little is known regarding the nutrient-removal performance and physiological responses of I. pseudacorus for brackish eutrophic water treatment due to high nutrients combined with certain salinity levels. In this study, I. pseudacorus-planted microcosms were established to evaluate the capacity of I. pseudacorus to remove excessive nutrients from fresh (salinity 0.05%) and brackish (salinity 0.5%) eutrophic waters. The degradation of total nitrogen and ammonia nitrogen were not affected by 0.5% salinity; 0.5% salinity promoted the degradation of nitrate nitrogen while severely inhibited the degradation of total phosphorus. Additionally, 0.5% salinity was found to induce stress responses quantified by measuring six physiological indexes. Compared to 0.05% salinity, 0.5% salinity resulted in significant decreases in the chlorophyll a, b and total chlorophyll contents of I. pseudacorus which closely related to photosynthesis (p < 0.05). Furthermore, the higher proline, malondialdehyde contents and antioxidant enzyme activities were detected in I. pseudacorus exposed to 0.5% salinity, which provided protection against reactive oxygen species. The results highlight that the cellular stress assays are efficient for monitoring the health of I. pseudacorus in salinity shock-associated constructed wetlands.

  18. Effect of imbalanced nutrients and immigration on Prymnesium parvum community dominance and toxicity: Results from in-lake microcosm experiments

    USGS Publications Warehouse

    Errera, R.M.; Roelke, D.L.; Kiesling, R.L.; Brooks, B.W.; Grover, J.P.; Schwierzke, L.; Urena-Boeck, F.; Baker, J.W.; Pinckney, J.L.

    2008-01-01

    Prymnesium parvum, a haptophyte species, forms harmful blooms, including those that have caused severe fish kills in Texas, USA, over the past 6 yr. We studied P. parvum dynamics using in situ microcosm experiments at Lake Possum Kingdom, Texas, during 3 seasons (fall 2004, winter and spring 2005). Experimental treatments included full and partial nutrient enrichment (encompassing nitrogen [N] and phosphorus [P] deficient treatments), P. parvum immigration and combinations of these factors. In the control and N and P deficient treatments, P. parvum populations dominated the community, but only in the N deficient treatments did P. parvum experience a significant growth in the population. In contrast, when nutrients were not limiting, P. parvum tended to lose its competitive edge to other taxa such as chlorophytes, euglenophytes and diatoms, which then dominated the community. Population growth of P. parvum was also stimulated through immigration, but only during the winter experiment, a period of the year when bloom initiation is common. This finding suggests that movement into the water column may be an important process leading to P. parvum bloom initiation. Toxicity of P. parvum to fish was also affected by the nutrient changes: during conditions of no nutrient addition P. parvum was most toxic; intermediate toxicity was observed under N and P deficient conditions, and full nutrient enrichments resulted in nearly non-toxic conditions. ?? Inter-Research 2008.

  19. Shifting nutrient-mediated interactions between algae and bacteria in a microcosm: evidence from alkaline phosphatase assay.

    PubMed

    Liu, Huali; Zhou, Yiyong; Xiao, Wenjuan; Ji, Lei; Cao, Xiuyun; Song, Chunlei

    2012-05-20

    The impacts of different nutrient additions (N + P, N + P + C, 4N + P, 4N + P + C, N + 2P) on the growth of algae and bacteria were studied in a microcosm experiment. Since alkaline phosphatase activity (APA) provides an indication of phosphorus deficiency, the higher value for algal APA in the treatments with excess nitrogen and for bacterial APA in the treatments with excess carbon suggested that, algal and bacterial phosphorus-limited status were induced by abundant nitrogen and carbon input, respectively. Bacterial phosphorus-limited status was weakened due to higher bacterial competition for phosphorus, compared to algae. In comparison with the bacterial and specific bacterial APA, higher values of algal and specific algal APA were found, which showed a gradual increase that coincided with the increase of chlorophyll a concentration. This fact indicated not only a stronger phosphorus demand by algae than by bacteria, but also a complementary relationship for phosphorus demand between algae and bacteria. However, this commensalism could be interfered by glucose input resulting in the decline of chlorophyll a concentration. Furthermore, the correlation between bacterial numbers and chlorophyll a concentration was positive in treatments without carbon and blurry in treatments with carbon. These observations validate a hypothesis that carbon addition can stimulate bacterial growth justifying bacterial nutrient demand, which decreases the availability of nutrients to algae and affects nutrient relationship between algae and bacteria. However, this interference would terminate after algal and bacterial adaption to carbon input.

  20. Can the algicidal material Ca-aminoclay be harmful when applied to a natural ecosystem? An assessment using microcosms.

    PubMed

    Jung, Seung Won; Yun, Suk Min; Yoo, Jae Won; Zhun, Li; Jang, Pung-Guk; Lim, Dhong-Il; Lee, Young-Chul; Lee, Hyun Uk; Lee, Taek-Kyun; Heo, Jinbee; Lee, Jin Hwan; Han, Myung-Soo

    2015-11-15

    We assessed the ability of an artificial clay (Ca-aminoclay) to suppress harmful algal bloom species (HABs) such as Cochlodinium polykrikoides and Chattonella marina and investigated the ecological responses in the closed and open microcosm systems. The Ca-aminoclay induced rapidly and selectively cell lysis in the HABs. However, applying Ca-aminoclay could cause adverse impacts in terms of biological and environmental changes. The bacterioplankton abundance increased and then, the abundances of heterotrophic nanoflagellates and ciliates increased rapidly. Extremely poor environmental conditions such as increase in nutrients and development of anoxic conditions were sustained continuously in a closed system, while the environmental conditions in open systems deteriorated before recovering to the initial conditions. We evaluated the potential for the occurrence of a bloom of another phytoplankton after HABs had been controlled using the Ca-aminoclay. The Ca-aminoclay controlled blooms of Chattonella marina in mixed cell cultures containing a Tetraselmis chui. However, T. chui increased over time and then bloomed. Therefore, caution should be taken when considering the direct application of Ca-aminoclay in natural environments even though it offers the rapid removal of HABs.

  1. Removal of diclofenac and sulfamethoxazole from synthetic municipal waste water in microcosm downflow constructed wetlands: Start-up results.

    PubMed

    Nowrotek, Monika; Sochacki, Adam; Felis, Ewa; Miksch, Korneliusz

    2016-01-01

    The objectives of this study were to investigate the start-up removal of pharmaceutical compounds diclofenac and sulfamethoxazole in microcosm downflow constructed wetlands and their effect on the performance of the studied constructed wetlands, and also to assess the effect of plants on the removal of these compounds. The experimental system that was used in this 86-day experiment consisted of 24 columns filled up to 70 cm with predominantly sandy material. Four types of columns were used (six replicates) depending on the presence of plants (Phalaris arundinacea L. var. picta L.) and the presence of pharmaceutical compounds in the influent. The influent was synthetic municipal waste water to which a mixture of 5 mg/L of diclofenac and 5 mg/L of sulfamethoxazole was added. The observed removal of diclofenac was moderate (approx. 50%) and the removal of sulfamethoxazole was relatively low (24-30%). It was found that the removal of diclofenac and sulfamethoxazole was not affected by the vegetation. The presence of diclofenac and sulfamethoxazole in the influent had significant effect on the effluent concentration of N-NO3 and the water loss in the columns, which in both cases were lower than in the control columns. The scope for further research was discussed.

  2. Biodegradation of phenanthrene in bioaugmented microcosm by consortium ASP developed from coastal sediment of Alang-Sosiya ship breaking yard.

    PubMed

    Patel, Vilas; Patel, Janki; Madamwar, Datta

    2013-09-15

    A phenanthrene-degrading bacterial consortium (ASP) was developed using sediment from the Alang-Sosiya shipbreaking yard at Gujarat, India. 16S rRNA gene-based molecular analyses revealed that the bacterial consortium consisted of six bacterial strains: Bacillus sp. ASP1, Pseudomonas sp. ASP2, Stenotrophomonas maltophilia strain ASP3, Staphylococcus sp. ASP4, Geobacillus sp. ASP5 and Alcaligenes sp. ASP6. The consortium was able to degrade 300 ppm of phenanthrene and 1000 ppm of naphthalene within 120 h and 48 h, respectively. Tween 80 showed a positive effect on phenanthrene degradation. The consortium was able to consume maximum phenanthrene at the rate of 46 mg/h/l and degrade phenanthrene in the presence of other petroleum hydrocarbons. A microcosm study was conducted to test the consortium's bioremediation potential. Phenanthrene degradation increased from 61% to 94% in sediment bioaugmented with the consortium. Simultaneously, bacterial counts and dehydrogenase activities also increased in the bioaugmented sediment. These results suggest that microbial consortium bioaugmentation may be a promising technology for bioremediation.

  3. Bioaccumulation of perfluoroalkyl acids including the isomers of perfluorooctane sulfonate in carp (Cyprinus carpio) in a sediment/water microcosm.

    PubMed

    Fang, Shuhong; Zhang, Yifeng; Zhao, Shuyan; Qiang, Liwen; Chen, Meng; Zhu, Lingyan

    2016-12-01

    Carp (Cyprinus carpio) were exposed to perfluoroalkyl acids (PFAAs) including perfluorooctane sulfonate (PFOS) isomers in an artificially contaminated sediment/water microcosm. The uptake constant of PFAAs increased with increasing carbon chain length, whereas the elimination coefficient displayed the opposite trend, suggesting that carbon chain length plays an important role in the bioaccumulation of PFAAs. When the contribution of suspended particulate matter was taken into account, the bioaccumulation factors (BAFs) became lower (3.61-600 L/kg) compared with BAFs derived from only considering the absorption from free PFAAs in water (3.85-97000 L/kg). The results indicate that suspended particulate matter in water constitutes an important source of exposure for aquatic organisms to long-chain PFAAs. Linear (n-)PFOS was preferentially accumulated compared with branched isomers in carp. Among the branched isomers, 1m-PFOS displayed the greatest bioaccumulation, whereas m2 -PFOS had the lowest. Linear PFOS displayed greater partitioning ability from blood to other tissues over branched PFOS (br-PFOS) isomers, leading to a relatively lower n-PFOS proportion in blood. In summary, suspended particulate matter made a contribution to the accumulation of long-chain PFAAs in aquatic organisms, and n-PFOS was preferentially accumulated compared with br-PFOS isomers. Environ Toxicol Chem 2016;35:3005-3013. © 2016 SETAC.

  4. Transfer of elements relevant to nuclear fuel cycle from soil to boreal plants and animals in experimental meso- and microcosms.

    PubMed

    Tuovinen, Tiina S; Kasurinen, Anne; Häikiö, Elina; Tervahauta, Arja; Makkonen, Sari; Holopainen, Toini; Juutilainen, Jukka

    2016-01-01

    Uranium (U), cobalt (Co), molybdenum (Mo), nickel (Ni), lead (Pb), thorium (Th) and zinc (Zn) occur naturally in soil but their radioactive isotopes can also be released into the environment during the nuclear fuel cycle. The transfer of these elements was studied in three different trophic levels in experimental mesocosms containing downy birch (Betula pubescens), narrow buckler fern (Dryopteris carthusiana) and Scandinavian small-reed (Calamagrostis purpurea ssp. Phragmitoides) as producers, snails (Arianta arbostorum) as herbivores, and earthworms (Lumbricus terrestris) as decomposers. To determine more precisely whether the element uptake of snails is mainly via their food (birch leaves) or both via soil and food, a separate microcosm experiment was also performed. The element uptake of snails did not generally depend on the presence of soil, indicating that the main uptake route was food, except for U, where soil contact was important for uptake when soil U concentration was high. Transfer of elements from soil to plants was not linear, i.e. it was not correctly described by constant concentration ratios (CR) commonly applied in radioecological modeling. Similar nonlinear transfer was found for the invertebrate animals included in this study: elements other than U were taken up more efficiently when element concentration in soil or food was low.

  5. Growing evidence for facultative biotrophy in saprotrophic fungi: data from microcosm tests with 201 species of wood-decay basidiomycetes.

    PubMed

    Smith, Gabriel R; Finlay, Roger D; Stenlid, Jan; Vasaitis, Rimvydas; Menkis, Audrius

    2017-04-06

    Ectomycorrhizal (ECM) symbioses have evolved a minimum of 78 times independently from saprotrophic lineages, indicating the potential for functional overlap between ECM and saprotrophic fungi. ECM fungi have the capacity to decompose organic matter, and although there is increasing evidence that some saprotrophic fungi exhibit the capacity to enter into facultative biotrophic relationships with plant roots without causing disease symptoms, this subject is still not well studied. In order to determine the extent of biotrophic capacity in saprotrophic wood-decay fungi and which systems may be useful models, we investigated the colonization of conifer seedling roots in vitro using an array of 201 basidiomycete wood-decay fungi. Microtome sectioning, differential staining and fluorescence microscopy were used to visualize patterns of root colonization in microcosm systems containing Picea abies or Pinus sylvestris seedlings and each saprotrophic fungus. Thirty-four (16.9%) of the tested fungal species colonized the roots of at least one tree species. Two fungal species showed formation of a mantle and one showed Hartig net-like structures. These features suggest the possibility of an active functional symbiosis between fungus and plant. The data indicate that the capacity for facultative biotrophic relationships in free-living saprotrophic basidiomycetes may be greater than previously supposed.

  6. Relative importance of nutrients and mortality factors on prokaryotic community composition in two lakes of different trophic status: microcosm experiments.

    PubMed

    Jardillier, Ludwig; Boucher, Delphine; Personnic, Sébastien; Jacquet, Stéphan; Thénot, Aurélie; Sargos, Denis; Amblard, Christian; Debroas, Didier

    2005-08-01

    The effect of nutrient resources (N and P enrichment) and of different grazing communities on the prokaryotic community composition (PCC) was investigated in two freshwater ecosystems: Sep reservoir (oligomesotrophic) and lake Aydat (eutrophic). An experimental approach using microcosms was chosen, that allowed control of both predation levels, by size fractionation of predators, and resources, by nutrient amendments. Changes in PCC were monitored by fluorescent in situ hybridization (FISH) and terminal-restriction fragment length polymorphism (T-RFLP). The main mortality agents were (i) heterotrophic nanoflagellates and virus-like particles in Aydat and (ii) cladocerans in Sep. All the nutritional elements assayed (N-NO3, P-PO4 and N-NH4) together with prokaryotic production (PP) always accounted for a significant part of the variations in PCC. Overall, prokaryotic diversity was mainly explained by resources in Sep, by a comparable contribution of resources and mortality factors in lake Aydat and, to a lesser extent, by the combined action of both.

  7. The effect of bioturbation by Lumbriculus variegatus on transport and distribution of lead in a freshwater microcosm.

    PubMed

    Blankson, Emmanuel R; Klerks, Paul L

    2016-05-01

    The present study investigated the effect of bioturbation by the oligochaete worm Lumbriculus variegatus on the transport and environmental distribution of lead (Pb). Experiments used L. variegatus at densities of 0 ind./m(2), 2093 ind./m(2), and 8372 ind./m(2), in freshwater microcosms with Pb-spiked sediment. At the end of the 14-d experiment, Pb levels in the water column, tissues of L. variegatus, and sediment were determined, and bioturbation was quantified using luminophores. The bioturbation by L. variegatus increased Pb transport from the sediment to the water column. However, it did not significantly affect Pb bioaccumulation by L. variegatus or Pb levels in the sediment. The biodiffusion coefficient (Db) was positively related to worm density, but did not differ between Pb-spiked sediment and uncontaminated sediment. The latter finding suggests that Pb at the 100 μg/g concentration used in the present study did not affect L. variegatus bioturbation. The present study shows that bioturbation can enhance Pb transfer across the sediment-water interface and thus enhance Pb availability to organisms in the water column.

  8. Community Interactions Modify the Effects of Pharmaceutical Exposure: A Microcosm Study on Responses to Propranolol in Baltic Sea Coastal Organisms

    PubMed Central

    Oskarsson, Hanna; Eriksson Wiklund, Ann-Kristin; Thorsén, Gunnar; Danielsson, Gabriela; Kumblad, Linda

    2014-01-01

    This study investigated the uptake and effects of a common human pharmaceutical, propranolol, on the structure and function of a coastal Baltic Sea model community consisting of macroalga (Ceramium tenuicorne), mussels (Mytilus edulis trossulus), amphipods (Gammarus spp.), water and sediment. The most sensitive species, the mussel, was affected to the same extent as in previous single species studies, while the effects on the amphipod and alga were smaller or even positive compared to experiments performed in less complex test systems. The observed cascade of beneficial effects was a result of inter-specific species interactions that buffered for more severe effects. The poor condition of the mussel led to a feeding shift from alga to mussel by the amphipods. The better food quality, due to the dietary shift, counteracted the effects of the exposure. Less amphipod grazing, together with increased levels of nutrients in the water was favourable for the alga, despite the negative effects of propranolol. This microcosm study showed effects on organisms on different organizational levels as well as interactions among the different components resulting in indirect exposure effects of both functional and structural nature. The combination of both direct and indirect effects would not have been detected using simpler single- or even two-species study designs. The observed structural changes would in the natural environment have a long-term influence on ecosystem function, especially in a low-biodiversity ecosystem like the Baltic Sea. PMID:24713620

  9. Shared ancestry influences community stability by altering competitive interactions: evidence from a laboratory microcosm experiment using freshwater green algae.

    PubMed

    Venail, Patrick A; Alexandrou, Markos A; Oakley, Todd H; Cardinale, Bradley J

    2013-10-07

    The impact of biodiversity on the stability of ecological communities has been debated among biologists for more than a century. Recently summarized empirical evidence suggests that biodiversity tends to enhance the temporal stability of community-level properties such as biomass; however, the underlying mechanisms driving this relationship remain poorly understood. Here, we report the results of a microcosm study in which we used simplified systems of freshwater microalgae to explore how the phylogenetic relatedness of species influences the temporal stability of community biomass by altering the nature of their competitive interactions. We show that combinations of two species that are more evolutionarily divergent tend to have lower temporal stability of biomass. In part, this is due to negative 'selection effects' in which bicultures composed of distantly related species are more likely to contain strong competitors that achieve low biomass. In addition, bicultures of distantly related species had on average weaker competitive interactions, which reduced compensatory dynamics and decreased the stability of community biomass. Our results demonstrate that evolutionary history plays a key role in controlling the mechanisms, which give rise to diversity-stability relationships. As such, patterns of shared ancestry may help us predict the ecosystem-level consequences of biodiversity loss.

  10. Small-scale soil water repellency in pine rizhosphere associated with ectomycorrhiza is affected by nutrient patchiness: a soil microcosms study