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Sample records for affect microbial activity

  1. Winter climate change affects growing-season soil microbial biomass and activity in northern hardwood forests.

    PubMed

    Durán, Jorge; Morse, Jennifer L; Groffman, Peter M; Campbell, John L; Christenson, Lynn M; Driscoll, Charles T; Fahey, Timothy J; Fisk, Melany C; Mitchell, Myron J; Templer, Pamela H

    2014-11-01

    Understanding the responses of terrestrial ecosystems to global change remains a major challenge of ecological research. We exploited a natural elevation gradient in a northern hardwood forest to determine how reductions in snow accumulation, expected with climate change, directly affect dynamics of soil winter frost, and indirectly soil microbial biomass and activity during the growing season. Soils from lower elevation plots, which accumulated less snow and experienced more soil temperature variability during the winter (and likely more freeze/thaw events), had less extractable inorganic nitrogen (N), lower rates of microbial N production via potential net N mineralization and nitrification, and higher potential microbial respiration during the growing season. Potential nitrate production rates during the growing season were particularly sensitive to changes in winter snow pack accumulation and winter soil temperature variability, especially in spring. Effects of elevation and winter conditions on N transformation rates differed from those on potential microbial respiration, suggesting that N-related processes might respond differently to winter climate change in northern hardwood forests than C-related processes.

  2. Zinc oxide nanoparticles cause inhibition of microbial denitrification by affecting transcriptional regulation and enzyme activity.

    PubMed

    Zheng, Xiong; Su, Yinglong; Chen, Yinguang; Wan, Rui; Liu, Kun; Li, Mu; Yin, Daqiang

    2014-12-02

    Over the past few decades, human activities have accelerated the rates and extents of water eutrophication and global warming through increasing delivery of biologically available nitrogen such as nitrate and large emissions of anthropogenic greenhouse gases. In particular, nitrous oxide (N2O) is one of the most important greenhouse gases, because it has a 300-fold higher global warming potential than carbon dioxide. Microbial denitrification is a major pathway responsible for nitrate removal, and also a dominant source of N2O emissions from terrestrial or aquatic environments. However, whether the release of zinc oxide nanoparticles (ZnO NPs) into the environment affects microbial denitrification is largely unknown. Here we show that the presence of ZnO NPs lead to great increases in nitrate delivery (9.8-fold higher) and N2O emissions (350- and 174-fold higher in the gas and liquid phases, respectively). Our data further reveal that ZnO NPs significantly change the transcriptional regulations of glycolysis and polyhydroxybutyrate synthesis, which causes the decrease in reducing powers available for the reduction of nitrate and N2O. Moreover, ZnO NPs substantially inhibit the gene expressions and catalytic activities of key denitrifying enzymes. These negative effects of ZnO NPs on microbial denitrification finally cause lower nitrate removal and higher N2O emissions, which is likely to exacerbate water eutrophication and global warming.

  3. Soil microbial activity is affected by Roundup WeatherMax and pesticides applied to cotton (Gossypium hirsutum).

    PubMed

    Lancaster, Sarah H; Haney, Richard L; Senseman, Scott A; Hons, Frank M; Chandler, James M

    2006-09-20

    Adoption of glyphosate-based weed control systems has led to increased use of the herbicide with continued use of additional pesticides. Combinations of pesticides may affect soil microbial activity differently than pesticides applied alone. Research was conducted to evaluate the influence of glyphosate-based cotton pest management systems on soil microbial activity. Soil was treated with commercial formulations of trifluralin, aldicarb, and mefenoxam + pentachloronitrobenzene (PCNB) with or without glyphosate (applied as Roundup WeatherMax). The soil microbial activity was measured by quantifying C and N mineralization. Soil microbial biomass was determined using the chloroform fumigation-incubation method. Soils treated with glyphosate alone exhibited greater cumulative C mineralization 30 days after treatment than all other treatments, which were similar to the untreated control. The addition of Roundup WeatherMax reduced C mineralization in soils treated with fluometuron, aldicarb, or mefenoxam + PCNB formulations. These results indicate that glyphosate-based herbicides alter the soil microbial response to other pesticides.

  4. CO2-induced shift in microbial activity affects carbon trapping and water quality in anoxic bioreactors

    NASA Astrophysics Data System (ADS)

    Kirk, Matthew F.; Santillan, Eugenio F. U.; Sanford, Robert A.; Altman, Susan J.

    2013-12-01

    Microbial activity is a potentially important yet poorly understood control on the fate and environmental impact of CO2 that leaks into aquifers from deep storage reservoirs. In this study we examine how variation in CO2 abundance affected competition between Fe(III) and SO42--reducers in anoxic bioreactors inoculated with a mixed-microbial community from a freshwater aquifer. We performed two sets of experiments: one with low CO2 partial pressure (∼0.02 atm) in the headspace of the reactors and one with high CO2 partial pressure (∼1 atm). A fluid residence time of 35 days was maintained in the reactors by replacing one-fifth of the aqueous volume with fresh medium every seven days. The aqueous medium was composed of groundwater amended with small amounts of acetate (250 μM), phosphate (1 μM), and ammonium (50 μM) to stimulate microbial activity. Synthetic goethite (1 mmol) and SO42- (500 μM influent concentration) were also available in each reactor to serve as electron acceptors. Results of this study show that higher CO2 abundance increased the ability of Fe(III) reducers to compete with SO42- reducers, leading to significant shifts in CO2 trapping and water quality. Mass-balance calculations and pyrosequencing results demonstrate that SO42- reducers were dominant in reactors with low CO2 content. They consumed 85% of the acetate after acetate consumption reached steady state while Fe(III) reducers consumed only 15% on average. In contrast, Fe(III) reducers were dominant during that same interval in reactors with high CO2 content, consuming at least 90% of the acetate while SO42- reducers consumed a negligible amount (<1%). The higher rate of Fe(III) reduction in the high-CO2 bioreactors enhanced CO2 solubility trapping relative to the low-CO2 bioreactors by increasing alkalinity generation (6X). Hence, the shift in microbial activity we observed was a positive feedback on CO2 trapping. More rapid Fe(III) reduction degraded water quality, however, by

  5. Vertical and horizontal distributions of microbial abundances and enzymatic activities in propylene-glycol-affected soils.

    PubMed

    Biró, Borbála; Toscano, Giuseppe; Horváth, Nikoletta; Matics, Heléna; Domonkos, Mónika; Scotti, Riccardo; Rao, Maria A; Wejden, Bente; French, Helen K

    2014-01-01

    The natural microbial activity in the unsaturated soil is vital for protecting groundwater in areas where high loads of biodegradable contaminants are supplied to the surface, which usually is the case for airports using aircraft de-icing fluids (ADF) in the cold season. Horizontal and vertical distributions of microbial abundance were assessed along the western runway of Oslo Airport (Gardermoen, Norway) to monitor the effect of ADF dispersion with special reference to the component with the highest chemical oxygen demand (COD), propylene glycol (PG). Microbial abundance was evaluated by several biondicators: colony-forming units (CFU) of some physiological groups (aerobic and anaerobic heterotrophs and microscopic fungi), most probable numbers (MPN) of PG degraders, selected catabolic enzymatic activities (fluorescein diacetate (FDA) hydrolase, dehydrogenase, and β-glucosidase). High correlations were found between the enzymatic activities and microbial counts in vertical soil profiles. All microbial abundance indicators showed a steep drop in the first meter of soil depth. The vertical distribution of microbial abundance can be correlated by a decreasing exponential function of depth. The horizontal trend of microbial abundance (evaluated as total aerobic CFU, MPN of PG-degraders, and FDA hydrolase activity) assessed in the surface soil at an increasing distance from the runway is correlated negatively with the PG and COD loads, suggesting the relevance of other chemicals in the modulation of microbial growth. The possible role of potassium formate, component of runway de-icers, has been tested in the laboratory by using mixed cultures of Pseudomonas spp., obtained by enrichment with a selective PG medium from soil samples taken at the most contaminated area near the runway. The inhibitory effect of formate on the growth of PG degraders is proven by the reduction of biomass yield on PG in the presence of formate.

  6. Microbial Activity in Organic Soils as Affected by Soil Depth and Crop †

    PubMed Central

    Tate, Robert L.

    1979-01-01

    The microbial activity of Pahokee muck, a lithic medisaprist, and the effect of various environmental factors, such as position in the profile and type of plant cover, were examined. Catabolic activity for [7-14C]salicylic acid, [1,4-14C]succinate, and [1,2-14C]acetate remained reasonably constant in surface (0 to 10 cm) soil samples from a fallow (bare) field from late in the wet season (May to September) through January. Late in January, the microbial activity toward all three compounds decreased approximately 50%. The microbial activity of the soil decreased with increasing depth of soil. Salicylate catabolism was the most sensitive to increasing moisture deep in the soil profile. At the end of the wet season, a 90% decrease in activity between the surface and the 60- to 70-cm depth occurred. Catabolism of acetate and succinate decreased approximately 75% in the same samples. Little effect of crop was observed. Variation in the microbial activity, as measured by the catabolism of labeled acetate, salicylate, or succinate, was not significant between a sugarcane (Saccharum officinarum L.) field and a fallow field. The activity with acetate was insignificantly different in a St. Augustine grass [Stenotaphrum secundatum (Walt) Kuntz] field, whereas the catabolism of the remaining substrates was elevated in the grass field. These results indicate that the total carbon evolved from the different levels of the soil profile by the microbial community oxidizing the soil organic matter decreased as the depth of the soil column increased. However, correction of the amount of carbon yielded at each level for the bulk density of that level reveals that the microbial contribution to the soil subsidence is approximately equivalent throughout the soil profile above the water table. PMID:16345393

  7. Salinity affects microbial activity and soil organic matter content in tidal wetlands.

    PubMed

    Morrissey, Ember M; Gillespie, Jaimie L; Morina, Joseph C; Franklin, Rima B

    2014-04-01

    Climate change-associated sea level rise is expected to cause saltwater intrusion into many historically freshwater ecosystems. Of particular concern are tidal freshwater wetlands, which perform several important ecological functions including carbon sequestration. To predict the impact of saltwater intrusion in these environments, we must first gain a better understanding of how salinity regulates decomposition in natural systems. This study sampled eight tidal wetlands ranging from freshwater to oligohaline (0-2 ppt) in four rivers near the Chesapeake Bay (Virginia). To help isolate salinity effects, sites were selected to be highly similar in terms of plant community composition and tidal influence. Overall, salinity was found to be strongly negatively correlated with soil organic matter content (OM%) and C : N, but unrelated to the other studied environmental parameters (pH, redox, and above- and below-ground plant biomass). Partial correlation analysis, controlling for these environmental covariates, supported direct effects of salinity on the activity of carbon-degrading extracellular enzymes (β-1, 4-glucosidase, 1, 4-β-cellobiosidase, β-D-xylosidase, and phenol oxidase) as well as alkaline phosphatase, using a per unit OM basis. As enzyme activity is the putative rate-limiting step in decomposition, enhanced activity due to salinity increases could dramatically affect soil OM accumulation. Salinity was also found to be positively related to bacterial abundance (qPCR of the 16S rRNA gene) and tightly linked with community composition (T-RFLP). Furthermore, strong relationships were found between bacterial abundance and/or composition with the activity of specific enzymes (1, 4-β-cellobiosidase, arylsulfatase, alkaline phosphatase, and phenol oxidase) suggesting salinity's impact on decomposition could be due, at least in part, to its effect on the bacterial community. Together, these results indicate that salinity increases microbial decomposition rates

  8. Microbial Functional Diversity, Biomass and Activity as Affected by Soil Surface Mulching in a Semiarid Farmland.

    PubMed

    Shen, Yufang; Chen, Yingying; Li, Shiqing

    2016-01-01

    Mulching is widely used to increase crop yield in semiarid regions in northwestern China, but little is known about the effect of different mulching systems on the microbial properties of the soil, which play an important role in agroecosystemic functioning and nutrient cycling. Based on a 4-year spring maize (Zea mays L.) field experiment at Changwu Agricultural and Ecological Experimental Station, Shaanxi, we evaluated the responses of soil microbial activity and crop to various management systems. The treatments were NMC (no mulching with inorganic N fertilizer), GMC (gravel mulching with inorganic N fertilizer), FMC (plastic-film mulching with inorganic N fertilizer) and FMO (plastic-film mulching with inorganic N fertilizer and organic manure addition). The results showed that the FMO soil had the highest contents of microbial biomass carbon and nitrogen, dehydrogenase activity, microbial activity and Shannon diversity index. The relative use of carbohydrates and amino acids by microbes was highest in the FMO soil, whereas the relative use of polymers, phenolic compounds and amines was highest in the soil in the NMC soil. Compared with the NMC, an increased but no significant trend of biomass production and nitrogen accumulation was observed under the GMC treatment. The FMC and FMO led a greater increase in biomass production than GMC and NMC. Compare with the NMC treatment, FMC increased grain yield, maize biomass and nitrogen accumulation by 62.2, 62.9 and 86.2%, but no significant difference was found between the FMO and FMC treatments. Some soil biological properties, i.e. microbial biomass carbon, microbial biomass nitrogen, being sensitive to the mulching and organic fertilizer, were significant correlated with yield and nitrogen availability. Film mulching over gravel mulching can serve as an effective measure for crop production and nutrient cycling, and plus organic fertilization additions may thus have improvements in the biological quality of the

  9. Microbial Functional Diversity, Biomass and Activity as Affected by Soil Surface Mulching in a Semiarid Farmland

    PubMed Central

    Shen, Yufang; Chen, Yingying; Li, Shiqing

    2016-01-01

    Mulching is widely used to increase crop yield in semiarid regions in northwestern China, but little is known about the effect of different mulching systems on the microbial properties of the soil, which play an important role in agroecosystemic functioning and nutrient cycling. Based on a 4-year spring maize (Zea mays L.) field experiment at Changwu Agricultural and Ecological Experimental Station, Shaanxi, we evaluated the responses of soil microbial activity and crop to various management systems. The treatments were NMC (no mulching with inorganic N fertilizer), GMC (gravel mulching with inorganic N fertilizer), FMC (plastic-film mulching with inorganic N fertilizer) and FMO (plastic-film mulching with inorganic N fertilizer and organic manure addition). The results showed that the FMO soil had the highest contents of microbial biomass carbon and nitrogen, dehydrogenase activity, microbial activity and Shannon diversity index. The relative use of carbohydrates and amino acids by microbes was highest in the FMO soil, whereas the relative use of polymers, phenolic compounds and amines was highest in the soil in the NMC soil. Compared with the NMC, an increased but no significant trend of biomass production and nitrogen accumulation was observed under the GMC treatment. The FMC and FMO led a greater increase in biomass production than GMC and NMC. Compare with the NMC treatment, FMC increased grain yield, maize biomass and nitrogen accumulation by 62.2, 62.9 and 86.2%, but no significant difference was found between the FMO and FMC treatments. Some soil biological properties, i.e. microbial biomass carbon, microbial biomass nitrogen, being sensitive to the mulching and organic fertilizer, were significant correlated with yield and nitrogen availability. Film mulching over gravel mulching can serve as an effective measure for crop production and nutrient cycling, and plus organic fertilization additions may thus have improvements in the biological quality of the

  10. Arid soil microbial enzymatic activity profile as affected by geographical location and soil degradation status

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Evaluating soil health is critical for any successful remediation effort. Arid lands, with their minimal carbon and water contents, low nutritional status and restricted, seasonal microbial activity pose specific challenges to soil health restoration and by extension, restoration of ecosystem repr...

  11. Repeated application of composted tannery sludge affects differently soil microbial biomass, enzymes activity, and ammonia-oxidizing organisms.

    PubMed

    Araújo, Ademir Sérgio Ferreira; Lima, Luciano Moura; Santos, Vilma Maria; Schmidt, Radomir

    2016-10-01

    Repeated application of composted tannery sludge (CTS) changes the soil chemical properties and, consequently, can affect the soil microbial properties. The aim of this study was to evaluate the responses of soil microbial biomass and ammonia-oxidizing organisms to repeated application of CTS. CTS was applied repeatedly during 6 years, and, at the sixth year, the soil microbial biomass, enzymes activity, and ammonia-oxidizing organisms were determined in the soil. The treatments consisted of 0 (without CTS application), 2.5, 5, 10, and 20 t ha(-1) of CTS (dry basis). Soil pH, EC, SOC, total N, and Cr concentration increased with the increase in CTS rate. Soil microbial biomass did not change significantly with the amendment of 2.5 Mg ha(-1), while it decreased at the higher rates. Total and specific enzymes activity responded differently after CTS application. The abundance of bacteria did not change with the 2.5-Mg ha(-1) CTS treatment and decreased after this rate, while the abundance of archaea increased significantly with the 2.5-Mg ha(-1) CTS treatment. Repeated application of different CTS rates for 6 years had different effects on the soil microbial biomass and ammonia-oxidizing organisms as a response to changes in soil chemical properties.

  12. Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland

    PubMed Central

    Gittel, Antje; Bárta, Jiří; Kohoutová, Iva; Schnecker, Jörg; Wild, Birgit; Čapek, Petr; Kaiser, Christina; Torsvik, Vigdis L.; Richter, Andreas; Schleper, Christa; Urich, Tim

    2014-01-01

    Permafrost-affected soils in the Northern latitudes store huge amounts of organic carbon (OC) that is prone to microbial degradation and subsequent release of greenhouse gasses to the atmosphere. In Greenland, the consequences of permafrost thaw have only recently been addressed, and predictions on its impact on the carbon budget are thus still highly uncertain. However, the fate of OC is not only determined by abiotic factors, but closely tied to microbial activity. We investigated eight soil profiles in northeast Greenland comprising two sites with typical tundra vegetation and one wet fen site. We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities. Sampling site and thus abiotic factors had a significant impact on microbial community structure, diversity and activity, the wet fen site exhibiting higher potential enzyme activities and presumably being a hot spot for anaerobic degradation processes such as fermentation and methanogenesis. Lowest fungal to bacterial ratios were found in topsoils that had been relocated by cryoturbation (“buried topsoils”), resulting from a decrease in fungal abundance compared to recent (“unburied”) topsoils. Actinobacteria (in particular Intrasporangiaceae) accounted for a major fraction of the microbial community in buried topsoils, but were only of minor abundance in all other soil horizons. It was indicated that the distribution pattern of Actinobacteria and a variety of other bacterial classes was related to the activity of phenol oxidases and peroxidases supporting the hypothesis that bacteria might resume the role of fungi in oxidative enzyme production and degradation of phenolic and other complex substrates in these soils. Our study sheds light on the highly diverse, but poorly-studied communities in permafrost-affected soils in Greenland and their role in OC degradation. PMID

  13. Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland.

    PubMed

    Gittel, Antje; Bárta, Jiří; Kohoutová, Iva; Schnecker, Jörg; Wild, Birgit; Capek, Petr; Kaiser, Christina; Torsvik, Vigdis L; Richter, Andreas; Schleper, Christa; Urich, Tim

    2014-01-01

    Permafrost-affected soils in the Northern latitudes store huge amounts of organic carbon (OC) that is prone to microbial degradation and subsequent release of greenhouse gasses to the atmosphere. In Greenland, the consequences of permafrost thaw have only recently been addressed, and predictions on its impact on the carbon budget are thus still highly uncertain. However, the fate of OC is not only determined by abiotic factors, but closely tied to microbial activity. We investigated eight soil profiles in northeast Greenland comprising two sites with typical tundra vegetation and one wet fen site. We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities. Sampling site and thus abiotic factors had a significant impact on microbial community structure, diversity and activity, the wet fen site exhibiting higher potential enzyme activities and presumably being a hot spot for anaerobic degradation processes such as fermentation and methanogenesis. Lowest fungal to bacterial ratios were found in topsoils that had been relocated by cryoturbation ("buried topsoils"), resulting from a decrease in fungal abundance compared to recent ("unburied") topsoils. Actinobacteria (in particular Intrasporangiaceae) accounted for a major fraction of the microbial community in buried topsoils, but were only of minor abundance in all other soil horizons. It was indicated that the distribution pattern of Actinobacteria and a variety of other bacterial classes was related to the activity of phenol oxidases and peroxidases supporting the hypothesis that bacteria might resume the role of fungi in oxidative enzyme production and degradation of phenolic and other complex substrates in these soils. Our study sheds light on the highly diverse, but poorly-studied communities in permafrost-affected soils in Greenland and their role in OC degradation.

  14. 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.

  15. DMPP-added nitrogen fertilizer affects soil N2O emission and microbial activity in Southern Italy

    NASA Astrophysics Data System (ADS)

    Vitale, Luca; De Marco, Anna; Maglione, Giuseppe; Polimeno, Franca; Di Tommasi, Paul; Magliulo, Vincenzo

    2014-05-01

    plots, whereas an opposite trend for basal respiration was observed, thus evidencing a stressful condition for nitrifying microbial population. After 57 and 71 DAS, when fertilizer was applied as 30 kg N ha-1, the microbial biomass was similar between C and DMPP plots, whereas basal respiration resulted statistically lower in DMPP plots than C plots. During these periods, average DMPP N2O fluxes were also comparable or lower. In conclusion, our data evidence a stressful condition for soil microbes and in particular for nitrifiers when a higher DMPP quantity is supplied. On the contrary, when lower quantities of DMPP-added fertilizers are supplied (e.s. 30 kg N ha-1) effectiveness of DMPP in reducing soil N2O emission is guaranteed by reducing the nitrifiers activity without negatively affecting their growth.

  16. The Role of EPS in Microhydrology and Transport Processes Affecting Microbial Activity in Unsaturated Porous Media

    NASA Astrophysics Data System (ADS)

    Or, D.; Phutane, S.

    2005-12-01

    Extra-cellular Polymeric Substances (EPS) refers to biopolymers excreted and surrounding soil bacterial cells (and other biota) forming the scaffolding for colonies and serving a wide array of transport, nutrient entrapment, and mechanical functions. In essence, EPS is a porous matrix through which aqueous, gaseous and nutrient fluxes flow to supply the embedded bacterial cells. The large water holding capacity and retarded water loss rates of EPS dampens rapid fluctuations in hydration status of host porous medium which sustain higher diffusion fluxes than in surrounding porous medium, and shelters microbial cells from effect of rapid desiccation or rewetting. The morphology of EPS changes from an open well-hydrated bioweb to dense and highly cross-linked structure under dry conditions. Such morphological changes are accompanied by enhanced mechanical strength and retardation of water loss that provide additional time for physiological adaptation to desiccation. Additional capacitance results from the disparity in dynamic hydrological properties between EPS and soil that promotes water entrapment in EPS during rapid drainage. EPS may also trap dissolved nutrients that may be unevenly distributed and irregularly supplied in unsaturated environments, thereby increasing nutrient availability in the microhabitat and offsetting decreased supply by diffusion during drying. The remarkable transport and mechanical properties of EPS makes it an important stabilizing agent for soil aggregation and even minute amounts of EPS may significantly alter macroscopic hydrological properties of host porous medium.

  17. Does anthracene affect microbial activities and organic matter decomposition? A comparative study in Pinus halepensis litters from Mediterranean coastal and inland areas.

    PubMed

    Qasemian, Leila; Guiral, Daniel; Ziarelli, Fabio; Ruaudel, Florence; Farnet, Anne-Marie

    2012-10-01

    The widespread concern about pollution caused by Polycyclic Aromatic Hydrocarbons (PAHs) raises the question of how they affect soil microbial communities which are potentially involved in the transformation of these pollutants. Using microcosms, we describe the effect of anthracene, a model PAH, on microbial communities inhabiting a Pinus halepensis litter from both coastal (COS) and inland (INL) Mediterranean sites. The microcosms were incubated over 3 months (25°C, 60% WHC) and the effects of anthracene on microbial activities of both litters were monitored. Different enzyme activities (laccase, cellulase, β-glucosidase and acid phosphatase) and microbial respiration were measured and variations in litter chemical composition over incubation were determined using (13)C Nuclear Magnetic Resonance (NMR) from both sites. Our results show that lignocellulolytic enzymes increased markedly after a 3-month incubation in COS microcosms, especially in the presence of anthracene, whereas INL microcosms were not similarly affected. These results show that anthracene not only has no toxic effect on the microbial activities tested but actually enhances the lignocellulolytic activities of the fungal communities from coastal litters, demonstrating the detoxification potential and resistance of stressed Mediterranean coastal ecosystems.

  18. Habitat management affects soil chemistry and allochthonous organic inputs mediating microbial structure and exo-enzyme activity in Wadden Sea salt-marsh soils

    NASA Astrophysics Data System (ADS)

    Mueller, Peter; Granse, Dirk; Thi Do, Hai; Weingartner, Magdalena; Nolte, Stefanie; Hoth, Stefan; Jensen, Kai

    2016-04-01

    The Wadden Sea (WS) region is Europe's largest wetland and home to approximately 20% of its salt marsh area. Mainland salt marshes of the WS are anthropogenically influenced systems and have traditionally been used for livestock grazing in wide parts. After foundation of WS National Parks in the late 1980s and early 1990s, artificial drainage has been abandoned; however, livestock grazing is still common in many areas of the National Parks and is under ongoing discussion as a habitat-management practice. While studies so far focused on effects of livestock grazing on biodiversity, little is known about how biogeochemical processes, element cycling, and particularly carbon sequestration are affected. Here, we present data from a recent field study focusing on grazing effects on soil properties, microbial exo-enzyme activity, microbial abundance and structure. Exo-enzyme activity was studied conducting digestive enzyme assays for various enzymes involved in C- and N cycling. Microbial abundance and structure was assessed measuring specific gene abundance of fungi and bacteria using quantitative PCR. Soil compaction induced by grazing led to higher bulk density and decreases in soil redox (∆ >100 mV). Soil pH was significantly lower in grazed parts. Further, the proportion of allochthonous organic matter (marine input) was significantly smaller in grazed vs. ungrazed sites, likely caused by a higher sediment trapping capacity of the taller vegetation in the ungrazed sites. Grazing induced changes in bulk density, pH and redox resulted in reduced activity of enzymes involved in microbial C acquisition; however, there was no grazing effect on enzymes involved in N acquisition. While changes in pH, bulk density or redox did not affect microbial abundance and structure, the relative amount of marine organic matter significantly reduced the relative abundance of fungi (F:B ratio). We conclude that livestock grazing directly affects microbial exo-enzyme activity, thus

  19. Experimental warming differentially affects microbial structure and activity in two contrasted moisture sites in a Sphagnum-dominated peatland.

    PubMed

    Delarue, Frédéric; Buttler, Alexandre; Bragazza, Luca; Grasset, Laurent; Jassey, Vincent E J; Gogo, Sébastien; Laggoun-Défarge, Fatima

    2015-04-01

    Several studies on the impact of climate warming have indicated that peat decomposition/mineralization will be enhanced. Most of these studies deal with the impact of experimental warming during summer when prevalent abiotic conditions are favorable to decomposition. Here, we investigated the effect of experimental air warming by open-top chambers (OTCs) on water-extractable organic matter (WEOM), microbial biomasses and enzymatic activities in two contrasted moisture sites named Bog and Fen sites, the latter considered as the wetter ones. While no or few changes in peat temperature and water content appeared under the overall effect of OTCs, we observed that air warming smoothed water content differences and led to a decrease in mean peat temperature at the warmed Bog sites. This thermal discrepancy between the two sites led to contrasting changes in microbial structure and activities: a rise in hydrolytic activity at the warmed Bog sites and a relative enhancement of bacterial biomass at the warmed Fen sites. These features were not associated with any change in WEOM properties namely carbon and sugar contents and aromaticity, suggesting that air warming did not trigger any shift in OM decomposition. Using various tools, we show that the use of single indicators of OM decomposition can lead to fallacious conclusions. Lastly, these patterns may change seasonally as a consequence of complex interactions between groundwater level and air warming, suggesting the need to improve our knowledge using a high time-resolution approach.

  20. Cry1Ac Transgenic Sugarcane Does Not Affect the Diversity of Microbial Communities and Has No Significant Effect on Enzyme Activities in Rhizosphere Soil within One Crop Season.

    PubMed

    Zhou, Dinggang; Xu, Liping; Gao, Shiwu; Guo, Jinlong; Luo, Jun; You, Qian; Que, Youxiong

    2016-01-01

    Cry1Ac transgenic sugarcane provides a promising way to control stem-borer pests. Biosafety assessment of soil ecosystem for cry1Ac transgenic sugarcane is urgently needed because of the important role of soil microorganisms in nutrient transformations and element cycling, however little is known. This study aimed to explore the potential impact of cry1Ac transgenic sugarcane on rhizosphere soil enzyme activities and microbial community diversity, and also to investigate whether the gene flow occurs through horizontal gene transfer. We found no horizontal gene flow from cry1Ac sugarcane to soil. No significant difference in the population of culturable microorganisms between the non-GM and cry1Ac transgenic sugarcane was observed, and there were no significant interactions between the sugarcane lines and the growth stages. A relatively consistent trend at community-level, represented by the functional diversity index, was found between the cry1Ac sugarcane and the non-transgenic lines. Most soil samples showed no significant difference in the activities of four soil enzymes: urease, protease, sucrose, and acid phosphate monoester between the non-transgenic and cry1Ac sugarcane lines. We conclude, based on one crop season, that the cry1Ac sugarcane lines may not affect the microbial community structure and functional diversity of the rhizosphere soil and have few negative effects on soil enzymes.

  1. Cry1Ac Transgenic Sugarcane Does Not Affect the Diversity of Microbial Communities and Has No Significant Effect on Enzyme Activities in Rhizosphere Soil within One Crop Season

    PubMed Central

    Zhou, Dinggang; Xu, Liping; Gao, Shiwu; Guo, Jinlong; Luo, Jun; You, Qian; Que, Youxiong

    2016-01-01

    Cry1Ac transgenic sugarcane provides a promising way to control stem-borer pests. Biosafety assessment of soil ecosystem for cry1Ac transgenic sugarcane is urgently needed because of the important role of soil microorganisms in nutrient transformations and element cycling, however little is known. This study aimed to explore the potential impact of cry1Ac transgenic sugarcane on rhizosphere soil enzyme activities and microbial community diversity, and also to investigate whether the gene flow occurs through horizontal gene transfer. We found no horizontal gene flow from cry1Ac sugarcane to soil. No significant difference in the population of culturable microorganisms between the non-GM and cry1Ac transgenic sugarcane was observed, and there were no significant interactions between the sugarcane lines and the growth stages. A relatively consistent trend at community-level, represented by the functional diversity index, was found between the cry1Ac sugarcane and the non-transgenic lines. Most soil samples showed no significant difference in the activities of four soil enzymes: urease, protease, sucrose, and acid phosphate monoester between the non-transgenic and cry1Ac sugarcane lines. We conclude, based on one crop season, that the cry1Ac sugarcane lines may not affect the microbial community structure and functional diversity of the rhizosphere soil and have few negative effects on soil enzymes. PMID:27014291

  2. Next-Generation Pyrosequencing Analysis of Microbial Biofilm Communities on Granular Activated Carbon in Treatment of Oil Sands Process-Affected Water

    PubMed Central

    Islam, M. Shahinoor; Zhang, Yanyan; McPhedran, Kerry N.

    2015-01-01

    The development of biodegradation treatment processes for oil sands process-affected water (OSPW) has been progressing in recent years with the promising potential of biofilm reactors. Previously, the granular activated carbon (GAC) biofilm process was successfully employed for treatment of a large variety of recalcitrant organic compounds in domestic and industrial wastewaters. In this study, GAC biofilm microbial development and degradation efficiency were investigated for OSPW treatment by monitoring the biofilm growth on the GAC surface in raw and ozonated OSPW in batch bioreactors. The GAC biofilm community was characterized using a next-generation 16S rRNA gene pyrosequencing technique that revealed that the phylum Proteobacteria was dominant in both OSPW and biofilms, with further in-depth analysis showing higher abundances of Alpha- and Gammaproteobacteria sequences. Interestingly, many known polyaromatic hydrocarbon degraders, namely, Burkholderiales, Pseudomonadales, Bdellovibrionales, and Sphingomonadales, were observed in the GAC biofilm. Ozonation decreased the microbial diversity in planktonic OSPW but increased the microbial diversity in the GAC biofilms. Quantitative real-time PCR revealed similar bacterial gene copy numbers (>109 gene copies/g of GAC) for both raw and ozonated OSPW GAC biofilms. The observed rates of removal of naphthenic acids (NAs) over the 2-day experiments for the GAC biofilm treatments of raw and ozonated OSPW were 31% and 66%, respectively. Overall, a relatively low ozone dose (30 mg of O3/liter utilized) combined with GAC biofilm treatment significantly increased NA removal rates. The treatment of OSPW in bioreactors using GAC biofilms is a promising technology for the reduction of recalcitrant OSPW organic compounds. PMID:25841014

  3. Next-generation pyrosequencing analysis of microbial biofilm communities on granular activated carbon in treatment of oil sands process-affected water.

    PubMed

    Islam, M Shahinoor; Zhang, Yanyan; McPhedran, Kerry N; Liu, Yang; Gamal El-Din, Mohamed

    2015-06-15

    The development of biodegradation treatment processes for oil sands process-affected water (OSPW) has been progressing in recent years with the promising potential of biofilm reactors. Previously, the granular activated carbon (GAC) biofilm process was successfully employed for treatment of a large variety of recalcitrant organic compounds in domestic and industrial wastewaters. In this study, GAC biofilm microbial development and degradation efficiency were investigated for OSPW treatment by monitoring the biofilm growth on the GAC surface in raw and ozonated OSPW in batch bioreactors. The GAC biofilm community was characterized using a next-generation 16S rRNA gene pyrosequencing technique that revealed that the phylum Proteobacteria was dominant in both OSPW and biofilms, with further in-depth analysis showing higher abundances of Alpha- and Gammaproteobacteria sequences. Interestingly, many known polyaromatic hydrocarbon degraders, namely, Burkholderiales, Pseudomonadales, Bdellovibrionales, and Sphingomonadales, were observed in the GAC biofilm. Ozonation decreased the microbial diversity in planktonic OSPW but increased the microbial diversity in the GAC biofilms. Quantitative real-time PCR revealed similar bacterial gene copy numbers (>10(9) gene copies/g of GAC) for both raw and ozonated OSPW GAC biofilms. The observed rates of removal of naphthenic acids (NAs) over the 2-day experiments for the GAC biofilm treatments of raw and ozonated OSPW were 31% and 66%, respectively. Overall, a relatively low ozone dose (30 mg of O3/liter utilized) combined with GAC biofilm treatment significantly increased NA removal rates. The treatment of OSPW in bioreactors using GAC biofilms is a promising technology for the reduction of recalcitrant OSPW organic compounds.

  4. Cr(Vi) reduction capacity of activated sludge as affected by nitrogen and carbon sources, microbial acclimation and cell multiplication.

    PubMed

    Ferro Orozco, A M; Contreras, E M; Zaritzky, N E

    2010-04-15

    The objectives of the present work were: (i) to analyze the capacity of activated sludge to reduce hexavalent chromium using different carbon sources as electron donors in batch reactors, (ii) to determine the relationship between biomass growth and the amount of Cr(VI) reduced considering the effect of the nitrogen to carbon source ratio, and (iii) to determine the effect of the Cr(VI) acclimation stage on the performance of the biological chromium reduction assessing the stability of the Cr(VI) reduction capacity of the activated sludge. The highest specific Cr(VI) removal rate (q(Cr)) was attained with cheese whey or lactose as electron donors decreasing in the following order: cheese whey approximately lactose>glucose>citrate>acetate. Batch assays with different nitrogen to carbon source ratio demonstrated that biological Cr(VI) reduction is associated to the cell multiplication phase; as a result, maximum Cr(VI) removal rates occur when there is no substrate limitation. The biomass can be acclimated to the presence of Cr(VI) and generate new cells that maintain the ability to reduce chromate. Therefore, the activated sludge process could be applied to a continuous Cr(VI) removal process.

  5. Microbial Carbon Cycling in Permafrost-Affected Soils

    SciTech Connect

    Vishnivetskaya, T.; Liebner, Susanne; Wilhelm, Ronald; Wagner, Dirk

    2011-01-01

    The Arctic plays a key role in Earth s climate system as global warming is predicted to be most pronounced at high latitudes and because one third of the global carbon pool is stored in ecosystems of the northern latitudes. In order to improve our understanding of the present and future carbon dynamics in climate sensitive permafrost ecosystems, present studies concentrate on investigations of microbial controls of greenhouse gas fluxes, on the activity and structure of the involved microbial communities, and on their response to changing environmental conditions. Permafrost-affected soils can function as both a source and a sink for carbon dioxide and methane. Under anaerobic conditions, caused by flooding of the active layer and the effect of backwater above the permafrost table, the mineralization of organic matter can only be realized stepwise by specialized microorganisms. Important intermediates of the organic matter decomposition are hydrogen, carbon dioxide and acetate, which can be further reduced to methane by methanogenic archaea. Evolution of methane fluxes across the subsurface/atmosphere boundary will thereby strongly depend on the activity of anaerobic methanogenic archaea and obligately aerobic methane oxidizing proteobacteria, which are known to be abundant and to significantly reduce methane emissions in permafrost-affected soils. Therefore current studies on methane-cycling microorganisms are the object of particular attention in permafrost studies, because of their key role in the Arctic methane cycle and consequently of their significance for the global methane budget.

  6. Ohmic resistance affects microbial community and ...

    EPA Pesticide Factsheets

    Multi-anode microbial electrochemical cells (MXCs) are considered as one of the most promising configurations for scale-up of MXCs, but fundamental understanding of anode kinetics governing current density is limited in the MXCs. In this study we first assessed microbial community and electrochemical kinetic parameters for biofilms on individual anodes in a multi-anode MXC to better comprehend anode fundamentals. Microbial community analysis using 16S rRNA illumine sequencing showed that Geobactor genus, one of the most kinetically efficient anode-respiring bacteria (ARB), was abundant (87%) only on the biofilm anode closest to a reference electrode in which current density was the highest among four anodes. In comparison, Geobacter populations were less than 11% for other three anodes more distant from the reference electrode, generating small current density. Half-saturation anode potential (EKA) was the lowest at -0.251 to -0.242 V (vs. standard hydrogen electrode) for the closest anode, while EKA was as high as -0.134 V for the farthest anode. Our study clearly proves that ohmic resistance changes anode potential which mainly causes different biofilm communities on individual anodes and consequently influences anode kinetics. This study explored the use of multiple anodes in microelectrochemical cells and the microbial community on these anodes, as a function of the efficiency in producing hydrogen peroxide.

  7. Biochar affects soil organic matter cycling and microbial functions but does not alter microbial community structure in a paddy soil.

    PubMed

    Tian, Jing; Wang, Jingyuan; Dippold, Michaela; Gao, Yang; Blagodatskaya, Evgenia; Kuzyakov, Yakov

    2016-06-15

    The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling.

  8. Altered precipitation regime affects the function and composition of soil microbial communities on multiple time scales.

    PubMed

    Zeglin, L H; Bottomley, P J; Jumpponen, A; Rice, C W; Arango, M; Lindsley, A; McGowan, A; Mfombep, P; Myrold, D D

    2013-10-01

    Climate change models predict that future precipitation patterns will entail lower-frequency but larger rainfall events, increasing the duration of dry soil conditions. Resulting shifts in microbial C cycling activity could affect soil C storage. Further, microbial response to rainfall events may be constrained by the physiological or nutrient limitation stress of extended drought periods; thus seasonal or multiannual precipitation regimes may influence microbial activity following soil wet-up. We quantified rainfall-driven dynamics of microbial processes that affect soil C loss and retention, and microbial community composition, in soils from a long-term (14-year) field experiment contrasting "Ambient" and "Altered" (extended intervals between rainfalls) precipitation regimes. We collected soil before, the day following, and five days following 2.5-cm rainfall events during both moist and dry periods (June and September 2011; soil water potential = -0.01 and -0.83 MPa, respectively), and measured microbial respiration, microbial biomass, organic matter decomposition potential (extracellular enzyme activities), and microbial community composition (phospholipid fatty acids). The equivalent rainfall events caused equivalent microbial respiration responses in both treatments. In contrast, microbial biomass was higher and increased after rainfall in the Altered treatment soils only, thus microbial C use efficiency (CUE) was higher in Altered than Ambient treatments (0.70 +/- 0.03 > 0.46 +/- 0.10). CUE was also higher in dry (September) soils. C-acquiring enzyme activities (beta-glucosidase, cellobiohydrolase, and phenol oxidase) increased after rainfall in moist (June), but not dry (September) soils. Both microbial biomass C:N ratios and fungal:bacterial ratios were higher at lower soil water contents, suggesting a functional and/or population-level shift in the microbiota at low soil water contents, and microbial community composition also differed following wet

  9. Microbial biomass, activity and community composition in constructed wetlands.

    PubMed

    Truu, Marika; Juhanson, Jaanis; Truu, Jaak

    2009-06-15

    The aim of the current article is to give an overview about microbial communities and their functioning but also about factors affecting microbial activity in the three most common types (surface flow and two types of sub-surface flow) of constructed wetlands. The paper reviews the community composition and structural diversity of the microbial biomass, analyzing different aspects of microbial activity with respect to wastewater properties, specific wetland type, and environmental parameters. A brief introduction about the application of different novel molecular techniques for the assessment of microbial communities in constructed wetlands is also given. Microbially mediated processes in constructed wetlands are mainly dependent on hydraulic conditions, wastewater properties, including substrate and nutrient quality and availability, filter material or soil type, plants, and different environmental factors. Microbial biomass is within similar ranges in both horizontal and vertical subsurface flow and surface flow constructed wetlands. Stratification of the biomass but also a stratified structural pattern of the bacterial community can be seen in subsurface flow systems. Microbial biomass C/N ratio is higher in horizontal flow systems compared to vertical flow systems, indicating the structural differences in microbial communities between those two constructed wetland types. The total activity of the microbial community is in the same range, but heterotrophic growth is higher in the subsurface (vertical flow) system compared to the surface flow systems. Available species-specific data about microbial communities in different types of wetlands is scarce and therefore it is impossible make any general conclusions about the dynamics of microbial community structure in wetlands, its relationship to removal processes and operational parameters.

  10. The subzero microbiome: microbial activity in frozen and thawing soils.

    PubMed

    Nikrad, Mrinalini P; Kerkhof, Lee J; Häggblom, Max M

    2016-06-01

    Most of the Earth's biosphere is characterized by low temperatures (<5°C) and cold-adapted microorganisms are widespread. These psychrophiles have evolved a complex range of adaptations of all cellular constituents to counteract the potentially deleterious effects of low kinetic energy environments and the freezing of water. Microbial life continues into the subzero temperature range, and this activity contributes to carbon and nitrogen flux in and out of ecosystems, ultimately affecting global processes. Microbial responses to climate warming and, in particular, thawing of frozen soils are not yet well understood, although the threat of microbial contribution to positive feedback of carbon flux is substantial. To date, several studies have examined microbial community dynamics in frozen soils and permafrost due to changing environmental conditions, and some have undertaken the complicated task of characterizing microbial functional groups and how their activity changes with changing conditions, either in situ or by isolating and characterizing macromolecules. With increasing temperature and wetter conditions microbial activity of key microbes and subsequent efflux of greenhouse gases also increase. In this review, we aim to provide an overview of microbial activity in seasonally frozen soils and permafrost. With a more detailed understanding of the microbiological activities in these vulnerable soil ecosystems, we can begin to predict and model future expectations for carbon release and climate change.

  11. Above- and belowground linkages in Sphagnum peatland: climate warming affects plant-microbial interactions.

    PubMed

    Jassey, Vincent E J; Chiapusio, Geneviève; Binet, Philippe; Buttler, Alexandre; Laggoun-Défarge, Fatima; Delarue, Frédéric; Bernard, Nadine; Mitchell, Edward A D; Toussaint, Marie-Laure; Francez, André-Jean; Gilbert, Daniel

    2013-03-01

    Peatlands contain approximately one third of all soil organic carbon (SOC). Warming can alter above- and belowground linkages that regulate soil organic carbon dynamics and C-balance in peatlands. Here we examine the multiyear impact of in situ experimental warming on the microbial food web, vegetation, and their feedbacks with soil chemistry. We provide evidence of both positive and negative impacts of warming on specific microbial functional groups, leading to destabilization of the microbial food web. We observed a strong reduction (70%) in the biomass of top-predators (testate amoebae) in warmed plots. Such a loss caused a shortening of microbial food chains, which in turn stimulated microbial activity, leading to slight increases in levels of nutrients and labile C in water. We further show that warming altered the regulatory role of Sphagnum-polyphenols on microbial community structure with a potential inhibition of top predators. In addition, warming caused a decrease in Sphagnum cover and an increase in vascular plant cover. Using structural equation modelling, we show that changes in the microbial food web affected the relationships between plants, soil water chemistry, and microbial communities. These results suggest that warming will destabilize C and nutrient recycling of peatlands via changes in above- and belowground linkages, and therefore, the microbial food web associated with mosses will feedback positively to global warming by destabilizing the carbon cycle. This study confirms that microbial food webs thus constitute a key element in the functioning of peatland ecosystems. Their study can help understand how mosses, as ecosystem engineers, tightly regulate biogeochemical cycling and climate feedback in peatlands.

  12. Seasonal distribution of microbial activity in bioaerosols in the outdoor environment of the Qingdao coastal region

    NASA Astrophysics Data System (ADS)

    Zhong, Xi; Qi, Jianhua; Li, Hongtao; Dong, Lijie; Gao, Dongmei

    2016-09-01

    Microbial activities in the atmosphere can indicate the physiological processes of microorganisms and can indirectly affect cloud formation and environmental health. In this study, the microbial activity in bioaerosols collected in the Qingdao coastal region was investigated using the fluorescein diacetate (FDA) hydrolysis method to detect the enzyme activity of microorganisms. The results showed that the microbial activity ranged from 5.49 to 102 ng/m3 sodium fluorescein from March 2013 to February 2014; the average value was 34.4 ng/m3. Microbial activity has no statistical correlation with total microbial quantity. Multiple linear regression analysis showed that meteorological factors such as atmospheric temperature, relative humidity and wind speed accounted for approximately 35.7% of the variation of the microbial activity, although their individual impacts on microbial activity varied. According to the correlation analysis, atmospheric temperature and wind speed had a significant positive and negative influence on microbial activity, respectively, whereas relative humidity and wind direction had no significant influence. The seasonal distribution of microbial activity in bioaerosols was in the order of summer > autumn > winter > spring, with high fluctuations in the summer and autumn. Microbial activity in bioaerosols differed in different weather conditions such as the sunny, foggy, and hazy days of different seasons. Further in situ observations in different weather conditions at different times and places are needed to understand the seasonal distribution characteristics of microbial activity in bioaerosols and the influence factors of microbial activity.

  13. Microbial activity at Yucca Mountain

    SciTech Connect

    Horn, J.M.; Meike, A.

    1995-09-25

    The U.S. Department of Energy is engaged in a suitability study for a potential geological repository at Yucca Mountain, Nevada, for the containment and storage of commercially generated spent fuel and defense high-level nuclear waste. There is growing recognition of the role that biotic factors could play in this repository, either directly through microbially induced corrosion (MIC), or indirectly by altering the chemical environment or contributing to the transport of radionuclides. As a first step toward describing and predicting these processes, a workshop was held on April 10-12, 1995, in Lafayette, California. The immediate aims of the workshop were: (1) To identify microbially related processes relevant to the design of a radioactive waste repository under conditions similar to those at Yucca Mountain. (2) To determine parameters that are critical to the evaluation of a disturbed subterranean environment. (3) To define the most effective means of investigating the factors thus identified.

  14. Microbial communities affecting albumen photography heritage: a methodological survey.

    PubMed

    Puškárová, Andrea; Bučková, Mária; Habalová, Božena; Kraková, Lucia; Maková, Alena; Pangallo, Domenico

    2016-02-11

    This study is one of the few investigations which analyze albumen prints, perhaps the most important photographic heritage of the late 19(th) and early 20(th) centuries. The chemical composition of photographic samples was assessed using Fourier-transform infrared spectroscopy and X-ray fluorescence. These two non-invasive techniques revealed the complex nature of albumen prints, which are composed of a mixture of proteins, cellulose and salts. Microbial sampling was performed using cellulose nitrate membranes which also permitted the trapped microflora to be observed with a scanning electron microscope. Microbial analysis was performed using the combination of culture-dependent (cultivation in different media, including one 3% NaCl) and culture-independent (bacterial and fungal cloning and sequencing) approaches. The isolated microorganisms were screened for their lipolytic, proteolytic, cellulolytic, catalase and peroxidase activities. The combination of the culture-dependent and -independent techniques together with enzymatic assays revealed a substantial microbial diversity with several deteriogen microorganisms from the genera Bacillus, Kocuria, Streptomyces and Geobacillus and the fungal strains Acrostalagmus luteoalbus, Bjerkandera adusta, Pleurotus pulmonarius and Trichothecium roseum.

  15. Microbial communities affecting albumen photography heritage: a methodological survey

    PubMed Central

    Puškárová, Andrea; Bučková, Mária; Habalová, Božena; Kraková, Lucia; Maková, Alena; Pangallo, Domenico

    2016-01-01

    This study is one of the few investigations which analyze albumen prints, perhaps the most important photographic heritage of the late 19th and early 20th centuries. The chemical composition of photographic samples was assessed using Fourier-transform infrared spectroscopy and X-ray fluorescence. These two non-invasive techniques revealed the complex nature of albumen prints, which are composed of a mixture of proteins, cellulose and salts. Microbial sampling was performed using cellulose nitrate membranes which also permitted the trapped microflora to be observed with a scanning electron microscope. Microbial analysis was performed using the combination of culture-dependent (cultivation in different media, including one 3% NaCl) and culture-independent (bacterial and fungal cloning and sequencing) approaches. The isolated microorganisms were screened for their lipolytic, proteolytic, cellulolytic, catalase and peroxidase activities. The combination of the culture-dependent and -independent techniques together with enzymatic assays revealed a substantial microbial diversity with several deteriogen microorganisms from the genera Bacillus, Kocuria, Streptomyces and Geobacillus and the fungal strains Acrostalagmus luteoalbus, Bjerkandera adusta, Pleurotus pulmonarius and Trichothecium roseum. PMID:26864429

  16. Microbial communities affecting albumen photography heritage: a methodological survey

    NASA Astrophysics Data System (ADS)

    Puškárová, Andrea; Bučková, Mária; Habalová, Božena; Kraková, Lucia; Maková, Alena; Pangallo, Domenico

    2016-02-01

    This study is one of the few investigations which analyze albumen prints, perhaps the most important photographic heritage of the late 19th and early 20th centuries. The chemical composition of photographic samples was assessed using Fourier-transform infrared spectroscopy and X-ray fluorescence. These two non-invasive techniques revealed the complex nature of albumen prints, which are composed of a mixture of proteins, cellulose and salts. Microbial sampling was performed using cellulose nitrate membranes which also permitted the trapped microflora to be observed with a scanning electron microscope. Microbial analysis was performed using the combination of culture-dependent (cultivation in different media, including one 3% NaCl) and culture-independent (bacterial and fungal cloning and sequencing) approaches. The isolated microorganisms were screened for their lipolytic, proteolytic, cellulolytic, catalase and peroxidase activities. The combination of the culture-dependent and -independent techniques together with enzymatic assays revealed a substantial microbial diversity with several deteriogen microorganisms from the genera Bacillus, Kocuria, Streptomyces and Geobacillus and the fungal strains Acrostalagmus luteoalbus, Bjerkandera adusta, Pleurotus pulmonarius and Trichothecium roseum.

  17. Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

    PubMed

    Haverkamp, Thomas H A; Hammer, Øyvind; Jakobsen, Kjetill S

    2014-01-01

    Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.

  18. Composition analysis of fractions of extracellular polymeric substances from an activated sludge culture and identification of dominant forces affecting microbial aggregation

    NASA Astrophysics Data System (ADS)

    Guo, Xuan; Wang, Xu; Liu, Junxin

    2016-06-01

    Extracellular polymeric substances (EPS) appear to play a critical role in the formation of bioaggregates, such as sludge flocs, in activated sludge processes. Here, we systematically investigated the composition and chemical structure of various EPS fractions excreted from an activated sludge culture using multi-analysis techniques to examine the ability of the sludge to aggregate. Chemical analysis was used with a three-dimensional excitation emission matrix and Fourier transform infrared spectroscopy, applying inter-particle forces theory. The combined findings revealed that hydrophobic groups, especially protein-related N–H, were present in a greater proportion in tightly bound EPS (TB-EPS). This result, which explained the specificity of TB-EPS in the chemical structure, was consistent with data indicating that TB-EPS contained a large amount of protein-like substances (86.7 mg/g of mixed liquor volatile suspended solids, 39.7% of the total EPS). Subsequently, a novel experimental procedure was developed to pinpoint key inter-particle forces in sludge aggregation. The result revealed that hydrogen bonds are the predominant triggers that promote sludge aggregation. This comprehensive analysis indicated that hydrophobic proteins in TB-EPS are responsible for the critical role played by hydrogen bonds in sludge formation. Our findings highlight the need to elucidate the mechanisms of TB-EPS-mediated flocculation in future efforts.

  19. Composition analysis of fractions of extracellular polymeric substances from an activated sludge culture and identification of dominant forces affecting microbial aggregation

    PubMed Central

    Guo, Xuan; Wang, Xu; Liu, Junxin

    2016-01-01

    Extracellular polymeric substances (EPS) appear to play a critical role in the formation of bioaggregates, such as sludge flocs, in activated sludge processes. Here, we systematically investigated the composition and chemical structure of various EPS fractions excreted from an activated sludge culture using multi-analysis techniques to examine the ability of the sludge to aggregate. Chemical analysis was used with a three-dimensional excitation emission matrix and Fourier transform infrared spectroscopy, applying inter-particle forces theory. The combined findings revealed that hydrophobic groups, especially protein-related N–H, were present in a greater proportion in tightly bound EPS (TB-EPS). This result, which explained the specificity of TB-EPS in the chemical structure, was consistent with data indicating that TB-EPS contained a large amount of protein-like substances (86.7 mg/g of mixed liquor volatile suspended solids, 39.7% of the total EPS). Subsequently, a novel experimental procedure was developed to pinpoint key inter-particle forces in sludge aggregation. The result revealed that hydrogen bonds are the predominant triggers that promote sludge aggregation. This comprehensive analysis indicated that hydrophobic proteins in TB-EPS are responsible for the critical role played by hydrogen bonds in sludge formation. Our findings highlight the need to elucidate the mechanisms of TB-EPS-mediated flocculation in future efforts. PMID:27311788

  20. Microbial activities in deep subsurface environments

    SciTech Connect

    Phelps, T.J.; Raione, E.G.; White, D.C. |; Fliermans, C.B.

    1988-12-31

    Activities of microorganisms residing in terrestrial deep subsurface sediments were examined in forty-six sediment samples from three aseptically sampled boreholes. Radiolabeled time course experiments assessing in situ microbial activities were initiated within 30 minutes of core recovery. [{sup 14}C-1-] Acetate incorporation into lipids. [methyl-{sup 3}H-]thymidine incorporation into DNA, [{sup 14}C-2-]acetate and [{sup 14}C-U-]glucose mineralization in addition to microbial enrichment and enumeration studies were examined in surface and subsurface sediments. Surface soils contained the greatest biomass and activities followed by the shallow aquifer zones. Water saturated subsurface sediments exhibited three to four orders of magnitude greater activity and culturable microorganisms than the dense clay zones. Regardless of depth, sediments which contained more than 20% clays exhibited the lowest activities and culturable microorganisms.

  1. Microbial activity in the marine deep biosphere: progress and prospects

    PubMed Central

    Orcutt, Beth N.; LaRowe, Douglas E.; Biddle, Jennifer F.; Colwell, Frederick S.; Glazer, Brian T.; Reese, Brandi Kiel; Kirkpatrick, John B.; Lapham, Laura L.; Mills, Heath J.; Sylvan, Jason B.; Wankel, Scott D.; Wheat, C. Geoff

    2013-01-01

    The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org). PMID:23874326

  2. [Effects of different straw recycling and tillage methods on soil respiration and microbial activity].

    PubMed

    Li, Xiao-sha; Wu, Ning; Liu, Ling; Feng, Yu-peng; Xu, Xu; Han, Hui-fang; Ning, Tang-yuan; Li, Zeng-jia

    2015-06-01

    To explore the effects of different tillage methods and straw recycling on soil respiration and microbial activity in summer maize field during the winter wheat and summer maize double cropping system, substrate induced respiration method and CO2 release method were used to determine soil microbial biomass carbon, microbial activity, soil respiration, and microbial respiratory quotient. The experiment included 3 tillage methods during the winter wheat growing season, i.e., no-tillage, subsoiling and conventional tillage. Each tillage method was companied with 2 straw management patterns, i.e., straw recycling and no straw. The results indicated that the conservation tillage methods and straw recycling mainly affected 0-10 cm soil layer. Straw recycling could significantly improve the microbial biomass carbon and microbial activity, while decrease microbial respiratory quotient. Straw recycling could improve the soil respiration at both seedling stage and anthesis, however, it could reduce the soil respiration at filling stage, wax ripeness, and harvest stage. Under the same straw application, compared with conventional tillage, the soil respiration and microbial respiratory quotient in both subsoiling and no-tillage were reduced, while the microbial biomass carbon and microbial activity were increased. During the summer maize growing season, soil microbial biomass carbon and microbial activity were increased in straw returning with conservation tillage, while the respiratory quotient was reduced. In 0-10 cm soil layer, compared with conventional tillage, straw recycling with subsoiling and no-tillage significantly increased soil microbial biomass carbon by 95.8% and 74.3%, and increased soil microbial activity by 97.1% and 74.2%, respectively.

  3. Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank

    PubMed Central

    Leite, Márcio F. A.; Pan, Yao; Bloem, Jaap; Berge, Hein ten; Kuramae, Eiko E.

    2017-01-01

    Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake. PMID:28198425

  4. Land use type significantly affects microbial gene transcription in soil.

    PubMed

    Nacke, Heiko; Fischer, Christiane; Thürmer, Andrea; Meinicke, Peter; Daniel, Rolf

    2014-05-01

    Soil microorganisms play an essential role in sustaining biogeochemical processes and cycling of nutrients across different land use types. To gain insights into microbial gene transcription in forest and grassland soil, we isolated mRNA from 32 sampling sites. After sequencing of generated complementary DNA (cDNA), a total of 5,824,229 sequences could be further analyzed. We were able to assign nonribosomal cDNA sequences to all three domains of life. A dominance of bacterial sequences, which were affiliated to 25 different phyla, was found. Bacterial groups capable of aromatic compound degradation such as Phenylobacterium and Burkholderia were detected in significantly higher relative abundance in forest soil than in grassland soil. Accordingly, KEGG pathway categories related to degradation of aromatic ring-containing molecules (e.g., benzoate degradation) were identified in high abundance within forest soil-derived metatranscriptomic datasets. The impact of land use type forest on community composition and activity is evidently to a high degree caused by the presence of wood breakdown products. Correspondingly, bacterial groups known to be involved in lignin degradation and containing ligninolytic genes such as Burkholderia, Bradyrhizobium, and Azospirillum exhibited increased transcriptional activity in forest soil. Higher solar radiation in grassland presumably induced increased transcription of photosynthesis-related genes within this land use type. This is in accordance with high abundance of photosynthetic organisms and plant-infecting viruses in grassland.

  5. Metalliferous Biosignatures for Deep Subsurface Microbial Activity

    NASA Astrophysics Data System (ADS)

    Parnell, John; Brolly, Connor; Spinks, Sam; Bowden, Stephen

    2016-03-01

    The interaction of microbes and metals is widely assumed to have occurred in surface or very shallow subsurface environments. However new evidence suggests that much microbial activity occurs in the deep subsurface. Fluvial, lacustrine and aeolian `red beds' contain widespread centimetre-scale reduction spheroids in which a pale reduced spheroid in otherwise red rocks contains a metalliferous core. Most of the reduction of Fe (III) in sediments is caused by Fe (III) reducing bacteria. They have the potential to reduce a range of metals and metalloids, including V, Cu, Mo, U and Se, by substituting them for Fe (III) as electron acceptors, which are all elements common in reduction spheroids. The spheroidal morphology indicates that they were formed at depth, after compaction, which is consistent with a microbial formation. Given that the consequences of Fe (III) reduction have a visual expression, they are potential biosignatures during exploration of the terrestrial and extraterrestrial geological record. There is debate about the energy available from Fe (III) reduction on Mars, but the abundance of iron in Martian soils makes it one of the most valuable prospects for life there. Entrapment of the microbes themselves as fossils is possible, but a more realistic target during the exploration of Mars would be the colour contrasts reflecting selective reduction or oxidation. This can be achieved by analysing quartz grains across a reduction spheroid using Raman spectroscopy, which demonstrates its suitability for life detection in subsurface environments. Microbial action is the most suitable explanation for the formation of reduction spheroids and may act as metalliferous biosignatures for deep subsurface microbial activity.

  6. Increasing concentrations of phenol progressively affect anaerobic digestion of cellulose and associated microbial communities.

    PubMed

    Chapleur, Olivier; Madigou, Céline; Civade, Raphaël; Rodolphe, Yohan; Mazéas, Laurent; Bouchez, Théodore

    2016-02-01

    Performance stability is a key issue when managing anaerobic digesters. However it can be affected by external disturbances caused by micropollutants. In this study the influence of phenol on the methanization of cellulose was evaluated through batch toxicity assays. Special attention was given to the dynamics of microbial communities by means of automated ribosomal intergenic spacer analysis. We observed that, as phenol concentrations increased, the different steps of anaerobic cellulose digestion were unevenly and progressively affected, methanogenesis being the most sensitive: specific methanogenic activity was half-inhibited at 1.40 g/L of phenol, whereas hydrolysis of cellulose and its fermentation to VFA were observed at up to 2.00 g/L. Depending on the level of phenol, microbial communities resisted either through physiological or structural adaptation. Thus, performances at 0.50 g/L were maintained in spite of the microbial community's shift. However, the communities' ability to adapt was limited and performances decreased drastically beyond 2.00 g/L of phenol.

  7. Community history affects the predictability of microbial ecosystem development.

    PubMed

    Pagaling, Eulyn; Strathdee, Fiona; Spears, Bryan M; Cates, Michael E; Allen, Rosalind J; Free, Andrew

    2014-01-01

    Microbial communities mediate crucial biogeochemical, biomedical and biotechnological processes, yet our understanding of their assembly, and our ability to control its outcome, remain poor. Existing evidence presents conflicting views on whether microbial ecosystem assembly is predictable, or inherently unpredictable. We address this issue using a well-controlled laboratory model system, in which source microbial communities colonize a pristine environment to form complex, nutrient-cycling ecosystems. When the source communities colonize a novel environment, final community composition and function (as measured by redox potential) are unpredictable, although a signature of the community's previous history is maintained. However, when the source communities are pre-conditioned to their new habitat, community development is more reproducible. This situation contrasts with some studies of communities of macro-organisms, where strong selection under novel environmental conditions leads to reproducible community structure, whereas communities under weaker selection show more variability. Our results suggest that the microbial rare biosphere may have an important role in the predictability of microbial community development, and that pre-conditioning may help to reduce unpredictability in the design of microbial communities for biotechnological applications.

  8. Community history affects the predictability of microbial ecosystem development

    PubMed Central

    Pagaling, Eulyn; Strathdee, Fiona; Spears, Bryan M; Cates, Michael E; Allen, Rosalind J; Free, Andrew

    2014-01-01

    Microbial communities mediate crucial biogeochemical, biomedical and biotechnological processes, yet our understanding of their assembly, and our ability to control its outcome, remain poor. Existing evidence presents conflicting views on whether microbial ecosystem assembly is predictable, or inherently unpredictable. We address this issue using a well-controlled laboratory model system, in which source microbial communities colonize a pristine environment to form complex, nutrient-cycling ecosystems. When the source communities colonize a novel environment, final community composition and function (as measured by redox potential) are unpredictable, although a signature of the community's previous history is maintained. However, when the source communities are pre-conditioned to their new habitat, community development is more reproducible. This situation contrasts with some studies of communities of macro-organisms, where strong selection under novel environmental conditions leads to reproducible community structure, whereas communities under weaker selection show more variability. Our results suggest that the microbial rare biosphere may have an important role in the predictability of microbial community development, and that pre-conditioning may help to reduce unpredictability in the design of microbial communities for biotechnological applications. PMID:23985743

  9. Factors affecting current production in microbial fuel cells using different industrial wastewaters.

    PubMed

    Velasquez-Orta, S B; Head, I M; Curtis, T P; Scott, K

    2011-04-01

    This study evaluated how different types of industrial wastewaters (bakery, brewery, paper and dairy) affect the performance of identical microbial fuel cells (MFCs); and the microbial composition and electrochemistry of MFC anodes. MFCs fed with paper wastewater produced the highest current density (125 ± 2 mA/m(2)) at least five times higher than dairy (25 ± 1 mA/m(2)), brewery and bakery wastewaters (10 ± 1 mA/m(2)). Such high current production was independent of substrate degradability. A comprehensive study was conducted to determine the factor driving current production when using the paper effluent. The microbial composition of anodic biofilms differed according to the type of wastewater used, and only MFC anodes fed with paper wastewater showed redox activity at -134 ± 5 mV vs NHE. Electrochemical analysis of this redox activity indicated that anodic bacteria produced a putative electron shuttling compound that increased the electron transfer rate through diffusion, and as a result the overall MFC performance.

  10. Influence of interfaces on microbial activity.

    PubMed Central

    van Loosdrecht, M C; Lyklema, J; Norde, W; Zehnder, A J

    1990-01-01

    Bacterial adhesion in natural and artificial systems has been critically reviewed to investigate the influences exerted by the presence of interfaces. Numerous investigations have demonstrated that, in the presence of a solid phase, the activity of bacterial cultures is changed. Reviewing relevant literature, two problems were encountered. One is of an experimental nature. Due to lack of similarity in experimental conditions, disparate experiments often cannot be compared; their results may even appear conflicting. The other problem is of an interpretational nature: several hypothetical theories exist which try to explain the effect of surfaces on microbial activity. These theories often confuse changes in the medium and limitations in mass transfer which are due to the presence of solid surfaces (indirect influences) with changes in cell properties (direct influences). Whenever a surface is reported to influence the metabolism of bacteria, the action is found almost exclusively to be due to changes in the medium or environment and is therefore indirect. Based on data reported in the literature, and by using thermodynamic and kinetic considerations, it is concluded that so far neither experimental nor theoretical evidence exists for a direct influence of interfaces on microbial activity. PMID:2181260

  11. Ohmic resistance affects microbial community and electrochemical kinetics in a multi-anode microbial electrochemical cell

    EPA Science Inventory

    Multi-anode microbial electrochemical cells (MXCs) are considered as one of the most promising configurations for scale-up of MXCs, but fundamental understanding of anode kinetics governing current density is limited in the MXCs. In this study we first assessed microbial communi...

  12. Activity assessment of microbial fibrinolytic enzymes.

    PubMed

    Kotb, Essam

    2013-08-01

    Conversion of fibrinogen to fibrin inside blood vessels results in thrombosis, leading to myocardial infarction and other cardiovascular diseases. In general, there are four therapy options: surgical operation, intake of antiplatelets, anticoagulants, or fibrinolytic enzymes. Microbial fibrinolytic enzymes have attracted much more attention than typical thrombolytic agents because of the expensive prices and the side effects of the latter. The fibrinolytic enzymes were successively discovered from different microorganisms, the most important among which is the genus Bacillus. Microbial fibrinolytic enzymes, especially those from food-grade microorganisms, have the potential to be developed as functional food additives and drugs to prevent or cure thrombosis and other related diseases. There are several assay methods for these enzymes; this may due to the insolubility of substrate, fibrin. Existing assay methods can be divided into three major groups. The first group consists of assay of fibrinolytic activity with natural proteins as substrates, e.g., fibrin plate methods. The second and third groups of assays are suitable for kinetic studies and are based on the determination of hydrolysis of synthetic peptide esters. This review will deal primarily with the microorganisms that have been reported in literature to produce fibrinolytic enzymes and the first review discussing the methods used to assay the fibrinolytic activity.

  13. Direct Observations Of Microbial Activity At Extreme Pressures

    NASA Astrophysics Data System (ADS)

    Sharma, A.; Scott, J. H.; Cody, G. D.; Fogel, M.; Hazen, R. M.; Hemley, R. J.; Huntress, W. T.

    2002-12-01

    Microbial communities adapt to a wide range of pressures, temperatures, salinities, pH, and oxidation states. Although, significant attention has been focused on the effects of high and low temperature on physiology, there is some evidence that elevated pressure may also manifest interesting effects on cellular physiology, such as enzyme inactivation, cell-membrane breach, and suppression of protein interactions with various substrates. However, exactly how these factors affect intact cells is not well understood. In this study, we have adapted diamond anvil cells to explore the effects of high pressure on microbial life. We used the rate of microbial formate oxidation as a probe of metabolic viability. The utilization of formate by microorganisms is a fundamental metabolic process in anaerobic environments. We monitored in-situ microbial formate oxidation via molecular spectroscopy for Shewanella oneidensis strain MR1 and Escherichia coli strain MG1655 at high pressures (68 to 1060 MPa). At pressures of 1200 to 1600 MPa, living bacteria resided in fluid inclusions in ice-VI crystals and continued to be viable upon subsequent release to ambient pressures (0.1 MPa). Furthermore, direct microscopic observations indicate that these cells maintain their ability for cellular division upon decompression from such high pressures. Evidence of microbial viability and activity at these extreme pressures expands by an order of magnitude the range of conditions representing the habitable zone in the solar system. These results imply that pressure may not be a significant impediment to life. The maximum pressure explored in this work is equivalent to a depth of ~ 50 km below Earth's crust, or ~ 160 km in a hypothetical ocean. The pressures encountered at the depths of thick ice caps and deep crustal subsurface may not be a limiting factor for the existence of life. This suggests that deep (water/ice) layers of Europa, Callisto, or Ganymede, subduction zones on Earth, and the

  14. Evidence of ancient microbial activity on Mars

    NASA Astrophysics Data System (ADS)

    Wallis, Jamie; Wickramasinghe, N. C.; Wallis, Daryl H.; Miyake, Nori; Wallis, M. K.; Hoover, Richard B.

    2015-09-01

    We report for the first time in situ observations of a relatively rare secondary iron arsenate-sulphate mineral named bukovskýite - Fe3+ 2(As5+O4)(S6+O4)(OH)•7(H2O) - found in a shock melt vein of the Tissint Martian meteorite. It is hypothesised that the mineral formed when high concentrations of aqueous H+, Fe(III), SO4 and AsO4 were maintained for long periods of time in microenvironments created within wet subsurface Martian clays. The aqueous H+, Fe(III), SO4 and AsO4 species arose from the microbial oxidation of FeS2 with concurrent release of sequestrated As. The availability of aqueous AsO4 would also be complemented by dissolution by-products of the microbial reduction of Feoxides influenced by dissolved organic matter that alters the redox state and the complexation of As, thus shifting As partitioning in favour of the solute phase. This hypothesis is substantially supported by SEM analysis of a 15μm spherical structure comprising of a carbonaceous outer coating with a inner core of FeS2 (pyrite) that showed the pyrite surface with spherical pits, and chains of pits, with morphologies distinct from abiotic alteration features. The pits and channels have a clustered, geometric distribution, typical of microbial activity, and are closely comparable to biologically mediated microstructures created by Fe- and S-oxidising microbes in the laboratory. These microstructures are interpreted as trace fossils resulting from the attachment of bacteria to the pyrite surfaces.

  15. Do long-lived ants affect soil microbial communities?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study was designed to test the hypothesis that desert ant species that build nests that remain viable at a particular point in space for more than a decade produce soil conditions that enhance microbial biomass and functional diversity. We studied the effects of a seed-harvester ant, Pogonomyrm...

  16. Effect of roundup ultra on microbial activity and biomass from selected soils.

    PubMed

    Haney, R L; Senseman, S A; Hons, F M

    2002-01-01

    Herbicides applied to soils potentially affect soil microbial activity. The quantity and frequency of Roundup Ultra [RU; N-(phosphonomethyl)glycine; Monsanto, St. Louis, MO] applications have escalated with the advent of Roundup-tolerant crops. The objective of this study was to determine the effect of Roundup Ultra on soil microbial biomass and activity across a range of soils varying in fertility. The isoproplyamine salt of glyphosate was applied in the form of RU at a rate of 234 mg active ingredient kg(-1) soil based on an assumed 2-mm glyphosate-soil interaction depth. Roundup Ultra significantly stimulated soil microbial activity as measured by C and N mineralization, as well as soil microbial biomass. Cumulative C mineralization as well as mineralization rate increased above background levels for all soils tested with addition of RU. There were strong linear relationships between C and N mineralized, as well as between soil microbial C and N (r2 = 0.96 and 0.95, respectively). The slopes of the relationships with RU addition approximated three. Since the isopropylamine salt of glyphosate has a C to N ratio of 3:1, the data strongly suggest that RU was the direct cause of the enhanced microbial activity. An increase in the C mineralization rate occurred the first day following RU addition and continued for 14 d. Roundup Ultra appeared to be rapidly degraded by soil microbes regardless of soil type or organic matter content, even at high application rates, without adversely affecting microbial activity.

  17. Energy and power limits for microbial activity

    NASA Astrophysics Data System (ADS)

    LaRowe, D.; Amend, J.

    2014-12-01

    The goal of this presentation is to describe a quantitative framework for determining how energy limits microbial activity, biomass and, ultimately, biogeochemical processes. Although this model can be applied to any environment, its utility is demonstrated in marine sediments, which are an attractive test habitat because they encompass a broad spectrum of energy levels, varying amounts of biomass and are ubiquitous. The potential number of active microbial cells in Arkonas Basin (Baltic Sea) sediments are estimated as a function of depth by quantifying the amount of energy that is available to them and the rate at which it is supplied: power. The amount of power supplied per cubic centimeter of sediment is determined by calculating the Gibbs energy of fermentation and sulfate reduction in combination with the rate of particulate organic carbon, POC, degradation. The Reactive Continuum Model (Boudreau and Ruddick, 1991), RCM, is used to determine the rate at which POC is made available for microbial consumption. The RCM represents POC as containing a range of different types of organic compounds whose ability to be consumed by microorganisms varies as a function of the age of the sediment and on the distribution of compound types that were initially deposited. The sediment age model and RCM parameters determined by (Mogollon et al., 2012) are used. The power available for fermentation and sulfate reduction coupled to H2 and acetate oxidation varies from 10-8 W cm-3 at the sediment water interface to between 10-11 - 10-12 W cm-3 at 3.5 meters below the seafloor, mbsf. Using values of maintenance powers for each of these catabolic activities taken from the literature, the total number of active cells in these sediments similarly decreases from just less than 108 cell cm-3 at the SWI to 4.6 x 104 cells cm-3 at 3.5 mbsf. The number of moles of POC decreases from 2.6 x 10-5 to 9.5 x 10-6, also becoming more recalcitrant with depth. Boudreau, B. P. and Ruddick, B. R

  18. Temperature and Microbial Activity Effects on Soil Carbon Stabilization

    NASA Astrophysics Data System (ADS)

    Fissore, C.; van Diepen, L.; Wixon, D.; Marin-Spiotta, E.; Giardina, C. P.

    2014-12-01

    Uncertainties on the importance of environmental controls on soil C stabilization and turnover limit accurate predictions of the rate and magnitude of the response of soils to climate change. Here we report results from a study of interactions among vegetation and soil microbial communities in North American forests across a highly constrained, 22OC gradient mean annual temperature (MAT) as a proxy for understanding changes with climate. Previous work indicated that turnover and amount of labile SOC responded negatively to MAT, whereas stable SOC was insensitive to temperature variation. Hardwood forests stored a larger amount of stable SOC, but with shorter mean residence times than paired pine forests. Our findings suggest that the interaction between vegetation composition and microbial communities may affect SOC accumulation and stabilization responses to rising temperature. To investigate these relationships, we characterized the microbial communities with Phospholipid Fatty Acid (PLFA) analysis. PLFA analyses indicate complex microbial responses to increased MAT and vegetation composition. Microbial biomass declined with MAT in conifer forests and increased in hardwood forests. Relative abundance of actinomycetes increased with MAT for both forest types, and was correlated with amount and turnover of active SOC. The relative abundance of fungi decreased with increasing MAT, while gram+ bacteria increased, such that fungi:bacteria ratio decreased with MAT, with this trend being more pronounced for hardwood cover type. These results are consistent with a long-term warming experiment in a hardwood forest at the Harvard Forest LTER site, where after 12 years of warming the relative abundance of gram positive bacteria and actinomycetes increased, while fungal biomass decreased. In contrast, relationships between microbial groups and the stable fraction of SOC along the gradient were only observed in conifers. Increases in mean residence time of stable SOC were

  19. Limited recovery of soil microbial activity after transient exposure to gasoline vapors.

    PubMed

    Modrzyński, Jakub J; Christensen, Jan H; Mayer, Philipp; Brandt, Kristian K

    2016-09-01

    During gasoline spills complex mixtures of toxic volatile organic compounds (VOCs) are released to terrestrial environments. Gasoline VOCs exert baseline toxicity (narcosis) and may thus broadly affect soil biota. We assessed the functional resilience (i.e. resistance and recovery of microbial functions) in soil microbial communities transiently exposed to gasoline vapors by passive dosing via headspace for 40 days followed by a recovery phase of 84 days. Chemical exposure was characterized with GC-MS, whereas microbial activity was monitored as soil respiration (CO2 release) and soil bacterial growth ([(3)H]leucine incorporation). Microbial activity was strongly stimulated and inhibited at low and high exposure levels, respectively. Microbial growth efficiency decreased with increasing exposure, but rebounded during the recovery phase for low-dose treatments. Although benzene, toluene, ethylbenzene and xylene (BTEX) concentrations decreased by 83-97% during the recovery phase, microbial activity in high-dose treatments did not recover and numbers of viable bacteria were 3-4 orders of magnitude lower than in control soil. Re-inoculation with active soil microorganisms failed to restore microbial activity indicating residual soil toxicity, which could not be attributed to BTEX, but rather to mixture toxicity of more persistent gasoline constituents or degradation products. Our results indicate a limited potential for functional recovery of soil microbial communities after transient exposure to high, but environmentally relevant, levels of gasoline VOCs which therefore may compromise ecosystem services provided by microorganisms even after extensive soil VOC dissipation.

  20. The effect of metal ions on the microbial attachment ability of flocculent activate sludge.

    PubMed

    Hao, Wen; Lv, Junping; Li, Yaochen; Chen, Lisha; Zhu, Jianrong

    2016-01-01

    As a kind of biofilm structure, microbial attachment was believed to play an important role in the aggregation and stability of flocculent activated sludge (FAS), and also its translation to aerobic granular activated sludge (AGAS). The aim of this study was to investigate the effect of Ca2+, Mg2+, Cu2+, Fe2+, Zn2+, K+, and Na+, which were frequently found in the biological wastewater-treatment systems on the microbial attachment of FAS, in order to provide a new strategy for the cultivation of FAS and AGAS. The results showed that different metal ions had different effects on the process of microbial attachment of FAS; in particular, Cu2+, Fe2+, and Zn2+ could increase the microbial attachment ability of FAS at appropriate concentrations, and disrupted the process at higher concentrations. Mg2+ would greatly enhance the microbial attachment of FAS at lower concentrations but then the biomass of attachment was fallen down to a level close to that of the control. However, Ca2+), K+, and Na+ always exhibited a positive impact on the microbial attachment of FAS. Besides, the concentration of FAS suspension and the culture time both had an effect on the microbial attachment of FAS. Moreover, the acyl-homoserine-lactones-based quorum-sensing system, the content of EPS, and the relative hydrophobicity of FAS had been greatly influenced by metal ions. As all these parameters had close relationships with microbial attachment process, changes in these parameters may affect the microbial attachment of FAS.

  1. Functional activity of soil microbial communities in post-fire pine stands of Tolyatti, Samara oblast

    NASA Astrophysics Data System (ADS)

    Maksimova, E. Yu.; Kudinova, A. G.; Abakumov, E. V.

    2017-02-01

    The state of microbial communities in gray-humus soils (Eutric Fluvic Arenosols (Ochric)) of pine stands in the city of Tolyatti after forest fires of 2010 is analyzed. It is shown that fires exert negative effects on the structure and metabolic activity of microbial communities in the postpyrogenic soils. The content of the carbon of microbial biomass and the intensity of microbial respiration in the upper organic horizons of the post-fire plots decrease by 6.5 and 3.4 times, respectively, in comparison with those in the soils of background plots. However, the fire has not affected the studied microbiological parameters of the soils at the depths of more than 10 cm. The maximum content of the carbon of microbial biomass carbon and the maximum intensity of microbial respiration have been found in the subsurface AY2 and AC horizons two-three years the fire. An increase in the microbial metabolic quotient (the ratio of soil respiration to microbial biomass) attests to the disturbance of the ecophysiological state of soil microbial communities after the pyrogenic impact.

  2. Changes in enzymatic activities and microbial properties in vermicompost of water hyacinth as affected by pre-composting and fungal inoculation: a comparative study of ergosterol and chitin for estimating fungal biomass.

    PubMed

    Pramanik, P

    2010-01-01

    In this experiment, three different fungal species, viz. Trichoderma viridae, Aspergillus niger and Phanerochaete chrysosporium, were inoculated in 7 day and 15 day partially decomposed water hyacinth to study their effect on enzymatic activities, microbial respiration and fungal biomass of the final stabilized product. The results suggested that increasing the duration of pre-composting from 7 days to 15 days did not show any significant effect on the activities of hydrolytic enzymes. Inoculation of fungi significantly (P < or = 0.05) increased cellulase, protease and acid and alkaline phosphatase activities. The highest value of ergosterol was recorded in A. niger-inoculated vermicomposts. Inoculation of P. chrysosporium in initial organic waste registered the highest chitin content in vermicompost. A comparison of fungal biomass and chitin content revealed a conversion factor of 2.628 with a standard deviation of 0.318. Due to significant correlation (r = 0.864), this conversion factor allows for the calculation of fungal biomass from chitin, which is comparatively more stable than ergosterol.

  3. Influence of earthworm activity on microbial communities related with the degradation of persistent pollutants.

    PubMed

    Natal-da-Luz, Tiago; Lee, Iwa; Verweij, Rudo A; Morais, Paula V; Van Velzen, Martin J M; Sousa, José Paulo; Van Gestel, Cornelis A M

    2012-04-01

    Earthworms may promote the biodegradation of polycyclic aromatic hydrocarbons (PAHs) in soil, but the mechanism through which they exert such influence is still unknown. To determine if the stimulation of PAH degradation by earthworms is related to changes in microbial communities, a microcosm experiment was conducted consisting of columns with natural uncontaminated soil covered with PAH-contaminated dredge sediment. Columns without and with low and high Eisenia andrei densities were prepared. Organic matter and PAH content, microbial biomass, and dehydrogenase activity (DHA) were measured in soil and sediment over time. Biolog Ecoplate™ and polymerase chain reaction using denaturing gradient gel electrophoresis were used to evaluate changes in metabolic and structural diversity of the microbial community, respectively. Earthworm activity promoted PAH degradation in soil, which was significant for biphenyl, benzo[a]pyrene, and benzo[e]pyrene. Microbial biomass and DHA activity generally did not change over the experiment. Earthworm activity did change microbial community structure, but this did not affect its functioning in terms of carbon substrate consumption. Results suggest no relationship between changes in the microbial community by earthworm activity and increased PAH disappearance. The role of shifts in soil microbial community structure induced by earthworms in PAH removal needs further investigation.

  4. Biofuel intercropping effects on soil carbon and microbial activity.

    PubMed

    Strickland, Michael S; Leggett, Zakiya H; Sucre, Eric B; Bradford, Mark A

    2015-01-01

    Biofuels will help meet rising demands for energy and, ideally, limit climate change associated with carbon losses from the biosphere to atmosphere. Biofuel management must therefore maximize energy production and maintain ecosystem carbon stocks. Increasingly, there is interest in intercropping biofuels with other crops, partly because biofuel production on arable land might reduce availability and increase the price of food. One intercropping approach involves growing biofuel grasses in forest plantations. Grasses differ from trees in both their organic inputs to soils and microbial associations. These differences are associated with losses of soil carbon when grasses become abundant in forests. We investigated how intercropping switchgrass (Panicum virgalum), a major candidate for cellulosic biomass production, in loblolly pine (Pinus taeda) plantations affects soil carbon, nitrogen, and microbial dynamics. Our design involved four treatments: two pine management regimes where harvest residues (i.e., biomass) were left in place or removed, and two switchgrass regimes where the grass was grown with pine under the same two biomass scenarios (left or removed). Soil variables were measured in four 1-ha replicate plots in the first and second year following switchgrass planting. Under switchgrass intercropping, pools of mineralizable and particulate organic matter carbon were 42% and 33% lower, respectively. These declines translated into a 21% decrease in total soil carbon in the upper 15 cm of the soil profile, during early stand development. The switchgrass effect, however, was isolated to the interbed region where switchgrass is planted. In these regions, switchgrass-induced reductions in soil carbon pools with 29%, 43%, and 24% declines in mineralizable, particulate, and total soil carbon, respectively. Our results support the idea that grass inputs to forests can prime the activity of soil organic carbon degrading microbes, leading to net reductions in stocks

  5. Ohmic resistance affects microbial community and electrochemical kinetics in a multi-anode microbial electrochemical cell

    NASA Astrophysics Data System (ADS)

    Dhar, Bipro Ranjan; Ryu, Hodon; Santo Domingo, Jorge W.; Lee, Hyung-Sool

    2016-11-01

    Multi-anode microbial electrochemical cells (MxCs) are considered as one of the most promising configurations for scale-up of MxCs, but understanding of anode kinetics in multiple anodes is limited in the MxCs. In this study we assessed microbial community and electrochemical kinetic parameters for biofilms on individual anodes in a multi-anode MxC to better comprehend anode fundamentals. Microbial community analysis targeting 16S rRNA Illumina sequencing showed that Geobacter genus was abundant (87%) only on the biofilm anode closest to a reference electrode (low ohmic energy loss) in which current density was the highest among three anodes. In comparison, Geobacter populations were less than 1% for biofilms on other two anodes distant from the reference electrode (high ohmic energy loss), generating small current density. Half-saturation anode potential (EKA) was the lowest at -0.251 to -0.242 V (vs. standard hydrogen electrode) for the closest biofilm anode to the reference electrode, while EKA was as high as -0.134 V for the farthest anode. Our study proves that electric potential of individual anodes changed by ohmic energy loss shifts biofilm communities on individual anodes and consequently influences electron transfer kinetics on each anode in the multi-anode MxC.

  6. Factors affecting the performance of microbial fuel cells for sulfur pollutants removal.

    PubMed

    Zhao, Feng; Rahunen, Nelli; Varcoe, John R; Roberts, Alexander J; Avignone-Rossa, Claudio; Thumser, Alfred E; Slade, Robert C T

    2009-03-15

    A microbial fuel cell (MFC) has been developed for removal of sulfur-based pollutants and can be used for simultaneous wastewater treatment and electricity generation. This fuel cell uses an activated carbon cloth+carbon fibre veil composite anode, air-breathing dual cathodes and the sulfate-reducing species Desulfovibrio desulfuricans. 1.16gdm(-3) sulfite and 0.97gdm(-3) thiosulfate were removed from the wastewater at 22 degrees C, representing sulfite and thiosulfate removal conversions of 91% and 86%, respectively. The anode potential was controlled by the concentration of sulfide in the compartment. The performance of the cathode assembly was affected by the concentration of protons in the cation-exchanging ionomer with which the electrocatalyst is co-bound at the three-phase (air, catalyst and support) boundary.

  7. Analysis of factors affecting the accuracy, reproducibility, and interpretation of microbial community carbon source utilization patterns

    USGS Publications Warehouse

    Haack, S.K.; Garchow, H.; Klug, M.J.; Forney, L.J.

    1995-01-01

    We determined factors that affect responses of bacterial isolates and model bacterial communities to the 95 carbon substrates in Biolog microliter plates. For isolates and communities of three to six bacterial strains, substrate oxidation rates were typically nonlinear and were delayed by dilution of the inoculum. When inoculum density was controlled, patterns of positive and negative responses exhibited by microbial communities to each of the carbon sources were reproducible. Rates and extents of substrate oxidation by the communities were also reproducible but were not simply the sum of those exhibited by community members when tested separately. Replicates of the same model community clustered when analyzed by principal- components analysis (PCA), and model communities with different compositions were clearly separated un the first PCA axis, which accounted for >60% of the dataset variation. PCA discrimination among different model communities depended on the extent to which specific substrates were oxidized. However, the substrates interpreted by PCA to be most significant in distinguishing the communities changed with reading time, reflecting the nonlinearity of substrate oxidation rates. Although whole-community substrate utilization profiles were reproducible signatures for a given community, the extent of oxidation of specific substrates and the numbers or activities of microorganisms using those substrates in a given community were not correlated. Replicate soil samples varied significantly in the rate and extent of oxidation of seven tested substrates, suggesting microscale heterogeneity in composition of the soil microbial community.

  8. Water level changes affect carbon turnover and microbial community composition in lake sediments.

    PubMed

    Weise, Lukas; Ulrich, Andreas; Moreano, Matilde; Gessler, Arthur; Kayler, Zachary E; Steger, Kristin; Zeller, Bernd; Rudolph, Kristin; Knezevic-Jaric, Jelena; Premke, Katrin

    2016-05-01

    Due to climate change, many lakes in Europe will be subject to higher variability of hydrological characteristics in their littoral zones. These different hydrological regimes might affect the use of allochthonous and autochthonous carbon sources. We used sandy sediment microcosms to examine the effects of different hydrological regimes (wet, desiccating, and wet-desiccation cycles) on carbon turnover. (13)C-labelled particulate organic carbon was used to trace and estimate carbon uptake into bacterial biomass (via phospholipid fatty acids) and respiration. Microbial community changes were monitored by combining DNA- and RNA-based real-time PCR quantification and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA. The shifting hydrological regimes in the sediment primarily caused two linked microbial effects: changes in the use of available organic carbon and community composition changes. Drying sediments yielded the highest CO2 emission rates, whereas hydrological shifts increased the uptake of allochthonous organic carbon for respiration. T-RFLP patterns demonstrated that only the most extreme hydrological changes induced a significant shift in the active and total bacterial communities. As current scenarios of climate change predict an increase of drought events, frequent variations of the hydrological regimes of many lake littoral zones in central Europe are anticipated. Based on the results of our study, this phenomenon may increase the intensity and amplitude in rates of allochthonous organic carbon uptake and CO2 emissions.

  9. Water level changes affect carbon turnover and microbial community composition in lake sediments

    PubMed Central

    Weise, Lukas; Ulrich, Andreas; Moreano, Matilde; Gessler, Arthur; E. Kayler, Zachary; Steger, Kristin; Zeller, Bernd; Rudolph, Kristin; Knezevic-Jaric, Jelena; Premke, Katrin

    2016-01-01

    Due to climate change, many lakes in Europe will be subject to higher variability of hydrological characteristics in their littoral zones. These different hydrological regimes might affect the use of allochthonous and autochthonous carbon sources. We used sandy sediment microcosms to examine the effects of different hydrological regimes (wet, desiccating, and wet-desiccation cycles) on carbon turnover. 13C-labelled particulate organic carbon was used to trace and estimate carbon uptake into bacterial biomass (via phospholipid fatty acids) and respiration. Microbial community changes were monitored by combining DNA- and RNA-based real-time PCR quantification and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA. The shifting hydrological regimes in the sediment primarily caused two linked microbial effects: changes in the use of available organic carbon and community composition changes. Drying sediments yielded the highest CO2 emission rates, whereas hydrological shifts increased the uptake of allochthonous organic carbon for respiration. T-RFLP patterns demonstrated that only the most extreme hydrological changes induced a significant shift in the active and total bacterial communities. As current scenarios of climate change predict an increase of drought events, frequent variations of the hydrological regimes of many lake littoral zones in central Europe are anticipated. Based on the results of our study, this phenomenon may increase the intensity and amplitude in rates of allochthonous organic carbon uptake and CO2 emissions. PMID:26902802

  10. Plant extracts affect in vitro rumen microbial fermentation.

    PubMed

    Busquet, M; Calsamiglia, S; Ferret, A; Kamel, C

    2006-02-01

    Different doses of 12 plant extracts and 6 secondary plant metabolites were incubated for 24 h in diluted ruminal fluid with a 50:50 forage:concentrate diet. Treatments were: control (no additive), plant extracts (anise oil, cade oil, capsicum oil, cinnamon oil, clove bud oil, dill oil, fenugreek, garlic oil, ginger oil, oregano oil, tea tree oil, and yucca), and secondary plant metabolites (anethol, benzyl salicylate, carvacrol, carvone, cinnamaldehyde, and eugenol). Each treatment was supplied at 3, 30, 300, and 3,000 mg/L of culture fluid. At 3,000 mg/L, most treatments decreased total volatile fatty acid concentration, but cade oil, capsicum oil, dill oil, fenugreek, ginger oil, and yucca had no effect. Different doses of anethol, anise oil, carvone, and tea tree oil decreased the proportion of acetate and propionate, which suggests that these compounds may not be nutritionally beneficial to dairy cattle. Garlic oil (300 and 3,000 mg/L) and benzyl salicylate (300 and 3,000 mg/L) reduced acetate and increased propionate and butyrate proportions, suggesting that methane production was inhibited. At 3,000 mg/L, capsicum oil, carvacrol, carvone, cinnamaldehyde, cinnamon oil, clove bud oil, eugenol, fenugreek, and oregano oil resulted in a 30 to 50% reduction in ammonia N concentration. Careful selection and combination of these extracts may allow the manipulation of rumen microbial fermentation.

  11. Long-term effects of nickel oxide nanoparticles on performance, microbial enzymatic activity, and microbial community of a sequencing batch reactor.

    PubMed

    Wang, Sen; Li, Zhiwei; Gao, Mengchun; She, Zonglian; Guo, Liang; Zheng, Dong; Zhao, Yangguo; Ma, Bingrui; Gao, Feng; Wang, Xuejiao

    2017-02-01

    The nitrogen and phosphorus removal, microbial enzymatic activity, and microbial community of a sequencing batch reactor (SBR) were evaluated under long-term exposure to nickel oxide nanoparticles (NiO NPs). High NiO NP concentration (over 5 mg L(-1)) affected the removal of chemical oxygen demand, nitrogen, and phosphorus. The presence of NiO NP inhibited the microbial enzymatic activities and reduced the nitrogen and phosphorus removal rates of activated sludge. The microbial enzymatic activities of the activated sludge showed a similar variation trend to the nitrogen and phosphorus removal rates with the increase in NiO NP concentration from 0 to 60 mg L(-1). The Ni content in the effluent and activated sludge showed an increasing trend with the increase in NiO NP concentration. Some NiO NPs were absorbed on the sludge surface or penetrate the cell membrane into the interior of microbial cells in the activated sludge. NiO NP facilitated the increase in reactive oxygen species by disturbing the balance between the oxidation and anti-oxidation processes, and the variation in lactate dehydrogenase demonstrated that NiO NP could destroy the cytomembrane and cause variations in the microbial morphology and physiological function. High-throughput sequencing demonstrated that the microbial community of SBR had some obvious changes at 0-60 mg L(-1) NiO NPs at the phyla, class and genus levels.

  12. Representation of Dormant and Active Microbial Dynamics for Ecosystem Modeling

    SciTech Connect

    Wang, Gangsheng; Mayes, Melanie; Gu, Lianhong; Schadt, Christopher Warren

    2014-01-01

    Dormancy is an essential strategy for microorganisms to cope with environmental stress. However, global ecosystem models typically ignore microbial dormancy, resulting in notable model uncertainties. To facilitate the consideration of dormancy in these large-scale models, we propose a new microbial physiology component that works for a wide range of substrate availabilities. This new model is based on microbial physiological states and the major parameters are the maximum specific growth and maintenance rates of active microbes and the ratio of dormant to active maintenance rates. A major improvement of our model over extant models is that it can explain the low active microbial fractions commonly observed in undisturbed soils. Our new model shows that the exponentially-increasing respiration from substrate-induced respiration experiments can only be used to determine the maximum specific growth rate and initial active microbial biomass, while the respiration data representing both exponentially-increasing and non-exponentially-increasing phases can robustly determine a range of key parameters including the initial total live biomass, initial active fraction, the maximum specific growth and maintenance rates, and the half-saturation constant. Our new model can be incorporated into existing ecosystem models to account for dormancy in microbially-driven processes and to provide improved estimates of microbial activities.

  13. Effects of Potassium Permanganate Oxidation on Subsurface Microbial Activity

    NASA Technical Reports Server (NTRS)

    Rowland, Martin A.; Brubaker, Gaylen R.; Westray, Mark; Morris, Damon; Kohler, Keisha; McCool, Alex (Technical Monitor)

    2001-01-01

    In situ chemical oxidation has the potential for degrading large quantities of organic contaminants and can be more effective and timely than traditional ex situ treatment methods. However, there is a need to better characterize the potential effects of this treatment on natural processes. This study focuses on potential inhibition to anaerobic dechlorination of trichloroethene (TCE) in soils from a large manufacturing facility as a result of in situ oxidation using potassium permanganate (KMn04)Previous microcosm studies established that natural attenuation occurs on-site and that it is enhanced by the addition of ethanol to the system. A potential remediation scheme for the site involves the use of potassium permanganate to reduce levels of TCE in heavily contaminated areas, then to inject ethanol into the system to "neutralize" excess oxidant and enhance microbial degradation. However, it is currently unknown whether the exposure of indigenous microbial populations to potassium permanganate may adversely affect biological reductive dechlorination by these microorganisms. Consequently, additional microcosm studies were conducted to evaluate this remediation scheme and assess the effect of potassium permanganate addition on biological reductive dechlorination of TCE. Samples of subsurface soil and groundwater were collected from a TCE-impacted area of the site. A portion of the soil was pretreated with nutrients and ethanol to stimulate microbial activity, while the remainder of the soil was left unamended. Soil/groundwater microcosms were prepared in sealed vials using the nutrient-amended and unamended soils, and the effects of potassium permanganate addition were evaluated using two permanganate concentrations (0.8 and 2.4 percent) and two contact times (1 and 3 weeks). TCE was then re-added to each microcosm and TCE and dichloroethene (DCE) concentrations were monitored to determine the degree to which microbial dechlorination occurred following chemical

  14. Effect of Malathion on the Microbial Ecology of Activated Sludge

    DTIC Science & Technology

    2015-03-26

    EFFECT OF MALATHION ON THE MICROBIAL ECOLOGY OF ACTIVATED SLUDGE THESIS Seth K. Martin, Senior Master Sergeant, USAF AFIT-ENV-MS-15-M-095 DEPARTMENT...Government and is not subject to copyright protection in the United States. AFIT-ENV-MS-15-M-095 EFFECT OF MALATHION ON THE MICROBIAL ECOLOGY OF ACTIVATED...UNLIMITED. AFIT-ENV-MS-15-M-095 EFFECT OF MALATHION ON THE MICROBIAL ECOLOGY OF ACTIVATED SLUDGE THESIS Seth K. Martin, B.S. Senior Master Sergeant

  15. Metabolically active microbial communities in uranium-contaminated subsurface sediments.

    PubMed

    Akob, Denise M; Mills, Heath J; Kostka, Joel E

    2007-01-01

    In order to develop effective bioremediation strategies for radionuclide contaminants, the composition and metabolic potential of microbial communities need to be better understood, especially in highly contaminated subsurface sediments for which little cultivation-independent information is available. In this study, we characterized metabolically active and total microbial communities associated with uranium-contaminated subsurface sediments along geochemical gradients. DNA and RNA were extracted and amplified from four sediment-depth intervals representing moderately acidic (pH 3.7) to near-neutral (pH 6.7) conditions. Phylotypes related to Proteobacteria (Alpha-, Beta-, Delta- and Gammaproteobacteria), Bacteroidetes, Actinobacteria, Firmicutes and Planctomycetes were detected in DNA- and RNA-derived clone libraries. Diversity and numerical dominance of phylotypes were observed to correspond to changes in sediment geochemistry and rates of microbial activity, suggesting that geochemical conditions have selected for well-adapted taxa. Sequences closely related to nitrate-reducing bacteria represented 28% and 43% of clones from the total and metabolically active fractions of the microbial community, respectively. This study provides the first detailed analysis of total and metabolically active microbial communities in radionuclide-contaminated subsurface sediments. Our microbial community analysis, in conjunction with rates of microbial activity, points to several groups of nitrate-reducers that appear to be well adapted to environmental conditions common to radionuclide-contaminated sites.

  16. Spatial Variations of Soil Microbial Activities in Saline Groundwater-Irrigated Soil Ecosystem

    NASA Astrophysics Data System (ADS)

    Chen, Li-Juan; Feng, Qi; Li, Chang-Sheng; Song, You-Xi; Liu, Wei; Si, Jian-Hua; Zhang, Bao-Gui

    2016-05-01

    Spatial variations of soil microbial activities and its relationship with environmental factors are very important for estimating regional soil ecosystem function. Based on field samplings in a typical saline groundwater-irrigated region, spatial variations of soil microbial metabolic activities were investigated. Combined with groundwater quality analysis, the relationship between microbial activities and water salinity was also studied. The results demonstrated that moderate spatial heterogeneity of soil microbial activities presented under the total dissolved solids (TDS) of groundwater ranging from 0.23 to 12.24 g L-1. Groundwater salinity and microbial activities had almost opposite distribution characteristics: slight saline water was mainly distributed in west Baqu and south Quanshan, while severe saline and briny water were dominant in east Baqu and west Huqu; however, total AWCD was higher in the east-center and southwest of Baqu and east Huqu, while it was lower in east Baqu and northwest Huqu. The results of correlation analyses demonstrated that high-salinity groundwater irrigation had significantly adverse effects on soil microbial activities. Major ions Ca2+, Mg2+, Cl_, and SO4 2- in groundwater decisively influenced the results. Three carbon sources, carbohydrates, amines, and phenols, which had minor utilization rates in all irrigation districts, were extremely significantly affected by high-salinity groundwater irrigation. The results presented here offer an approach for diagnosing regional soil ecosystem function changes under saline water irrigation.

  17. Spatial Variations of Soil Microbial Activities in Saline Groundwater-Irrigated Soil Ecosystem.

    PubMed

    Chen, Li-Juan; Feng, Qi; Li, Chang-Sheng; Song, You-Xi; Liu, Wei; Si, Jian-Hua; Zhang, Bao-Gui

    2016-05-01

    Spatial variations of soil microbial activities and its relationship with environmental factors are very important for estimating regional soil ecosystem function. Based on field samplings in a typical saline groundwater-irrigated region, spatial variations of soil microbial metabolic activities were investigated. Combined with groundwater quality analysis, the relationship between microbial activities and water salinity was also studied. The results demonstrated that moderate spatial heterogeneity of soil microbial activities presented under the total dissolved solids (TDS) of groundwater ranging from 0.23 to 12.24 g L(-1). Groundwater salinity and microbial activities had almost opposite distribution characteristics: slight saline water was mainly distributed in west Baqu and south Quanshan, while severe saline and briny water were dominant in east Baqu and west Huqu; however, total AWCD was higher in the east-center and southwest of Baqu and east Huqu, while it was lower in east Baqu and northwest Huqu. The results of correlation analyses demonstrated that high-salinity groundwater irrigation had significantly adverse effects on soil microbial activities. Major ions Ca(2+), Mg(2+), Cl(-), and SO4(2-) in groundwater decisively influenced the results. Three carbon sources, carbohydrates, amines, and phenols, which had minor utilization rates in all irrigation districts, were extremely significantly affected by high-salinity groundwater irrigation. The results presented here offer an approach for diagnosing regional soil ecosystem function changes under saline water irrigation.

  18. Microbial community changes along the active seepage site of one cold seep in the Red Sea

    PubMed Central

    Cao, Huiluo; Zhang, Weipeng; Wang, Yong; Qian, Pei-Yuan

    2015-01-01

    The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep. PMID:26284035

  19. Microbial community changes along the active seepage site of one cold seep in the Red Sea.

    PubMed

    Cao, Huiluo; Zhang, Weipeng; Wang, Yong; Qian, Pei-Yuan

    2015-01-01

    The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.

  20. Microbial Ecology of Thailand Tsunami and Non-Tsunami Affected Terrestrials

    PubMed Central

    Somboonna, Naraporn; Wilantho, Alisa; Jankaew, Kruawun; Assawamakin, Anunchai; Sangsrakru, Duangjai; Tangphatsornruang, Sithichoke; Tongsima, Sissades

    2014-01-01

    The effects of tsunamis on microbial ecologies have been ill-defined, especially in Phang Nga province, Thailand. This ecosystem was catastrophically impacted by the 2004 Indian Ocean tsunami as well as the 600 year-old tsunami in Phra Thong island, Phang Nga province. No study has been conducted to elucidate their effects on microbial ecology. This study represents the first to elucidate their effects on microbial ecology. We utilized metagenomics with 16S and 18S rDNA-barcoded pyrosequencing to obtain prokaryotic and eukaryotic profiles for this terrestrial site, tsunami affected (S1), as well as a parallel unaffected terrestrial site, non-tsunami affected (S2). S1 demonstrated unique microbial community patterns than S2. The dendrogram constructed using the prokaryotic profiles supported the unique S1 microbial communities. S1 contained more proportions of archaea and bacteria domains, specifically species belonging to Bacteroidetes became more frequent, in replacing of the other typical floras like Proteobacteria, Acidobacteria and Basidiomycota. Pathogenic microbes, including Acinetobacter haemolyticus, Flavobacterium spp. and Photobacterium spp., were also found frequently in S1. Furthermore, different metabolic potentials highlighted this microbial community change could impact the functional ecology of the site. Moreover, the habitat prediction based on percent of species indicators for marine, brackish, freshwater and terrestrial niches pointed the S1 to largely comprise marine habitat indicating-species. PMID:24710002

  1. Microbial ecology of Thailand tsunami and non-tsunami affected terrestrials.

    PubMed

    Somboonna, Naraporn; Wilantho, Alisa; Jankaew, Kruawun; Assawamakin, Anunchai; Sangsrakru, Duangjai; Tangphatsornruang, Sithichoke; Tongsima, Sissades

    2014-01-01

    The effects of tsunamis on microbial ecologies have been ill-defined, especially in Phang Nga province, Thailand. This ecosystem was catastrophically impacted by the 2004 Indian Ocean tsunami as well as the 600 year-old tsunami in Phra Thong island, Phang Nga province. No study has been conducted to elucidate their effects on microbial ecology. This study represents the first to elucidate their effects on microbial ecology. We utilized metagenomics with 16S and 18S rDNA-barcoded pyrosequencing to obtain prokaryotic and eukaryotic profiles for this terrestrial site, tsunami affected (S1), as well as a parallel unaffected terrestrial site, non-tsunami affected (S2). S1 demonstrated unique microbial community patterns than S2. The dendrogram constructed using the prokaryotic profiles supported the unique S1 microbial communities. S1 contained more proportions of archaea and bacteria domains, specifically species belonging to Bacteroidetes became more frequent, in replacing of the other typical floras like Proteobacteria, Acidobacteria and Basidiomycota. Pathogenic microbes, including Acinetobacter haemolyticus, Flavobacterium spp. and Photobacterium spp., were also found frequently in S1. Furthermore, different metabolic potentials highlighted this microbial community change could impact the functional ecology of the site. Moreover, the habitat prediction based on percent of species indicators for marine, brackish, freshwater and terrestrial niches pointed the S1 to largely comprise marine habitat indicating-species.

  2. Microbial ecology of terrestrial Antarctica: Are microbial systems at risk from human activities?

    SciTech Connect

    White, G.J.

    1996-08-01

    Many of the ecological systems found in continental Antarctica are comprised entirely of microbial species. Concerns have arisen that these microbial systems might be at risk either directly through the actions of humans or indirectly through increased competition from introduced species. Although protection of native biota is covered by the Protocol on Environmental Protection to the Antarctic Treaty, strict measures for preventing the introduction on non-native species or for protecting microbial habitats may be impractical. This report summarizes the research conducted to date on microbial ecosystems in continental Antarctica and discusses the need for protecting these ecosystems. The focus is on communities inhabiting soil and rock surfaces in non-coastal areas of continental Antarctica. Although current polices regarding waste management and other operations in Antarctic research stations serve to reduce the introduction on non- native microbial species, importation cannot be eliminated entirely. Increased awareness of microbial habitats by field personnel and protection of certain unique habitats from physical destruction by humans may be necessary. At present, small-scale impacts from human activities are occurring in certain areas both in terms of introduced species and destruction of habitat. On a large scale, however, it is questionable whether the introduction of non-native microbial species to terrestrial Antarctica merits concern.

  3. Microbial Activity and Silica Degradation in Rice Straw

    NASA Astrophysics Data System (ADS)

    Kim, Esther Jin-kyung

    Abundantly available agricultural residues like rice straw have the potential to be feedstocks for bioethanol production. Developing optimized conditions for rice straw deconstruction is a key step toward utilizing the biomass to its full potential. One challenge associated with conversion of rice straw to bioenergy is its high silica content as high silica erodes machinery. Another obstacle is the availability of enzymes that hydrolyze polymers in rice straw under industrially relevant conditions. Microbial communities that colonize compost may be a source of enzymes for bioconversion of lignocellulose to products because composting systems operate under thermophilic and high solids conditions that have been shown to be commercially relevant. Compost microbial communities enriched on rice straw could provide insight into a more targeted source of enzymes for the breakdown of rice straw polysaccharides and silica. Because rice straw is low in nitrogen it is important to understand the impact of nitrogen concentrations on the production of enzyme activity by the microbial community. This study aims to address this issue by developing a method to measure microbial silica-degrading activity and measure the effect of nitrogen amendment to rice straw on microbial activity and extracted enzyme activity during a high-solids, thermophilic incubation. An assay was developed to measure silica-degrading enzyme or silicase activity. This process included identifying methods of enzyme extraction from rice straw, identifying a model substrate for the assay, and optimizing measurement techniques. Rice straw incubations were conducted with five different levels of nitrogen added to the biomass. Microbial activity was measured by respiration and enzyme activity. A microbial community analysis was performed to understand the shift in community structure with different treatments. With increased levels of nitrogen, respiration and cellulose and hemicellulose degrading activity

  4. Association of Microbial Community Composition and Activity with Lead, Chromium, and Hydrocarbon Contamination

    PubMed Central

    Shi, W.; Becker, J.; Bischoff, M.; Turco, R. F.; Konopka, A. E.

    2002-01-01

    Microbial community composition and activity were characterized in soil contaminated with lead (Pb), chromium (Cr), and hydrocarbons. Contaminant levels were very heterogeneous and ranged from 50 to 16,700 mg of total petroleum hydrocarbons (TPH) kg of soil−1, 3 to 3,300 mg of total Cr kg of soil−1, and 1 to 17,100 mg of Pb kg of soil−1. Microbial community compositions were estimated from the patterns of phospholipid fatty acids (PLFA); these were considerably different among the 14 soil samples. Statistical analyses suggested that the variation in PLFA was more correlated with soil hydrocarbons than with the levels of Cr and Pb. The metal sensitivity of the microbial community was determined by extracting bacteria from soil and measuring [3H]leucine incorporation as a function of metal concentration. Six soil samples collected in the spring of 1999 had IC50 values (the heavy metal concentrations giving 50% reduction of microbial activity) of approximately 2.5 mM for CrO42− and 0.01 mM for Pb2+. Much higher levels of Pb were required to inhibit [14C]glucose mineralization directly in soils. In microcosm experiments with these samples, microbial biomass and the ratio of microbial biomass to soil organic C were not correlated with the concentrations of hydrocarbons and heavy metals. However, microbial C respiration in samples with a higher level of hydrocarbons differed from the other soils no matter whether complex organic C (alfalfa) was added or not. The ratios of microbial C respiration to microbial biomass differed significantly among the soil samples (P < 0.05) and were relatively high in soils contaminated with hydrocarbons or heavy metals. Our results suggest that the soil microbial community was predominantly affected by hydrocarbons. PMID:12147482

  5. Association of microbial community composition and activity with lead, chromium, and hydrocarbon contamination.

    PubMed

    Shi, W; Becker, J; Bischoff, M; Turco, R F; Konopka, A E

    2002-08-01

    Microbial community composition and activity were characterized in soil contaminated with lead (Pb), chromium (Cr), and hydrocarbons. Contaminant levels were very heterogeneous and ranged from 50 to 16,700 mg of total petroleum hydrocarbons (TPH) kg of soil(-1), 3 to 3,300 mg of total Cr kg of soil(-1), and 1 to 17,100 mg of Pb kg of soil(-1). Microbial community compositions were estimated from the patterns of phospholipid fatty acids (PLFA); these were considerably different among the 14 soil samples. Statistical analyses suggested that the variation in PLFA was more correlated with soil hydrocarbons than with the levels of Cr and Pb. The metal sensitivity of the microbial community was determined by extracting bacteria from soil and measuring [(3)H]leucine incorporation as a function of metal concentration. Six soil samples collected in the spring of 1999 had IC(50) values (the heavy metal concentrations giving 50% reduction of microbial activity) of approximately 2.5 mM for CrO(4)2- and 0.01 mM for Pb2+. Much higher levels of Pb were required to inhibit [14C]glucose mineralization directly in soils. In microcosm experiments with these samples, microbial biomass and the ratio of microbial biomass to soil organic C were not correlated with the concentrations of hydrocarbons and heavy metals. However, microbial C respiration in samples with a higher level of hydrocarbons differed from the other soils no matter whether complex organic C (alfalfa) was added or not. The ratios of microbial C respiration to microbial biomass differed significantly among the soil samples (P < 0.05) and were relatively high in soils contaminated with hydrocarbons or heavy metals. Our results suggest that the soil microbial community was predominantly affected by hydrocarbons.

  6. Arabinoxylan‐oligosaccharides (AXOS) affect the protein/carbohydrate fermentation balance and microbial population dynamics of the Simulator of Human Intestinal Microbial Ecosystem

    PubMed Central

    Sanchez, J. I.; Marzorati, M.; Grootaert, C.; Baran, M.; Van Craeyveld, V.; Courtin, C. M.; Broekaert, W. F.; Delcour, J. A.; Verstraete, W.; Van de Wiele, T.

    2009-01-01

    Summary Arabinoxylan‐oligosaccharides (AXOS) are a recently newly discovered class of candidate prebiotics as – depending on their structure – they are fermented in different regions of gastrointestinal tract. This can have an impact on the protein/carbohydrate fermentation balance in the large intestine and, thus, affect the generation of potentially toxic metabolites in the colon originating from proteolytic activity. In this study, we screened different AXOS preparations for their impact on the in vitro intestinal fermentation activity and microbial community structure. Short‐term fermentation experiments with AXOS with an average degree of polymerization (avDP) of 29 allowed part of the oligosaccharides to reach the distal colon, and decreased the concentration of proteolytic markers, whereas AXOS with lower avDP were primarily fermented in the proximal colon. Additionally, prolonged supplementation of AXOS with avDP 29 to the Simulator of Human Intestinal Microbial Ecosystem (SHIME) reactor decreased levels of the toxic proteolytic markers phenol and p‐cresol in the two distal colon compartments and increased concentrations of beneficial short‐chain fatty acids (SCFA) in all colon vessels (25–48%). Denaturant gradient gel electrophoresis (DGGE) analysis indicated that AXOS supplementation only slightly modified the total microbial community, implying that the observed effects on fermentation markers are mainly caused by changes in fermentation activity. Finally, specific quantitative PCR (qPCR) analysis showed that AXOS supplementation significantly increased the amount of health‐promoting lactobacilli as well as of Bacteroides–Prevotella and Clostridium coccoides–Eubacterium rectale groups. These data allow concluding that AXOS are promising candidates to modulate the microbial metabolism in the distal colon. PMID:21261885

  7. [Soil microbial activity variation after land use changes in savannah, Llanos Orientales, Venezuela].

    PubMed

    Gómez, Yrma; Paolini, Jorge

    2011-03-01

    In West plains of Venezuela, the traditional land use of the Trachypogon savannah, has been the extensive grazing. The pressure over these savannahs to obtain a major animal productivity has stimulated the introduction of exotic forage plants, such as Brachiaria brizantha and Andropogon gayanus. In spite that great savannah extensions have been subject to this land use change, information about the effect that pastures and grazing activity have on microbial activity in these soils is scarce. So the objective of this study was to determine the impact that the extensive grazing and cover substitution have on microbial activity. The soil sampling was carried out during the dry and rainy seasons. The employed parameters to determine changes in soil microbial activity were the substrate induced respiration (SIR), basal respiration (BR), the dehydrogenase activity (DHS), the fluorescein diacetate hydrolysis (FDA) and the arginene ammonification (AA). The similarity of the structural soil characteristics studied allows us to infer, that the differences in the microbiological parameters are determined by climatic conditions and soil management. The results show that there is a low microbial activity in these soils. The rainy season caused an increase in all the microbiological parameters determined. B. brizantha made a greater contribution to soil carbon and promoted a greater heterotrophic activity. The extensive grazing and the low stocking rate in the West plain savannas did not affect the microbial activity in these soils.

  8. Top-down control of carbon sequestration: grazing affects microbial structure and function in salt marsh soils.

    PubMed

    Mueller, Peter; Granse, Dirk; Nolte, Stefanie; Do, Hai Thi; Weingartner, Magdalena; Hoth, Stefan; Jensen, Kai

    2017-03-20

    Tidal wetlands have been increasingly recognized as long-term carbon sinks in recent years. Work on carbon sequestration and decomposition processes in tidal wetlands focused so far mainly on effects of global-change factors such as sea-level rise and increasing temperatures. However, little is known about effects of land use, such as livestock grazing, on organic matter decomposition and ultimately carbon sequestration. The present work aims at understanding the mechanisms by which large herbivores can affect organic matter decomposition in tidal wetlands. This was achieved by studying both direct animal-microbe interactions and indirect animal-plant-microbe interactions in grazed and ungrazed areas of two long-term experimental field sites at the German North Sea coast. We assessed bacterial and fungal gene abundance using quantitative PCR, as well as the activity of microbial exo-enzymes by conducting fluorometric assays. We demonstrate that grazing can have a profound impact on the microbial community structure of tidal wetland soils, by consistently increasing the fungi-to-bacteria ratio by 38-42%, and therefore potentially exerts important control over carbon turnover and sequestration. The observed shift in the microbial community was primarily driven by organic matter source, with higher contributions of recalcitrant autochthonous (terrestrial) vs. easily degradable allochthonous (marine) sources in grazed areas favoring relative fungal abundance. We propose a novel and indirect form of animal-plant-microbe interaction: top-down control of aboveground vegetation structure determines the capacity of allochthonous organic matter trapping during flooding and thus the structure of the microbial community. Furthermore, our data provide the first evidence that grazing slows down microbial exo-enzyme activity and thus decomposition through changes in soil redox chemistry. Activities of enzymes involved in C cycling were reduced by 28-40%, while activities of

  9. Soil microbial diversity and soil functioning affect competition among grasses in experimental microcosms.

    PubMed

    Bonkowski, Michael; Roy, Jacques

    2005-03-01

    A gradient of microbial diversity in soil was established by inoculating pasteurized soil with microbial populations of different complexity, which were obtained by a combination of soil fumigation and filtering techniques. Four different soil diversity treatments were planted with six different grass species either in monoculture or in polyculture to test how changes of general microbial functions, such as catabolic diversity and nutrient recycling efficiency would affect the performance of the plant communities. Relatively harsh soil treatments were necessary to elicit visible effects on major soil processes such as decomposition and nitrogen cycling due to the high redundancy and resilience of soil microbial communities. The strongest effects of soil diversity manipulations on plant growth occurred in polycultures where interspecific competition between plants was high. In polycultures, soil diversity reduction led to a gradual, linear decline in biomass production of one subordinate grass species (Bromus hordeaceus), which was compensated by increased growth of two intermediate competitors (Aegilops geniculata, B. madritensis). This negative covariance in growth of competing grass species smoothed the effects of soil diversity manipulations at the plant community level. As a result, total shoot biomass production remained constant. Apparently the effects of soil diversity manipulations were buffered because functional redundancy at both, the microbial and the plant community level complemented each other. The results further suggests that small trade-offs in plant fitness due to general functional shifts at the microbial level can be significant for the outcome of competition in plant communities and thus diversity at much larger scales.

  10. Measurements of Microbial Community Activities in Individual Soil Macroaggregates

    SciTech Connect

    Bailey, Vanessa L.; Bilskis, Christina L.; Fansler, Sarah J.; McCue, Lee Ann; Smith, Jeff L.; Konopka, Allan

    2012-05-01

    The functional potential of single soil aggregates may provide insights into the localized distribution of microbial activities better than traditional assays conducted on bulk quantities of soil. Thus, we scaled down enzyme assays for {beta}-glucosidase, N-acetyl-{beta}-D-glucosaminidase, lipase, and leucine aminopeptidase to measure of the enzyme potential of individual aggregates (250-1000 {mu}m diameter). Across all enzymes, the smallest aggregates had the greatest activity and the range of enzyme activities observed in all aggregates supports the hypothesis that functional potential in soil may be distributed in a patchy fashion. Paired analyses of ATP as a surrogate for active microbial biomass and {beta}-glucosidase on the same aggregates suggest the presence of both extracellular {beta}-glucosidase functioning in aggregates with no detectable ATP and also of relatively active microbial communities (high ATP) that have low {beta}-glucosidase potentials. Studying function at a scale more consistent with microbial habitat presents greater opportunity to link microbial community structure to microbial community function.

  11. Factors affecting virus dynamics and microbial host-virus interactions in marine environments.

    PubMed

    Mojica, Kristina D A; Brussaard, Corina P D

    2014-09-01

    Marine microorganisms constitute the largest percentage of living biomass and serve as the major driving force behind nutrient and energy cycles. While viruses only comprise a small percentage of this biomass (i.e., 5%), they dominate in numerical abundance and genetic diversity. Through host infection and mortality, viruses affect microbial population dynamics, community composition, genetic evolution, and biogeochemical cycling. However, the field of marine viral ecology is currently limited by a lack of data regarding how different environmental factors regulate virus dynamics and host-virus interactions. The goal of the present minireview was to contribute to the evolution of marine viral ecology, through the assimilation of available data regarding the manner and degree to which environmental factors affect viral decay and infectivity as well as influence latent period and production. Considering the ecological importance of viruses in the marine ecosystem and the increasing pressure from anthropogenic activity and global climate change on marine systems, a synthesis of existing information provides a timely framework for future research initiatives in viral ecology.

  12. Denitrifying Bacterial Communities Affect Current Production and Nitrous Oxide Accumulation in a Microbial Fuel Cell

    PubMed Central

    Vilar-Sanz, Ariadna; Puig, Sebastià; García-Lledó, Arantzazu; Trias, Rosalia; Balaguer, M. Dolors; Colprim, Jesús; Bañeras, Lluís

    2013-01-01

    The biocathodic reduction of nitrate in Microbial Fuel Cells (MFCs) is an alternative to remove nitrogen in low carbon to nitrogen wastewater and relies entirely on microbial activity. In this paper the community composition of denitrifiers in the cathode of a MFC is analysed in relation to added electron acceptors (nitrate and nitrite) and organic matter in the cathode. Nitrate reducers and nitrite reducers were highly affected by the operational conditions and displayed high diversity. The number of retrieved species-level Operational Taxonomic Units (OTUs) for narG, napA, nirS and nirK genes was 11, 10, 31 and 22, respectively. In contrast, nitrous oxide reducers remained virtually unchanged at all conditions. About 90% of the retrieved nosZ sequences grouped in a single OTU with a high similarity with Oligotropha carboxidovorans nosZ gene. nirS-containing denitrifiers were dominant at all conditions and accounted for a significant amount of the total bacterial density. Current production decreased from 15.0 A·m−3 NCC (Net Cathodic Compartment), when nitrate was used as an electron acceptor, to 14.1 A·m−3 NCC in the case of nitrite. Contrarily, nitrous oxide (N2O) accumulation in the MFC was higher when nitrite was used as the main electron acceptor and accounted for 70% of gaseous nitrogen. Relative abundance of nitrite to nitrous oxide reducers, calculated as (qnirS+qnirK)/qnosZ, correlated positively with N2O emissions. Collectively, data indicate that bacteria catalysing the initial denitrification steps in a MFC are highly influenced by main electron acceptors and have a major influence on current production and N2O accumulation. PMID:23717427

  13. Primary succession of soil enzyme activity and heterotrophic microbial communities along the chronosequence of Tianshan Mountains No. 1 Glacier, China.

    PubMed

    Zeng, Jun; Wang, Xiao-Xia; Lou, Kai; Eusufzai, Moniruzzaman Khan; Zhang, Tao; Lin, Qing; Shi, Ying-Wu; Yang, Hong-Mei; Li, Zhong-Qing

    2015-02-01

    We investigated the primary successions of soil enzyme activity and heterotrophic microbial communities at the forefields of the Tianshan Mountains No. 1 Glacier by investigating soil microbial processes (microbial biomass and nitrogen mineralization), enzyme activity and community-level physiological profiling. Soils deglaciated between 1959 and 2008 (0, 5, 17, 31 and 44 years) were collected. Soils >1,500 years in age were used as a reference (alpine meadow soils). Soil enzyme activity and carbon-source utilization ability significantly increased with successional time. Amino-acid utilization rates were relatively higher in early, unvegetated soils (0 and 5 years), but carbohydrate utilization was higher in later stages (from 31 years to the reference soil). Discriminant analysis, including data on microbial processes and soil enzyme activities, revealed that newly exposed soils (0-5 years) and older soils (17-44 years) were well-separated from each other and obviously different from the reference soil. Correlation analysis revealed that soil organic carbon, was the primary factor influencing soil enzyme activity and heterotrophic microbial community succession. Redundancy analysis suggested that soil pH and available P were also affect microbial activity to a considerable degree. Our results indicated that glacier foreland soils have continued to develop over 44 years and soils were significantly affected by the geographic location of the glacier and the local topography. Soil enzyme activities and heterotrophic microbial communities were also significantly influenced by these variables.

  14. Factors limiting microbial activity in volcanic tuff at Yucca Mountain

    SciTech Connect

    Kieft, T.L.; Kovacik, W.P.; Taylor, J.

    1996-09-01

    Samples of tuff aseptically collected from 10 locations in the Exploratory Shaft Facility at the site of the proposed high-level nuclear waste repository at Yucca Mountain, Nevada Test Site were analyzed for microbiological populations, activities, and factors limiting microbial activity. Radiotracer assays ({sup 14}C-labeled organic substrate mineralization), direct microscopic counts, and plate counts were used. Radiolabeled substrates were glucose, acetate, and glutamate. Radiotracer experiments were carried out with and without moisture and inorganic nutrient amendments to determine factors limiting to microbial activities. Nearly all samples showed the presence of microorganisms with the potential to mineralize organic substrates. Addition of inorganic nutrients stimulated activities in a small number of samples. The presence of viable microbial communities within the tuff has implications for transport of contaminants.

  15. Rhizosphere Microbial Community Composition Affects Cadmium and Zinc Uptake by the Metal-Hyperaccumulating Plant Arabidopsis halleri

    PubMed Central

    Muehe, E. Marie; Weigold, Pascal; Adaktylou, Irini J.; Planer-Friedrich, Britta; Kraemer, Ute; Kappler, Andreas

    2015-01-01

    The remediation of metal-contaminated soils by phytoextraction depends on plant growth and plant metal accessibility. Soil microorganisms can affect the accumulation of metals by plants either by directly or indirectly stimulating plant growth and activity or by (im)mobilizing and/or complexing metals. Understanding the intricate interplay of metal-accumulating plants with their rhizosphere microbiome is an important step toward the application and optimization of phytoremediation. We compared the effects of a “native” and a strongly disturbed (gamma-irradiated) soil microbial communities on cadmium and zinc accumulation by the plant Arabidopsis halleri in soil microcosm experiments. A. halleri accumulated 100% more cadmium and 15% more zinc when grown on the untreated than on the gamma-irradiated soil. Gamma irradiation affected neither plant growth nor the 1 M HCl-extractable metal content of the soil. However, it strongly altered the soil microbial community composition and overall cell numbers. Pyrosequencing of 16S rRNA gene amplicons of DNA extracted from rhizosphere samples of A. halleri identified microbial taxa (Lysobacter, Streptomyces, Agromyces, Nitrospira, “Candidatus Chloracidobacterium”) of higher relative sequence abundance in the rhizospheres of A. halleri plants grown on untreated than on gamma-irradiated soil, leading to hypotheses on their potential effect on plant metal uptake. However, further experimental evidence is required, and wherefore we discuss different mechanisms of interaction of A. halleri with its rhizosphere microbiome that might have directly or indirectly affected plant metal accumulation. Deciphering the complex interactions between A. halleri and individual microbial taxa will help to further develop soil metal phytoextraction as an efficient and sustainable remediation strategy. PMID:25595759

  16. Culture Independent Geochemical Tools for Adressing Microbial Activity

    NASA Astrophysics Data System (ADS)

    Lomstein, B. A.; Langerhuus, A. T.; Jørgensen, B. B.; Alperin, M. J.

    2014-12-01

    Decades of ocean drilling have demonstrated wide-spread microbial life in deep sub-seafloor sediment, and surprisingly high numbers of microbial cells and endospores. Despite the ubiquity of life in the deep biosphere, the large community sizes are not yet understood given the extremely low energy fluxes. We have developed and applied new approaches to the deep sub-seafloor to quantify distributions and turnover times of living microbial biomass, endospores and microbial necromass. The approach combines sensitive analyses of unique bacterial marker molecules (muramic acid and d-amino acids) and the bacterial endospore marker (dipicolinic acid) with a series of models that link microscopic (e.g., racemization dynamics of stereo-isomeric amino acids) and macroscopic (e.g., porewater geochemistry) properties. Model output includes production rates and turnover times of microbial biomass and necromass, concentration profiles of reactive organic carbon, and rates of organic carbon decomposition. In combination, these results allow us to assess the role of microbial activity in the sub-seafloor carbon budget. One key result is that the turnover time of biomass is far longer than turnover times found in cultures and active surface sediments.

  17. Will anticipated future climatic conditions affect belowground C utilization? - Insights into the role of microbial functional groups in a temperate heath/grassland.

    NASA Astrophysics Data System (ADS)

    Reinsch, Sabine; Michelsen, Anders; Sárossy, Zsuzsa; Egsgaard, Helge; Kappel Schmidt, Inger; Jakobsen, Iver; Ambus, Per

    2013-04-01

    The global terrestrial soil organic matter stock is the biggest terrestrial carbon pool (1500 Pg C) of which about 4 % is turned over annually. Thus, terrestrial ecosystems have the potential to accelerate or diminish atmospheric climate change effects via belowground carbon processes. We investigated the effect of elevated CO2 (510 ppm), prolonged spring/summer droughts and increased temperature (1 ˚C) on belowground carbon allocation and on the recovery of carbon by the soil microbial community. An in-situ 13C-carbon pulse-labeling experiment was carried out in a temperate heath/grassland (Denmark) in May 2011. Recently assimilated 13C-carbon was traced into roots, soil and microbial biomass 1, 2 and 8 days after pulse-labeling. The importance of the microbial community in C utilization was investigated using 13C enrichment patterns in microbial functional groups on the basis of phospholipid fatty acids (PLFAs) in roots. Gram-negative and gram-positive bacteria were distinguished from the decomposer groups of actinomycetes (belonging to the group of gram-positive bacteria) and saprophytic fungi. Mycorrhizal fungi specific PLFAs were not detected probably due to limited sample size in combination with restricted sensitivity of the used GC-c-IRMS setup. Climate treatments did not affect 13C allocation into roots, soil and microbial biomass carbon and also the total microbial biomass size stayed unchanged as frequently observed. However, climate treatments changed the composition of the microbial community: elevated CO2 significantly reduced the abundance of gram-negative bacteria (17:0cy) but did not affect the abundance of decomposers. Drought favored the bacterial community whereas increased temperatures showed reduced abundance of gram-negative bacteria (19:0cy) and changed the actinomycetes community (10Me16:0, 10Me18:0). However, not only the microbial community composition was affected by the applied climatic conditions, but also the activity of microbial

  18. Secondary Mineralization of Ferrihydrite Affects Microbial Methanogenesis in Geobacter-Methanosarcina Cocultures

    PubMed Central

    Tang, Jia; Ma, Jinlian; Tang, Ziyang; Yu, Zhen

    2016-01-01

    ABSTRACT The transformation of ferrihydrite to stable iron oxides over time has important consequences for biogeochemical cycling of many metals and nutrients. The response of methanogenic activity to the presence of iron oxides depends on the type of iron mineral, but the effects of changes in iron mineralogy on methanogenesis have not been characterized. To address these issues, we constructed methanogenic cocultures of Geobacter and Methanosarcina strains with different ferrihydrite mineralization pathways. In this system, secondary mineralization products from ferrihydrite are regulated by the presence or absence of phosphate. In cultures producing magnetite as the secondary mineralization product, the rates of methanogenesis from acetate and ethanol increased by 30.2% and 135.3%, respectively, compared with a control lacking ferrihydrite. Biogenic magnetite was proposed to promote direct interspecies electron transfer between Geobacter and Methanosarcina in a manner similar to that of c-type cytochrome and thus facilitate methanogenesis. Vivianite biomineralization from ferrihydrite in the presence of phosphate did not significantly influence the methanogenesis processes. The correlation between magnetite occurrence and facilitated methanogenesis was supported by increased rates of methane production from acetate and ethanol with magnetite supplementation in the defined cocultures. Our data provide a new perspective on the important role of iron biomineralization in biogeochemical cycling of carbon in diverse anaerobic environments. IMPORTANCE It has been found that microbial methanogenesis is affected by the presence of iron minerals, and their influences on methanogenesis are associated with the mineralogical properties of the iron minerals. However, how changes in iron mineralogy affect microbial methanogenesis has not been characterized. To address this issue, we constructed methanogenic cocultures of Geobacter and Methanosarcina strains with different

  19. Soil microbial biomass, basal respiration and enzyme activity of main forest types in the Qinling Mountains.

    PubMed

    Cheng, Fei; Peng, Xiaobang; Zhao, Peng; Yuan, Jie; Zhong, Chonggao; Cheng, Yalong; Cui, Cui; Zhang, Shuoxin

    2013-01-01

    Different forest types exert essential impacts on soil physical-chemical characteristics by dominant tree species producing diverse litters and root exudates, thereby further regulating size and activity of soil microbial communities. However, the study accuracy is usually restricted by differences in climate, soil type and forest age. Our objective is to precisely quantify soil microbial biomass, basal respiration and enzyme activity of five natural secondary forest (NSF) types with the same stand age and soil type in a small climate region and to evaluate relationship between soil microbial and physical-chemical characters. We determined soil physical-chemical indices and used the chloroform fumigation-extraction method, alkali absorption method and titration or colorimetry to obtain the microbial data. Our results showed that soil physical-chemical characters remarkably differed among the NSFs. Microbial biomass carbon (Cmic) was the highest in wilson spruce soils, while microbial biomass nitrogen (Nmic) was the highest in sharptooth oak soils. Moreover, the highest basal respiration was found in the spruce soils, but mixed, Chinese pine and spruce stands exhibited a higher soil qCO2. The spruce soils had the highest Cmic/Nmic ratio, the greatest Nmic/TN and Cmic/Corg ratios were found in the oak soils. Additionally, the spruce soils had the maximum invertase activity and the minimum urease and catalase activities, but the maximum urease and catalase activities were found in the mixed stand. The Pearson correlation and principle component analyses revealed that the soils of spruce and oak stands obviously discriminated from other NSFs, whereas the others were similar. This suggested that the forest types affected soil microbial properties significantly due to differences in soil physical-chemical features.

  20. Which Members of the Microbial Communities Are Active? Microarrays

    NASA Astrophysics Data System (ADS)

    Morris, Brandon E. L.

    only at the early stages of understanding the microbial processes that occur in petroliferous formations and the surrounding subterranean environment. Important first steps in characterising the microbiology of oilfield systems involve identifying the microbial community structure and determining how population diversity changes are affected by the overall geochemical and biological parameters of the system. This is relatively easy to do today by using general 16S rRNA primers for PCR and building clone libraries. For example, previous studies using molecular methods characterised many dominant prokaryotes in petroleum reservoirs (Orphan et al., 2000) and in two Alaskan North Slope oil facilities (Duncan et al., 2009; Pham et al., 2009). However, the problem is that more traditional molecular biology approaches, such as 16S clone libraries, fail to detect large portions of the community perhaps missing up to half of the biodiversity (see Hong et al., 2009) and require significant laboratory time to construct large libraries necessary to increase the probability of detecting the majority of even bacterial biodiversity. In the energy sector, the overarching desire would be to quickly assess the extent of in situ hydrocarbon biodegradation or to disrupt detrimental processes such as biofouling, and in these cases it may not be necessary to identify specific microbial species. Rather, it would be more critical to evaluate metabolic processes or monitor gene products that are implicated in the specific activity of interest. Research goals such as these are well suited for a tailored application of microarray technology.

  1. Agricultural management and labile carbon additions affect soil microbial community structure and interact with carbon and nitrogen cycling.

    PubMed

    Berthrong, Sean T; Buckley, Daniel H; Drinkwater, Laurie E

    2013-07-01

    We investigated how conversion from conventional agriculture to organic management affected the structure and biogeochemical function of soil microbial communities. We hypothesized the following. (1) Changing agricultural management practices will alter soil microbial community structure driven by increasing microbial diversity in organic management. (2) Organically managed soil microbial communities will mineralize more N and will also mineralize more N in response to substrate addition than conventionally managed soil communities. (3) Microbial communities under organic management will be more efficient and respire less added C. Soils from organically and conventionally managed agroecosystems were incubated with and without glucose ((13)C) additions at constant soil moisture. We extracted soil genomic DNA before and after incubation for TRFLP community fingerprinting of soil bacteria and fungi. We measured soil C and N pools before and after incubation, and we tracked total C respired and N mineralized at several points during the incubation. Twenty years of organic management altered soil bacterial and fungal community structure compared to continuous conventional management with the bacterial differences caused primarily by a large increase in diversity. Organically managed soils mineralized twice as much NO3 (-) as conventionally managed ones (44 vs. 23 μg N/g soil, respectively) and increased mineralization when labile C was added. There was no difference in respiration, but organically managed soils had larger pools of C suggesting greater efficiency in terms of respiration per unit soil C. These results indicate that the organic management induced a change in community composition resulting in a more diverse community with enhanced activity towards labile substrates and greater capacity to mineralize N.

  2. Autophagy protein Rubicon mediates phagocytic NADPH oxidase activation in response to microbial infection or TLR stimulation.

    PubMed

    Yang, Chul-Su; Lee, Jong-Soo; Rodgers, Mary; Min, Chan-Ki; Lee, June-Yong; Kim, Hee Jin; Lee, Kwang-Hoon; Kim, Chul-Joong; Oh, Byungha; Zandi, Ebrahim; Yue, Zhenyu; Kramnik, Igor; Liang, Chengyu; Jung, Jae U

    2012-03-15

    Phagocytosis and autophagy are two important and related arms of the host's first-line defense against microbial invasion. Rubicon is a RUN domain containing cysteine-rich protein that functions as part of a Beclin-1-Vps34-containing autophagy complex. We report that Rubicon is also an essential, positive regulator of the NADPH oxidase complex. Upon microbial infection or Toll-like-receptor 2 (TLR2) activation, Rubicon interacts with the p22phox subunit of the NADPH oxidase complex, facilitating its phagosomal trafficking to induce a burst of reactive oxygen species (ROS) and inflammatory cytokines. Consequently, ectopic expression or depletion of Rubicon profoundly affected ROS, inflammatory cytokine production, and subsequent antimicrobial activity. Rubicon's actions in autophagy and in the NADPH oxidase complex are functionally and genetically separable, indicating that Rubicon functions in two ancient innate immune machineries, autophagy and phagocytosis, depending on the environmental stimulus. Rubicon may thus be pivotal to generating an optimal intracellular immune response against microbial infection.

  3. Deep-Subterranean Microbial Habitats in the Hishikari Epithermal Gold Mine: Active Thermophilic Microbial Communities and Endolithic Ancient Microbial Relicts.

    NASA Astrophysics Data System (ADS)

    Hirayama, H.; Takai, K.; Inagaki, F.; Horikoshi, K.

    2001-12-01

    Deep subterranean microbial community structures in an epithermal gold-silver deposit, Hishikari gold mine, southern part of Kyusyu Japan, were evaluated through the combined use of enrichment culture methods and culture-independent molecular surveys. The geologic setting of the Hishikari deposit is composed of three lithologies; basement oceanic sediments of the Cretaceous Shimanto Supergroup, Quaternary andesites, and auriferous quartz vein. We studied the drilled core rock of these, and the geothermal hot waters from the basement aquifers collected by means of the dewatering system located at the deepest level in the mining sites. Culture-independent molecular phylogenetic analyses of PCR-amplified ribosomal DNA (rDNA) recovered from drilled cores suggested that the deep-sea oceanic microbial communities were present as ancient indigenous relicts confined in the Shimanto basement. On the other hand, genetic signals of active thermophilic microbial communities, mainly consisting of thermophilic hydrogen-oxidizer within Aquificales, thermophilic methanotroph within g-Proteobacteria and yet-uncultivated bacterium OPB37 within b-Proteobacteria, were detected with these of oceanic relicts from the subterranean geothermal hot aquifers (temp. 70-100ºC). Successful cultivation and FISH analyses strongly supported that these thermophilic lithotrophic microorganisms could be exactly active and they grew using geochemically produced hydrogen and methane gasses as nutrients. Based on these results, the deep-subsurface biosphere occurring in the Hishikari epithermal gold mine was delineated as endolithic ancient microbial relicts and modern habitats raising active lithotrophic thermophiles associated with the geological and geochemical features of the epithermal gold deposit.

  4. Using dispersants after oil spills: impacts on the composition and activity of microbial communities.

    PubMed

    Kleindienst, Sara; Paul, John H; Joye, Samantha B

    2015-06-01

    Dispersants are globally and routinely applied as an emergency response to oil spills in marine ecosystems with the goal of chemically enhancing the dissolution of oil into water, which is assumed to stimulate microbially mediated oil biodegradation. However, little is known about how dispersants affect the composition of microbial communities or their biodegradation activities. The published findings are controversial, probably owing to variations in laboratory methods, the selected model organisms and the chemistry of different dispersant-oil mixtures. Here, we argue that an in-depth assessment of the impacts of dispersants on microorganisms is needed to evaluate the planning and use of dispersants during future responses to oil spills.

  5. Submersible microbial fuel cell sensor for monitoring microbial activity and BOD in groundwater: focusing on impact of anodic biofilm on sensor applicability.

    PubMed

    Zhang, Yifeng; Angelidaki, Irini

    2011-10-01

    A sensor, based on a submersible microbial fuel cell (SUMFC), was developed for in situ monitoring of microbial activity and biochemical oxygen demand (BOD) in groundwater. Presence or absence of a biofilm on the anode was a decisive factor for the applicability of the sensor. Fresh anode was required for application of the sensor for microbial activity measurement, while biofilm-colonized anode was needed for utilizing the sensor for BOD content measurement. The current density of SUMFC sensor equipped with a biofilm-colonized anode showed linear relationship with BOD content, to up to 250 mg/L (∼233 ± 1 mA/m(2)), with a response time of <0.67 h. This sensor could, however, not measure microbial activity, as indicated by the indifferent current produced at varying active microorganisms concentration, which was expressed as microbial adenosine-triphosphate (ATP) concentration. On the contrary, the current density (0.6 ± 0.1 to 12.4 ± 0.1 mA/m(2)) of the SUMFC sensor equipped with a fresh anode showed linear relationship, with active microorganism concentrations from 0 to 6.52 nmol-ATP/L, while no correlation between the current and BOD was observed. It was found that temperature, pH, conductivity, and inorganic solid content were significantly affecting the sensitivity of the sensor. Lastly, the sensor was tested with real contaminated groundwater, where the microbial activity and BOD content could be detected in <3.1 h. The microbial activity and BOD concentration measured by SUMFC sensor fitted well with the one measured by the standard methods, with deviations ranging from 15% to 22% and 6% to 16%, respectively. The SUMFC sensor provides a new way for in situ and quantitative monitoring contaminants content and biological activity during bioremediation process in variety of anoxic aquifers.

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  7. Microbial Succession and Nitrogen Cycling in Cultured Biofilms as Affected by the Inorganic Nitrogen Availability.

    PubMed

    Li, Shuangshuang; Peng, Chengrong; Wang, Chun; Zheng, Jiaoli; Hu, Yao; Li, Dunhai

    2017-01-01

    Biofilms play important roles in nutrients and energy cycling in aquatic ecosystems. We hypothesized that as eutrophication could change phytoplankton community and decrease phytoplankton diversity, ambient inorganic nitrogen level will affect the microbial community and diversity of biofilms and the roles of biofilms in nutrient cycling. Biofilms were cultured using a flow incubator either with replete inorganic nitrogen (N-rep) or without exogenous inorganic nitrogen supply (N-def). The results showed that the biomass and nitrogen and phosphorous accumulation of biofilms were limited by N deficiency; however, as expected, the N-def biofilms had significantly higher microbial diversity than that of N-rep biofilms. The microbial community of biofilms shifted in composition and abundance in response to ambient inorganic nitrogen level. For example, as compared between the N-def and the N-rep biofilms, the former consisted of more diazotrophs, while the latter consisted of more denitrifying bacteria. As a result of the shift of the functional microbial community, the N concentration of N-rep medium kept decreasing, while that of N-def medium showed an increasing trend in the late stage. This indicates that biofilms can serve as the source or the sink of nitrogen in aquatic ecosystems, and it depends on the inorganic nitrogen availability.

  8. Influence of Macrofaunal Burrows on Extracellular Enzyme Activity and Microbial Abundance in Subtropical Mangrove Sediment.

    PubMed

    Luo, Ling; Gu, Ji-Dong

    2016-09-13

    Bioturbation and bioirrigation induced by burrowing macrofauna are recognized as important processes in aquatic sediment since macrofaunal activities lead to the alteration of sediment characteristics. However, there is a lack of information on how macrofauna influence microbial abundance and extracellular enzyme activity in mangrove sediment. In this study, the environmental parameters, extracellular enzyme activities, and microbial abundance were determined and their relationships were explored. Sediment samples were taken from the surface (S) and lower layer (L) without burrow, as well as crab burrow wall (W) and bottom of crab burrow (B) located at the Mai Po Nature Reserve, Hong Kong. The results showed that the burrowing crabs could enhance the activities of oxidase and hydrolases. The highest activities of phenol oxidase and acid phosphatase were generally observed in B sediment, while the highest activity of N-acetyl-glucosaminidase was found in W sediment. The enzymatic stoichiometry indicated that the crab-affected sediment had similar microbial nitrogen (N) and phosphorous (P) availability relative to carbon (C), lower than S but higher than L sediment. Furthermore, it was found that the highest abundance of both bacteria and fungi was shown in S sediment, and B sediment presented the lowest abundance. Moreover, the concentrations of phosphorus and soluble phenolics in crab-affected sediment were almost higher than the non-affected sediment. The alterations of phenolics, C/P and N/P ratios as well as undetermined environmental factors by the activities of crabs might be the main reasons for the changes of enzyme activity and microbial abundance. Finally, due to the important role of phenol oxidase and hydrolases in sediment organic matter (SOM) decomposition, it is necessary to take macrofaunal activities into consideration when estimating the C budget in mangrove ecosystem in the future.

  9. Effects of nutrient enrichment on the decomposition of wood and associated microbial activity in streams

    USGS Publications Warehouse

    Gulis, V.; Rosemond, A.D.; Suberkropp, K.; Weyers, H.S.; Benstead, J.P.

    2004-01-01

    1. We determined the effects of nutrient enrichment on wood decomposition rates and microbial activity during a 3-year study in two headwater streams at Coweeta Hydrologic Laboratory, NC, U.S.A. After a 1-year pretreatment period, one of the streams was continuously enriched with inorganic nutrients (nitrogen and phosphorus) for 2 years while the other stream served as a reference. We determined the effects of enrichment on both wood veneers and sticks, which have similar carbon quality but differ in physical characteristics (e.g. surface area to volume ratios, presence of bark) that potentially affect microbial colonisation and activity. 2. Oak wood veneers (0.5 mm thick) were placed in streams monthly and allowed to decompose for approximately 90 days. Nutrient addition stimulated ash-free dry mass loss and increased mean nitrogen content, fungal biomass and microbial respiration on veneers in the treatment stream compared with the reference. The magnitude of the response to enrichment was great, with mass loss 6.1 times, and per cent N, fungal biomass and microbial respiration approximately four times greater in the treatment versus reference stream. 3. Decomposition rate and nitrogen content of maple sticks (ca. 1-2 cm diameter) also increased; however, the effect was less pronounced than for veneers. Wood response overall was greater than that determined for leaves in a comparable study, supporting the hypothesis that response to enrichment may be greater for lower quality organic matter (high C:N) than for higher quality (low C:N) substrates. 4. Our results show that moderate nutrient enrichment can profoundly affect decomposition rate and microbial activity on wood in streams. Thus, the timing and availability of wood that provides retention, structure, attachment sites and food in stream ecosystems may be affected by nutrient concentrations raised by human activities.

  10. Soil disturbance increases soil microbial enzymatic activity in arid ecoregion

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Functional diversity of the soil microbial community is commonly used in the assessment of soil health as it relates to the activity of soil microflora involved in carbon cycling. Soil microbes in different microenvironments will have varying responses to different substrates, thus catabolic fingerp...

  11. Measurements of microbial community activities in individual soil macroaggregates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The functional potential of single soil aggregates may provide insights into the localized distribution of microbial activities better than traditional assays conducted on bulk quantities of soil. Thus, we scaled down enzyme assays for ß-glucosidase, N-acetyl-ß-D-glucosaminidase, lipase, and leucine...

  12. Microbial Biomass and Activity in Geomorphic Features in Forested and Urban Restored and Degraded Streams

    EPA Science Inventory

    Geomorphic spatial heterogeneity affects sediment denitrification, an anaerobic microbial process that results in the loss of nitrogen (N), and other anaerobic microbial processes such as methanogenesis in urban streams. We measured sediment denitrification potential (DEA), metha...

  13. Variation in Honey Bee Gut Microbial Diversity Affected by Ontogenetic Stage, Age and Geographic Location

    PubMed Central

    Hroncova, Zuzana; Havlik, Jaroslav; Killer, Jiri; Doskocil, Ivo; Tyl, Jan; Kamler, Martin; Titera, Dalibor; Hakl, Josef; Mrazek, Jakub; Bunesova, Vera; Rada, Vojtech

    2015-01-01

    Social honey bees, Apis mellifera, host a set of distinct microbiota, which is similar across the continents and various honey bee species. Some of these bacteria, such as lactobacilli, have been linked to immunity and defence against pathogens. Pathogen defence is crucial, particularly in larval stages, as many pathogens affect the brood. However, information on larval microbiota is conflicting. Seven developmental stages and drones were sampled from 3 colonies at each of the 4 geographic locations of A. mellifera carnica, and the samples were maintained separately for analysis. We analysed the variation and abundance of important bacterial groups and taxa in the collected bees. Major bacterial groups were evaluated over the entire life of honey bee individuals, where digestive tracts of same aged bees were sampled in the course of time. The results showed that the microbial tract of 6-day-old 5th instar larvae were nearly equally rich in total microbial counts per total digestive tract weight as foraging bees, showing a high percentage of various lactobacilli (Firmicutes) and Gilliamella apicola (Gammaproteobacteria 1). However, during pupation, microbial counts were significantly reduced but recovered quickly by 6 days post-emergence. Between emergence and day 6, imago reached the highest counts of Firmicutes and Gammaproteobacteria, which then gradually declined with bee age. Redundancy analysis conducted using denaturing gradient gel electrophoresis identified bacterial species that were characteristic of each developmental stage. The results suggest that 3-day 4th instar larvae contain low microbial counts that increase 2-fold by day 6 and then decrease during pupation. Microbial succession of the imago begins soon after emergence. We found that bacterial counts do not show only yearly cycles within a colony, but vary on the individual level. Sampling and pooling adult bees or 6th day larvae may lead to high errors and variability, as both of these stages may

  14. Microbial biomass governs enzyme activity decay during aging of worm-worked substrates through vermicomposting.

    PubMed

    Aira, Manuel; Monroy, Fernando; Domínguez, Jorge

    2007-01-01

    Vermicomposting is the biooxidation and stabilization of organic matter involving the joint action of earthworms and microorganisms, thereby turning wastes into a valuable soil amendment called vermicompost. Studies have focused on the changes in the type of substrates available before and after vermicomposting, but little is known on how these changes take place, especially those changes related with maturation of vermicompost. This study investigated the effects of aging on the microbiological properties of fresh vermicompost produced from pig slurry by analyzing the substrate after the earthworms had left it. We incubated 16-wk-old vermicompost and sampled it after 15, 30, 45, and 60 d analyzing microbial biomass and activity (assessed as microbial biomass N and basal respiration respectively) and four enzymatic activities (beta-glucosidase, cellulase, protease, and alkaline phosphatase). Aging of vermicompost resulted in decreases of microbial biomass and activity. Three of the four enzymes analyzed also showed decrease. An initial increase followed by a rapid decrease in alkaline phosphatase was also recorded. High and significant correlations between microbial biomass and beta-glucosidase (r = 0.62, P < 0.001), cellulase (r = 0.56, P < 0.01), and protease (r = 0.82, P < 0.001) were found. Results suggest that there may be two steps involved in the aging dynamics of vermicompost with regards to extracellular enzyme activity; the first step was characterized by a decrease in microbial populations, which resulted in a reduction in the synthesis of new enzymes. The second step was the degradation of the pool of remaining enzymes. This dynamic does not seem to be affected by earthworms because similar decaying patterns of microbial biomass and activity were found in substrate where earthworms were present.

  15. Comparison between geochemical and biological estimates of subsurface microbial activities.

    PubMed

    Phelps, T J; Murphy, E M; Pfiffner, S M; White, D C

    1994-01-01

    Geochemical and biological estimates of in situ microbial activities were compared from the aerobic and microaerophilic sediments of the Atlantic Coastal Plain. Radioisotope time-course experiments suggested oxidation rates greater than millimolar quantities per year for acetate and glucose. Geochemical analyses assessing oxygen consumption, soluble organic carbon utilization, sulfate reduction, and carbon dioxide production suggested organic oxidation rates of nano- to micromolar quantities per year. Radiotracer timecourse experiments appeared to overestimate rates of organic carbon oxidation, sulfate reduction, and biomass production by a factor of 10(3)-10(6) greater than estimates calculated from groundwater analyses. Based on the geochemical evidence, in situ microbial metabolism was estimated to be in the nano- to micromolar range per year, and the average doubling time for the microbial community was estimated to be centuries.

  16. Plant diversity increases soil microbial activity and soil carbon storage.

    PubMed

    Lange, Markus; Eisenhauer, Nico; Sierra, Carlos A; Bessler, Holger; Engels, Christoph; Griffiths, Robert I; Mellado-Vázquez, Perla G; Malik, Ashish A; Roy, Jacques; Scheu, Stefan; Steinbeiss, Sibylle; Thomson, Bruce C; Trumbore, Susan E; Gleixner, Gerd

    2015-04-07

    Plant diversity strongly influences ecosystem functions and services, such as soil carbon storage. However, the mechanisms underlying the positive plant diversity effects on soil carbon storage are poorly understood. We explored this relationship using long-term data from a grassland biodiversity experiment (The Jena Experiment) and radiocarbon ((14)C) modelling. Here we show that higher plant diversity increases rhizosphere carbon inputs into the microbial community resulting in both increased microbial activity and carbon storage. Increases in soil carbon were related to the enhanced accumulation of recently fixed carbon in high-diversity plots, while plant diversity had less pronounced effects on the decomposition rate of existing carbon. The present study shows that elevated carbon storage at high plant diversity is a direct function of the soil microbial community, indicating that the increase in carbon storage is mainly limited by the integration of new carbon into soil and less by the decomposition of existing soil carbon.

  17. Evasion of inflammasome activation by microbial pathogens

    PubMed Central

    Ulland, Tyler K.; Ferguson, Polly J.; Sutterwala, Fayyaz S.

    2015-01-01

    Activation of the inflammasome occurs in response to infection with a wide array of pathogenic microbes. The inflammasome serves as a platform to activate caspase-1, which results in the subsequent processing and secretion of the proinflammatory cytokines IL-1β and IL-18 and the initiation of an inflammatory cell death pathway termed pyroptosis. Effective inflammasome activation is essential in controlling pathogen replication as well as initiating adaptive immune responses against the offending pathogens. However, a number of pathogens have developed strategies to evade inflammasome activation. In this Review, we discuss these pathogen evasion strategies as well as the potential infectious complications of therapeutic blockade of IL-1 pathways. PMID:25642707

  18. Long-term effects of cupric oxide nanoparticles (CuO NPs) on the performance, microbial community and enzymatic activity of activated sludge in a sequencing batch reactor.

    PubMed

    Wang, Sen; Li, Zhiwei; Gao, Mengchun; She, Zonglian; Ma, Bingrui; Guo, Liang; Zheng, Dong; Zhao, Yangguo; Jin, Chunji; Wang, Xuejiao; Gao, Feng

    2017-02-01

    The long-term effects of cupric oxide nanoparticles (CuO NPs) on the performance, microbial activity and microbial community of activated sludge were investigated in a sequencing batch reactor (SBR). The SBR performance had no evident change at 0-10 mg/L CuO NPs, whereas the CuO NPs concentration at 30-60 mg/L affected the COD, NH4(+)-N and soluble orthophosphate (SOP) removal, nitrogen and phosphorus removal rate and microbial enzymatic activity of activated sludge. Some CuO NPs might be absorbed on the surface of activated sludge or penetrate the microbial cytomembrane into the microbial cell interior of activated sludge. Compared to 0 mg/L CuO NPs, the reactive oxygen species (ROS) production and lactate dehydrogenase (LDH) release increased by 43.6% and 56.4% at 60 mg/L CuO NPs, respectively. The variations of ROS production and LDH release demonstrated that CuO NPs could induce the toxicity towards the microorganisms and destroy the integrity of microbial cytomembrane in the activated sludge. High throughput sequencing of 16S rDNA indicated that CuO NPs could evidently impact on the microbial richness, diversity and composition of activated sludge in the SBR.

  19. Microbial production of sensory-active miraculin.

    PubMed

    Ito, Keisuke; Asakura, Tomiko; Morita, Yuji; Nakajima, Ken-ichiro; Koizumi, Ayako; Shimizu-Ibuka, Akiko; Masuda, Katsuyoshi; Ishiguro, Masaji; Terada, Tohru; Maruyama, Jun-ichi; Kitamoto, Katsuhiko; Misaka, Takumi; Abe, Keiko

    2007-08-24

    Miraculin (MCL), a tropical fruit protein, is unique in that it has taste-modifying activity to convert sourness to sweetness, though flat in taste at neutral pH. To obtain a sufficient amount of MCL to examine the mechanism involved in this sensory event at the molecular level, we transformed Aspergillus oryzae by introducing the MCL gene. Transformants were expressed and secreted a sensory-active form of MCL yielding 2 mg/L. Recombinant MCL resembled native MCL in the secondary structure and the taste-modifying activity to generate sweetness at acidic pH. Since the observed pH-sweetness relation seemed to reflect the imidazole titration curve, suggesting that histidine residues might be involved in the taste-modifying activity. H30A and H30,60A mutants were generated using the A. oryzae-mediated expression system. Both mutants found to have lost the taste-modifying activity. The result suggests that the histidine-30 residue is important for the taste-modifying activity of MCL.

  20. Promoting uranium immobilization by the activities of microbial phophatases

    SciTech Connect

    Sobecky, Patricia A.; Martial Taillefert

    2006-06-01

    The following is a summary of progress in our project ''Promoting uranium immobilization by the activities of microbial phosphatases'' during the second year of the project. (1). Assignment of microbial phosphatases to molecular classes. One objective of this project is to determine the relationship of phosphatase activity to metal resistance in subsurface strains and possible contributions of horizontal gene transfer (HGT) to the dissemination of nonspecific acid phosphatase genes. Non-specific acid phosphohydrolases are a broad group of secreted microbial phosphatases that function in acidic-to-neutral pH ranges and utilize a wide range of organophosphate substrates. To address this objective we have designed a collection of PCR primer sets based on known microbial acid phosphatase sequences. Genomic DNA is extracted from subsurface FRC isolates and amplicons of the expected sizes are sequenced and searched for conserved signature motifs. During this reporting period we have successfully designed and tested a suite of PCR primers for gram-positive and gram-negative groups of the following phosphatase classes: (1) Class A; (2) Class B; and (3) Class C (gram negative). We have obtained specific PCR products for each of the classes using the primers we have designed using control strains as well as with subsurface isolates.

  1. Distribution of chromium contamination and microbial activity in soil aggregates.

    PubMed

    Tokunaga, Tetsu K; Wan, Jiamin; Hazen, Terry C; Schwartz, Egbert; Firestone, Mary K; Sutton, Stephen R; Newville, Matthew; Olson, Keith R; Lanzirotti, Antonio; Rao, William

    2003-01-01

    Biogeochemical transformations of redox-sensitive chemicals in soils can be strongly transport-controlled and localized. This was tested through experiments on chromium diffusion and reduction in soil aggregates that were exposed to chromate solutions. Reduction of soluble Cr(VI) to insoluble Cr(II) occurred only within the surface layer of aggregates with higher available organic carbon and higher microbial respiration. Sharply terminated Cr diffusion fronts develop when the reduction rate increases rapidly with depth. The final state of such aggregates consists of a Cr-contaminated exterior, and an uncontaminated core, each having different microbial community compositions and activity. Microbial activity was significantly higher in the more reducing soils, while total microbial biomass was similar in all of the soils. The small fraction of Cr(VI) remaining unreduced resides along external surfaces of aggregates, leaving it potentially available to future transport down the soil profile. Using the Thiele modulus, Cr(VI) reduction in soil aggregates is shown to be diffusion rate- and reaction rate-limited in anaerobic and aerobic aggregates, respectively. Thus, spatially resolved chemical and microbiological measurements are necessary within anaerobic soil aggregates to characterize and predict the fate of Cr contamination. Typical methods of soil sampling and analyses that average over redox gradients within aggregates can erase important biogeochemical spatial relations necessary for understanding these environments.

  2. Harnessing microbial activities for environmental cleanup.

    PubMed

    Löffler, Frank E; Edwards, Elizabeth A

    2006-06-01

    Human activities have released large amounts of toxic organic and inorganic chemicals into the environment. Toxic waste streams threaten dwindling drinking water supplies and impact terrestrial, estuarine and marine ecosystems. Cleanup is technically challenging and the costs based on traditional technologies are exceeding the economic capabilities of even the richest countries. Recent advances in our understanding of the microbiology contributing to contaminant transformation and detoxification has led to successful field demonstrations. Hence, harnessing the activity of naturally occurring bacteria, particularly the power of anaerobic reductive processes, is a promising approach to restore contaminated subsurface environments, protect drinking water reservoirs and to safeguard ecosystem health.

  3. Soil microbial activity as influenced by compaction and straw mulching

    NASA Astrophysics Data System (ADS)

    Siczek, A.; Frąc, M.

    2012-02-01

    Field study was performed on Haplic Luvisol soil to determine the effects of soil compaction and straw mulching on microbial parameters of soil under soybean. Treatments with different compaction were established on unmulched and mulched with straw soil. The effect of soil compaction and straw mulching on the total bacteria number and activities of dehydrogenases, protease, alkaline and acid phosphatases was studied. The results of study indicated the decrease of enzymes activities in strongly compacted soil and their increase in medium compacted soil as compared to no-compacted treatment. Mulch application caused stimulation of the bacteria total number and enzymatic activity in the soil under all compaction levels. Compaction and mulch effects were significant for all analyzed microbial parameters (P<0.001).

  4. Power generation and oil sands process-affected water treatment in microbial fuel cells.

    PubMed

    Choi, Jeongdong; Liu, Yang

    2014-10-01

    Oil sands process-affected water (OSPW), a product of bitumen isolation in the oil sands industry, is a source of pollution if not properly treated. In present study, OSPW treatment and voltage generation were examined in a single chamber air-cathode microbial fuel cell (MFC) under the effect of inoculated carbon source and temperature. OSPW treatment with an anaerobic sludge-inoculated MFC (AS-MFC) generated 0.55 ± 0.025 V, whereas an MFC inoculated with mature-fine tailings (MFT-MFC) generated 0.41 ± 0.01 V. An additional carbon source (acetate) significantly improved generated voltage. The voltage detected increased to 20-23% in MFCs when the condition was switched from ambient to mesophilic. The mesophilic condition increased OSPW treatment efficiency in terms of lowering the chemical oxygen demand and acid-extractable organics. Pyrosequencing analysis of microbial consortia revealed that Proteobacteria were the most abundant in MFCs and microbial communities in the AS-MFC were more diverse than those in the MFT-MFC.

  5. Microbial Community Structure and Enzyme Activities in Semiarid Agricultural Soils

    NASA Astrophysics Data System (ADS)

    Acosta-Martinez, V. A.; Zobeck, T. M.; Gill, T. E.; Kennedy, A. C.

    2002-12-01

    The effect of agricultural management practices on the microbial community structure and enzyme activities of semiarid soils of different textures in the Southern High Plains of Texas were investigated. The soils (sandy clay loam, fine sandy loam and loam) were under continuous cotton (Gossypium hirsutum L.) or in rotations with peanut (Arachis hypogaea L.), sorghum (Sorghum bicolor L.) or wheat (Triticum aestivum L.), and had different water management (irrigated or dryland) and tillage (conservation or conventional). Microbial community structure was investigated using fatty acid methyl ester (FAME) analysis by gas chromatography and enzyme activities, involved in C, N, P and S cycling of soils, were measured (mg product released per kg soil per h). The activities of b-glucosidase, b-glucosaminidase, alkaline phosphatase, and arylsulfatase were significantly (P<0.05) increased in soils under cotton rotated with sorghum or wheat, and due to conservation tillage in comparison to continuous cotton under conventional tillage. Principal component analysis showed FAME profiles of these soils separated distinctly along PC1 (20 %) and PC2 (13 %) due to their differences in soil texture and management. No significant differences were detected in FAME profiles due to management practices for the same soils in this sampling period. Enzyme activities provide early indications of the benefits in microbial populations and activities and soil organic matter under crop rotations and conservation tillage in comparison to the typical practices in semiarid regions of continuous cotton and conventional tillage.

  6. Distributions of microbial activities in deep subseafloor sediments

    NASA Technical Reports Server (NTRS)

    D'Hondt, Steven; Jorgensen, Bo Barker; Miller, D. Jay; Batzke, Anja; Blake, Ruth; Cragg, Barry A.; Cypionka, Heribert; Dickens, Gerald R.; Ferdelman, Timothy; Hinrichs, Kai-Uwe; Holm, Nils G.; Mitterer, Richard; Spivack, Arthur; Wang, Guizhi; Bekins, Barbara; Engelen, Bert; Ford, Kathryn; Gettemy, Glen; Rutherford, Scott D.; Sass, Henrik; Skilbeck, C. Gregory; Aiello, Ivano W.; Guerin, Gilles; House, Christopher H.; Inagaki, Fumio

    2004-01-01

    Diverse microbial communities and numerous energy-yielding activities occur in deeply buried sediments of the eastern Pacific Ocean. Distributions of metabolic activities often deviate from the standard model. Rates of activities, cell concentrations, and populations of cultured bacteria vary consistently from one subseafloor environment to another. Net rates of major activities principally rely on electron acceptors and electron donors from the photosynthetic surface world. At open-ocean sites, nitrate and oxygen are supplied to the deepest sedimentary communities through the underlying basaltic aquifer. In turn, these sedimentary communities may supply dissolved electron donors and nutrients to the underlying crustal biosphere.

  7. New and highly active microbial phosphotriesterase sources.

    PubMed

    Santillan, Julia Y; Dettorre, Lucas A; Lewkowicz, Elizabeth S; Iribarren, Adolfo M

    2016-12-01

    Many toxic insecticides used worldwide as well as some chemical warfare agents are phosphotriester derivatives. Therefore, detoxification of organophosphorus compounds has become the subject of many studies and in particular bioremediation, based on the phosphotriesterase catalysed hydrolysis of these compounds, has shown to be an effective and ecological methodology. In order to identify new bacterial phosphotriesterases, a simple and sensitive fluorimetric screening method on solid media was employed that allowed the selection of six strains with phosphotriesterase activity. Since pH and temperature are important parameters for bioremediation of contaminated soils and waters, the influence of these variables on the rate of the enzymatic hydrolysis was assessed. This study afforded notable results, being the most remarkable one the increased activity exhibited by Nocardia asteroides and Streptomyces setonii strains at 50°C, 7 and 30 times higher than at 30°C, respectively. Compared with the results obtained with Brevundimonas diminuta, whose activity is usually considered as reference, an increase of 26 and 75 times is observed, respectively.

  8. Targeted Proteomics Approaches To Monitor Microbial Activity In Basalt Aquifer

    NASA Astrophysics Data System (ADS)

    Paszczynski, A. J.; Paidisetti, R.

    2007-12-01

    Microorganisms play a major role in biogeochemical cycles of the Earth. Information regarding microbial community composition can be very useful for environmental monitoring since the short generation times of microorganisms allows them to respond rapidly to changing environmental conditions. Microbial mediated attenuation of toxic chemicals offers great potential for the restoration of contaminated environments in an ecologically acceptable manner. Current knowledge regarding the structure and functional activities of microbial communities is limited, but more information is being acquired every day through many genomic- and proteomic- based methods. As of today, only a small fraction of the Earth's microorganisms has been cultured, and so most of the information regarding the biodegradation and therapeutic potentials of these uncultured microorganisms remains unknown. Sequence analysis of DNA and/or RNA has been used for identifying specific microorganisms, to study the community composition, and to monitor gene expression providing limited information about metabolic state of given microbial system. Proteomic studies can reveal information regarding the real-time metabolic state of the microbial communities thereby aiding in understanding their interaction with the environment. In research described here the involvement of microbial communities in the degradation of anthropogenic contaminants such as trichloroethylene (TCE) was studied using mass spectrometry-based proteomics. The co- metabolic degradation of TCE in the groundwater of the Snake River Plain Aquifer at the Test Area North (TAN) site of Idaho National Laboratory (INL) was monitored by the characterization of peptide sequences of enzymes such as methane monooxygenases (MMOs). MMOs, expressed by methanotrophic bacteria are involved in the oxidation of methane and non-specific co-metabolic oxidation of TCE. We developed a time- course cell lysis method to release proteins from complex microbial

  9. Soil contamination with olive mill wastes negatively affects microbial communities, invertebrates and plants.

    PubMed

    Hentati, Olfa; Oliveira, Vanessa; Sena, Clara; Bouji, Mohamed Seddik Mahmoud; Wali, Ahmed; Ksibi, Mohamed

    2016-10-01

    The aim of the present study was to evaluate the ecotoxicological effects of olive mill waste (OMW) on soil habitat function. To this end, soil samples from OMW evaporating ponds (S1-S5) located at Agareb (Sfax, Tunisia) and a reference soil (R) were collected. The effects of OMW on the springtails Folsomia candida (F.c.), the earthworm species Eisenia fetida (E.f.), Enchytraeus crypticus (E.c.) reproduction and on the soil living microbial communities were investigated. E.f. reproduction and tomato growth assays were performed in the reference soil amended with 0.43 to 7.60 % (wOMW/wref-soil) mass ratios of dried OMW. Changes in microbial function diversity were explored using sole-carbon-source utilization profiles (BiologEcoPlates(®)). E.f. absolutely avoided (100 %) the most polluted soil (S4) while the F.c. moderately avoided (37.5 ± 7.5 %) the same soil. E.c. reproduction in S4 was significantly lower than in S1, S2, S3 and S5, and was the highest in R soil. Estimated effect concentration EC50 for juveniles' production by E.f., and for tomato fresh weight and chlorophyll content were 0.138, 0.6 and 1.13 %, respectively. Community level physiological profiles (CLPPs) were remarkably different in R and S4 and a higher similarity was observed between soils S1, S2, S3 and S5. Principal component analysis (PCA) revealed that differences between soil microbial functional diversity were mainly due to high polyphenol concentrations, while the salinity negatively affected E.c. reproduction in OMW contaminated soils. These results clearly reflect the high toxicity of dried OMW when added to agricultural soils, causing severe threats to terrestrial ecosystem functions and services provided by invertebrates and microbial communities.

  10. Metals other than uranium affected microbial community composition in a historical uranium-mining site.

    PubMed

    Sitte, Jana; Löffler, Sylvia; Burkhardt, Eva-Maria; Goldfarb, Katherine C; Büchel, Georg; Hazen, Terry C; Küsel, Kirsten

    2015-12-01

    To understand the links between the long-term impact of uranium and other metals on microbial community composition, ground- and surface water-influenced soils varying greatly in uranium and metal concentrations were investigated at the former uranium-mining district in Ronneburg, Germany. A soil-based 16S PhyloChip approach revealed 2358 bacterial and 35 archaeal operational taxonomic units (OTU) within diverse phylogenetic groups with higher OTU numbers than at other uranium-contaminated sites, e.g., at Oak Ridge. Iron- and sulfate-reducing bacteria (FeRB and SRB), which have the potential to attenuate uranium and other metals by the enzymatic and/or abiotic reduction of metal ions, were found at all sites. Although soil concentrations of solid-phase uranium were high, ranging from 5 to 1569 μg·g (dry weight) soil(-1), redundancy analysis (RDA) and forward selection indicated that neither total nor bio-available uranium concentrations contributed significantly to the observed OTU distribution. Instead, microbial community composition appeared to be influenced more by redox potential. Bacterial communities were also influenced by bio-available manganese and total cobalt and cadmium concentrations. Bio-available cadmium impacted FeRB distribution while bio-available manganese and copper as well as solid-phase zinc concentrations in the soil affected SRB composition. Archaeal communities were influenced by the bio-available lead as well as total zinc and cobalt concentrations. These results suggest that (i) microbial richness was not impacted by heavy metals and radionuclides and that (ii) redox potential and secondary metal contaminants had the strongest effect on microbial community composition, as opposed to uranium, the primary source of contamination.

  11. Structure and Function of Subsurface Microbial Communities Affecting Radionuclide Transport and Bio-immobilization

    SciTech Connect

    Kerkhof, Lee

    2013-10-23

    The goal of this research project was to employ a multi-disciplinary team to investigate the DOE-ERSP Field Research Center at Oak Ridge, TN (ORFRC), which contains well-defined subsurface contaminant plumes with contrasting pH and redox conditions. Part of the team would pursue cultivation-independent characterization of the microbial groups catalyzing relevant biogeochemical reactions to gain an understanding of the physiological mechanisms controlling radionuclide immobilization. Other team members would focus on cultivation and physiological characterization of model microorganisms from the site using single cell sorting methods. In order to understand and predict the in situ function of microbial communities, the PIs hope to develop new strategies for cultivation and to couple phylogenetic structure with microbial community function. Specific objectives by the Rutgers group was to discern the active bacteria at the Oak Ridge Research Field Challenge Site: 1. by applying stable isotope probing techniques to enrichment cultures developed from Florida State University; 2. by fingerprinting intact rRNA from groundwater samples obtained along the various flow pathways at ORFRC; and 3. by identifying functional genes for N and S cycling along the flowpaths to aid in detection of active bacteria.

  12. Active microbial sulfur disproportionation in the Mesoproterozoic.

    PubMed

    Johnston, David T; Wing, Boswell A; Farquhar, James; Kaufman, Alan J; Strauss, Harald; Lyons, Timothy W; Kah, Linda C; Canfield, Donald E

    2005-12-02

    The environmental expression of sulfur compound disproportionation has been placed between 640 and 1050 million years ago (Ma) and linked to increases in atmospheric oxygen. These arguments have their basis in temporal changes in the magnitude of 34S/32S fractionations between sulfate and sulfide. Here, we present a Proterozoic seawater sulfate isotope record that includes the less abundant sulfur isotope 33S. These measurements imply that sulfur compound disproportionation was an active part of the sulfur cycle by 1300 Ma and that progressive Earth surface oxygenation may have characterized the Mesoproterozoic.

  13. Microbial killing activity of peracetic acid.

    PubMed

    Thamlikitkul, V; Trakulsomboon, S; Louisirirotchanakul, S; Chaiprasert, A; Foongladda, S; Thipsuvan, K; Arjratanakool, W; Kunyok, R; Wasi, C; Santiprasitkul, S; Danchaivijitr, S

    2001-10-01

    In vitro killing activity of peracetic acid (Perasafe) at a concentration of 0.26 per cent w/v was tested against Escherichia coli, Enterobacter cloacae, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella typhi, Salmonella paratyphi A, Acinetobacter baumannii, Sternotrophomonas maltophilia, Enterococcus faecium, Enterococcus faecalis, methicillin-resistant Staphylococcus aureus (MRSA), Bacillus subtilis spore, Mycobacterium tuberculosis and human immuno-deficiency virus type I. Exposure to Peracetic acid (0.26% w/v) for 10 minutes resulted in massive killing of all the aforementioned organisms and spore.

  14. 28 CFR 55.15 - Affected activities.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... RIGHTS ACT REGARDING LANGUAGE MINORITY GROUPS Minority Language Materials and Assistance § 55.15 Affected... of applicable language minority groups to be effectively informed of and participate effectively in voting-connected activities. Accordingly, the quoted language should be broadly construed to apply to...

  15. 28 CFR 55.15 - Affected activities.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... RIGHTS ACT REGARDING LANGUAGE MINORITY GROUPS Minority Language Materials and Assistance § 55.15 Affected... of applicable language minority groups to be effectively informed of and participate effectively in voting-connected activities. Accordingly, the quoted language should be broadly construed to apply to...

  16. 28 CFR 55.15 - Affected activities.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... RIGHTS ACT REGARDING LANGUAGE MINORITY GROUPS Minority Language Materials and Assistance § 55.15 Affected... of applicable language minority groups to be effectively informed of and participate effectively in voting-connected activities. Accordingly, the quoted language should be broadly construed to apply to...

  17. 28 CFR 55.15 - Affected activities.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... RIGHTS ACT REGARDING LANGUAGE MINORITY GROUPS Minority Language Materials and Assistance § 55.15 Affected... of applicable language minority groups to be effectively informed of and participate effectively in voting-connected activities. Accordingly, the quoted language should be broadly construed to apply to...

  18. 28 CFR 55.15 - Affected activities.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... RIGHTS ACT REGARDING LANGUAGE MINORITY GROUPS Minority Language Materials and Assistance § 55.15 Affected... of applicable language minority groups to be effectively informed of and participate effectively in voting-connected activities. Accordingly, the quoted language should be broadly construed to apply to...

  19. Land-use and soil depth affect resource and microbial stoichiometry in a tropical mountain rainforest region of southern Ecuador.

    PubMed

    Tischer, Alexander; Potthast, Karin; Hamer, Ute

    2014-05-01

    Global change phenomena, such as forest disturbance and land-use change, significantly affect elemental balances as well as the structure and function of terrestrial ecosystems. However, the importance of shifts in soil nutrient stoichiometry for the regulation of belowground biota and soil food webs have not been intensively studied for tropical ecosystems. In the present account, we examine the effects of land-use change and soil depth on soil and microbial stoichiometry along a land-use sequence (natural forest, pastures of different ages, secondary succession) in the tropical mountain rainforest region of southern Ecuador. Furthermore, we analyzed (PLFA-method) whether shifts in the microbial community structure were related to alterations in soil and microbial stoichiometry. Soil and microbial stoichiometry were affected by both land-use change and soil depth. After forest disturbance, significant decreases of soil C:N:P ratios at the pastures were followed by increases during secondary succession. Microbial C:N ratios varied slightly in response to land-use change, whereas no fixed microbial C:P and N:P ratios were observed. Shifts in microbial community composition were associated with soil and microbial stoichiometry. Strong positive relationships between PLFA-markers 18:2n6,9c (saprotrophic fungi) and 20:4 (animals) and negative associations between 20:4 and microbial N:P point to land-use change affecting the structure of soil food webs. Significant deviations from global soil and microbial C:N:P ratios indicated a major force of land-use change to alter stoichiometric relationships and to structure biological systems. Our results support the idea that soil biotic communities are stoichiometrically flexible in order to adapt to alterations in resource stoichiometry.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    PubMed Central

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

    2016-01-01

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

  2. Uranium Biomineralization By Natural Microbial Phosphatase Activities in the Subsurface

    SciTech Connect

    Taillefert, Martial

    2015-04-01

    This project investigated the geochemical and microbial processes associated with the biomineralization of radionuclides in subsurface soils. During this study, it was determined that microbial communities from the Oak Ridge Field Research subsurface are able to express phosphatase activities that hydrolyze exogenous organophosphate compounds and result in the non-reductive bioimmobilization of U(VI) phosphate minerals in both aerobic and anaerobic conditions. The changes of the microbial community structure associated with the biomineralization of U(VI) was determined to identify the main organisms involved in the biomineralization process, and the complete genome of two isolates was sequenced. In addition, it was determined that both phytate, the main source of natural organophosphate compounds in natural environments, and polyphosphate accumulated in cells could also be hydrolyzed by native microbial population to liberate enough orthophosphate and precipitate uranium phosphate minerals. Finally, the minerals produced during this process are stable in low pH conditions or environments where the production of dissolved inorganic carbon is moderate. These findings suggest that the biomineralization of U(VI) phosphate minerals is an attractive bioremediation strategy to uranium bioreduction in low pH uranium-contaminated environments. These efforts support the goals of the SBR long-term performance measure by providing key information on "biological processes influencing the form and mobility of DOE contaminants in the subsurface".

  3. Microbial H2 cycling does not affect δ2H values of ground water

    USGS Publications Warehouse

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

    2000-01-01

    Stable hydrogen-isotope values of ground water (δ2H) and dissolved hydrogen concentrations (H(2(aq)) were quantified in a petroleum-hydrocarbon contaminated aquifer to determine whether the production/consumption of H2 by subsurface microorganisms affects ground water &delta2H values. The range of &delta2H observed in monitoring wells sampled (-27.8 ‰c to -15.5 ‰c) was best explained, however, by seasonal differences in recharge temperature as indicated using ground water δ18O values, rather than isotopic exchange reactions involving the microbial cycling of H2 during anaerobic petroleum-hydrocarbon biodegradation. The absence of a measurable hydrogen-isotope exchange between microbially cycled H2 and ground water reflects the fact that the amount of H2 available from the anaerobic decomposition of petroleum hydrocarbons is small relative to the amount of hydrogen present in water, even though milligram per liter concentrations of readily biodegradable contaminants are present at the study site. Additionally, isotopic fractionation calculations indicate that in order for H2 cycling processes to affect δ2H values of ground water, relatively high concentrations of H2 (>0.080 M) would have to be maintained, considerably higher than the 0.2 to 26 nM present at this site and characteristic of anaerobic conditions in general. These observations suggest that the conventional approach of using δ2H and δ18O values to determine recharge history is appropriate even for those ground water systems characterized by anaerobic conditions and extensive microbial H2 cycling.

  4. Direct Experimental Assessment of Microbial Activity in North Pond Sediments

    NASA Astrophysics Data System (ADS)

    Ferdelman, T. G.; Picard, A.; Morando, M.; Ziebis, W.

    2009-12-01

    North Pond, an isolated sediment pond located at 22°45’N on the western flank of the Mid-Atlantic Ridge, offered the opportunity to study microbial activities in deeply-buried low-activity sediments. About 8 x 15 km in size with sediment maximum thickness of about 300 m, North Pond is completely surrounded by exposed 7 Ma old basement. North Pond lies above the carbonate compensation depth at a water depth about 4500 m; hydrostatic pressure at the seafloor is about 45 MPa and the temperature is near 2°C. During the a R/V MS Merian cruise (MSM-11/1) in February -March 2009, 14 gravity cores of up to 9 m length were successfully obtained, from which samples were taken with 1-m resolution for experimental activity measurements. The goal of the experimental work was 1) to examine potential metabolic pathways in North Pond sediments and carbon assimilation pathways in this low-energy environment, and 2) explore the effects of pressure on microbial metabolic activities. As dissolved oxygen penetrated through all depths, sediments were aerobically sampled, processed and incubated at 4°C. Selected samples were immediately stored at in situ pressure until further use. The microbial uptake of both organic and inorganic carbon in selected North Pond sediment samples was investigated by following the fate of 14C in radio-labeled organic and organic compounds in North Pond sediment slurry incubations. Shipboard and on-shore experiments using 14C-leucine, 14C-glucose and 14C-bicarbonate were performed on selected cores. Day- to month- incubations were performed at 4°C. Parallel incubations were conducted at atmospheric pressure (0.1 MPa) and in situ pressure (~45 MPa). Either whole cell extraction (Kallmeyer et al., Limnol. Oceanogr.: Methods 6, 2008, 238-245) or protein-DNA extraction was carried on after various incubations to determine the fraction of 14C incorporated into cellular components. Formation of 14C-labeled CO2 was determined on samples incubated with 14C

  5. Soil microbial activities beneath Stipa tenacissima L. and in surrounding bare soil

    NASA Astrophysics Data System (ADS)

    Novosadová, I.; Ruiz Sinoga, J. D.; Záhora, J.; Fišerová, H.

    2010-05-01

    Open steppes dominated by Stipa tenacissima L. constitute one of the most representative ecosystems of the semi-arid zones of Eastern Mediterranean Basin (Iberian Peninsula, North of Africa). These steppes show a higher degree of variability in composition and structure. Ecosystem functioning is strongly related to the spatial pattern of grass tussocks. Soils beneath S. tenacissima grass show higher fertility and improved microclimatic conditions, favouring the formation of "resource islands" (Maestre et al., 2007). On the other hand in "resource islands" and in surrounding bare soil exists the belowground zone of influence. The competition for water and resources between plants and microorganisms is strong and mediated trough an enormous variety of exudates and resource depletion intended to regulate soil microbial communities in the rhizosphere, control herbivory, encourage beneficial symbioses, and change chemical and physical properties in soil (Pugnaire et Armas, 2008). Secondary compounds and allelopathy restrict other species growth and contribute to patchy plant distribution. Active root segregation affects not only neighbourś growth but also soil microbial activities. The objective of this study was to assess the effect of Stipa tenacissima on the key soil microbial activities under controlled incubation conditions (basal and potential respiration; net nitrogen mineralization). The experimental plots were located in the province Almería in Sierra de los Filabres Mountains near the village Gérgal (southeast Spain) in the small catchment which is situated between 1090 - 1165 m a.s.l. The area with extent of 82 000 m2 is affected by soil degradation. The climate is semiarid Mediterranean. The mean annual rainfall is of about 240 mm mostly concentrated in autumn and spring. The mean annual temperature is 13.9° C. The studied soil has a loam to sandy clay texture and is classified as Lithosol (FAO-ISRIC and ISSS, 1998). The vegetation of these areas is an

  6. Benthic microbial abundance and activities in an intensively trawled ecosystem (Thermaikos Gulf, Aegean Sea)

    NASA Astrophysics Data System (ADS)

    Polymenakou, Paraskevi N.; Pusceddu, Antonio; Tselepides, Anastasios; Polychronaki, Thalia; Giannakourou, Antonia; Fiordelmondo, Carla; Hatziyanni, Eleni; Danovaro, Roberto

    2005-12-01

    Abundance of benthic bacteria, heterotrophic nanoflagellates and ciliates, extracellular enzymatic activities, bacterial C production, C mineralisation and sediment community oxygen consumption rates were measured in the Thermaikos Gulf (Northeastern Mediterranean), before (September 2001), and during intense trawling activities (October 2001 and February 2002). The biochemical composition of sedimentary organic matter has revealed that bottom trawling had an effect on the trophic state of Thermaikos Gulf. Changes on the benthic microbial food web were also recorded, during the three sampling seasons. Even though trawling-induced sediment resuspension did not alter significantly the abundance of the microbial components, with the exception of the most impacted station, it determined changes regarding their relative importance. Thus, the ratios of bacterium to nanoflagellates and ciliate to nanoflagellates abundance increased in the trawled stations, causing a sudden increase in bacterial C production, in comparison to the non-trawled station. Four months later, the effects of trawling on the microbial food web were less evident, masked possibly by the drastic decrease in the water temperature. The results of the present work suggest that bottom trawling induces alteration of the sedimentological variables and can be considered as a factor affecting the function of the microbial food web in marine coastal ecosystems. These alterations cause faster mobilisation of organic C buried in the sediment and increase nutrient concentrations and availability in the system, thus inducing an effect that could lead to coastal eutrophication.

  7. Do recreational activities affect coastal biodiversity?

    NASA Astrophysics Data System (ADS)

    Riera, Rodrigo; Menci, Cristiano; Sanabria-Fernández, José Antonio; Becerro, Mikel A.

    2016-09-01

    Human activities are largely affecting coastal communities worldwide. Recreational perturbations have been overlooked in comparison to other perturbations, yet they are potential threats to marine biodiversity. They affect coastal communities in different ways, underpinning consistent shifts in fish and invertebrates assemblages. Several sites were sampled subjected to varying effects by recreational fishermen (low and high pressure) and scuba divers (low and high) in an overpopulated Atlantic island. Non-consistent differences in ecological, trophic and functional diversity were found in coastal communities, considering both factors ("diving" and "fishing"). Multivariate analyses only showed significant differences in benthic invertebrates between intensively-dived and non-dived sites. The lack of clear trends may be explained by the depletion of coastal resources in the study area, an extensively-affected island by overfishing.

  8. Drought induced changes of plant belowground carbon allocation affect soil microbial community function in a subalpine meadow

    NASA Astrophysics Data System (ADS)

    Fuchslueger, L.; Bahn, M.; Fritz, K.; Hasibeder, R.; Richter, A.

    2012-12-01

    There is growing evidence that climate extremes may affect ecosystem carbon dynamics more strongly than gradual changes in temperatures or precipitation. Climate projections suggest more frequent heat waves accompanied by extreme drought periods in many parts of Europe, including the Alps. Drought is considered to decrease plant C uptake and turnover, which may in turn decrease belowground C allocation and potentially has significant consequences for microbial community composition and functioning. However, information on effects of drought on C dynamics at the plant-soil interface in real ecosystems is still scarce. Our study aimed at understanding how summer drought affects soil microbial community composition and the uptake of recently assimilated plant C by different microbial groups in grassland. We hypothesized that under drought 1) the microbial community shifts, fungi being less affected than bacteria, 2) plants decrease belowground C allocation, which further reduces C transfer to soil microbes and 3) the combined effects of belowground C allocation, reduced soil C transport due to reduced soil moisture and shift in microbial communities cause an accumulation of extractable organic C in the soil. Our study was conducted as part of a rain-exclusion experiment in a subalpine meadow in the Austrian Central Alps. After eight weeks of rain exclusion we pulse labelled drought and control plots with 13CO2 and traced C in plant biomass, extractable organic C (EOC) and soil microbial communities using phospholipid fatty acids (PLFA). Drought induced a shift of the microbial community composition: gram-positive bacteria became more dominant, whereas gram-negative bacteria were not affected by drought. Also the relative abundance of fungal biomass was not affected by drought. While total microbial biomass (as estimated by total microbial PLFA content) increased during drought, less 13C was taken up. This reduction was pronounced for bacterial biomarkers. It reflects

  9. Assessing Microbial Activity in Marcellus Shale Hydraulic Fracturing Fluids

    NASA Astrophysics Data System (ADS)

    Wishart, J. R.; Morono, Y.; Itoh, M.; Ijiri, A.; Hoshino, T.; Inagaki, F.; Verba, C.; Torres, M. E.; Colwell, F. S.

    2014-12-01

    Hydraulic fracturing (HF) produces millions of gallons of waste fluid which contains a microbial community adapted to harsh conditions such as high temperatures, high salinities and the presence of heavy metals and radionuclides. Here we present evidence for microbial activity in HF production fluids. Fluids collected from a Marcellus shale HF well were supplemented with 13C-labeled carbon sources and 15N-labeled ammonium at 25°C under aerobic or anaerobic conditions. Samples were analyzed for 13C and 15N incorporation at sub-micrometer scale by ion imaging with the JAMSTEC NanoSIMS to determine percent carbon and nitrogen assimilation in individual cells. Headspace CO2 and CH4 were analyzed for 13C enrichment using irm-GC/MS. At 32 days incubation carbon assimilation was observed in samples containing 1 mM 13C-labeled glucose under aerobic and anaerobic conditions with a maximum of 10.4 and 6.5% total carbon, respectively. Nitrogen assimilation of 15N ammonium observed in these samples were 0.3 and 0.8% of total nitrogen, respectively. Head space gas analysis showed 13C enrichment in CH4 in anaerobic samples incubated with 1mM 13C-labeled bicarbonate (2227 ‰) or methanol (98943 ‰). Lesser 13C enrichment of CO2 was observed in anaerobic samples containing 1 mM 13C-labeled acetate (13.7 ‰), methanol (29.9 ‰) or glucose (85.4 ‰). These results indicate metabolic activity and diversity in microbial communities present in HF flowback fluids. The assimilation of 13C-labeled glucose demonstrates the production of biomass, a critical part of cell replication. The production of 13CO2 and 13CH4 demonstrate microbial metabolism in the forms of respiration and methanogenesis, respectively. Methanogenesis additionally indicates the presence of an active archaeal community. This research shows that HF production fluid chemistry does not entirely inhibit microbial activity or growth and encourages further research regarding biogeochemical processes occurring in

  10. Effects of heat shocks on microbial community structure and microbial activity of a methanogenic enrichment degrading benzoate.

    PubMed

    Mei, R; Narihiro, T; Nobu, M K; Liu, W-T

    2016-11-01

    In anaerobic digesters, temperature fluctuation could lead to process instability and failure. It is still not well understood how digester microbiota as a whole respond to heat shock, and what specific organisms are vulnerable to perturbation or responsible for process recovery after perturbation. To address these questions, a mesophilic benzoate-degrading methanogenic culture enriched from digester was subjected to different levels of heat shock. Three types of methane production profiles after perturbation were observed in comparison to the control: uninhibited, inhibited with later recovery, and inhibited without recovery. These responses were correlated with the microbial community compositions based on the analyses of 16S rRNA and 16S rRNA gene. Specifically, the primary benzoate-degrading syntroph was highly affected by heat shock, and its abundance and activity were both crucial to the restoration of benzoate degradation after heat shock. In contrast, methanogens were stable regardless whether methane production was inhibited. Populations related to 'Candidatus Cloacimonetes' and Firmicutes showed stimulated growth. These observations indicated distinct physiological traits and ecological niches associated with individual microbial groups. The results obtained after exposure to heat shock can be critical to more comprehensive characterization of digester ecology under perturbations.

  11. Fractionating soluble microbial products in the activated sludge process.

    PubMed

    Ni, Bing-Jie; Zeng, Raymond J; Fang, Fang; Xie, Wen-Ming; Sheng, Guo-Ping; Yu, Han-Qing

    2010-04-01

    Soluble microbial products (SMP) are the pool of organic compounds originating from microbial growth and decay, and are usually the major component of the soluble organic matters in effluents from biological treatment processes. In this work, SMP in activated sludge were characterized, fractionized, and quantified using integrated chemical analysis and mathematical approach. The utilization-associated products (UAP) in SMP, produced in the substrate-utilization process, were found to be carbonaceous compounds with a molecular weight (MW) lower than 290 kDa which were quantified separately from biomass-associated products (BAP). The BAP were mainly cellular macromolecules with an MW in a range of 290-5000 kDa, and for the first time were further classified into the growth-associated BAP (GBAP) with an MW of 1000 kDa, which were produced in the microbial growth phase, and the endogeny-associated BAP (EBAP) with an MW of 4500 kDa, which were generated in the endogenous phase. Experimental and modeling results reveal that the UAP could be utilized by the activated sludge and that the BAP would accumulate in the system. The GBAP and EBAP had different formation rates from the hydrolysis of extracellular polymeric substances and distinct biodegradation kinetics. This study provides better understanding of SMP formation mechanisms and becomes useful for subsequent effluent treatment.

  12. Microbial decomposition of wood in streams: distribution of microflora and factors affecting [C]lignocellulose mineralization.

    PubMed

    Aumen, N G; Bottomley, P J; Ward, G M; Gregory, S V

    1983-12-01

    The distribution and lignocellulolytic activity of the microbial community was determined on a large log of Douglas fir (Pseudotsuga menziesii) in a Pacific Northwest stream. Scanning electron microscopy, plate counts, and degradation of [C]lignocelluloses prepared from Douglas fir and incubated with samples of wood taken from the surface and within the log revealed that most of the microbial colonization and lignocellulose-degrading activity occurred on the surface. Labeled lignocellulose and surface wood samples were incubated in vitro with nutrient supplements to determine potential limiting factors of [C]lignocellulose degradation. Incubations carried out in a nitrogenless mineral salts and trace elements solution were no more favorable to degradation than those carried out in distilled water alone. Incubations supplemented with either (NH(4))(2)SO(4) or organic nitrogen sources showed large increases in the rates of mineralization over incubations with mineral salts and trace elements alone, with the greatest effect being observed from an addition of (NH(4))(2)SO(4). Subsequent incubations with (NH(4))(2)SO(4), KNO(3), and NH(4)NO(3) revealed that KNO(3) was the most favorable for lignin degradation, whereas all three supplements were equally favorable for cellulose degradation. Supplementation with glucose repressed both lignin and cellulose mineralization. The results reported in this study indicate that nitrogen limitation of wood decomposition may exist in streams of the Pacific Northwest. The radiotracer technique was shown to be a sensitive and useful tool for assessing relative patterns of lignocellulose decay and microbial activity in wood, along with the importance of thoroughly characterizing the experimental system before its general acceptance.

  13. Long-term effects of ZnO nanoparticles on nitrogen and phosphorus removal, microbial activity and microbial community of a sequencing batch reactor.

    PubMed

    Wang, Sen; Gao, Mengchun; She, Zonglian; Zheng, Dong; Jin, Chunji; Guo, Liang; Zhao, Yangguo; Li, Zhiwei; Wang, Xuejiao

    2016-09-01

    The performance, microbial activity, and microbial community of a sequencing batch reactor (SBR) were investigated under the long-term exposure of ZnO nanoparticles (ZnO NPs). Low ZnO NPs concentration (less than 5mg/L) had no obvious effect on the SBR performance, whereas the removals of COD, NH4(+)-N, and phosphorus were affected at 10-60mg/L ZnO NPs. The variation trend of nitrogen and phosphorus removal rate was similar to that of microbial enzymatic activity with the increase of ZnO NPs concentrations. The richness and diversity of microbial community showed obvious variations at different ZnO NPs concentrations. ZnO NPs appeared on the surface and cell interior of activated sludge, and the Zn contents in the effluent and activated sludge increased with the increase of ZnO NPS concentration. The present results provide use information to understand the effect of ZnO NPS on the performance of wastewater biological treatment systems.

  14. Comparative resistance and resilience of soil microbial communities and enzyme activities in adjacent native forest and agricultural soils.

    PubMed

    Chaer, Guilherme; Fernandes, Marcelo; Myrold, David; Bottomley, Peter

    2009-08-01

    Degradation of soil properties following deforestation and long-term soil cultivation may lead to decreases in soil microbial diversity and functional stability. In this study, we investigated the differences in the stability (resistance and resilience) of microbial community composition and enzyme activities in adjacent soils under either native tropical forest (FST) or in agricultural cropping use for 14 years (AGR). Mineral soil samples (0 to 5 cm) from both areas were incubated at 40 degrees C, 50 degrees C, 60 degrees C, or 70 degrees C for 15 min in order to successively reduce the microbial biomass. Three and 30 days after the heat shocks, fluorescein diacetate (FDA) hydrolysis, cellulase and laccase activities, and phospholipid-derived fatty acids-based microbial community composition were measured. Microbial biomass was reduced up to 25% in both soils 3 days after the heat shocks. The higher initial values of microbial biomass, enzyme activity, total and particulate soil organic carbon, and aggregate stability in the FST soil coincided with higher enzymatic stability after heat shocks. FDA hydrolysis activity was less affected (more resistance) and cellulase and laccase activities recovered more rapidly (more resilience) in the FST soil relative to the AGR counterpart. In the AGR soil, laccase activity did not show resilience to any heat shock level up to 30 days after the disturbance. Within each soil type, the microbial community composition did not differ between heat shock and control samples at day 3. However, at day 30, FST soil samples treated at 60 degrees C and 70 degrees C contained a microbial community significantly different from the control and with lower biomass regardless of high enzyme resilience. Results of this study show that deforestation followed by long-term cultivation changed microbial community composition and had differential effects on microbial functional stability. Both soils displayed similar resilience to FDA hydrolysis, a

  15. Does the preferential microbial colonisation of ferromagnesian minerals affect mineral weathering in soil?

    PubMed

    Wilson, Michael J; Certini, Giacomo; Campbell, Colin D; Anderson, Ian C; Hillier, Stephen

    2008-09-01

    Fungal activity is thought to play a direct and effective role in the breakdown and dissolution of primary minerals and in the synthesis of clay minerals in soil environments, with important consequences for plant growth and ecosystem functioning. We have studied primary mineral weathering in volcanic soils developed on trachydacite in southern Tuscany using a combination of qualitative and quantitative mineralogical and microbiological techniques. Specifically, we characterized the weathering and microbiological colonization of the magnetically separated ferromagnesian minerals (biotite and orthopyroxene) and non-ferromagnesian constituents (K-feldspar and volcanic glass) of the coarse sand fraction (250-1,000 microm). Our results show that in the basal horizons of the soils, the ferromagnesian minerals are much more intensively colonized by microorganisms than K-feldspar and glass, but that the composition of the microbial communities living on the two mineral fractions is similar. Moreover, X-ray diffraction, optical and scanning electron microscope observations show that although the ferromagnesian minerals are preferentially associated with an embryonic form of the clay mineral halloysite, they are still relatively fresh. We interpret our results as indicating that in this instance microbial activity, and particularly fungal activity, has not been an effective agent of mineral weathering, that the association with clay minerals is indirect, and that fungal weathering of primary minerals may not be as important a source of plant nutrients as previously claimed.

  16. From field barley to malt: detection and specification of microbial activity for quality aspects.

    PubMed

    Noots, I; Delcour, J A; Michiels, C W

    1999-01-01

    Barley grain carries a numerous, variable, and complex microbial population that mainly consists of bacteria, yeasts, and filamentous fungi and that can partly be detected and quantified using plating methods and microscopic and molecular techniques. The extent and the activity of this microflora are determined by the altering state of the grain and the environmental conditions in the malt production chain. Three ecological systems can be distinguished: the growing cereal in the field, the dry barley grain under storage, and the germinating barley kernel during actual malting. Microorganisms interact with the malting process both by their presence and by their metabolic activity. In this respect, interference with the oxygen uptake by the barley grain and secretion of enzymes, hormones, toxins, and acids that may affect the plant physiological processes have been studied. As a result of the interaction, microorganisms can cause important losses and influence malt quality as measured by brewhouse performance and beer quality. Of particular concern is the occurrence of mycotoxins that may affect the safety of malt. The development of the microflora during malt production can to a certain extent be controlled by the selection of appropriate process conditions. Physical and chemical treatments to inactivate the microbial population on the barley grain are suggested. Recent developments, however, aim to control the microbial activity during malt production by promoting the growth of desirable microbial cultures, selected either as biocontrol agents inhibiting mycotoxin-producing molds or as starter cultures actively contributing to malt modification. Such techniques may offer natural opportunities to improve the quality and safety of malt.

  17. Effect of antimony on the microbial growth and the activities of soil enzymes.

    PubMed

    An, Youn-Joo; Kim, Minjin

    2009-02-01

    The effects of antimony (Sb) on microbial growth inhibition and activities of soil enzymes were investigated in the present study. Test bacterial species were Escherichia coli, Bacillus subtilis and Streptococcus aureus. Among the microorganisms tested, S. aureus was the most sensitive. The 50% effects on the inhibition of specific growth rate of E. coli, B. subtilis, and, S. aureus were 555, 18.4, and 15.8 mg Sb L(-1), respectively. A silt loam soil was amended with antimony and incubated in a controlled condition. Microbial activities of dehydrogenase, acid phosphatase (P cycle), arylsulfatase (S cycle), beta-glucosidase (C cycle), urease (N cycle), and fluorescein diacetate hydrolase in soil were measured. Activities of urease and dehydrogenase were related with antimony and can be an early indication of antimony contamination. The maximum increase in soil urease activity by antimony was up to 168% after 3d compared with the control. The activities of other four enzymes (acid phosphatase, fluorescein diacetate hydrolase, arylsulfatase and ss-glucosidase) were less affected by antimony. This study suggested that antimony affects nitrogen cycle in soil by changing urease activity under the neutral pH, however, soil enzyme activities may not be a good protocol due to their complex response patterns to antimony pollution.

  18. Dissipation and effects of tricyclazole on soil microbial communities and rice growth as affected by amendment with alperujo compost.

    PubMed

    García-Jaramillo, M; Redondo-Gómez, S; Barcia-Piedras, J M; Aguilar, M; Jurado, V; Hermosín, M C; Cox, L

    2016-04-15

    The presence of pesticides in surface and groundwater has grown considerably in the last decades as a consequence of the intensive farming activity. Several studies have shown the benefits of using organic amendments to prevent losses of pesticides from runoff or leaching. A particular soil from the Guadalquivir valley was placed in open air ponds and amended at 1 or 2% (w/w) with alperujo compost (AC), a byproduct from the olive oil industry. Tricyclazole dissipation, rice growth and microbial diversity were monitored along an entire rice growing season. An increase in the net photosynthetic rate of Oryza sativa plants grown in the ponds with AC was observed. These plants produced between 1100 and 1300kgha(-1) more rice than plants from the unamended ponds. No significant differences were observed in tricyclazole dissipation, monitored for a month in soil, surface and drainage water, between the amended and unamended ponds. The structure and diversity of bacteria and fungi communities were also studied by the use of the polymerase chain reaction denaturing gel electrophoresis (PCR-DGGE) from DNA extracted directly from soil samples. The banding pattern was similar for all treatments, although the density of bands varied throughout the time. Apparently, tricyclazole did not affect the structure and diversity of bacteria and fungi communities, and this was attributed to its low bioavailability. Rice cultivation under paddy field conditions may be more efficient under the effects of this compost, due to its positive effects on soil properties, rice yield, and soil microbial diversity.

  19. Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics

    PubMed Central

    Brum, Jennifer R; Hurwitz, Bonnie L; Schofield, Oscar; Ducklow, Hugh W; Sullivan, Matthew B

    2016-01-01

    Rapid warming in the highly productive western Antarctic Peninsula (WAP) region of the Southern Ocean has affected multiple trophic levels, yet viral influences on microbial processes and ecosystem function remain understudied in the Southern Ocean. Here we use cultivation-independent quantitative ecological and metagenomic assays, combined with new comparative bioinformatic techniques, to investigate double-stranded DNA viruses during the WAP spring–summer transition. This study demonstrates that (i) temperate viruses dominate this region, switching from lysogeny to lytic replication as bacterial production increases, and (ii) Southern Ocean viral assemblages are genetically distinct from lower-latitude assemblages, primarily driven by this temperate viral dominance. This new information suggests fundamentally different virus–host interactions in polar environments, where intense seasonal changes in bacterial production select for temperate viruses because of increased fitness imparted by the ability to switch replication strategies in response to resource availability. Further, temperate viral dominance may provide mechanisms (for example, bacterial mortality resulting from prophage induction) that help explain observed temporal delays between, and lower ratios of, bacterial and primary production in polar versus lower-latitude marine ecosystems. Together these results suggest that temperate virus–host interactions are critical to predicting changes in microbial dynamics brought on by warming in polar marine systems. PMID:26296067

  20. Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics.

    PubMed

    Brum, Jennifer R; Hurwitz, Bonnie L; Schofield, Oscar; Ducklow, Hugh W; Sullivan, Matthew B

    2016-02-01

    Rapid warming in the highly productive western Antarctic Peninsula (WAP) region of the Southern Ocean has affected multiple trophic levels, yet viral influences on microbial processes and ecosystem function remain understudied in the Southern Ocean. Here we use cultivation-independent quantitative ecological and metagenomic assays, combined with new comparative bioinformatic techniques, to investigate double-stranded DNA viruses during the WAP spring-summer transition. This study demonstrates that (i) temperate viruses dominate this region, switching from lysogeny to lytic replication as bacterial production increases, and (ii) Southern Ocean viral assemblages are genetically distinct from lower-latitude assemblages, primarily driven by this temperate viral dominance. This new information suggests fundamentally different virus-host interactions in polar environments, where intense seasonal changes in bacterial production select for temperate viruses because of increased fitness imparted by the ability to switch replication strategies in response to resource availability. Further, temperate viral dominance may provide mechanisms (for example, bacterial mortality resulting from prophage induction) that help explain observed temporal delays between, and lower ratios of, bacterial and primary production in polar versus lower-latitude marine ecosystems. Together these results suggest that temperate virus-host interactions are critical to predicting changes in microbial dynamics brought on by warming in polar marine systems.

  1. Microbial diversity in European alpine permafrost and active layers.

    PubMed

    Frey, Beat; Rime, Thomas; Phillips, Marcia; Stierli, Beat; Hajdas, Irka; Widmer, Franco; Hartmann, Martin

    2016-03-01

    Permafrost represents a largely understudied genetic resource. Thawing of permafrost with global warming will not only promote microbial carbon turnover with direct feedback on greenhouse gases, but also unlock an unknown microbial diversity. Pioneering metagenomic efforts have shed light on the permafrost microbiome in polar regions, but temperate mountain permafrost is largely understudied. We applied a unique experimental design coupled to high-throughput sequencing of ribosomal markers to characterize the microbiota at the long-term alpine permafrost study site 'Muot-da-Barba-Peider' in eastern Switzerland with an approximate radiocarbon age of 12 000 years. Compared to the active layers, the permafrost community was more diverse and enriched with members of the superphylum Patescibacteria (OD1, TM7, GN02 and OP11). These understudied phyla with no cultured representatives proposedly feature small streamlined genomes with reduced metabolic capabilities, adaptations to anaerobic fermentative metabolisms and potential ectosymbiotic lifestyles. The permafrost microbiota was also enriched with yeasts and lichenized fungi known to harbour various structural and functional adaptation mechanisms to survive under extreme sub-zero conditions. These data yield an unprecedented view on microbial life in temperate mountain permafrost, which is increasingly important for understanding the biological dynamics of permafrost in order to anticipate potential ecological trajectories in a warming world.

  2. Soil pH, total phosphorus, climate and distance are the major factors influencing microbial activity at a regional spatial scale

    NASA Astrophysics Data System (ADS)

    Cao, Haichuan; Chen, Ruirui; Wang, Libing; Jiang, Lanlan; Yang, Fen; Zheng, Shixue; Wang, Gejiao; Lin, Xiangui

    2016-05-01

    Considering the extensive functional redundancy in microbial communities and great difficulty in elucidating it based on taxonomic structure, studies on the biogeography of soil microbial activity at large spatial scale are as important as microbial community structure. Eighty-four soil samples were collected across a region from south to north China (about 1,000 km) to address the questions if microbial activity displays biogeographic patterns and what are driving forces. These samples represented different soil types, land use and climate. Redundancy analysis and nonmetric multidimensional scaling clearly revealed that soil microbial activities showed distinct differentiation at different sites over a regional spatial scale, which were strongly affected by soil pH, total P, rainfall, temperature, soil type and location. In addition, microbial community structure was greatly influenced by rainfall, location, temperature, soil pH and soil type and was correlated with microbial activity to some extent. Our results suggest that microbial activities display a clear geographic pattern that is greatly altered by geographic distance and reflected by climate, soil pH and total P over large spatial scales. There are common (distance, climate, pH and soil type) but differentiated aspects (TP, SOC and N) in the biogeography of soil microbial community structure and activity.

  3. Soil pH, total phosphorus, climate and distance are the major factors influencing microbial activity at a regional spatial scale

    PubMed Central

    Cao, Haichuan; Chen, Ruirui; Wang, Libing; Jiang, Lanlan; Yang, Fen; Zheng, Shixue; Wang, Gejiao; Lin, Xiangui

    2016-01-01

    Considering the extensive functional redundancy in microbial communities and great difficulty in elucidating it based on taxonomic structure, studies on the biogeography of soil microbial activity at large spatial scale are as important as microbial community structure. Eighty-four soil samples were collected across a region from south to north China (about 1,000 km) to address the questions if microbial activity displays biogeographic patterns and what are driving forces. These samples represented different soil types, land use and climate. Redundancy analysis and nonmetric multidimensional scaling clearly revealed that soil microbial activities showed distinct differentiation at different sites over a regional spatial scale, which were strongly affected by soil pH, total P, rainfall, temperature, soil type and location. In addition, microbial community structure was greatly influenced by rainfall, location, temperature, soil pH and soil type and was correlated with microbial activity to some extent. Our results suggest that microbial activities display a clear geographic pattern that is greatly altered by geographic distance and reflected by climate, soil pH and total P over large spatial scales. There are common (distance, climate, pH and soil type) but differentiated aspects (TP, SOC and N) in the biogeography of soil microbial community structure and activity. PMID:27170469

  4. Soil pH, total phosphorus, climate and distance are the major factors influencing microbial activity at a regional spatial scale.

    PubMed

    Cao, Haichuan; Chen, Ruirui; Wang, Libing; Jiang, Lanlan; Yang, Fen; Zheng, Shixue; Wang, Gejiao; Lin, Xiangui

    2016-05-12

    Considering the extensive functional redundancy in microbial communities and great difficulty in elucidating it based on taxonomic structure, studies on the biogeography of soil microbial activity at large spatial scale are as important as microbial community structure. Eighty-four soil samples were collected across a region from south to north China (about 1,000 km) to address the questions if microbial activity displays biogeographic patterns and what are driving forces. These samples represented different soil types, land use and climate. Redundancy analysis and nonmetric multidimensional scaling clearly revealed that soil microbial activities showed distinct differentiation at different sites over a regional spatial scale, which were strongly affected by soil pH, total P, rainfall, temperature, soil type and location. In addition, microbial community structure was greatly influenced by rainfall, location, temperature, soil pH and soil type and was correlated with microbial activity to some extent. Our results suggest that microbial activities display a clear geographic pattern that is greatly altered by geographic distance and reflected by climate, soil pH and total P over large spatial scales. There are common (distance, climate, pH and soil type) but differentiated aspects (TP, SOC and N) in the biogeography of soil microbial community structure and activity.

  5. Energy balance affected by electrolyte recirculation and operating modes in microbial fuel cells.

    PubMed

    Jacobson, Kyle S; Kelly, Patrick T; He, Zhen

    2015-03-01

    Energy recovery and consumption in a microbial fuel cell (MFC) can be significantly affected by the operating conditions. This study investigated the effects of electrolyte recirculation and operation mode (continuous vs sequence batch reactor) on the energy balance in a tubular MFC. It was found that decreasing the anolyte recirculation also decreased the energy recovery. Because of the open environment of the cathode electrode, the catholyte recirculation consumed 10 to 50 times more energy than the anolyte recirculation, and resulted in negative energy balances despite the reduction of the anolyte recirculation. Reducing the catholyte recirculation to 20% led to a positive energy balance of 0.0288 kWh m(-3). The MFC operated as a sequence batch reactor generated less energy and had a lower energy balance than the one with continuous operation. Those results encourage the further development of MFC technology to achieve neutral or even positive energy output.

  6. The microbial community structure of drinking water biofilms can be affected by phosphorus availability.

    PubMed

    Keinänen, Minna M; Korhonen, Leena K; Lehtola, Markku J; Miettinen, Ilkka T; Martikainen, Pertti J; Vartiainen, Terttu; Suutari, Merja H

    2002-01-01

    Microbial communities in biofilms grown for 4 and 11 weeks under the flow of drinking water supplemented with 0, 1, 2, and 5 microg of phosphorus liter(-1) and in drinking and warm waters were compared by using phospholipid fatty acids (PLFAs) and lipopolysaccharide 3-hydroxy fatty acids (LPS 3-OH-FAs). Phosphate increased the proportion of PLFAs 16:1 omega 7c and 18:1 omega 7c and affected LPS 3-OH-FAs after 11 weeks of growth, indicating an increase in gram-negative bacteria and changes in their community structure. Differences in community structures between biofilms and drinking and warm waters can be assumed from PLFAs and LPS 3-OH-FAs, concomitantly with adaptive changes in fatty acid chain length, cyclization, and unsaturation.

  7. No tillage combined with crop rotation improves soil microbial community composition and metabolic activity.

    PubMed

    Sun, Bingjie; Jia, Shuxia; Zhang, Shixiu; McLaughlin, Neil B; Liang, Aizhen; Chen, Xuewen; Liu, Siyi; Zhang, Xiaoping

    2016-04-01

    Soil microbial community can vary with different agricultural managements, which in turn can affect soil quality. The objective of this work was to evaluate the effects of long-term tillage practice (no tillage (NT) and conventional tillage (CT)) and crop rotation (maize-soybean (MS) rotation and monoculture maize (MM)) on soil microbial community composition and metabolic capacity in different soil layers. Long-term NT increased the soil organic carbon (SOC) and total nitrogen (TN) mainly at the 0-5 cm depth which was accompanied with a greater microbial abundance. The greater fungi-to-bacteria (F/B) ratio was found in NTMS at the 0-5 cm depth. Both tillage and crop rotation had a significant effect on the metabolic activity, with the greatest average well color development (AWCD) value in NTMS soil at all three soil depths. Redundancy analysis (RDA) showed that the shift in microbial community composition was accompanied with the changes in capacity of utilizing different carbon substrates. Therefore, no tillage combined with crop rotation could improve soil biological quality and make agricultural systems more sustainable.

  8. Heavy metal pollution decreases microbial abundance, diversity and activity within particle-size fractions of a paddy soil.

    PubMed

    Chen, Junhui; He, Feng; Zhang, Xuhui; Sun, Xuan; Zheng, Jufeng; Zheng, Jinwei

    2014-01-01

    Chemical and microbial characterisations of particle-size fractions (PSFs) from a rice paddy soil subjected to long-term heavy metal pollution (P) and nonpolluted (NP) soil were performed to investigate whether the distribution of heavy metals (Cd, Cu, Pb and Zn) regulates microbial community activity, abundance and diversity at the microenvironment scale. The soils were physically fractionated into coarse sand, fine sand, silt and clay fractions. Long-term heavy metal pollution notably decreased soil basal respiration (a measurement of the total activity of the soil microbial community) and microbial biomass carbon (MBC) across the fractions by 3-45% and 21-53%, respectively. The coarse sand fraction was more affected by pollution than the clay fraction and displayed a significantly lower MBC content and respiration and dehydrogenase activity compared with the nonpolluted soils. The abundances and diversities of bacteria were less affected within the PSFs under pollution. However, significant decreases in the abundances and diversities of fungi were noted, which may have strongly contributed to the decrease in MBC. Sequencing of denaturing gradient gel electrophoresis bands revealed that the groups Acidobacteria, Ascomycota and Chytridiomycota were clearly inhibited under pollution. Our findings suggest that long-term heavy metal pollution decreased the microbial biomass, activity and diversity in PSFs, particularly in the large-size fractions.

  9. Solar activity affects avian timing of reproduction

    PubMed Central

    Visser, Marcel E.; Sanz, Juan José

    2009-01-01

    Avian timing of reproduction is strongly affected by ambient temperature. Here we show that there is an additional effect of sunspots on laying date, from five long-term population studies of great and blue tits (Parus major and Cyanistes caeruleus), demonstrating for the first time that solar activity not only has an effect on population numbers but that it also affects the timing of animal behaviour. This effect is statistically independent of ambient temperature. In years with few sunspots, birds initiate laying late while they are often early in years with many sunspots. The sunspot effect may be owing to a crucial difference between the method of temperature measurements by meteorological stations (in the shade) and the temperatures experienced by the birds. A better understanding of the impact of all the thermal components of weather on the phenology of ecosystems is essential when predicting their responses to climate change. PMID:19574283

  10. Internal porosity of mineral coating supports microbial activity in rapid sand filters for groundwater treatment.

    PubMed

    Gülay, Arda; Tatari, Karolina; Musovic, Sanin; Mateiu, Ramona V; Albrechtsen, Hans-Jørgen; Smets, Barth F

    2014-11-01

    A mineral coating develops on the filter grain surface when groundwater is treated via rapid sand filtration in drinking water production. The coating changes the physical and chemical properties of the filter material, but little is known about its effect on the activity, colonization, diversity, and abundance of microbiota. This study reveals that a mineral coating can positively affect the colonization and activity of microbial communities in rapid sand filters. To understand this effect, we investigated the abundance, spatial distribution, colonization, and diversity of all and of nitrifying prokaryotes in filter material with various degrees of mineral coating. We also examined the physical and chemical characteristics of the mineral coating. The amount of mineral coating correlated positively with the internal porosity, the packed bulk density, and the biologically available surface area of the filter material. The volumetric NH4 (+) removal rate also increased with the degree of mineral coating. Consistently, bacterial 16S rRNA and amoA abundances positively correlated with increased mineral coating levels. Microbial colonization could be visualized mainly within the outer periphery (60.6 ± 35.6 μm) of the mineral coating, which had a thickness of up to 600 ± 51 μm. Environmental scanning electron microscopic (E-SEM) observations suggested an extracellular polymeric substance-rich matrix and submicron-sized bacterial cells. Nitrifier diversity profiles were similar irrespective of the degree of mineral coating, as indicated by pyrosequencing analysis. Overall, our results demonstrate that mineral coating positively affects microbial colonization and activity in rapid sand filters, most likely due to increased volumetric cell abundances facilitated by the large surface area of internal mineral porosity accessible for microbial colonization.

  11. Connecting plant-microbial interactions above and belowground: a fungal endophyte affects decomposition.

    PubMed

    Lemons, Alisha; Clay, Keith; Rudgers, Jennifer A

    2005-10-01

    Mutualisms can strongly affect the structure of communities, but their influence on ecosystem processes is not well resolved. Here we show that a plant-microbial mutualism affects the rate of leaf litter decomposition using the widespread interaction between tall fescue grass (Lolium arundinaceum) and the fungal endophyte Neotyphodium coenophialum. In grasses, fungal endophytes live symbiotically in the aboveground tissues, where the fungi gain protection and nutrients from their host and often protect host plants from biotic and abiotic stress. In a field experiment, decomposition rate depended on a complex interaction between the litter source (collected from endophyte-infected or endophyte-free plots), the decomposition microenvironment (endophyte-infected or endophyte-free plots), and the presence of mesoinvertebrates (manipulated by the mesh size of litter bags). Over all treatments, decomposition was slower for endophyte-infected fescue litter than for endophyte-free litter. When mesoinvertebrates were excluded using fine mesh and litter was placed in a microenvironment with the endophyte, the difference between endophyte-infected and endophyte-free litter was strongest. In the presence of mesoinvertebrates, endophyte-infected litter decomposed faster in microenvironments with the endophyte than in microenvironments lacking the endophyte, suggesting that plots differ in the detritivore assemblage. Indeed, the presence of the endophyte in plots shifted the composition of Collembola, with more Hypogastruridae in the presence of the endophyte and more Isotomidae in endophyte-free plots. In a separate outdoor pot experiment, we did not find strong effects of the litter source or the soil microbial/microinvertebrate community on decomposition, which may reflect differences between pot and field conditions or other differences in methodology. Our work is among the first to demonstrate an effect of plant-endophyte mutualisms on ecosystem processes under field

  12. Representing Microbial Dormancy in Soil Decomposition Models Improves Model Performance and Reveals Key Ecosystem Controls on Microbial Activity

    NASA Astrophysics Data System (ADS)

    He, Y.; Yang, J.; Zhuang, Q.; Wang, G.; Liu, Y.

    2014-12-01

    Climate feedbacks from soils can result from environmental change and subsequent responses of plant and microbial communities and nutrient cycling. Explicit consideration of microbial life history traits and strategy may be necessary to predict climate feedbacks due to microbial physiology and community changes and their associated effect on carbon cycling. In this study, we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of dormancy at six temperate forest sites with observed soil efflux ranged from 4 to 10 years across different forest types. We then extrapolated the model to all temperate forests in the Northern Hemisphere (25-50°N) to investigate spatial controls on microbial and soil C dynamics. Both models captured the observed soil heterotrophic respiration (RH), yet no-dormancy model consistently exhibited large seasonal amplitude and overestimation in microbial biomass. Spatially, the total RH from temperate forests based on dormancy model amounts to 6.88PgC/yr, and 7.99PgC/yr based on no-dormancy model. However, no-dormancy model notably overestimated the ratio of microbial biomass to SOC. Spatial correlation analysis revealed key controls of soil C:N ratio on the active proportion of microbial biomass, whereas local dormancy is primarily controlled by soil moisture and temperature, indicating scale-dependent environmental and biotic controls on microbial and SOC dynamics. These developments should provide essential support to modeling future soil carbon dynamics and enhance the avenue for collaboration between empirical soil experiment and modeling in the sense that more microbial physiological measurements are needed to better constrain and evaluate the models.

  13. Inflammasome Activity in Non-Microbial Lung Inflammation

    PubMed Central

    Ather, Jennifer L.; Martin, Rebecca A.; Ckless, Karina; Poynter, Matthew E.

    2015-01-01

    The understanding of interleukin-1 (IL-1) family cytokines in inflammatory disease has rapidly developed, due in part to the discovery and characterization of inflammasomes, which are multi-subunit intracellular protein scaffolds principally enabling recognition of a myriad of cellular stimuli, leading to the activation of caspase-1 and the processing of IL-1β and IL-18. Studies continue to elucidate the role of inflammasomes in immune responses induced by both microbes and environmental factors. This review focuses on the current understanding of inflammasome activity in the lung, with particular focus on the non-microbial instigators of inflammasome activation, including inhaled antigens, oxidants, cigarette smoke, diesel exhaust particles, mineral fibers, and engineered nanomaterials, as well as exposure to trauma and pre-existing inflammatory conditions such as metabolic syndrome. Inflammasome activity in these sterile inflammatory states contribute to diseases including asthma, chronic obstructive disease, acute lung injury, ventilator-induced lung injury, pulmonary fibrosis, and lung cancer. PMID:25642415

  14. Evaluation of Potential Impacts of Microbial Activity on Drift Chemistry

    SciTech Connect

    Y. Wang

    2004-11-18

    ''Evaluation of Potential Impacts of Microbial Activity on Drift Chemistry'' focuses on the potential for microbial communities that could be active in repository emplacement drifts to influence the in-drift bulk chemical environment. This report feeds analyses to support the inclusion or exclusion of features, events, and processes (FEPs) in the total system performance assessment (TSPA) for the license application (LA), but this work is not expected to generate direct feeds to the TSPA-LA. The purpose was specified by, and the evaluation was performed and is documented in accordance with, ''Technical Work Plan For: Near-Field Environment and Transport In-Drift Geochemistry Analyses'' (BSC 2004 [DIRS 172402], Section 2.1). This report addresses all of the FEPs assigned by the technical work plan (TWP), including the development of exclusion arguments for FEPs that are not carried forward to the TSPA-LA. Except for an editorial correction noted in Section 6.2, there were no other deviations from the TWP. This report documents the completion of all assigned tasks, as follows (BSC 2004 DIRS 172402, Section 1.2.1): (1) Perform analyses to evaluate the potential for microbial activity in the waste emplacement drift under the constraints of anticipated physical and chemical conditions. (2) Evaluate uncertainties associated with these analyses. (3) Determine whether the potential for microbes warrants a feed to TSPA-LA to account for predicted effects on repository performance. (4) Provide information to address the ''Yucca Mountain Review Plan, Final Report'' (NUREG-1804) (NRC 2003 [DIRS 163274]) and Key Technical Issues and agreements, as appropriate. (5) Develop information for inclusion or exclusion of FEPs.

  15. Effects of Picoxystrobin and 4-n-Nonylphenol on Soil Microbial Community Structure and Respiration Activity

    PubMed Central

    Stenrød, Marianne; Klemsdal, Sonja S.; Norli, Hans Ragnar; Eklo, Ole Martin

    2013-01-01

    There is widespread use of chemical amendments to meet the demands for increased productivity in agriculture. Potentially toxic compounds, single or in mixtures, are added to the soil medium on a regular basis, while the ecotoxicological risk assessment procedures mainly follow a chemical by chemical approach. Picoxystrobin is a fungicide that has caused concern due to studies showing potentially detrimental effects to soil fauna (earthworms), while negative effects on soil microbial activities (nitrification, respiration) are shown to be transient. Potential mixture situations with nonylphenol, a chemical frequently occurring as a contaminant in sewage sludge used for land application, infer a need to explore whether these chemicals in mixture could alter the potential effects of picoxystrobin on the soil microflora. The main objective of this study was to assess the effects of picoxystrobin and nonylphenol, as single chemicals and mixtures, on soil microbial community structure and respiration activity in an agricultural sandy loam. Effects of the chemicals were assessed through measurements of soil microbial respiration activity and soil bacterial and fungal community structure fingerprints, together with a degradation study of the chemicals, through a 70 d incubation period. Picoxystrobin caused a decrease in the respiration activity, while 4-n-nonylphenol caused an increase in respiration activity concurring with a rapid degradation of the substance. Community structure fingerprints were also affected, but these results could not be directly interpreted in terms of positive or negative effects, and were indicated to be transient. Treatment with the chemicals in mixture caused less evident changes and indicated antagonistic effects between the chemicals in soil. In conclusion, the results imply that the application of the fungicide picoxystrobin and nonylphenol from sewage sludge application to agricultural soil in environmentally relevant concentrations, as

  16. Effects of picoxystrobin and 4-n-nonylphenol on soil microbial community structure and respiration activity.

    PubMed

    Stenrød, Marianne; Klemsdal, Sonja S; Norli, Hans Ragnar; Eklo, Ole Martin

    2013-01-01

    There is widespread use of chemical amendments to meet the demands for increased productivity in agriculture. Potentially toxic compounds, single or in mixtures, are added to the soil medium on a regular basis, while the ecotoxicological risk assessment procedures mainly follow a chemical by chemical approach. Picoxystrobin is a fungicide that has caused concern due to studies showing potentially detrimental effects to soil fauna (earthworms), while negative effects on soil microbial activities (nitrification, respiration) are shown to be transient. Potential mixture situations with nonylphenol, a chemical frequently occurring as a contaminant in sewage sludge used for land application, infer a need to explore whether these chemicals in mixture could alter the potential effects of picoxystrobin on the soil microflora. The main objective of this study was to assess the effects of picoxystrobin and nonylphenol, as single chemicals and mixtures, on soil microbial community structure and respiration activity in an agricultural sandy loam. Effects of the chemicals were assessed through measurements of soil microbial respiration activity and soil bacterial and fungal community structure fingerprints, together with a degradation study of the chemicals, through a 70 d incubation period. Picoxystrobin caused a decrease in the respiration activity, while 4-n-nonylphenol caused an increase in respiration activity concurring with a rapid degradation of the substance. Community structure fingerprints were also affected, but these results could not be directly interpreted in terms of positive or negative effects, and were indicated to be transient. Treatment with the chemicals in mixture caused less evident changes and indicated antagonistic effects between the chemicals in soil. In conclusion, the results imply that the application of the fungicide picoxystrobin and nonylphenol from sewage sludge application to agricultural soil in environmentally relevant concentrations, as

  17. Microbial solar cells: applying photosynthetic and electrochemically active organisms.

    PubMed

    Strik, David P B T B; Timmers, Ruud A; Helder, Marjolein; Steinbusch, Kirsten J J; Hamelers, Hubertus V M; Buisman, Cees J N

    2011-01-01

    Microbial solar cells (MSCs) are recently developed technologies that utilize solar energy to produce electricity or chemicals. MSCs use photoautotrophic microorganisms or higher plants to harvest solar energy, and use electrochemically active microorganisms in the bioelectrochemical system to generate electrical current. Here, we review the principles and performance of various MSCs in an effort to identify the most promising systems, as well as the bottlenecks and potential solutions, for "real-life" MSC applications. We present an outlook on future applications based on the intrinsic advantages of MSCs, specifically highlighting how these living energy systems can facilitate the development of an electricity-producing green roof.

  18. Chromium Isotope Behaviour During Aerobic Microbial Reduction Activities

    NASA Astrophysics Data System (ADS)

    Zhang, Q.; Amor, K.; Porcelli, D.; Thompson, I.

    2014-12-01

    Microbial activity is a very important, and possibly even the dominant, reduction mechanism for many metals in natural water systems. Isotope fractionations during microbial metal reduction can reflect one major mechanism in metal cycling in the environment, and isotopic signatures can be used to identify and quantify reduction processes during biogeochemical cycling in the present environment as well as in the past. There are many Cr (VI)-reducing bacteria that have been discovered and isolated from the environment, and Cr isotopes were found to be fractionated during microbial reduction processes. In this study, Cr reduction experiments have been undertaken to determine the conditions under which Cr is reduced and the corresponding isotope signals that are generated. The experiments have been done with a facultative bacteria Pseudomonas fluorescens LB 300, and several parameters that have potential impact on reduction mechanisms have been investigated. Electron donors are important for bacteria growth and metabolism. One factor that can control the rate of Cr reduction is the nature of the electron donor. The results show that using citrate as an electron donor can stimulate bacteria reduction activity to a large extent; the reduction rate is much higher (15.10 mgˑL-1hour-1) compared with experiments using glucose (6.65 mgˑL-1ˑhour-1), acetate (4.88 mgˑL-1hour-1) or propionate (4.85 mgˑL-1hour-1) as electron donors. Groups with higher electron donor concentrations have higher reduction rates. Chromium is toxic, and when increasing Cr concentrations in the medium, the bacteria reduction rate is also higher, which reflects bacteria adapting to the toxic environment. In the natural environment, under different pH conditions, bacteria may metabolise in different ways. In our experiments with pH, bacteria performed better in reducing Cr (VI) when pH = 8, and there are no significant differences between groups with pH = 4 or pH = 6. To investigate this further, Cr

  19. Phosphate oxygen isotope ratio proxy for specific microbial activity in marine sediments (Peru Margin)

    NASA Astrophysics Data System (ADS)

    Liang, Y.; Blake, R. E.

    2005-12-01

    Oxygen (O) isotope ratios of biogenic apatites have been widely used as paleotemperature and environmental geochemical proxies. With improved knowledge of the phosphate O isotope effects of different P cycling pathways, the δ18O value of inorganic phosphate (δ18OP) has been proposed as a useful proxy and tracer of biological reactions and P cycling in natural environments[1,2,3,4]. Being the only way of removing P from oceanic water, sedimentary P burial is one of the most important processes during biogeochemical cycling of P. The high concentrations of organic matter and pronounced microbial activity at ODP Site 1230 along the Peru Margin result in unusually high interstitial water phosphate concentrations, which provides a unique opportunity to use δ18OP to investigate inorganic phosphate (Pi) regeneration and P cycling pathways in marine sediments. The isotopic measurements of both dissolved inorganic phosphate (DIP) and bulk sediment Pi show that DIP δ18OP values are affected by three different processes, which are all induced by specific microbial activities present in the sediments. In sediments at ~ 65 to 120 mbsf, porewater DIP is derived from dissolved organophosphorus compounds (DOP) through enzymatic degradation pathways, evidenced by both DIP δ18OP values and interstitial water chemistry. Measured porewater DIP δ18OP values also suggest that 4 to 8% of interstitial water DIP reflects regeneration of Pi from Porg by microbially-synthesized enzymes. Throughout the sediment column and especially at ~ 120 to 150 mbsf, DIP is released from the sediments by microbially-induced reductive dissolution of Fe-oxides, which contributes to the overall high DIP concentrations at Site 1230. The third and dominant process controlling measured DIP δ18OP values is microbial turnover of regenerated Pi. The presence of high microbial activities in organic-rich Site 1230 sediments promotes the remobilization of P and affects marine P cycling by potentially enhancing

  20. Metaproteomic analysis reveals microbial metabolic activities in the deep ocean

    NASA Astrophysics Data System (ADS)

    Wang, Da-Zhi; Xie, Zhang-Xian; Zhang, Shu-Feng; Wang, Ming-Hua; Zhang, Hao; Kong, Ling-Fen; Lin, Lin

    2016-04-01

    The deep sea is the largest habitat on earth and holds many and varied microbial life forms. However, little is known about their metabolic activities in the deep ocean. Here, we characterized protein profiles of particulate (>0.22 μm) and dissolved (between 10 kDa and 0.22 μm) fractions collected from the deep South China Sea using a shotgun proteomic approach. SAR324, Alteromonadales and SAR11 were the most abundant groups, while Prasinophyte contributed most to eukaryotes and cyanophage to viruses. The dominant heterotrophic activity was evidenced by the abundant transporters (33%). Proteins participating in nitrification, methanogenesis, methyltrophy and CO2 fixation were detected. Notably, the predominance of unique cellular proteins in dissolved fraction suggested the presence of membrane structures. Moreover, the detection of translation proteins related to phytoplankton indicated that other process rather than sinking particles might be the downward export of living cells. Our study implied that novel extracellular activities and the interaction of deep water with its overlying water could be crucial to the microbial world of deep sea.

  1. Uranium Biomineralization by Natural Microbial Phosphatase Activities in the Subsurface

    SciTech Connect

    Sobecky, Patricia A.

    2015-04-06

    In this project, inter-disciplinary research activities were conducted in collaboration among investigators at The University of Alabama (UA), Georgia Institute of Technology (GT), Lawrence Berkeley National Laboratory (LBNL), Brookhaven National Laboratory (BNL), the DOE Joint Genome Institute (JGI), and the Stanford Synchrotron Radiation Light source (SSRL) to: (i) confirm that phosphatase activities of subsurface bacteria in Area 2 and 3 from the Oak Ridge Field Research Center result in solid U-phosphate precipitation in aerobic and anaerobic conditions; (ii) investigate the eventual competition between uranium biomineralization via U-phosphate precipitation and uranium bioreduction; (iii) determine subsurface microbial community structure changes of Area 2 soils following organophosphate amendments; (iv) obtain the complete genome sequences of the Rahnella sp. Y9-602 and the type-strain Rahnella aquatilis ATCC 33071 isolated from these soils; (v) determine if polyphosphate accumulation and phytate hydrolysis can be used to promote U(VI) biomineralization in subsurface sediments; (vi) characterize the effect of uranium on phytate hydrolysis by a new microorganism isolated from uranium-contaminated sediments; (vii) utilize positron-emission tomography to label and track metabolically-active bacteria in soil columns, and (viii) study the stability of the uranium phosphate mineral product. Microarray analyses and mineral precipitation characterizations were conducted in collaboration with DOE SBR-funded investigators at LBNL. Thus, microbial phosphorus metabolism has been shown to have a contributing role to uranium immobilization in the subsurface.

  2. Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors

    PubMed Central

    Frossard, Aline; Gerull, Linda; Mutz, Michael; Gessner, Mark O

    2012-01-01

    A fundamental issue in microbial and general ecology is the question to what extent environmental conditions dictate the structure of communities and the linkages with functional properties of ecosystems (that is, ecosystem function). We approached this question by taking advantage of environmental gradients established in soil and sediments of small stream corridors in a recently created, early successional catchment. Specifically, we determined spatial and temporal patterns of bacterial community structure and their linkages with potential microbial enzyme activities along the hydrological flow paths of the catchment. Soil and sediments were sampled in a total of 15 sites on four occasions spread throughout a year. Denaturing gradient gel electrophoresis (DGGE) was used to characterize bacterial communities, and substrate analogs linked to fluorescent molecules served to track 10 different enzymes as specific measures of ecosystem function. Potential enzyme activities varied little among sites, despite contrasting environmental conditions, especially in terms of water availability. Temporal changes, in contrast, were pronounced and remarkably variable among the enzymes tested. This suggests much greater importance of temporal dynamics than spatial heterogeneity in affecting specific ecosystem functions. Most strikingly, bacterial community structure revealed neither temporal nor spatial patterns. The resulting disconnect between bacterial community structure and potential enzyme activities indicates high functional redundancy within microbial communities even in the physically and biologically simplified stream corridors of early successional landscapes. PMID:22030674

  3. A Relationship Between Microbial Activity in Soils and Phosphate Levels in Tributaries to Lake Champlain

    NASA Astrophysics Data System (ADS)

    Larose, R.; Lee, S.; Lane, T.

    2015-12-01

    Lake Champlain is a large natural freshwater lake. It forms the western boundary of Vermont and drains over half of the state. It is bordered by the state of New York on its western side and drains to the north into Quebec, Canada. Lake Champlain is the source of fresh drinking water for over quarter of a million people and provides for the livelihoods and recreational opportunities of many well beyond its borders. The health of this lake is important. During the summer month's algae blooms plague the lake. These unsightly growths, which affect other aquatic organisms, are the result of excess phosphate flowing into the lake from many sources. Examining whether there is a relationship between microbial activity in the soils bordering tributaries to Lake Champlain and phosphate levels in those tributaries sheds insight into the origins and paths by which phosphate moves into Lake Champlain. Understanding the how phosphate moves into the water system may assist in mitigation efforts.Total Phosphate levels and Total Suspended Solids were measured in second and third order streams in the Lake Champlain Basin over a three-year period. In addition microbial activity was measured within the toe, bank and upland riparian zone areas of these streams during the summer months. In general in areas showing greater microbial activity in the soil(s) there were increased levels of phosphate in the streams.

  4. Biogas digestates affect crop P uptake and soil microbial community composition.

    PubMed

    Hupfauf, Sebastian; Bachmann, Silvia; Fernández-Delgado Juárez, Marina; Insam, Heribert; Eichler-Löbermann, Bettina

    2016-01-15

    Fermentation residues from biogas production are known as valuable organic fertilisers. This study deals with the effect of cattle slurry, co-digested cattle slurry, co-digested energy crops and mineral fertilisers on the activity and composition of soil microbiota. Furthermore, the effect of solid-liquid separation as a common pre-treatment of digestate was tested. The fertilising effects were analysed in an 8-week pot experiment on loamy sand using two crops, Amaranthus cruentus and Sorghum bicolor. Amaranth, as a crop with significantly higher P uptake, triggered stress for occurring soil microbes and thereby caused a reduction of microbial biomass C in the soil. Irrespective of the crop, microbial basal respiration and metabolic quotient were higher with the digestates than with the untreated slurry or the mineral treatments. Community level physiological profiles with MicroResp showed considerable differences among the treatments, with particularly strong effects of solid-liquid separation. Similar results were also found on a structural level (PCR-DGGE). Alkaline phosphatase gene analyses revealed high sensitivity to different fertilisation regimes.

  5. Impact of different antibiotics on methane production using waste-activated sludge: mechanisms and microbial community dynamics.

    PubMed

    Mustapha, Nurul Asyifah; Sakai, Kenji; Shirai, Yoshihito; Maeda, Toshinari

    2016-11-01

    Anaerobic digestion is an effective method for reducing the by-product of waste-activated sludge (WAS) from wastewater treatment plants and for producing bioenergy from WAS. However, only a limited number of studies have attempted to improve anaerobic digestion by targeting the microbial interactions in WAS. In this study, we examined whether different antibiotics positively, negatively, or neutrally influence methane fermentation by evaluating changes in the microbial community and functions in WAS. Addition of azithromycin promoted the microbial communities related to the acidogenic and acetogenic stages, and a high concentration of soluble proteins and a high activity of methanogens were detected. Chloramphenicol inhibited methane production but did not affect the bacteria that contribute to the hydrolysis, acidogenesis, and acetogenesis digestion stages. The addition of kanamycin, which exhibits the same methane productivity as a control (antibiotic-free WAS), did not affect all of the microbial communities during anaerobic digestion. This study demonstrates the simultaneous functions and interactions of diverse bacteria and methanogenic Archaea in different stages of the anaerobic digestion of WAS. The ratio of Caldilinea, Methanosarcina, and Clostridium may correspond closely to the trend of methane production in each antibiotic. The changes in microbial activities and function by antibiotics facilitate a better understanding of bioenergy production.

  6. Microbial community structure and activity in arsenic-, chromium- and copper-contaminated soils.

    PubMed

    Turpeinen, Riina; Kairesalo, Timo; Häggblom, Max M

    2004-01-01

    Microbial community structure, potential microbial activity and As resistance were affected by arsenic (As), chromium (Cr) and copper (Cu) contamination in soils of abandoned wood impregnating plants. Contaminated soils differed in the concentrations of soil acid-soluble and total water-soluble As, Cr and Cu, and in the concentration of bioavailable As analyzed with a bacterial sensor. Phospholipid fatty acid (PLFA) and 16S rRNA gene terminal restriction fragment length polymorphism (t-RFLP) profiles indicated that exposure to high metal contamination or subsequent effects of this exposure permanently changed microbial community structure. The total number of colony forming units (CFU) was not affected by metal contamination and the As(V)-resistant bacterial ratio to total heterotrophic plate counts was high (0.5-1.1) and relatively independent of the concentration of As. In contrast, the proportion of As(III)-resistant bacteria was dependent on the concentration of As in the soils and a significant positive relationship was found between the bioavailability of As and the proportion of As(III)-resistant bacteria. Dominant As-resistant isolates from contaminated soils were identified by their fatty acid methyl ester (FAME) profiles as Acinetobacter, Edwardsiella, Enterobacter, Pseudomonas, Salmonella and Serratia species. No differences were noted in glucose mineralization among contaminated and control soil samples within sites. Based on [(14)C]glucose mineralization the community was able to compensate for the reduced diversity. According to t-RFLP results, this was not due to a reversion towards the unexposed community, but mainly due to the appearance of new dominating species. This study, combining complementary culture-dependent and -independent methods, suggests that microbes are able to respond to soil metal contamination and maintain metabolic activity apparently through changes in microbial community structure and selection for resistance.

  7. Imidacloprid induces changes in the structure, genetic diversity and catabolic activity of soil microbial communities.

    PubMed

    Cycoń, Mariusz; Markowicz, Anna; Borymski, Sławomir; Wójcik, Marcin; Piotrowska-Seget, Zofia

    2013-12-15

    This is the first report describing the effect of imidacloprid applied at field rate (FR, 1 mg/kg of soil) and 10 times the FR (10*FR, 10 mg/kg of soil) on the structural, genetic and physiological diversity of soil bacterial community as determined by the phospholipid fatty acid (PLFA), the denaturing gradient gel electrophoresis (DGGE), and the community level physiological profile (CLPP) approaches. PLFA profiles showed that imidacloprid significantly shifted the microbial community structure and decreased the biomass of the total, bacterial and fungal PLFAs, however, this effect was transient at the FR dosage. The alterations in DGGE patterns caused by imidacloprid application, confirmed considerable changes in the overall richness and diversity of dominant bacteria. Although, as a result of imidacloprid application, the metabolic activity of microbial communities was generally lower, the richness and functional biodiversity of the soil microbial community were not negatively affected. In general, the analysis of the variance indicated that the measured parameters were significantly affected by treatment and the incubation time, however, the incubation time effect explained most of the observed variance. Imidacloprid degradation and the appearance of some new bands in DGGE profiles suggest the evolution of bacteria capable of degrading imidacloprid among indigenous microflora.

  8. Changes in the Size of the Active Microbial Pool Explain Short-Term Soil Respiratory Responses to Temperature and Moisture

    PubMed Central

    Salazar-Villegas, Alejandro; Blagodatskaya, Evgenia; Dukes, Jeffrey S.

    2016-01-01

    Heterotrophic respiration contributes a substantial fraction of the carbon flux from soil to atmosphere, and responds strongly to environmental conditions. However, the mechanisms through which short-term changes in environmental conditions affect microbial respiration still remain unclear. Microorganisms cope with adverse environmental conditions by transitioning into and out of dormancy, a state in which they minimize rates of metabolism and respiration. These transitions are poorly characterized in soil and are generally omitted from decomposition models. Most current approaches to model microbial control over soil CO2 production relate responses to total microbial biomass (TMB) and do not differentiate between microorganisms in active and dormant physiological states. Indeed, few data for active microbial biomass (AMB) exist with which to compare model output. Here, we tested the hypothesis that differences in soil microbial respiration rates across various environmental conditions are more closely related to differences in AMB (e.g., due to activation of dormant microorganisms) than in TMB. We measured basal respiration (SBR) of soil incubated for a week at two temperatures (24 and 33°C) and two moisture levels (10 and 20% soil dry weight [SDW]), and then determined TMB, AMB, microbial specific growth rate, and the lag time before microbial growth (tlag) using the Substrate-Induced Growth Response (SIGR) method. As expected, SBR was more strongly correlated with AMB than with TMB. This relationship indicated that each g active biomass C contributed ~0.04 g CO2-C h−1 of SBR. TMB responded very little to short-term changes in temperature and soil moisture and did not explain differences in SBR among the treatments. Maximum specific growth rate did not respond to environmental conditions, suggesting that the dominant microbial populations remained similar. However, warmer temperatures and increased soil moisture both reduced tlag, indicating that favorable

  9. [Comparisons of Microbial Numbers, Biomasses and Soil Enzyme Activities Between Paddy Field and Drvland Origins in Karst Cave Wetland].

    PubMed

    Jin, Zhen-jiang; Zeng, Hong-hu; Li, Qiang; Cheng, Ya-ping; Tang, Hua-feng; Li, Min; Huang, Bing-fu

    2016-01-15

    The purpose of this study is to compare microbial number, microbial biomass as well as soil enzyme activity between paddy field and dryland originated karst wetland ecosystems. The soil samples (0-20 cm) of uncultivated wetland, paddy field and dryland were collected in Huixian karst cave wetland, Guilin, China. Microbial numbers and biomass were detected using dilute plate incubation counting and chloroform fumigation-extraction, respectively. Microbial DNA was extracted according to the manufacturer's instructions of the kit. Microbial activity was examined using soil enzyme assays as well. The result showed that the bacteria number in paddy filed was (4.36 +/- 2.25) x 10(7) CFU x g(-1), which was significantly higher than those in wetland and dryland. Fungi numbers were (6.41 +/- 2.16) x 10(4) CFU x g(-1) in rice paddy and (6.52 +/- 1.55) x 10(4) CFU x g(-1) in wetland, which were higher than that in dryland. Actinomycetes number was (2.65 +/- 0.72) x 10(6) CFU x g(-1) in dryland, which was higher than that in wetland. Microbial DNA concentration in rice paddy was (11.92 +/- 3.69) microg x g(-1), which was higher than that in dryland. Invertase activity was (66.87 +/- 18.61) mg x (g x 24 h)(-1) in rice paddy and alkaline phosphatase activity was (2.07 +/- 0.99) mg x (g x 2 h)(-1) in wetland, both of which were higher than those in dryland. Statistical analysis showed there was a significant positive correlation of microbial DNA content, alkaline phosphatase activity and microbial carbon with soil pH, soil organic carbon (SOC), total nitrogen, alkali-hydrolyzable nitrogen, soil moisture, exchangeable Ca2+ and exchangeable Mg2+, as well as a significant positive correlation of intervase activity with the former three microbial factors. The above results indicated that microbial biomass and function responded much more sensitively to land-use change than microbial number in karst cave wetland system. Soil moisture, SOC and some factors induced by land-use change

  10. Uncharted Microbial World: Microbes and Their Activities in the Environment

    SciTech Connect

    Harwood, Caroline; Buckley, Merry

    2007-12-31

    Microbes are the foundation for all of life. From the air we breathe to the soil we rely on for farming to the water we drink, everything humans need to survive is intimately coupled with the activities of microbes. Major advances have been made in the understanding of disease and the use of microorganisms in the industrial production of drugs, food products and wastewater treatment. However, our understanding of many complicated microbial environments (the gut and teeth), soil fertility, and biogeochemical cycles of the elements is lagging behind due to their enormous complexity. Inadequate technology and limited resources have stymied many lines of investigation. Today, most environmental microorganisms have yet to be isolated and identified, let alone rigorously studied. The American Academy of Microbiology convened a colloquium in Seattle, Washington, in February 2007, to deliberate the way forward in the study of microorganisms and microbial activities in the environment. Researchers in microbiology, marine science, pathobiology, evolutionary biology, medicine, engineering, and other fields discussed ways to build on and extend recent successes in microbiology. The participants made specific recommendations for targeting future research, improving methodologies and techniques, and enhancing training and collaboration in the field. Microbiology has made a great deal of progress in the past 100 years, and the useful applications for these new discoveries are numerous. Microorganisms and microbial products are now used in industrial capacities ranging from bioremediation of toxic chemicals to probiotic therapies for humans and livestock. On the medical front, studies of microbial communities have revealed, among other things, new ways for controlling human pathogens. The immediate future for research in this field is extremely promising. In order to optimize the effectiveness of community research efforts in the future, scientists should include manageable

  11. Design and composition of synthetic fungal-bacterial microbial consortia that improve lignocellulolytic enzyme activity.

    PubMed

    Hu, Jiajun; Xue, Yiyun; Guo, Hongcheng; Gao, Min-Tian; Li, Jixiang; Zhang, Shiping; Tsang, Yiu Fai

    2017-03-01

    Microbial interactions are important for metabolism as they can improve or reduce metabolic efficiency. To improve lignocellulolytic enzyme activity, a series of synergistic microbial consortia of increasing diversity and complexity were devised using fungal strains, including Trichoderma reesei, Penicillium decumbens, Aspergillus tubingensis, and Aspergillus niger. However, when a screened microbial community with cellulolytic capacity was added to the consortia to increase the number of strains, it engendered more microbial interactions with the above strains and universally improved the β-glucosidase activity of the consortia. Analysis of the microbial community structure revealed that the bacteria in the consortia are more important for lignocellulolytic enzyme activity than the fungi. One fungal and 16 bacterial genera in the consortia may interact with T. reesei and are potential members of a devised synergistic microbial consortium. Such devised microbial consortia may potentially be applied to effectively and economically degrade lignocellulose.

  12. Antimicrobial and mosquitocidal activity of microbial synthesized silver nanoparticles.

    PubMed

    Soni, Namita; Prakash, Soam

    2015-03-01

    Microbial synthesis of nanoparticles is a green approach that interconnects nanotechnology and microbial biotechnology. Here, we synthesized the silver nanoparticles (AgNPs) using bacterial strains of Listeria monocytogenes, Bacillus subtilius and Streptomyces anulatus. We tested the efficacy of AgNPs against the larvae, pupae and adults of Anopheles stephensi and Culex quinquefasciatus. We have also investigated the antifungal activity of AgNPs against the soil keratinophilic fungus of Chrysosporium keratinophilum. The efficacy tests were then performed at different concentrations and varying numbers of hours by probit analysis. The results were obtained using a UV-visible spectrophotometer, and the images were recorded with a transmission electron microscope (TEM). The synthesized AgNPs were in varied shape and sizes. The larvae and pupae of Cx. quinquefasciatus were found highly susceptible to AgNPs synthesized using the L. monocytogenes, B. subtilius and S. anulatus than the An. stephensi, while the adults of An. stephensi were found more susceptible to the AgNPs synthesized using the L. monocytogenes, B. subtilius and S. anulatus the Cx. quinquefasciatus. Further, these nanoparticles have also been tested as antifungal activity against the entomopathogenic fungus C. keratinophilum. The higher zone of inhibition occurred at the concentration level of 50 μl. This study gives an innovative approach to develop eco-friendly AgNPs which act as an effective antifungal agent/fungicide and insecticide.

  13. Set anode potentials affect the electron fluxes and microbial community structure in propionate-fed microbial electrolysis cells.

    PubMed

    Hari, Ananda Rao; Katuri, Krishna P; Logan, Bruce E; Saikaly, Pascal E

    2016-12-09

    Anode potential has been shown to be a critical factor in the rate of acetate removal in microbial electrolysis cells (MECs), but studies with fermentable substrates and set potentials are lacking. Here, we examined the impact of three different set anode potentials (SAPs; -0.25, 0, and 0.25 V vs. standard hydrogen electrode) on the electrochemical performance, electron flux to various sinks, and anodic microbial community structure in two-chambered MECs fed with propionate. Electrical current (49-71%) and CH4 (22.9-41%) were the largest electron sinks regardless of the potentials tested. Among the three SAPs tested, 0 V showed the highest electron flux to electrical current (71 ± 5%) and the lowest flux to CH4 (22.9 ± 1.2%). In contrast, the SAP of -0.25 V had the lowest electron flux to current (49 ± 6%) and the highest flux to CH4 (41.1 ± 2%). The most dominant genera detected on the anode of all three SAPs based on 16S rRNA gene sequencing were Geobacter, Smithella and Syntrophobacter, but their relative abundance varied among the tested SAPs. Microbial community analysis implies that complete degradation of propionate in all the tested SAPs was facilitated by syntrophic interactions between fermenters and Geobacter at the anode and ferementers and hydrogenotrophic methanogens in suspension.

  14. Set anode potentials affect the electron fluxes and microbial community structure in propionate-fed microbial electrolysis cells

    PubMed Central

    Hari, Ananda Rao; Katuri, Krishna P.; Logan, Bruce E.; Saikaly, Pascal E.

    2016-01-01

    Anode potential has been shown to be a critical factor in the rate of acetate removal in microbial electrolysis cells (MECs), but studies with fermentable substrates and set potentials are lacking. Here, we examined the impact of three different set anode potentials (SAPs; −0.25, 0, and 0.25 V vs. standard hydrogen electrode) on the electrochemical performance, electron flux to various sinks, and anodic microbial community structure in two-chambered MECs fed with propionate. Electrical current (49–71%) and CH4 (22.9–41%) were the largest electron sinks regardless of the potentials tested. Among the three SAPs tested, 0 V showed the highest electron flux to electrical current (71 ± 5%) and the lowest flux to CH4 (22.9 ± 1.2%). In contrast, the SAP of −0.25 V had the lowest electron flux to current (49 ± 6%) and the highest flux to CH4 (41.1 ± 2%). The most dominant genera detected on the anode of all three SAPs based on 16S rRNA gene sequencing were Geobacter, Smithella and Syntrophobacter, but their relative abundance varied among the tested SAPs. Microbial community analysis implies that complete degradation of propionate in all the tested SAPs was facilitated by syntrophic interactions between fermenters and Geobacter at the anode and ferementers and hydrogenotrophic methanogens in suspension. PMID:27934925

  15. Physicochemical properties influencing denitrification rate and microbial activity in denitrification bioreactors

    NASA Astrophysics Data System (ADS)

    Schmidt, C. A.

    2012-12-01

    The use of N-based fertilizer will need to increase to meet future demands, yet existing applications have been implicated as the main source of coastal eutrophication and hypoxic zones. Producing sufficient crops to feed a growing planet will require efficient production in combination with sustainable treatment solutions. The long-term success of denitrification bioreactors to effectively remove nitrate (NO¬3), indicates this technology is a feasible treatment option. Assessing and quantifying the media properties that affect NO¬3 removal rate and microbial activity can improve predictions on bioreactor performance. It was hypothesized that denitrification rates and microbial biomass would be correlated with total C, NO¬3 concentration, metrics of organic matter quality, media surface area and laboratory measures of potential denitrification rate. NO¬3 removal rates and microbial biomass were evaluated in mesocosms filled with different wood treatments and the unique influence of these predictor variables was determined using a multiple linear regression analysis. NO3 reduction rates were independent of NO¬3 concentration indicating zero order reaction kinetics. Temperature was strongly correlated with denitrification rate (r2=0.87; Q10=4.7), indicating the variability of bioreactor performance in differing climates. Fiber quality, and media surface area were strong (R>0.50), unique predictors of rates and microbial biomass, although C:N ratio and potential denitrification rate did not predict actual denitrification rate or microbial biomass. Utilizing a stepwise multiple linear regression, indicates that the denitrification rate can be effectively (r2=0.56;p<0.0001) predicted if the groundwater temperature, neutral detergent fiber and surface area alone are quantified. These results will assist with the widespread implementation of denitrification bioreactors to achieve significant N load reductions in large watersheds. The nitrate reduction rate as a

  16. Compositional Changes and Baking Performance of Rye Dough As Affected by Microbial Transglutaminase and Xylanase.

    PubMed

    Grossmann, Isabel; Döring, Clemens; Jekle, Mario; Becker, Thomas; Koehler, Peter

    2016-07-20

    Doughs supplemented with endoxylanase (XYL) and varying amounts of microbial transglutaminase (TG) were analyzed by sequential protein extraction, quantitation of protein fractions and protein types, and determination of water-extractable arabinoxylans. With increasing TG activity, the concentration of prolamins and glutelins decreased and increased, respectively, and the prolamin-to-glutelin ratio strongly declined. The overall amount of extractable protein decreased with increasing TG level showing that cross-linking by TG provided high-molecular-weight protein aggregates. The decrease of the high-molecular-weight arabinoxylan fraction and the concurrent increase of the medium-molecular-weight fraction confirmed the degradation of arabinoxylans by XYL. However, XYL addition did not lead to significant improved cross-linking of rye proteins by TG. Volume and crumb hardness measurements of bread showed increased protein connectivity induced by XYL and TG. Significant positive effects on the final bread quality were especially obtained by XYL addition.

  17. Geophysical Monitoring of Microbial Activity within a Wetland Soil

    NASA Astrophysics Data System (ADS)

    O'Brien, M.; Zhang, C.; Ntarlagiannis, D.; Slater, L.; Yee, N.

    2007-05-01

    We performed Induced Polarization (IP) and Self Potential (SP) measurements to record the geoelectrical signatures of microbial activity within a wetland soil. The experiment was conducted in laboratory, utilizing an open flow column set up. Soil samples from Kearny Marsh (KM), a shallow water wetland, were collected and stored at 4o Celsius prior to the start of the experiment. Two columns were dry packed with a mix of KM soil and sterile Ottawa sand (50% by weight). One column was sterilized and used as a control while the other column retained the biologically active soil sample. Both columns were saturated with a minimal salts medium capable of supporting microbial life; after saturation, a steady flow rate of one pore volume per day was maintained throughout the experiment. Ambient temperature and pressure changes (at the inflow and outflow of each column) were continuously monitored throughout the experiment. Common geochemical parameters, such as Eh, pH, and fluid conductivity were measured at the inflow and outflow of each column at regular intervals. IP and SP responses were continuously recorded on both columns utilizing a series of electrodes along the column length; additionally for the SP measurements we used a reference electrode at the inflow tube. Strong SP anomalies were observed for all the locations along the active column. Black visible mineral precipitant also formed in the active column. The observed precipitation coincided with the times that SP anomalies developed at each electrode position. These responses are associated with microbial induced sulfide mineralization. We interpret the SP signal as the result of redox processes associated with this mineralization driven by gradients in ionic concentration and mobility within the column, similar to a galvanic cell mechanism. IP measurements show no correlation with these visual and SP responses. Destructive analysis of the samples followed the termination of the experiment. Scanning electron

  18. Wood ant nests as hot spots of microbial activity in forest ecosystems

    NASA Astrophysics Data System (ADS)

    Jilkova, Veronika; Frouz, Jan

    2015-04-01

    Wood ants build large and long-lasting nests from organic materials and mineral soil which have a very special structure. Nests are well-aerated due to numerous chambers and galleries and stable temperature and moisture are maintained there thanks to ant activities. These conditions together with the constant input of easily available nutrients from food of ants support microbial activity. Due to respiration of ants and microbes, wood ant nests are known as hot spots of CO2 production in forest ecosystems. Although the main source of CO2 is represented by ant respiration, a significant amount of CO2 originates also from microbial decomposition of organic materials. Several conditions affect microbial respiration, such as moisture of nest material, changes in temperatures or food input. As mineral nutrients are released from organic materials, wood ant nests represent hot spots of mineral nutrients in forest ecosystems which can be exploited by other organisms, such as roots of trees, and can also cause heterogeneity in species abundance and composition.

  19. Modification of soil microbial activity and several hydrolases in a forest soil artificially contaminated with copper

    NASA Astrophysics Data System (ADS)

    Bellas, Rosa; Leirós, Mā Carmen; Gil-Sotres, Fernando; Trasar-Cepeda, Carmen

    2010-05-01

    Soils have long been exposed to the adverse effects of human activities, which negatively affect soil biological activity. As a result of their functions and ubiquitous presence microorganisms can serve as environmental indicators of soil pollution. Some features of soil microorganisms, such as the microbial biomass size, respiration rate, and enzyme activity are often used as bioindicators of the ecotoxicity of heavy metals. Although copper is essential for microorganisms, excessive concentrations have a negative influence on processes mediated by microorganisms. In this study we measured the response of some microbial indicators to Cu pollution in a forest soil, with the aim of evaluating their potential for predicting Cu contamination. Samples of an Ah horizon from a forest soil under oakwood vegetation (Quercus robur L.) were contaminated in the laboratory with copper added at different doses (0, 120, 360, 1080 and 3240 mg kg-1) as CuCl2×2H2O. The soil samples were kept for 7 days at 25 °C and at a moisture content corresponding to the water holding capacity, and thereafter were analysed for carbon and nitrogen mineralization capacity, microbial biomass C, seed germination and root elongation tests, and for urease, phosphomonoesterase, catalase and ß-glucosidase activities. In addition, carbon mineralization kinetics were studied, by plotting the log of residual C against incubation time, and the metabolic coefficient, qCO2, was estimated. Both organic carbon and nitrogen mineralization were lower in polluted samples, with the greatest decrease observed in the sample contaminated with 1080 mg kg-1. In all samples carbon mineralization followed first order kinetics; the C mineralization constant was lower in contaminated than in uncontaminated samples and, in general, decreased with increasing doses of copper. Moreover, it appears that copper contamination not only reduced the N mineralization capacity, but also modified the N mineralization process, since in

  20. Elevated atmospheric CO2 increases microbial growth rates and enzymes activity in soil

    NASA Astrophysics Data System (ADS)

    Blagodatskaya, Evgenia; Blagodatsky, Sergey; Dorodnikov, Maxim; Kuzyakov, Yakov

    2010-05-01

    Increasing the belowground translocation of assimilated carbon by plants grown under elevated CO2 can cause a shift in the structure and activity of the microbial community responsible for the turnover of organic matter in soil. We investigated the long-term effect of elevated CO2 in the atmosphere on microbial biomass and specific growth rates in root-free and rhizosphere soil. The experiments were conducted under two free air carbon dioxide enrichment (FACE) systems: in Hohenheim and Braunschweig, as well as in the intensively managed forest mesocosm of the Biosphere 2 Laboratory (B2L) in Oracle, AZ. Specific microbial growth rates (μ) were determined using the substrate-induced respiration response after glucose and/or yeast extract addition to the soil. We evaluated the effect of elevated CO2 on b-glucosidase, chitinase, phosphatase, and sulfatase to estimate the potential enzyme activity after soil amendment with glucose and nutrients. For B2L and both FACE systems, up to 58% higher μ were observed under elevated vs. ambient CO2, depending on site, plant species and N fertilization. The μ-values increased linearly with atmospheric CO2 concentration at all three sites. The effect of elevated CO2 on rhizosphere microorganisms was plant dependent and increased for: Brassica napus=Triticum aestivumaffected microbial growth rates directly (N limitation) and indirectly (changing the quantity of fine roots). So, 50% decrease in N fertilization caused the overall increase or decrease of microbial growth rates depending on plant species. The μ-value increase was lower for microorganisms growing on yeast extract then for those growing on glucose, i.e. the effect of elevated CO2 was smoothed on rich vs. simple substrate. So, the r/K strategies ratio can be better revealed by studying growth on simple (glucose) than on rich substrate mixtures (yeast extract). After adding glucose, enzyme activities under elevated CO2 were

  1. Uranium Biomineralization by Natural Microbial Phosphatase Activities in the Subsurface

    NASA Astrophysics Data System (ADS)

    Martinez, R.; Wu, C. H.; Beazley, M. J.; Andersen, G. L.; Hazen, T. C.; Taillefert, M.; Sobecky, P. A.

    2011-12-01

    Soils and groundwater contaminated with heavy metals and radionuclides remain a legacy of Cold War nuclear weapons development. Due to the scale of environmental contamination, in situ sequestration of heavy metals and radionuclides remain the most cost-effective strategy for remediation. We are currently investigating a remediation approach that utilizes periplasmic and extracellular microbial phosphatase activity of soil bacteria capable promoting in situ uranium phosphate sequestration. Our studies focus on the contaminated soils from the DOE Field Research Center (ORFRC) in Oak Ridge, TN. We have previously demonstrated that ORFRC strains with phosphatase-positive phenotypes were capable of promoting the precpitation of >95% U(VI) as a low solubility phosphate mineral during growth on glycerol phosphate as a sole carbon and phosphorus source. Here we present culture-independent soil slurry studies aimed at understanding microbial community dynamics resulting from exogenous organophosphate additions. Soil slurries containing glycerol-2-phosphate (G2P) or glycerol-3-phosphate (G3P) and nitrate as the sole C, P and N sources were incubated under oxic growth conditions at pH 5.5 or pH 6.8. Following treatments, total DNA was extracted and prokaryotic diversity was assessed using high-density 16S oligonucleotide microarray (PhyloChip) analysis. Treatments at pH 5.5 and pH 6.8 amended with G2P required 36 days to accumulate 4.8mM and 2.2 mM phosphate, respectively. In contrast, treatments at pH 5.5 and pH 6.8 amended with G3P accumulated 8.9 mM and 8.7 mM phosphate, respectively, after 20 days. A total of 2120 unique taxa representing 46 phyla, 66 classes, 110 orders, and 186 families were detected among all treatment conditions. The phyla that significantly (P<0.05) increased in abundance relative to incubations lacking organophosphate amendments included: Crenarchaeota, Euryarchaeota, Bacteroidetes, and Proteobacteria. Members from the classes Bacteroidetes

  2. Single-walled carbon nanotube release affects the microbial enzyme-catalyzed oxidation processes of organic pollutants and lignin model compounds in nature.

    PubMed

    Chen, Ming; Qin, Xiaosheng; Zeng, Guangming

    2016-11-01

    The question how microbial enzyme-catalyzed oxidation processes of organic pollutants and lignin model compounds (LMCs) are affected by the release of single-walled carbon nanotube (SWCNT) into the environment remains to be addressed at the molecular level. We have, therefore concentrated the effects of SWCNT on some important properties associated with enzyme activity and function during microbial oxidation of polycyclic aromatic hydrocarbons (benzo(a)pyrene, acenaphthene and anthracene), LMCs (2,6-dimethoxyphenol, guaiacol and veratryl alcohol) and β-hexachlorocyclohexane, including the behaviour of water molecules, hydrogen bonds (HBs) and hydrophobic interactions (HYs) between ligand and the enzyme, and conformational dynamics in N- and C-terminus. Our study revealed that SWCNT significantly affected the behaviour of water molecules within 5 Å of both these substrates and their respective enzymes during oxidation (p < 0.01), by increasing or decreasing the water number near them. SWCNT tended to significantly enhance or reduce the stability of atom pairs that formed the HBs and HYs (p < 0.01). N- and C-terminus conformations underwent transitions between positive and negative states or between positive state or between negative state in all analyzed complexes. Significant conformational transitions were found for all C-terminus, but only for a part of N-terminus after the inclusion of the SWCNT. These results showed that SWCNT release would significantly affect the microbial enzyme-catalyzed processes of organic pollutants and LMCs in nature.

  3. A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning

    USGS Publications Warehouse

    Wallenstein, Matthew D.; Hall, Edward K.

    2012-01-01

    As the earth system changes in response to human activities, a critical objective is to predict how biogeochemical process rates (e.g. nitrification, decomposition) and ecosystem function (e.g. net ecosystem productivity) will change under future conditions. A particular challenge is that the microbial communities that drive many of these processes are capable of adapting to environmental change in ways that alter ecosystem functioning. Despite evidence that microbes can adapt to temperature, precipitation regimes, and redox fluctuations, microbial communities are typically not optimally adapted to their local environment. For example, temperature optima for growth and enzyme activity are often greater than in situ temperatures in their environment. Here we discuss fundamental constraints on microbial adaptation and suggest specific environments where microbial adaptation to climate change (or lack thereof) is most likely to alter ecosystem functioning. Our framework is based on two principal assumptions. First, there are fundamental ecological trade-offs in microbial community traits that occur across environmental gradients (in time and space). These trade-offs result in shifting of microbial function (e.g. ability to take up resources at low temperature) in response to adaptation of another trait (e.g. limiting maintenance respiration at high temperature). Second, the mechanism and level of microbial community adaptation to changing environmental parameters is a function of the potential rate of change in community composition relative to the rate of environmental change. Together, this framework provides a basis for developing testable predictions about how the rate and degree of microbial adaptation to climate change will alter biogeochemical processes in aquatic and terrestrial ecosystems across the planet.

  4. [The influence of Acinetobacter calcoaceticus K-4 surface-active substances on the efficiency of microbial destruction of oil pollutants].

    PubMed

    Pyroh, T P; Antoniuk, S I; Sorokina, A I

    2009-01-01

    The possibility of the use of Acinetobacter calcoaceticus K-4 surface-active substances (SAS) for water purification from oil was shown. The efficiency of oil degradation (2.6 g/l) in the presence of SAS preparations (5-15 %) in the form of postfermentation of cultural liquid or its supernatant was established to be 81-95 %. Intensification of oil destruction was determined by SAS affecting the activity of oil-oxidizing microbial population.

  5. Rumen development process in goats as affected by supplemental feeding v. grazing: age-related anatomic development, functional achievement and microbial colonisation.

    PubMed

    Jiao, Jinzhen; Li, Xiaopeng; Beauchemin, Karen A; Tan, Zhiliang; Tang, Shaoxun; Zhou, Chuanshe

    2015-03-28

    The aim of the present study was to describe age-related changes in anatomic, functional and microbial variables during the rumen development process, as affected by the feeding system (supplemental feeding v. grazing), in goats. Goats were slaughtered at seven time points that were selected to reflect the non-rumination (0, 7 and 14 d), transition (28 and 42 d) and rumination (56 and 70 d) phases of rumen development. Total volatile fatty acid (TVFA) concentration (P= 0·002), liquid-associated bacterial and archaeal copy numbers (P< 0·01) were greater for supplemental feeding v. grazing, while rumen pH (P< 0·001), acetate molar proportion (P= 0·003) and solid-associated microbial copy numbers (P< 0·05) were less. Rumen papillae length (P= 0·097) and extracellular (P= 0·093) and total (P= 0·073) protease activity potentials in supplemented goats tended to be greater than those in grazing goats. Furthermore, from 0 to 70 d, irrespective of the feeding system, rumen weight, rumen wall thickness, rumen papillae length and area, TVFA concentration, xylanase, carboxymethylcellulase activity potentials, and microbial copy numbers increased (P< 0·01) with age, while the greatest amylase and protease activity potentials occurred at 28 d. Most anatomic and functional variables evolved progressively from 14 to 42 d, while microbial colonisation was fastest from birth to 28 d. These outcomes suggest that the supplemental feeding system is more effective in promoting rumen development than the grazing system; in addition, for both the feeding systems, microbial colonisation in the rumen is achieved at 1 month, functional achievement at 2 months, and anatomic development after 2 months.

  6. Titanium dioxide nanoparticles strongly impact soil microbial function by affecting archaeal nitrifiers

    PubMed Central

    Simonin, Marie; Richaume, Agnès; Guyonnet, Julien P.; Dubost, Audrey; Martins, Jean M. F.; Pommier, Thomas

    2016-01-01

    Soils are facing new environmental stressors, such as titanium dioxide nanoparticles (TiO2-NPs). While these emerging pollutants are increasingly released into most ecosystems, including agricultural fields, their potential impacts on soil and its function remain to be investigated. Here we report the response of the microbial community of an agricultural soil exposed over 90 days to TiO2-NPs (1 and 500 mg kg−1 dry soil). To assess their impact on soil function, we focused on the nitrogen cycle and measured nitrification and denitrification enzymatic activities and by quantifying specific representative genes (amoA for ammonia-oxidizers, nirK and nirS for denitrifiers). Additionally, diversity shifts were examined in bacteria, archaea, and the ammonia-oxidizing clades of each domain. With strong negative impacts on nitrification enzyme activities and the abundances of ammonia-oxidizing microorganism, TiO2-NPs triggered cascading negative effects on denitrification enzyme activity and a deep modification of the bacterial community structure after just 90 days of exposure to even the lowest, realistic concentration of NPs. These results appeal further research to assess how these emerging pollutants modify the soil health and broader ecosystem function. PMID:27659196

  7. Titanium dioxide nanoparticles strongly impact soil microbial function by affecting archaeal nitrifiers

    NASA Astrophysics Data System (ADS)

    Simonin, Marie; Richaume, Agnès; Guyonnet, Julien P.; Dubost, Audrey; Martins, Jean M. F.; Pommier, Thomas

    2016-09-01

    Soils are facing new environmental stressors, such as titanium dioxide nanoparticles (TiO2-NPs). While these emerging pollutants are increasingly released into most ecosystems, including agricultural fields, their potential impacts on soil and its function remain to be investigated. Here we report the response of the microbial community of an agricultural soil exposed over 90 days to TiO2-NPs (1 and 500 mg kg‑1 dry soil). To assess their impact on soil function, we focused on the nitrogen cycle and measured nitrification and denitrification enzymatic activities and by quantifying specific representative genes (amoA for ammonia-oxidizers, nirK and nirS for denitrifiers). Additionally, diversity shifts were examined in bacteria, archaea, and the ammonia-oxidizing clades of each domain. With strong negative impacts on nitrification enzyme activities and the abundances of ammonia-oxidizing microorganism, TiO2-NPs triggered cascading negative effects on denitrification enzyme activity and a deep modification of the bacterial community structure after just 90 days of exposure to even the lowest, realistic concentration of NPs. These results appeal further research to assess how these emerging pollutants modify the soil health and broader ecosystem function.

  8. Yeast culture supplement during nursing and transport affects immunity and intestinal microbial ecology of weanling pigs.

    PubMed

    Weedman, S M; Rostagno, M H; Patterson, J A; Yoon, I; Fitzner, G; Eicher, S D

    2011-06-01

    The objectives of this study were to determine the influence of a Saccharomyces cerevisiae fermentation product on innate immunity and intestinal microbial ecology after weaning and transport stress. In a randomized complete block design, before weaning and in a split-plot analysis of a 2 × 2 factorial arrangement of yeast culture (YY) and transport (TT) after weaning, 3-d-old pigs (n = 108) were randomly assigned within litter (block) to either a control (NY, milk only) or yeast culture diet (YY; delivered in milk to provide 0.1 g of yeast culture product/kg of BW) from d 4 to 21. At weaning (d 21), randomly, one-half of the NY and YY pigs were assigned to a 6-h transport (NY-TT and YY-TT) before being moved to nursery housing, and the other one-half were moved directly to nursery housing (NY-NT and YY-NT, where NT is no transport). The yeast treatment was a 0.2% S. cerevisiae fermentation product and the control treatment was a 0.2% grain blank in feed for 2 wk. On d 1 before transport and on d 1, 4, 7, and 14 after transport, blood was collected for leukocyte assays, and mesenteric lymph node, jejunal, and ileal tissue, and jejunal, ileal, and cecal contents were collected for Toll-like receptor expression (TLR); enumeration of Escherichia coli, total coliforms, and lactobacilli; detection of Salmonella; and microbial analysis. After weaning, a yeast × transport interaction for ADG was seen (P = 0.05). Transport affected (P = 0.09) ADFI after weaning. Yeast treatment decreased hematocrit (P = 0.04). A yeast × transport interaction was found for counts of white blood cells (P = 0.01) and neutrophils (P = 0.02) and for the neutrophil-to-lymphocyte ratio (P = 0.02). Monocyte counts revealed a transport (P = 0.01) effect. Interactions of yeast × transport (P = 0.001) and yeast × transport × day (P = 0.09) for TLR2 and yeast × transport (P = 0.08) for TLR4 expression in the mesenteric lymph node were detected. Day affected lactobacilli, total coliform, and E

  9. Unravelling the active microbial community in a thermophilic anaerobic digester-microbial electrolysis cell coupled system under different conditions.

    PubMed

    Cerrillo, Míriam; Viñas, Marc; Bonmatí, August

    2017-03-01

    Thermophilic anaerobic digestion (AD) of pig slurry coupled to a microbial electrolysis cell (MEC) with a recirculation loop was studied at lab-scale as a strategy to increase AD stability when submitted to organic and nitrogen overloads. The system performance was studied, with the recirculation loop both connected and disconnected, in terms of AD methane production, chemical oxygen demand removal (COD) and volatile fatty acid (VFA) concentrations. Furthermore, the microbial population was quantitatively and qualitatively assessed through DNA and RNA-based qPCR and high throughput sequencing (MiSeq), respectively to identify the RNA-based active microbial populations from the total DNA-based microbial community composition both in the AD and MEC reactors under different operational conditions. Suppression of the recirculation loop reduced the AD COD removal efficiency (from 40% to 22%) and the methane production (from 0.32 to 0.03 m(3) m(-3) d(-1)). Restoring the recirculation loop led to a methane production of 0.55 m(3) m(-3) d(-1) concomitant with maximum MEC COD and ammonium removal efficiencies of 29% and 34%, respectively. Regarding microbial analysis, the composition of the AD and MEC anode populations differed from really active microorganisms. Desulfuromonadaceae was revealed as the most active family in the MEC (18%-19% of the RNA relative abundance), while hydrogenotrophic methanogens (Methanobacteriaceae) dominated the AD biomass.

  10. Effect of oxygen on the microbial activities of thermophilic anaerobic biomass.

    PubMed

    Pedizzi, C; Regueiro, L; Rodriguez-Verde, I; Lema, J M; Carballa, M

    2016-07-01

    Low oxygen levels (μgO2L(-1)) in anaerobic reactors are quite common and no relevant consequences are expected. On the contrary, higher concentrations could affect the process. This work aimed to study the influence of oxygen (4.3 and 8.8mgO2L(-1), respectively) on the different microbial activities (hydrolytic, acidogenic and methanogenic) of thermophilic anaerobic biomass and on the methanogenic community structure. Batch tests in presence of oxygen were conducted using specific substrates for each biological activity and a blank (with minimum oxygen) was included. No effect of oxygen was observed on the hydrolytic and acidogenic activities. In contrast, the methane production rate decreased by 40% in all oxygenated batches and the development of active archaeal community was slower in presence of 8.8mgO2L(-1). However, despite this sensitivity of methanogens to oxygen at saturation levels, the inhibition was reversible.

  11. Effect of monospecific and mixed sea-buckthorn (Hippophae rhamnoides) plantations on the structure and activity of soil microbial communities.

    PubMed

    Yu, Xuan; Liu, Xu; Zhao, Zhong; Liu, Jinliang; Zhang, Shunxiang

    2015-01-01

    This study aims to evaluate the effect of different afforestation models on soil microbial composition in the Loess Plateau in China. In particular, we determined soil physicochemical properties, enzyme activities, and microbial community structures in the top 0 cm to 10 cm soil underneath a pure Hippophae rhamnoides (SS) stand and three mixed stands, namely, H. rhamnoides and Robinia pseucdoacacia (SC), H. rhamnoides and Pinus tabulaeformis (SY), and H. rhamnoides and Platycladus orientalis (SB). Results showed that total organic carbon (TOC), total nitrogen, and ammonium (NH4(+)) contents were higher in SY and SB than in SS. The total microbial biomass, bacterial biomass, and Gram+ biomass of the three mixed stands were significantly higher than those of the pure stand. However, no significant difference was found in fungal biomass. Correlation analysis suggested that soil microbial communities are significantly and positively correlated with some chemical parameters of soil, such as TOC, total phosphorus, total potassium, available phosphorus, NH4(+) content, nitrate content (NH3(-)), and the enzyme activities of urease, peroxidase, and phosphatase. Principal component analysis showed that the microbial community structures of SB and SS could clearly be discriminated from each other and from the others, whereas SY and SC were similar. In conclusion, tree species indirectly but significantly affect soil microbial communities and enzyme activities through soil physicochemical properties. In addition, mixing P. tabulaeformis or P. orientalis in H. rhamnoides plantations is a suitable afforestation model in the Loess Plateau, because of significant positive effects on soil nutrient conditions, microbial community, and enzyme activities over pure plantations.

  12. Bioprospecting for microbial products that affect ice crystal formation and growth.

    PubMed

    Christner, Brent C

    2010-01-01

    At low temperatures, some organisms produce proteins that affect ice nucleation, ice crystal structure, and/or the process of recrystallization. Based on their ice-interacting properties, these proteins provide an advantage to species that commonly experience the phase change from water to ice or rarely experience temperatures above the melting point. Substances that bind, inhibit or enhance, and control the size, shape, and growth of ice crystals could offer new possibilities for a number of agricultural, biomedical, and industrial applications. Since their discovery more than 40 years ago, ice nucleating and structuring proteins have been used in cryopreservation, frozen food preparation, transgenic crops, and even weather modification. Ice-interacting proteins have demonstrated commercial value in industrial applications; however, the full biotechnological potential of these products has yet to be fully realized. The Earth's cold biosphere contains an almost endless diversity of microorganisms to bioprospect for microbial compounds with novel ice-interacting properties. Microorganisms are the most appropriate biochemical factories to cost effectively produce ice nucleating and structuring proteins on large commercial scales.

  13. Hydrogeology, chemical and microbial activity measurement through deep permafrost

    SciTech Connect

    Stotler, R.L.; Frape, S.K.; Freifeld, B.M.; Holden, B.; Onstott, T.C.; Ruskeeniemi, T.; Chan, E.

    2010-04-01

    Little is known about hydrogeochemical conditions beneath thick permafrost, particularly in fractured crystalline rock, due to difficulty in accessing this environment. The purpose of this investigation was to develop methods to obtain physical, chemical, and microbial information about the subpermafrost environment from a surface-drilled borehole. Using a U-tube, gas and water samples were collected, along with temperature, pressure, and hydraulic conductivity measurements, 420 m below ground surface, within a 535 m long, angled borehole at High Lake, Nunavut, Canada, in an area with 460-m-thick permafrost. Piezometric head was well above the base of the permafrost, near land surface. Initial water samples were contaminated with drill fluid, with later samples <40% drill fluid. The salinity of the non-drill fluid component was <20,000 mg/L, had a Ca/Na ratio above 1, with {delta}{sup 18}O values {approx}5{per_thousand} lower than the local surface water. The fluid isotopic composition was affected by the permafrost-formation process. Nonbacteriogenic CH{sub 4} was present and the sample location was within methane hydrate stability field. Sampling lines froze before uncontaminated samples from the subpermafrost environment could be obtained, yet the available time to obtain water samples was extended compared to previous studies. Temperature measurements collected from a distributed temperature sensor indicated that this issue can be overcome easily in the future. The lack of methanogenic CH{sub 4} is consistent with the high sulfate concentrations observed in cores. The combined surface-drilled borehole/U-tube approach can provide a large amount of physical, chemical, and microbial data from the subpermafrost environment with few, controllable, sources of contamination.

  14. Hydrogeology, chemical and microbial activity measurement through deep permafrost.

    PubMed

    Stotler, Randy L; Frape, Shaun K; Freifeld, Barry M; Holden, Brian; Onstott, Tullis C; Ruskeeniemi, Timo; Chan, Eric

    2011-01-01

    Little is known about hydrogeochemical conditions beneath thick permafrost, particularly in fractured crystalline rock, due to difficulty in accessing this environment. The purpose of this investigation was to develop methods to obtain physical, chemical, and microbial information about the subpermafrost environment from a surface-drilled borehole. Using a U-tube, gas and water samples were collected, along with temperature, pressure, and hydraulic conductivity measurements, 420 m below ground surface, within a 535 m long, angled borehole at High Lake, Nunavut, Canada, in an area with 460-m-thick permafrost. Piezometric head was well above the base of the permafrost, near land surface. Initial water samples were contaminated with drill fluid, with later samples <40% drill fluid. The salinity of the non-drill fluid component was <20,000 mg/L, had a Ca/Na ratio above 1, with δ(18) O values ∼5‰ lower than the local surface water. The fluid isotopic composition was affected by the permafrost-formation process. Nonbacteriogenic CH(4) was present and the sample location was within methane hydrate stability field. Sampling lines froze before uncontaminated samples from the subpermafrost environment could be obtained, yet the available time to obtain water samples was extended compared to previous studies. Temperature measurements collected from a distributed temperature sensor indicated that this issue can be overcome easily in the future. The lack of methanogenic CH(4) is consistent with the high sulfate concentrations observed in cores. The combined surface-drilled borehole/U-tube approach can provide a large amount of physical, chemical, and microbial data from the subpermafrost environment with few, controllable, sources of contamination.

  15. Hydrogeology, Chemical and Microbial Activity Measurement Through Deep Permafrost

    USGS Publications Warehouse

    Stotler, R.L.; Frape, S.K.; Freifeld, B.M.; Holden, B.; Onstott, T.C.; Ruskeeniemi, T.; Chan, E.

    2011-01-01

    Little is known about hydrogeochemical conditions beneath thick permafrost, particularly in fractured crystalline rock, due to difficulty in accessing this environment. The purpose of this investigation was to develop methods to obtain physical, chemical, and microbial information about the subpermafrost environment from a surface-drilled borehole. Using a U-tube, gas and water samples were collected, along with temperature, pressure, and hydraulic conductivity measurements, 420 m below ground surface, within a 535 m long, angled borehole at High Lake, Nunavut, Canada, in an area with 460-m-thick permafrost. Piezometric head was well above the base of the permafrost, near land surface. Initial water samples were contaminated with drill fluid, with later samples <40% drill fluid. The salinity of the non-drill fluid component was <20,000 mg/L, had a Ca/Na ratio above 1, with ??18O values ???5??? lower than the local surface water. The fluid isotopic composition was affected by the permafrost-formation process. Nonbacteriogenic CH4 was present and the sample location was within methane hydrate stability field. Sampling lines froze before uncontaminated samples from the subpermafrost environment could be obtained, yet the available time to obtain water samples was extended compared to previous studies. Temperature measurements collected from a distributed temperature sensor indicated that this issue can be overcome easily in the future. The lack of methanogenic CH4 is consistent with the high sulfate concentrations observed in cores. The combined surface-drilled borehole/U-tube approach can provide a large amount of physical, chemical, and microbial data from the subpermafrost environment with few, controllable, sources of contamination. ?? 2010 The Author(s). Journal compilation ?? 2010 National Ground Water Association.

  16. Impact of Nano-Silver Exposure on Microbial Activity

    NASA Astrophysics Data System (ADS)

    Morales, V. L.; Braga, R. A., Jr.; Spiers, A. J.

    2012-04-01

    A key gap in environmental impact assessments of emerging contaminants is the change in biological activity of microorganisms exposed to toxic substances. Silver-nanoparticles are among the top cytotoxic nanomaterials suspected to threaten microbial functions of natural and engineered systems. In this study, a novel light-interference technique termed 'bio-speckle' is employed to determine real-time biological activity of monocultures and biologically complex samples. Bio-speckle uses laser illumination of biological samples to create interference patterns of the scattered light that can be used to quantify intracellular organelle movement as a measurement of biological activity. To test the potential of bio-speckle technique for toxicity assays, filter paper microcosms of the model environmental bacterium Pseudomonas fluorescens strain SBW25 were exposed to uncoated nano-silver suspensions for 2, 24, 48, and 72 hours. At the end of each exposure period, biological activity was quantitatively determined as the dynamic speckle pattern's moment of inertia. Results suggest that the biological activity of bacteria decreases exponentially with the time of exposure of the colonies to the silver nanoparticles.

  17. Antibiotic Treatment Affects Intestinal Permeability and Gut Microbial Composition in Wistar Rats Dependent on Antibiotic Class.

    PubMed

    Tulstrup, Monica Vera-Lise; Christensen, Ellen Gerd; Carvalho, Vera; Linninge, Caroline; Ahrné, Siv; Højberg, Ole; Licht, Tine Rask; Bahl, Martin Iain

    2015-01-01

    Antibiotics are frequently administered orally to treat bacterial infections not necessarily related to the gastrointestinal system. This has adverse effects on the commensal gut microbial community, as it disrupts the intricate balance between specific bacterial groups within this ecosystem, potentially leading to dysbiosis. We hypothesized that modulation of community composition and function induced by antibiotics affects intestinal integrity depending on the antibiotic administered. To address this a total of 60 Wistar rats (housed in pairs with 6 cages per group) were dosed by oral gavage with either amoxicillin (AMX), cefotaxime (CTX), vancomycin (VAN), metronidazole (MTZ), or water (CON) daily for 10-11 days. Bacterial composition, alpha diversity and caecum short chain fatty acid levels were significantly affected by AMX, CTX and VAN, and varied among antibiotic treatments. A general decrease in diversity and an increase in the relative abundance of Proteobacteria was observed for all three antibiotics. Additionally, the relative abundance of Bifidobacteriaceae was increased in the CTX group and both Lactobacillaceae and Verrucomicrobiaceae were increased in the VAN group compared to the CON group. No changes in microbiota composition or function were observed following MTZ treatment. Intestinal permeability to 4 kDa FITC-dextran decreased after CTX and VAN treatment and increased following MTZ treatment. Plasma haptoglobin levels were increased by both AMX and CTX but no changes in expression of host tight junction genes were found in any treatment group. A strong correlation between the level of caecal succinate, the relative abundance of Clostridiaceae 1 family in the caecum, and the level of acute phase protein haptoglobin in blood plasma was observed. In conclusion, antibiotic-induced changes in microbiota may be linked to alterations in intestinal permeability, although the specific interactions remain to be elucidated as changes in permeability did

  18. Citrate and malonate increase microbial activity and alter microbial community composition in uncontaminated and diesel-contaminated soil microcosms

    NASA Astrophysics Data System (ADS)

    Martin, Belinda C.; George, Suman J.; Price, Charles A.; Shahsavari, Esmaeil; Ball, Andrew S.; Tibbett, Mark; Ryan, Megan H.

    2016-09-01

    Petroleum hydrocarbons (PHCs) are among the most prevalent sources of environmental contamination. It has been hypothesized that plant root exudation of low molecular weight organic acid anions (carboxylates) may aid degradation of PHCs by stimulating heterotrophic microbial activity. To test their potential implication for bioremediation, we applied two commonly exuded carboxylates (citrate and malonate) to uncontaminated and diesel-contaminated microcosms (10 000 mg kg-1; aged 40 days) and determined their impact on the microbial community and PHC degradation. Every 48 h for 18 days, soil received 5 µmol g-1 of (i) citrate, (ii) malonate, (iii) citrate + malonate or (iv) water. Microbial activity was measured daily as the flux of CO2. After 18 days, changes in the microbial community were assessed by a community-level physiological profile (CLPP) and 16S rRNA bacterial community profiles determined by denaturing gradient gel electrophoresis (DGGE). Saturated PHCs remaining in the soil were assessed by gas chromatography-mass spectrometry (GC-MS). Cumulative soil respiration increased 4- to 6-fold with the addition of carboxylates, while diesel contamination resulted in a small, but similar, increase across all carboxylate treatments. The addition of carboxylates resulted in distinct changes to the microbial community in both contaminated and uncontaminated soils but only a small increase in the biodegradation of saturated PHCs as measured by the n-C17 : pristane biomarker. We conclude that while the addition of citrate and malonate had little direct effect on the biodegradation of saturated hydrocarbons present in diesel, their effect on the microbial community leads us to suggest further studies using a variety of soils and organic acids, and linked to in situ studies of plants, to investigate the role of carboxylates in microbial community dynamics.

  19. Microbial activities and dissolved organic matter dynamics in oil-contaminated surface seawater from the Deepwater Horizon oil spill site.

    PubMed

    Ziervogel, Kai; McKay, Luke; Rhodes, Benjamin; Osburn, Christopher L; Dickson-Brown, Jennifer; Arnosti, Carol; Teske, Andreas

    2012-01-01

    The Deepwater Horizon oil spill triggered a complex cascade of microbial responses that reshaped the dynamics of heterotrophic carbon degradation and the turnover of dissolved organic carbon (DOC) in oil contaminated waters. Our results from 21-day laboratory incubations in rotating glass bottles (roller bottles) demonstrate that microbial dynamics and carbon flux in oil-contaminated surface water sampled near the spill site two weeks after the onset of the blowout were greatly affected by activities of microbes associated with macroscopic oil aggregates. Roller bottles with oil-amended water showed rapid formation of oil aggregates that were similar in size and appearance compared to oil aggregates observed in surface waters near the spill site. Oil aggregates that formed in roller bottles were densely colonized by heterotrophic bacteria, exhibiting high rates of enzymatic activity (lipase hydrolysis) indicative of oil degradation. Ambient waters surrounding aggregates also showed enhanced microbial activities not directly associated with primary oil-degradation (β-glucosidase; peptidase), as well as a twofold increase in DOC. Concurrent changes in fluorescence properties of colored dissolved organic matter (CDOM) suggest an increase in oil-derived, aromatic hydrocarbons in the DOC pool. Thus our data indicate that oil aggregates mediate, by two distinct mechanisms, the transfer of hydrocarbons to the deep sea: a microbially-derived flux of oil-derived DOC from sinking oil aggregates into the ambient water column, and rapid sedimentation of the oil aggregates themselves, serving as vehicles for oily particulate matter as well as oil aggregate-associated microbial communities.

  20. Promoting uranium immobilization by the activities of microbial phophatases

    SciTech Connect

    Sobecky, Patricia A.

    2005-06-01

    The first objective of this project is to determine the relationship of phosphatase activity to metal resistance in subsurface strains and the role of lateral gene transfer (LGT) in dissemination of nonspecific acid phosphatase genes. Nonspecific acid phosphohydrolases are a broad group of secreted microbial phosphatases that function in acidic-to-neutral pH ranges and utilize a wide range of organophosphate substrates. We have previously shown that PO43- accumulation during growth on a model organophosphorus compound was attributable to the overproduction of alkaline phosphatase by genetically modified subsurface pseudomonads [Powers et al. (2002) FEMS Microbiol. Ecol. 41:115-123]. During this report period, we have extended these results to include indigenous metal resistant subsurface microorganisms cultivated from the Field Research Center (FRC), in Oak Ridge Tennessee.

  1. Post-Biostimulation Biogenic U(IV) Stability and Microbial Community Structure that Affects its Dynamics

    NASA Astrophysics Data System (ADS)

    Jaffe, P. R.; Long, P. E.; Moon, H.; N'Guessan, L.; Peacock, A.; Sinha, M.; Tan, H.; Traub, D.; Williams, K. H.

    2010-12-01

    Flow-through sediment column experiments were conducted to determine the stability of biogenic U(IV) after biostimulation has been discontinued, and to isolate the key biogeochemical processes that affect the post-biostimulation U(IV) stability. Columns, packed with sediments from an UMTRA site (Rifle Colorado) were biostimulated for two months by injecting groundwater containing 3 mM acetate and 20 uM U(VI) at flow rates typically encountered at the Rifle site. After the biostimulation period, acetate injection was discontinued, and groundwater containing dissolved oxygen was allowed to enter the columns. Columns were then sacrificed at two week intervals to examine the sediment geochemistry and associated microbial community. Results showed that iron sulfide precipitates, that formed during the bioreduction phase, acted as a buffer to partially prevent biogenic U(IV) oxidation during the month post stimulation period. Groundwater and sediment microbial community compositions were analyzed over a period of one month post-biostimulation. The results indicate that two distinct biological processes, characterized by oxygen utilization, played important roles during this period. Within two weeks post stimulation, organisms such as Hydrogenophaga sp. and Thiobacillus sp. were observed in the columns. These bacteria, are able to use Fe(II), sulfide, or thiosulfate as their electron donor in the presence of O2. Furthermore, organisms closely related to Lysobacter sp. and Sterolibacterium sp. were also detected in the groundwater and sediment. It was suggested that these organisms may be feeding on decaying biomass and consuming O2 in the process. The presence of these oxidizing and spoilage bacteria is thought to have resulted in the consumption of oxygen, therefore protecting the biogenic U(IV) from being reoxidized in the sediment columns. To simulate the in situ U(IV) stability under post biostimulation conditions, columns bioreduced in the laboratory, as described

  2. Coarse Woody Debris Increases Microbial Community Functional Diversity but not Enzyme Activities in Reclaimed Oil Sands Soils.

    PubMed

    Kwak, Jin-Hyeob; Chang, Scott X; Naeth, M Anne; Schaaf, Wolfgang

    2015-01-01

    Forest floor mineral soil mix (FMM) and peat mineral soil mix (PMM) are cover soils commonly used for upland reclamation post open-pit oil sands mining in northern Alberta, Canada. Coarse woody debris (CWD) can be used to regulate soil temperature and water content, to increase organic matter content, and to create microsites for the establishment of microorganisms and vegetation in upland reclamation. We studied the effects of CWD on soil microbial community level physiological profile (CLPP) and soil enzyme activities in FMM and PMM in a reclaimed landscape in the oil sands. This experiment was conducted with a 2 (FMM vs PMM) × 2 (near CWD vs away from CWD) factorial design with 6 replications. The study plots were established with Populus tremuloides (trembling aspen) CWD placed on each plot between November 2007 and February 2008. Soil samples were collected within 5 cm from CWD and more than 100 cm away from CWD in July, August and September 2013 and 2014. Microbial biomass was greater (p<0.05) in FMM than in PMM, in July, and August 2013 and July 2014, and greater (p<0.05) near CWD than away from CWD in FMM in July and August samplings. Soil microbial CLPP differed between FMM and PMM (p<0.01) according to a principal component analysis and CWD changed microbial CLPP in FMM (p<0.05) but not in PMM. Coarse woody debris increased microbial community functional diversity (average well color development in Biolog Ecoplates) in both cover soils (p<0.05) in August and September 2014. Carbon degrading soil enzyme activities were greater in FMM than in PMM (p<0.05) regardless of distance from CWD but were not affected by CWD. Greater microbial biomass and enzyme activities in FMM than in PMM will increase organic matter decomposition and nutrient cycling, improving plant growth. Enhanced microbial community functional diversity by CWD application in upland reclamation has implications for accelerating upland reclamation after oil sands mining.

  3. Effect of activated carbon on microbial bioavailability of phenanthrene in soils

    SciTech Connect

    Yang, Y.; Hunter, W.; Tao, S.; Crowley, D.; Gan, J.

    2009-11-15

    Bioavailability is a governing factor that controls the rate of biological degradation of hydrophobic organic contaminants in soil. Among the solid phases that can adsorb hydrophobic organic contaminants in soil, black carbon (BC) exerts a particularly significant effect on phase distribution. However, knowledge on the effect of BC on the microbial availability of polycyclic aromatic hydrocarbons in soil is still limited. In the present study, the effect of a coal-derived activated carbon on the bioavailability of phenanthrene (PHE) during its degradation by Mycobacterium vanbaalenii PYR-1 was measured in three soils. The freely dissolved concentration of PHE was concurrently determined in soil solutions using disposable polydimethylsiloxane fibers. The results showed that PHE mineralization was significantly inhibited after addition of activated carbon in all test soils. After 216 h, only 5.20, 5.83, and 6.85% of PHE was degraded in the 0.5% BC-amended soils initially containing organic carbon at 0.23, 2.1, and 7.1%, respectively. Significant correlation was found between PHE degradability and freely dissolved concentration, suggesting that BC affected PHE bioavailability by decreasing chemical activity. The effect of activated carbon in the amended soils was attributed to its enhancement of soil surface areas and pore volumes. Results from the present study clearly highlighted the importance of BC for influencing the microbial availability of polycyclic aromatic hydrocarbons in soils.

  4. Anion effects on anti-microbial activity of poly[1-vinyl-3-(2-sulfoethyl imidazolium betaine)].

    PubMed

    Garg, Godawari; Chauhan, Ghanshyam S; Gupta, Reena; Ahn, J-H

    2010-04-01

    Recent investigations in the anti-microbial properties of the functional polymers are predominantly focused on the structure of the cationic moieties. In the present study, we investigated that the nature of the anion present in polysulfobetaines affects activity against certain microorganisms and their anti-microbial properties have been rationalized in terms of the structure-activity relationship. Vinyl imidazolium-based polysulfobetaines were prepared by the quaternization of poly(N-vinyl imidazole) with sodium salt of 2-bromo ethanesulfonic acid. The bromide counter anion of the resulting polymer was exchanged with different anions to generate a series of polymers. These were characterized by FTIR, DSC, XRD, SEM, elemental analysis (C, H, N and S) and viscosity measurements. The anti-microbial activity studies were carried against three fungi (Aspergillus niger, Byssochlamys fulva and Mucor circenelliods) and two bacteria (Bacillus coagulans BTS-3 and Pseudomonas aeruginosa BTS-2). The nature of the anion affects the structure of polysulfobetaine by realignment of polymer chains. The anion-dependent anti-microbial properties of polysulfobetaines result from the interaction of the microbes at the polymer interface.

  5. Effects of Carbon in Flooded Paddy Soils: Implications for Microbial Activity and Arsenic Mobilization

    NASA Astrophysics Data System (ADS)

    Avancha, S.; Boye, K.

    2014-12-01

    In the Mekong delta in Cambodia, naturally occurring arsenic (originating from erosion in the Himalaya Mountains) in paddy soils is mobilized during the seasonal flooding. As a consequence, rice grown on the flooded soils may take up arsenic and expose people eating the rice to this carcinogenic substance. Microbial activity will enhance or decrease the mobilization of arsenic depending on their metabolic pathways. Among the microbes naturally residing in the soil are denitrifying bacteria, sulfate reducers, metal reducers (Fe, Mn), arsenic reducers, methanogens, and fermenters, whose activity varies based on the presence of oxygen. The purpose of the experiment was to assess how different amendments affect the microbial activity and the arsenic mobilization during the transition from aerobic to anaerobic metabolism after flooding of naturally contaminated Cambodian soil. In a batch experiment, we investigated how the relative metabolic rate of naturally occurring microbes could vary with different types of organic carbon. The experiment was designed to measure the effects of various sources of carbon (dried rice straw, charred rice straw, manure, and glucose) on the microbial activity and arsenic release in an arsenic-contaminated paddy soil from Cambodia under flooded conditions. All amendments were added based on the carbon content in order to add 0.036 g of carbon per vial. The soil was flooded with a 10mM TRIS buffer solution at pH 7.04 in airtight 25mL serum vials and kept at 25 °C. We prepared 14 replicates per treatment to sample both gas and solution. On each sampling point, the solution replicates were sampled destructively. The gas replicates continued on and were sampled for both gas and solution on the final day of the experiment. We measured pH, total arsenic, methane, carbon dioxide, and nitrous oxide at 8 hours, 1.5 days, 3.33 days, and 6.33 days from the start of the experiment.

  6. Spreading Topsoil Encourages Ecological Restoration on Embankments: Soil Fertility, Microbial Activity and Vegetation Cover

    PubMed Central

    Rivera, Desirée; Mejías, Violeta; Jáuregui, Berta M.; López-Archilla, Ana Isabel; Peco, Begoña

    2014-01-01

    The construction of linear transport infrastructure has severe effects on ecosystem functions and properties, and the restoration of the associated roadslopes contributes to reduce its impact. This restoration is usually approached from the perspective of plant cover regeneration, ignoring plant-soil interactions and the consequences for plant growth. The addition of a 30 cm layer of topsoil is a common practice in roadslope restoration projects to increase vegetation recovery. However topsoil is a scarce resource. This study assesses the effects of topsoil spreading and its depth (10 to 30 cm) on two surrogates of microbial activity (β-glucosidase and phosphatase enzymes activity and soil respiration), and on plant cover, plant species richness and floristic composition of embankment vegetation. The study also evaluates the differences in selected physic-chemical properties related to soil fertility between topsoil and the original embankment substrate. Topsoil was found to have higher values of organic matter (11%), nitrogen (44%), assimilable phosphorous (50%) and silt content (54%) than the original embankment substrate. The topsoil spreading treatment increased microbial activity, and its application increased β-glucosidase activity (45%), phosphatase activity (57%) and soil respiration (60%). Depth seemed to affect soil respiration, β-glucosidase and phosphatase activity. Topsoil application also enhanced the species richness of restored embankments in relation to controls. Nevertheless, the depth of the spread topsoil did not significantly affect the resulting plant cover, species richness or floristic composition, suggesting that both depths could have similar effects on short-term recovery of the vegetation cover. A significant implication of these results is that it permits the application of thinner topsoil layers, with major savings in this scarce resource during the subsequent slope restoration work, but the quality of topsoil relative to the

  7. Spreading topsoil encourages ecological restoration on embankments: soil fertility, microbial activity and vegetation cover.

    PubMed

    Rivera, Desirée; Mejías, Violeta; Jáuregui, Berta M; Costa-Tenorio, Marga; López-Archilla, Ana Isabel; Peco, Begoña

    2014-01-01

    The construction of linear transport infrastructure has severe effects on ecosystem functions and properties, and the restoration of the associated roadslopes contributes to reduce its impact. This restoration is usually approached from the perspective of plant cover regeneration, ignoring plant-soil interactions and the consequences for plant growth. The addition of a 30 cm layer of topsoil is a common practice in roadslope restoration projects to increase vegetation recovery. However topsoil is a scarce resource. This study assesses the effects of topsoil spreading and its depth (10 to 30 cm) on two surrogates of microbial activity (β-glucosidase and phosphatase enzymes activity and soil respiration), and on plant cover, plant species richness and floristic composition of embankment vegetation. The study also evaluates the differences in selected physic-chemical properties related to soil fertility between topsoil and the original embankment substrate. Topsoil was found to have higher values of organic matter (11%), nitrogen (44%), assimilable phosphorous (50%) and silt content (54%) than the original embankment substrate. The topsoil spreading treatment increased microbial activity, and its application increased β-glucosidase activity (45%), phosphatase activity (57%) and soil respiration (60%). Depth seemed to affect soil respiration, β-glucosidase and phosphatase activity. Topsoil application also enhanced the species richness of restored embankments in relation to controls. Nevertheless, the depth of the spread topsoil did not significantly affect the resulting plant cover, species richness or floristic composition, suggesting that both depths could have similar effects on short-term recovery of the vegetation cover. A significant implication of these results is that it permits the application of thinner topsoil layers, with major savings in this scarce resource during the subsequent slope restoration work, but the quality of topsoil relative to the

  8. Microbial Activity in the Subseafloor Sediments of ODP Leg 201

    NASA Astrophysics Data System (ADS)

    D'Honst, S.; Joergensen, B. B.; Blake, R.; Dickens, G.; Hinrichs, K.; Holm, N.; Mitterer, R.; Spivack, A.

    2002-12-01

    Ocean Drilling Program Leg 201 was the first ocean drilling expedition dedicated to the study of life deep beneath the seafloor. Its equatorial Pacific and Peru Margin sites were selected to represent the general range of subsurface environments that exists in marine sediments throughout most of the world's oceans. In water depths as great as 5300 meters and as shallow as 150 meters, the expedition drilled up to 420 meters into oceanic sediments and the underlying basaltic crust. The sediments ranged in temperature from 1° C to 25° C and in age from 0 to almost 40 million years. Leg 201 scientists found biogeochemical evidence of metabolic activity throughout the sediment column at every site. This activity is supported at all sites by the diffusion of sulfate down from the overlying ocean, as well as by the dissolution of iron- and manganese-bearing minerals. At the open ocean sites, metabolic activity deep beneath the seafloor is also supported by the transport of sulfate, nitrate and oxygen from water circulating through the underlying basaltic crust. At both the open ocean sites and the Peru margin sites, multiple metabolic activities (sulfate reduction, iron reduction, manganese reduction and methanogenesis) co-occur. Chemical flux estimates suggest that sulfate is generally the principal terminal electron acceptor in these subseafloor sediments. However, at the open ocean sites with the lowest rates of microbial respiration, manganese may rival sulfate as a terminal electron acceptor. The recovered sediments and fluids are being studied further to document the controls on rates of subsurface activity, the influence of past oceanographic conditions on current activity in deeply buried sediments, and the effects of subseafloor biogeochemical processes on Earth's surface world.

  9. Structure and function of subsurface microbial communities affecting radionuclide transport and bioimmobilization

    SciTech Connect

    Kostka, Joel E.; Prakash, Om; Green, Stefan J.; Akob, Denise; Jasrotia, Puja; Kerkhof, Lee; Chin, Kuk-Jeong; Sheth, Mili; Keller, Martin; Venkateswaran, Amudhan; Elkins, James G.; Stucki, Joseph W.

    2012-05-01

    Our objectives were to: 1) isolate and characterize novel anaerobic prokaryotes from subsurface environments exposed to high levels of mixed contaminants (U(VI), nitrate, sulfate), 2) elucidate the diversity and distribution of metabolically active metal- and nitrate-reducing prokaryotes in subsurface sediments, and 3) determine the biotic and abiotic mechanisms linking electron transport processes (nitrate, Fe(III), and sulfate reduction) to radionuclide reduction and immobilization. Mechanisms of electron transport and U(VI) transformation were examined under near in situ conditions in sediment microcosms and in field investigations. Field sampling was conducted at the Oak Ridge Field Research Center (ORFRC), in Oak Ridge, Tennessee. The ORFRC subsurface is exposed to mixed contamination predominated by uranium and nitrate. In short, we effectively addressed all 3 stated objectives of the project. In particular, we isolated and characterized a large number of novel anaerobes with a high bioremediation potential that can be used as model organisms, and we are now able to quantify the function of subsurface sedimentary microbial communities in situ using state-of-the-art gene expression methods (molecular proxies).

  10. Impact of Faba Bean-Seed Rhizobial Inoculation on Microbial Activity in the Rhizosphere Soil during Growing Season

    PubMed Central

    Siczek, Anna; Lipiec, Jerzy

    2016-01-01

    Inoculation of legume seeds with Rhizobium affects soil microbial community and processes, especially in the rhizosphere. This study aimed at assessing the effect of Rhizobium inoculation on microbial activity in the faba bean rhizosphere during the growing season in a field experiment on a Haplic Luvisol derived from loess. Faba bean (Vicia faba L.) seeds were non-inoculated (NI) or inoculated (I) with Rhizobium leguminosarum bv. viciae and sown. The rhizosphere soil was analyzed for the enzymatic activities of dehydrogenases, urease, protease and acid phosphomonoesterase, and functional diversity (catabolic potential) using the Average Well Color Development, Shannon-Weaver, and Richness indices following the community level physiological profiling from Biolog EcoPlate™. The analyses were done on three occasions corresponding to the growth stages of: 5–6 leaf, flowering, and pod formation. The enzymatic activities were higher in I than NI (p < 0.05) throughout the growing season. However, none of the functional diversity indices differed significantly under both treatments, regardless of the growth stage. This work showed that the functional diversity of the microbial communities was a less sensitive tool than enzyme activities in assessment of rhizobial inoculation effects on rhizosphere microbial activity. PMID:27213363

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  13. Stability of soil microbial structure and activity depends on microbial diversity.

    PubMed

    Tardy, Vincent; Mathieu, Olivier; Lévêque, Jean; Terrat, Sébastien; Chabbi, Abad; Lemanceau, Philippe; Ranjard, Lionel; Maron, Pierre-Alain

    2014-04-01

    Despite the central role of microbes in soil processes, empirical evidence concerning the effect of their diversity on soil stability remains controversial. Here, we addressed the ecological insurance hypothesis by examining the stability of microbial communities along a gradient of soil microbial diversity in response to mercury pollution and heat stress. Diversity was manipulated by dilution extinction approach. Structural and functional stabilities of microbial communities were assessed from patterns of genetic structure and soil respiration after the stress. Dilution led to the establishment of a consistent diversity gradient, as revealed by 454 sequencing of ribosomal genes. Diversity stability was enhanced in species-rich communities whatever the stress whereas functional stability was improved with increasing diversity after heat stress, but not after mercury pollution. This discrepancy implies that the relevance of ecological insurance for soil microbial communities might depend on the type of stress. Our results also suggest that the significance of microbial diversity for soil functional stability might increase with available soil resources. This could have strong repercussions in the current 'global changes' context because it suggests that the combined increased frequencies of extreme climatic events, nutrient loading and biotic exploitation may amplify the functional consequences of diversity decrease.

  14. Microbial fuel cells with highly active aerobic biocathodes

    NASA Astrophysics Data System (ADS)

    Milner, Edward M.; Popescu, Dorin; Curtis, Tom; Head, Ian M.; Scott, Keith; Yu, Eileen H.

    2016-08-01

    Microbial fuel cells (MFCs), which convert organic waste to electricity, could be used to make the wastewater infrastructure more energy efficient and sustainable. However, platinum and other non-platinum chemical catalysts used for the oxygen reduction reaction (ORR) at the cathode of MFCs are unsustainable due to their high cost and long-term degradation. Aerobic biocathodes, which use microorganisms as the biocatalysts for cathode ORR, are a good alternative to chemical catalysts. In the current work, high-performing aerobic biocathodes with an onset potential for the ORR of +0.4 V vs. Ag/AgCl were enriched from activated sludge in electrochemical half-cells poised at -0.1 and + 0.2 V vs. Ag/AgCl. Gammaproteobacteria, distantly related to any known cultivated gammaproteobacterial lineage, were identified as dominant in these working electrode biofilms (23.3-44.3% of reads in 16S rRNA gene Ion Torrent libraries), and were in very low abundance in non-polarised control working electrode biofilms (0.5-0.7%). These Gammaproteobacteria were therefore most likely responsible for the high activity of biologically catalysed ORR. In MFC tests, a high-performing aerobic biocathode increased peak power 9-fold from 7 to 62 μW cm-2 in comparison to an unmodified carbon cathode, which was similar to peak power with a platinum-doped cathode at 70 μW cm-2.

  15. Active microbial soil communities in different agricultural managements

    NASA Astrophysics Data System (ADS)

    Landi, S.; Pastorelli, R.

    2009-04-01

    We studied the composition of active eubacterial microflora by RNA extraction from soil (bulk and rhizosphere) under different environmental impact managements, in a hilly basin in Gallura (Sardinia). We contrasted grassy vineyard, in which the soil had been in continuous contact with plant roots for a long period of time, with traditional tilled vineyard. Moreover, we examined permanent grassland, in which plants had been present for some years, with temporary grassland, in which varying plants had been present only during the respective growing seasons. Molecular analysis of total population was carried out by electrophoretic separation by Denaturing Gradient Gel Electrophoresis (DGGE) of amplified cDNA fragments obtained from 16S rRNA. In vineyards UPGMA (Unweighted Pair Group Mathematical Average) analysis made up separate clusters depending on soil management. In spring both clusters showed similarity over 70%, while in autumn the similarity increased, 84% and 90% for grassy and conventional tilled vineyard respectively. Permanent and temporary grassland joined in a single cluster in spring, while in autumn a partial separation was evidenced. The grassy vineyard, permanent and temporary grassland showed higher richness and diversity Shannon-Weiner index values than vineyard with conventional tillage although no significant. In conclusion the expected effect of the rhizosphere was visible: the grass cover influenced positively the diversity of active microbial population.

  16. Microbial community composition and denitrifying enzyme activities in salt marsh sediments.

    PubMed

    Cao, Yiping; Green, Peter G; Holden, Patricia A

    2008-12-01

    Denitrifying microbial communities and denitrification in salt marsh sediments may be affected by many factors, including environmental conditions, nutrient availability, and levels of pollutants. The objective of this study was to examine how microbial community composition and denitrification enzyme activities (DEA) at a California salt marsh with high nutrient loading vary with such factors. Sediments were sampled from three elevations, each with different inundation and vegetation patterns, across 12 stations representing various salinity and nutrient conditions. Analyses included determination of cell abundance, total and denitrifier community compositions (by terminal restriction fragment length polymorphism), DEA, nutrients, and eluted metals. Total bacterial (16S rRNA) and denitrifier (nirS) community compositions and DEA were analyzed for their relationships to environmental variables and metal concentrations via multivariate direct gradient and regression analyses, respectively. Community composition and DEA were highly variable within the dynamic salt marsh system, but each was strongly affected by elevation (i.e., degree of inundation) and carbon content as well as by selected metals. Carbon content was highly related to elevation, and the relationships between DEA and carbon content were found to be elevation specific when evaluated across the entire marsh. There were also lateral gradients in the marsh, as evidenced by an even stronger association between community composition and elevation for a marsh subsystem. Lastly, though correlated with similar environmental factors and selected metals, denitrifier community composition and function appeared uncoupled in the marsh.

  17. ETBE (ethyl tert butyl ether) and TAME (tert amyl methyl ether) affect microbial community structure and function in soils.

    PubMed

    Bartling, Johanna; Esperschütz, Jürgen; Wilke, Berndt-Michael; Schloter, Michael

    2011-03-15

    Ethyl tert butyl ether (ETBE) and tert amyl methyl ether (TAME) are oxygenates used in gasoline in order to reduce emissions from vehicles. The present study investigated their impact on a soil microflora that never was exposed to any contamination before. Therefore, soil was artificially contaminated and incubated over 6 weeks. Substrate induced respiration (SIR) measurements and phospholipid fatty acid (PLFA) analysis indicated shifts in both, microbial function and structure during incubation. The results showed an activation of microbial respiration in the presence of ETBE and TAME, suggesting biodegradation by the microflora. Furthermore, PLFA concentrations decreased in the presence of ETBE and TAME and Gram-positive bacteria became more dominant in the microbial community.

  18. Soil biological activity as affected by tillage intensity

    NASA Astrophysics Data System (ADS)

    Gajda, A.; Przewłoka, B.

    2012-02-01

    The effect of tillage intensity on changes of microbiological activity and content of particulate organic matter in soil under winter wheat duirng 3 years was studied. Microbial response related to the tillage-induced changes in soil determined on the content of biomass C and N, the rate of CO2 evolution, B/F ratio, the activity of dehydrogenases, acid and alkaline phosphatases, soil C/N ratio and microbial biomass C/N ratio confirmed the high sensitivity of soil microbial populations to the tillage system applied. After three year studies, the direct sowing system enhanced the increase of labile fraction of organic matter content in soil. There were no significant changes in the labile fraction quantity observed in soil under conventional tillage. Similar response related to the tillage intensity was observed in particulate organic matter quantities expressed as a percentage of total organic matter in soil. A high correlation coefficients calculated between contents of soil microbial biomass C and N, particulate organic matter and potentially mineralizable N, and the obtained yields of winter wheat grown on experimental fields indicated on a high importance of biological quality of status of soil for agricultural crop production.

  19. [Carbon source metabolic diversity of soil microbial community under different climate types in the area affected by Wenchuan earthquake].

    PubMed

    Zhang, Guang-Shuai; Lin, Yong-Ming; Ma, Rui-Feng; Deng, Hao-Jun; Du, Kun; Wu, Cheng-Zhen; Hong, Wei

    2015-02-01

    The MS8.0 Wenchuan earthquake in 2008 led to huge damage to land covers in northwest Sichuan, one of the critical fragile eco-regions in China which can be divided into Semi-arid dry hot climate zone (SDHC) and Subtropical humid monsoon climate zone (SHMC). Using the method of Bilog-ECO-microplate technique, this paper aimed to determine the functional diversity of soil microbial community in the earthquake-affected areas which can be divided into undamaged area (U), recover area (R) and damaged area without recovery (D) under different climate types, in order to provide scientific basis for ecological recovery. The results indicated that the average-well-color-development (AWCD) in undamaged area and recovery area showed SDHC > SHMC, which was contrary to the AWCD in the damaged area without recovery. The AWCD of damaged area without recovery was the lowest in both climate zones. The number of carbon source utilization types of soil microbial in SHMC zone was significantly higher than that in SDHC zone. The carbon source utilization types in both climate zones presented a trend of recover area > undamaged area > damaged area without recovery. The carbon source metabolic diversity characteristic of soil microbial community was significantly different in different climate zones. The diversity index and evenness index both showed a ranking of undamaged area > recover area > damaged area without recovery. In addition, the recovery area had the highest richness index. The soil microbial carbon sources metabolism characteristic was affected by soil nutrient, aboveground vegetation biomass and vegetation coverage to some extent. In conclusion, earthquake and its secondary disasters influenced the carbon source metabolic diversity characteristic of soil microbial community mainly through the change of aboveground vegetation and soil environmental factors.

  20. Microcalorimetric study the toxic effect of hexavalent chromium on microbial activity of Wuhan brown sandy soil: an in vitro approach.

    PubMed

    Yao, Jun; Tian, Lin; Wang, Yanxin; Djah, Atakora; Wang, Fei; Chen, Huilun; Su, Chunli; Zhuang, Rensheng; Zhou, Yong; Choi, Martin M F; Bramanti, Emilia

    2008-02-01

    A multi-channel thermal activity monitor was applied to study soil microbial activity in Wuhan brown sandy soil in the presence of different concentrations of hexavalent chromium (K(2)Cr(2)O(7)). In order to stimulate the soil microbial activity, 5.0mg of glucose and 5.0mg of ammonium sulfate were added to a 1.20-g soil sample under a controlled humidity of 35%. The results show that the poisonous species of K(2)Cr(2)O(7) at an half inhibitory concentration (IC(50)) value of 4.27 microg mL(-1) against soil microbe, and an increase of the amount of hexavalent chromium is associated to a decrease in the microbial activity of the soil, probably due to an increase in the toxicity of hexavalent chromium, affecting strongly the life in this soil microbial environment. Our work also suggests that microcalorimetry is a fast, simple and more sensitive method that can be easily performed to study the toxicity of different species of heavy metals on microorganism compared to other biological methods.

  1. Microbial Community Analysis of a Coastal Salt Marsh Affected by the Deepwater Horizon Oil Spill

    PubMed Central

    Beazley, Melanie J.; Martinez, Robert J.; Rajan, Suja; Powell, Jessica; Piceno, Yvette M.; Tom, Lauren M.; Andersen, Gary L.; Hazen, Terry C.; Van Nostrand, Joy D.; Zhou, Jizhong; Mortazavi, Behzad; Sobecky, Patricia A.

    2012-01-01

    Coastal salt marshes are highly sensitive wetland ecosystems that can sustain long-term impacts from anthropogenic events such as oil spills. In this study, we examined the microbial communities of a Gulf of Mexico coastal salt marsh during and after the influx of petroleum hydrocarbons following the Deepwater Horizon oil spill. Total hydrocarbon concentrations in salt marsh sediments were highest in June and July 2010 and decreased in September 2010. Coupled PhyloChip and GeoChip microarray analyses demonstrated that the microbial community structure and function of the extant salt marsh hydrocarbon-degrading microbial populations changed significantly during the study. The relative richness and abundance of phyla containing previously described hydrocarbon-degrading bacteria (Proteobacteria, Bacteroidetes, and Actinobacteria) increased in hydrocarbon-contaminated sediments and then decreased once hydrocarbons were below detection. Firmicutes, however, continued to increase in relative richness and abundance after hydrocarbon concentrations were below detection. Functional genes involved in hydrocarbon degradation were enriched in hydrocarbon-contaminated sediments then declined significantly (p<0.05) once hydrocarbon concentrations decreased. A greater decrease in hydrocarbon concentrations among marsh grass sediments compared to inlet sediments (lacking marsh grass) suggests that the marsh rhizosphere microbial communities could also be contributing to hydrocarbon degradation. The results of this study provide a comprehensive view of microbial community structural and functional dynamics within perturbed salt marsh ecosystems. PMID:22815990

  2. Microbial Survey of a Full-Scale, Biologically Active Filter for Treatment of Drinking Water

    PubMed Central

    DeBry, Ronald W.; Lytle, Darren A.

    2012-01-01

    The microbial community of a full-scale, biologically active drinking water filter was surveyed using molecular techniques. Nitrosomonas, Nitrospira, Sphingomonadales, and Rhizobiales dominated the clone libraries. The results elucidate the microbial ecology of biological filters and demonstrate that biological treatment of drinking water should be considered a viable alternative to physicochemical methods. PMID:22752177

  3. Microbial survey of a full-scale, biologically active filter for treatment of drinking water.

    PubMed

    White, Colin P; Debry, Ronald W; Lytle, Darren A

    2012-09-01

    The microbial community of a full-scale, biologically active drinking water filter was surveyed using molecular techniques. Nitrosomonas, Nitrospira, Sphingomonadales, and Rhizobiales dominated the clone libraries. The results elucidate the microbial ecology of biological filters and demonstrate that biological treatment of drinking water should be considered a viable alternative to physicochemical methods.

  4. Contrasting effects of biochar versus manure on soil microbial communities and enzyme activities in an Aridisol

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biochar has been shown to increase microbial activity, alter microbial community structure, and increase soil fertility in arid and semi-arid soils, but at relatively high rates that may be impractical for large-scale field studies. This contrasts with organic amendments such as manure, which can be...

  5. Microbial diversity and activity in seafloor brine lake sediments (Alaminos Canyon block 601, Gulf of Mexico).

    PubMed

    Crespo-Medina, M; Bowles, M W; Samarkin, V A; Hunter, K S; Joye, S B

    2016-09-01

    The microbial communities thriving in deep-sea brines are sustained largely by energy rich substrates supplied through active seepage. Geochemical, microbial activity, and microbial community composition data from different habitats at a Gulf of Mexico brine lake in Alaminos Canyon revealed habitat-linked variability in geochemistry that in turn drove patterns in microbial community composition and activity. The bottom of the brine lake was the most geochemically extreme (highest salinity and nutrient concentrations) habitat and its microbial community exhibited the highest diversity and richness indices. The habitat at the upper halocline of the lake hosted the highest rates of sulfate reduction and methane oxidation, and the largest inventories of dissolved inorganic carbon, particulate organic carbon, and hydrogen sulfide. Statistical analyses indicated a significant positive correlation between the bacterial and archaeal diversity in the bottom brine sample and NH4+ inventories. Other environmental factors with positive correlation with microbial diversity indices were DOC, H2 S, and DIC concentrations. The geochemical regime of different sites within this deep seafloor extreme environment exerts a clear selective force on microbial communities and on patterns of microbial activity.

  6. Sediment Microbial Enzyme Activity as an Indicator of Nutrient Limitation in Great Lakes Coastal Wetlands

    EPA Science Inventory

    This study, the first to link microbial enzyme activities to regional-scale anthropogenic stressors, suggests that microbial enzyme regulation of carbon and nutrient dynamics may be sensitive indicators of nutrient dynamics in aquatic ecosystems, but further work is needed to elu...

  7. Biogeochemical drivers of microbial community convergence across actively retreating glaciers

    SciTech Connect

    Castle, Sarah C.; Nemergut, Diana R.; Grandy, A. Stuart; Leff, Jonathan W.; Graham, Emily B.; Hood, Eran; Schmidt, Steven K.; Wickings, Kyle; Cleveland, Cory C.

    2016-10-01

    The ecological processes that influence biogeographical patterns of microorganisms are actively debated. To investigate how such patterns emerge during ecosystem succession, we examined the biogeochemical drivers of bacterial community assembly in soils over two environmentally distinct, recently deglaciated chronosequences separated by a distance of more than 1,300 kilometers. Our results show that despite different geographic, climatic, and soil chemical and physical characteristics at the two sites, soil bacterial community structure and decomposer function converged during plant succession. In a comparative analysis, we found that microbial communities in early succession soils were compositionally distinct from a group of diverse, mature forest soils, but that the differences between successional soils and mature soils decreased from early to late stages of succession. Differences in bacterial community composition across glacial sites were largely explained by pH. However, successional patterns and community convergence across sites were more consistently related to soil organic carbon and organic matter chemistry, which appeared to be tightly coupled with bacterial community structure across both young and mature soils.

  8. Biological soil crusts: a microenvironment characterized by complex microbial interrelations affected by the presence of the exopolysaccharidic matrix.

    NASA Astrophysics Data System (ADS)

    De Philippis, Roberto

    2015-04-01

    Biological Soil Crusts (BSCs) are complex microbial communities, commonly found in arid and semiarid areas of the world. The capability of the microorganisms residing in BSCs to withstand the harsh environmental conditions typical of these habitats, namely drought and high solar irradiation, is related with the presence of a matrix constituted by microbial-produced extracellular polysaccharides (EPSs), which also accomplish for a wide array of key ecological roles. EPSs represent a huge carbon source directly available to heterotrophic organisms, affect soil characteristics, water regimes, and establish complex interactions with plants. The induction of BSCs on degraded soils is considered a feasible approach to amend and maintain land fertility, as it was reported in a number of recent studies. It was recently shown that BSC induction is beneficial in enhancing SOC (Soil Organic Carbon) and in increasing the abundance of phototrophic organisms and vegetation cover. This lecture will describe the results of a study showing that cyanobacterial-EPS resulted advantageous to the growth and metabolism of seedlings of Caragana korshinskii, a desert sub-shrub widely diffused in the area under study, also contributing a defensive effect against the damaging effects of reactive oxygen species (ROS), generated under UV-irradiation, salt stress and desiccation. A study aimed at investigating the possible correlation between the chemical composition and the macromolecular features of the EPS matrix of induced BSCs of different age, collected in the hyper-arid plateau of Hobq desert, Inner Mongolia, China, will be also presented. The results of this study showed that the characteristics of the EPS of the matrix of the investigated IBSCs cannot be put only in relation with the age of the crusts and the activity of phototrophic microorganisms but, more properly, it has to be taken into account the biotic interactions ongoing between EPS producers (cyanobacteria, green microalgae

  9. Organic matter quantity and source affects microbial community structure and function following volcanic eruption on Kasatochi Island, Alaska

    USGS Publications Warehouse

    Zeglin, Lydia H.; Wang, Bronwen; Waythomas, Christopher F.; Rainey, Frederick; Talbot, Sandra

    2016-01-01

    In August 2008, Kasatochi volcano erupted and buried a small island in pyroclastic deposits and fine ash; since then, microbes, plants and birds have begun to re-colonize the initially sterile surface. Five years post-eruption, bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) copy numbers and extracellular enzyme activity (EEA) potentials were one to two orders of magnitude greater in pyroclastic materials with organic matter (OM) inputs relative to those without, despite minimal accumulation of OM (< 0.2%C). When normalized by OM levels, post-eruptive surfaces with OM inputs had the highest β-glucosidase, phosphatase, NAGase and cellobiohydrolase activities, and had microbial population sizes approaching those in reference soils. In contrast, the strongest factor determining bacterial community composition was the dominance of plants versus birds as OM input vectors. Although soil pH ranged from 3.9 to 7.0, and %C ranged 100×, differentiation between plant- and bird-associated microbial communities suggested that cell dispersal or nutrient availability are more likely drivers of assembly than pH or OM content. This study exemplifies the complex relationship between microbial cell dispersal, soil geochemistry, and microbial structure and function; and illustrates the potential for soil microbiota to be resilient to disturbance.

  10. Temperature Effects on Microbial CH4 and CO2 Production in Permafrost-Affected Soils From the Barrow Environmental Observatory

    NASA Astrophysics Data System (ADS)

    Graham, D. E.; Roy Chowdhury, T.; Zheng, J.; Moon, J. W.; Yang, Z.; Gu, B.; Wullschleger, S. D.

    2015-12-01

    Warmer Arctic temperatures are increasing the annual soil thaw depth and prolonging the thaw season in Alaskan permafrost zones. This change exposes organic matter buried in the soils and permafrost to microbial degradation and mineralization to form CO2 and CH4. The proportion and fluxes of these greenhouse gases released into the atmosphere control the global feedback on warming. To improve representations of these biogeochemical processes in terrestrial ecosystem models we compared soil properties and microbial activities in core samples of polygonal tundra from the Barrow Environmental Observatory. Measurements of soil water potential through the soil column characterized water binding to the organic and mineral components. This suction combines with temperature to control freezing, gas diffusion and microbial activity. The temperature-dependence of CO2 and CH4 production from anoxic soil incubations at -2, +4 or +8 °C identified a significant lag in methanogenesis relative to CO2 production by anaerobic respiration and fermentation. Changes in the abundance of methanogen signature genes during incubations indicate that microbial population shifts caused by thawing and warmer temperatures drive changes in the mixtures of soil carbon degradation products. Comparisons of samples collected across the microtopographic features of ice-wedge polygons address the impacts of water saturation, iron reduction and organic matter content on CH4 production and oxidation. These combined measurements build process understanding that can be applied across scales to constrain key response factors in models that address Arctic soil warming.

  11. Nearshore Pelagic Microbial Community Abundance Affects Recruitment Success of Giant Kelp, Macrocystis pyrifera

    PubMed Central

    Morris, Megan M.; Haggerty, John M.; Papudeshi, Bhavya N.; Vega, Alejandro A.; Edwards, Matthew S.; Dinsdale, Elizabeth A.

    2016-01-01

    Marine microbes mediate key ecological processes in kelp forest ecosystems and interact with macroalgae. Pelagic and biofilm-associated microbes interact with macroalgal propagules at multiple stages of recruitment, yet these interactions have not been described for Macrocystis pyrifera. Here we investigate the influence of microbes from coastal environments on recruitment of giant kelp, M. pyrifera. Through repeated laboratory experiments, we tested the effects of altered pelagic microbial abundance on the settlement and development of the microscopic propagules of M. pyrifera during recruitment. M. pyrifera zoospores were reared in laboratory microcosms exposed to environmental microbial communities from seawater during the complete haploid stages of the kelp recruitment cycle, including zoospore release, followed by zoospore settlement, to gametophyte germination and development. We altered the microbial abundance states differentially in three independent experiments with repeated trials, where microbes were (a) present or absent in seawater, (b) altered in community composition, and (c) altered in abundance. Within the third experiment, we also tested the effect of nearshore versus offshore microbial communities on the macroalgal propagules. Distinct pelagic microbial communities were collected from two southern California temperate environments reflecting contrasting intensity of human influence, the nearshore Point Loma kelp forest and the offshore Santa Catalina Island kelp forest. The Point Loma kelp forest is a high impacted coastal region adjacent to the populous San Diego Bay; whereas the kelp forest at Catalina Island is a low impacted region of the Channel Islands, 40 km offshore the southern California coast, and is adjacent to a marine protected area. Kelp gametophytes reared with nearshore Point Loma microbes showed lower survival, growth, and deteriorated morphology compared to gametophytes with the offshore Catalina Island microbial community

  12. Microbial respiration and kinetics of extracellular enzymes activities through rhizosphere and detritusphere at agricultural site

    NASA Astrophysics Data System (ADS)

    Löppmann, Sebastian; Blagodatskaya, Evgenia; Kuzyakov, Yakov

    2014-05-01

    Rhizosphere and detritusphere are soil microsites with very high resource availability for microorganisms affecting their biomass, composition and functions. In the rhizosphere low molecular compounds occur with root exudates and low available polymeric compounds, as belowground plant senescence. In detritusphere the substrate for decomposition is mainly a polymeric material of low availability. We hypothesized that microorganisms adapted to contrasting quality and availability of substrates in the rhizosphere and detritusphere are strongly different in affinity of hydrolytic enzymes responsible for decomposition of organic compounds. According to common ecological principles easily available substrates are quickly consumed by microorganisms with enzymes of low substrate affinity (i.e. r-strategists). The slow-growing K-strategists with enzymes of high substrate affinity are better adapted for growth on substrates of low availability. Estimation of affinity of enzyme systems to the substrate is based on Michaelis-Menten kinetics, reflecting the dependency of decomposition rates on substrate amount. As enzymes-mediated reactions are substrate-dependent, we further hypothesized that the largest differences in hydrolytic activity between the rhizosphere and detritusphere occur at substrate saturation and that these differences are smoothed with increasing limitation of substrate. Affected by substrate limitation, microbial species follow a certain adaptation strategy. To achieve different depth gradients of substrate availability 12 plots on an agricultural field were established in the north-west of Göttingen, Germany: 1) 4 plots planted with maize, reflecting lower substrate availability with depth; 2) 4 unplanted plots with maize litter input (0.8 kg m-2 dry maize residues), corresponding to detritusphere; 3) 4 bare fallow plots as control. Maize litter was grubbed homogenously into the soil at the first 5 cm to ensure comparable conditions for the herbivore and

  13. Temperature sensitivity of microbial respiration, nitrogen mineralization, and potential soil enzyme activities in organic alpine soils

    NASA Astrophysics Data System (ADS)

    Koch, Oliver; Tscherko, Dagmar; Kandeler, Ellen

    2007-12-01

    Investigations focusing on the temperature sensitivity of microbial activity and nutrient turnover in soils improve our understanding of potential effects of global warming. This study investigates the temperature sensitivity of C mineralization, N mineralization, and potential enzyme activities involved in the C and N cycle (tyrosine amino-peptidase, leucine amino-peptidase, ß-glucosidase, ß-xylosidase, N-acetyl-ß-glucosaminidase). Four different study sites in the Austrian alpine zone were selected, and soils were sampled in three seasons (summer, autumn, and winter). A simple first-order exponential equation was used to calculate constant Q10 values for the C and N mineralization over the investigated temperature range (0-30°C). The Q10 values of the C mineralization (average 2.0) for all study sites were significantly higher than for the N mineralization (average 1.7). The Q10 values of both activities were significantly negatively related to a soil organic matter quality index calculated by the ratios of respiration to the organic soil carbon and mineralized N to the total soil nitrogen. The chemical soil properties or microbial biomass did not affect the Q10 values of C and N mineralization. Moreover, the Q10 values showed no distinct pattern according to sampling date, indicating that the substrate quality and other factors are more important. Using a flexible model function, the analysis of relative temperature sensitivity (RTS) showed that the temperature sensitivity of activities increased with decreasing temperature. The C and N mineralization and potential amino-peptidase activities (tyrosine and leucine) showed an almost constant temperature dependence over 0-30°C. In contrast, ß-glucosidase, ß-xylosidase, and N-acetyl-ß-glucosaminidase showed a distinctive increase in temperature sensitivity with decreasing temperature. Low temperature at the winter sampling date caused a greater increase in the RTS of all microbial activities than for the

  14. Soil Microbial Activity Provides Insight to Carbon Cycling in Shrub Ecotones of Sub-Arctic Sweden

    NASA Astrophysics Data System (ADS)

    Marek, E.; Kashi, N. N.; Chen, J.; Hobbie, E. A.; Schwan, M. R.; Varner, R. K.

    2015-12-01

    Shrubs are expanding in Arctic and sub-Arctic regions due to rising atmospheric temperatures. Microbial activity increases as growing temperatures cause permafrost warming and subsequent thaw, leading to a greater resource of soil nutrients enabling shrub growth. Increased carbon inputs from shrubs is predicted to result in faster carbon turnover by microbial decomposition. Further understanding of microbial activity underneath shrubs could uncover how microbes and soil processes interact to promote shrub expansion and carbon cycling. To address how higher soil carbon input from shrubs influences decomposition, soil samples were taken across a heath, shrub, and forest ecotone gradient at two sites near Abikso, Sweden. Samples were analyzed for soluble carbon and nitrogen, microbial abundance, and microbial activity of chitinase, glucosidase, and phosphatase to reflect organic matter decomposition and availability of nitrogen, carbon, and phosphate respectively. Chitinase activity positively correlated with shrub cover, suggesting microbial demands for nitrogen increase with higher shrub cover. Glucosidase activity negatively correlated with shrub cover and soluble carbon, suggesting decreased microbial demand for carbon as shrub cover and carbon stores increase. Lower glucosidase activity in areas with high carbon input from shrubs implies that microbes are decomposing carbon less readily than carbon is being put into the soil. Increasing soil carbon stores in shrub covered areas can lead to shrubs becoming a net carbon sink and a negative feedback to changing climate.

  15. Assessing microbial activities in metal contaminated agricultural volcanic soils--An integrative approach.

    PubMed

    Parelho, C; Rodrigues, A S; Barreto, M C; Ferreira, N G C; Garcia, P

    2016-07-01

    Volcanic soils are unique naturally fertile resources, extensively used for agricultural purposes and with particular physicochemical properties that may result in accumulation of toxic substances, such as trace metals. Trace metal contaminated soils have significant effects on soil microbial activities and hence on soil quality. The aim of this study is to determine the soil microbial responses to metal contamination in volcanic soils under different agricultural land use practices (conventional, traditional and organic), based on a three-tier approach: Tier 1 - assess soil microbial activities, Tier 2 - link the microbial activity to soil trace metal contamination and, Tier 3 - integrate the microbial activity in an effect-based soil index (Integrative Biological Response) to score soil health status in metal contaminated agricultural soils. Our results showed that microbial biomass C levels and soil enzymes activities were decreased in all agricultural soils. Dehydrogenase and β-glucosidase activities, soil basal respiration and microbial biomass C were the most sensitive responses to trace metal soil contamination. The Integrative Biological Response value indicated that soil health was ranked as: organic>traditional>conventional, highlighting the importance of integrative biomarker-based strategies for the development of the trace metal "footprint" in Andosols.

  16. STRUCTURE AND FUNCTION OF SUBSURFACE MICROBIAL COMMUNITIES AFFECTING RADIONUCLIDE TRANSPORT AND BIOIMMOBILIZATION

    SciTech Connect

    Joel E. Kostka; Lee Kerkhof; Kuk-Jeong Chin; Martin Keller; Joseph W. Stucki

    2011-06-15

    to science all show high sequence identity to sequences retrieved from ORFRC subsurface. (2) Based on physiological and phylogenetic characterization, two new species of subsurface bacteria were described: the metal-reducer Geobacter daltonii, and the denitrifier Rhodanobacter denitrificans. (3) Strains isolated from the ORFRC show that Rhodanobacter species are well adapted to the contaminated subsurface. Strains 2APBS1 and 116-2 grow at high salt (3% NaCl), low pH (3.5) and tolerate high concentrations of nitrate (400mM) and nitrite (100mM). Strain 2APBS1 was demonstrated to grow at in situ acidic pHs down to 2.5. (4) R. denitrificans strain 2APBS1 is the first described Rhodanobacter species shown to denitrify. Nitrate is almost entirely converted to N2O, which may account for the large accumulation of N2O in the ORFRC subsurface. (5) G. daltonii, isolated from uranium- and hydrocarbon-contaminated subsurface sediments of the ORFRC, is the first organism from the subsurface clade of the genus Geobacter that is capable of growth on aromatic hydrocarbons. (6) High quality draft genome sequences and a complete eco-physiological description are completed for R. denitrificans strain 2APBS1 and G. daltonii strain FRC-32. (7) Given their demonstrated relevance to DOE remediation efforts and the availability of detailed genotypic/phenotypic characterization, Rhodanobacter denitrificans strain 2APBS1 and Geobacter daltonii strain FRC-32 represent ideal model organisms to provide a predictive understanding of subsurface microbial activity through metabolic modeling. Tasks II and III-Diversity and distribution of active anaerobes and Mechanisms linking electron transport and the fate of radionuclides: (1) Our study showed that members of genus Rhodanobacter and Geobacter are abundant and active in the uranium and nitrate contaminated subsurface. In the contaminant source zone of the Oak Ridge site, Rhodanobacter spp. are the predominant, active organisms detected (comprising

  17. The soil carbon/nitrogen ratio and moisture affect microbial community structures in alkaline permafrost-affected soils with different vegetation types on the Tibetan plateau.

    PubMed

    Zhang, Xinfang; Xu, Shijian; Li, Changming; Zhao, Lin; Feng, Huyuan; Yue, Guangyang; Ren, Zhengwei; Cheng, Guogdong

    2014-01-01

    In the Tibetan permafrost region, vegetation types and soil properties have been affected by permafrost degradation, but little is known about the corresponding patterns of their soil microbial communities. Thus, we analyzed the effects of vegetation types and their covariant soil properties on bacterial and fungal community structure and membership and bacterial community-level physiological patterns. Pyrosequencing and Biolog EcoPlates were used to analyze 19 permafrost-affected soil samples from four principal vegetation types: swamp meadow (SM), meadow (M), steppe (S) and desert steppe (DS). Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria dominated bacterial communities and the main fungal phyla were Ascomycota, Basidiomycota and Mucoromycotina. The ratios of Proteobacteria/Acidobacteria decreased in the order: SM>M>S>DS, whereas the Ascomycota/Basidiomycota ratios increased. The distributions of carbon and nitrogen cycling bacterial genera detected were related to soil properties. The bacterial communities in SM/M soils degraded amines/amino acids very rapidly, while polymers were degraded rapidly by S/DS communities. UniFrac analysis of bacterial communities detected differences among vegetation types. The fungal UniFrac community patterns of SM differed from the others. Redundancy analysis showed that the carbon/nitrogen ratio had the main effect on bacteria community structures and their diversity in alkaline soil, whereas soil moisture was mainly responsible for structuring fungal communities. Thus, microbial communities and their functioning are probably affected by soil environmental change in response to permafrost degradation.

  18. Microbial activities and phosphorus cycling: An application of oxygen isotope ratios in phosphate

    NASA Astrophysics Data System (ADS)

    Stout, Lisa M.; Joshi, Sunendra R.; Kana, Todd M.; Jaisi, Deb P.

    2014-08-01

    Microorganisms carry out biochemical transformations of nutrients that make up their cells. Therefore, understanding how these nutrients are transformed or cycled in natural environments requires knowledge of microbial activity. Commonly used indicators for microbial activity typically include determining microbial respiration by O2/CO2 measurements, cell counts, and measurement of enzyme activities. However, coupled studies on nutrient cycling and microbial activity are not given enough emphasis. Here we apply phosphate oxygen isotope ratios (δ18OP) as a tool for measurement of microbial activity and compare the rate of isotope exchange with methods of measuring microbial activities that are more commonly applied in environmental studies including respiration, dehydrogenase activity, alkaline phosphatase activity, and cell counts. Our results show that different bacteria may have different strategies for P uptake, storage and release, their respiration and consequently expression of DHA and APase activities, but in general the trend of their enzyme activities are comparable. Phosphate δ18OP values correlated well with these other parameters used to measure microbial activity with the strongest linear relationships between δ18OP and CO2 evolution (r = -0.99). Even though the rate of isotope exchange for each microorganism used in this study is different, the rate per unit CO2 respiration showed one general trend, where δ18OP values move towards equilibrium while CO2 is generated. While this suggests that P cycling among microorganisms used in this study can be generalized, further research is needed to determine whether the microorganism-specific isotope exchange trend may occur in natural environments. In summary, phosphate oxygen isotope measurements may offer an alternative for use as a tracer to measure microbial activity in soils, sediments, and many other natural environments.

  19. Effect of altitude and season on microbial activity, abundance and community structure in Alpine forest soils.

    PubMed

    Siles, José A; Cajthaml, Tomas; Minerbi, Stefano; Margesin, Rosa

    2016-03-01

    In the current context of climate change, the study of microbial communities along altitudinal gradients is especially useful. Only few studies considered altitude and season at the same time. We characterized four forest sites located in the Italian Alps, along an altitude gradient (545-2000 m a.s.l.), to evaluate the effect of altitude in spring and autumn on soil microbial properties. Each site in each season was characterized with regard to soil temperature, physicochemical properties, microbial activities (respiration, enzymes), community level physiological profiles (CLPP), microbial abundance and community structure (PLFA). Increased levels of soil organic matter (SOM) and nutrients were found at higher altitudes and in autumn, resulting in a significant increase of (soil dry-mass related) microbial activities and abundance at higher altitudes. Significant site- and season-specific effects were found for enzyme production. The significant interaction of the factors site and incubation temperature for soil microbial activities indicated differences in microbial communities and their responses to temperature among sites. CLPP revealed site-specific effects. Microbial community structure was influenced by altitudinal, seasonal and/or site-specific effects. Correlations demonstrated that altitude, and not season, was the main factor determining the changes in abiotic and biotic characteristics at the sites investigated.

  20. Microbial Community-Level Physiological Profiles (CLPP) and herbicide mineralization potential in groundwater affected by agricultural land use

    NASA Astrophysics Data System (ADS)

    Janniche, Gry Sander; Spliid, Henrik; Albrechtsen, Hans-Jørgen

    2012-10-01

    Diffuse groundwater pollution from agricultural land use may impact the microbial groundwater community, which was investigated as Community-Level Physiological Profiles (CLPP) using EcoPlate™. Water was sampled from seven piezometers and a spring in a small agricultural catchment with diffuse herbicide and nitrate pollution. Based on the Shannon-Wiener and Simpson's diversity indices the diversity in the microbial communities was high. The response from the EcoPlates™ showed which substrates support groundwater bacteria, and all 31 carbon sources were utilized by organisms from at least one water sample. However, only nine carbon sources were utilized by all water samples: D-Mannitol, N-acetyl-D-glucosamine, putrescine, D-galacturonic acid, itaconic acid, 4-hydroxy benzoic acid, tween 40, tween 80, and L-asparagine. In all water samples the microorganisms preferred D-mannitol, D-galacturonic acid, tween 40, and 4-hydroxy benzoic acid as substrates, whereas none preferred 2-hydroxy benzoic acid, α-D-lactose, D,L-α-glycerol phosphate, α-ketobutyric acid, L-threonine and glycyl-L-glutamic acid. Principal Component Analysis of the CLPP's clustered the most agriculturally affected groundwater samples, indicating that the agricultural land use affects the groundwater microbial communities. Furthermore, the ability to mineralize atrazine and isoproturon, which have been used in the catchment, was also associated with this cluster.

  1. Soil microbial activities in Mediterranean environment as desertification indicators along a pluviometric gradient.

    NASA Astrophysics Data System (ADS)

    Novosadova, I.; Zahora, J.; Ruiz Sinoga, J. D.

    2009-04-01

    In the Mediterranean areas of Southern Spain, unsuitable agricultural practices with adverse environmental conditions (López Bermúdez and Albaladejo, 1990), have led to a permanent degradation and loss of soil fertility. This includes deterioration of the natural plant cover, which protects against erosion by contributing organic matter, the main prerequisite of ecosystem sustainability (Grace et al., 1994). Physico-chemical, microbiological and biochemical soil properties are very responsive and provide immediate and precise information on small changes occurring in soil (Dick and Tabatabai, 1993). There is increasing evidence that such parameters are also sensitive indicators of ecology stress suffered by a soil and its recovery, since microbial activity has a direct influence on the stability and fertility of ecosystems (Smith and Papendick, 1993). One method for recovering degraded soils of such semiarid regions, with their low organic matter content, is to enhance primary productivity and carbon sequestration without any additional nitrogen fertilization and preferably without incorporation of leguminous plants (Martinez Mena et al., 2008). Carbon rich materials can sustain microbial activity and growth, thus enhancing biogeochemical nutrient cycles (Pascual et al., 1997). The present study is focused in the role of physico-chemical and microbial soil properties in Mediterranean environment, in terms of in situ and ex situ microbial transformation of soil carbon and nitrogen, in order to characterise the key soil microbial activities which could strongly affect carbon and nitrogen turnover in soil and hereby soil fertility and soil organic matter "quality". These microbial activities could at unsuitable agricultural practices with adverse environmental conditions induce unfavourable hydrologycal tempo-spatial response. The final results shown modifications in the soil properties studied with the increasing of the aridity. Such changes suppose the soil

  2. (A)synchronous Availabilities of N and P Regulate the Activity and Structure of the Microbial Decomposer Community.

    PubMed

    Fanin, Nicolas; Hättenschwiler, Stephan; Chavez Soria, Paola F; Fromin, Nathalie

    2015-01-01

    Nitrogen (N) and phosphorus (P) availability both control microbial decomposers and litter decomposition. However, these two key nutrients show distinct release patterns from decomposing litter and are unlikely available at the same time in most ecosystems. Little is known about how temporal differences in N and P availability affect decomposers and litter decomposition, which may be particularly critical for tropical rainforests growing on old and nutrient-impoverished soils. Here we used three chemically contrasted leaf litter substrates and cellulose paper as a widely accessible substrate containing no nutrients to test the effects of temporal differences in N and P availability in a microcosm experiment under fully controlled conditions. We measured substrate mass loss, microbial activity (by substrate induced respiration, SIR) as well as microbial community structure (using phospholipid fatty acids, PLFAs) in the litter and the underlying soil throughout the initial stages of decomposition. We generally found a stronger stimulation of substrate mass loss and microbial respiration, especially for cellulose, with simultaneous NP addition compared to a temporally separated N and P addition. However, litter types with a relatively high N to P availability responded more to initial P than N addition and vice versa. A third litter species showed no response to fertilization regardless of the sequence of addition, likely due to strong C limitation. Microbial community structure in the litter was strongly influenced by the fertilization sequence. In particular, the fungi to bacteria ratio increased following N addition alone, a shift that was reversed with complementary P addition. Opposite to the litter layer microorganisms, the soil microbial community structure was more strongly influenced by the identity of the decomposing substrate than by fertilization treatments, reinforcing the idea that C availability can strongly constrain decomposer communities

  3. (A)synchronous Availabilities of N and P Regulate the Activity and Structure of the Microbial Decomposer Community

    PubMed Central

    Fanin, Nicolas; Hättenschwiler, Stephan; Chavez Soria, Paola F.; Fromin, Nathalie

    2016-01-01

    Nitrogen (N) and phosphorus (P) availability both control microbial decomposers and litter decomposition. However, these two key nutrients show distinct release patterns from decomposing litter and are unlikely available at the same time in most ecosystems. Little is known about how temporal differences in N and P availability affect decomposers and litter decomposition, which may be particularly critical for tropical rainforests growing on old and nutrient-impoverished soils. Here we used three chemically contrasted leaf litter substrates and cellulose paper as a widely accessible substrate containing no nutrients to test the effects of temporal differences in N and P availability in a microcosm experiment under fully controlled conditions. We measured substrate mass loss, microbial activity (by substrate induced respiration, SIR) as well as microbial community structure (using phospholipid fatty acids, PLFAs) in the litter and the underlying soil throughout the initial stages of decomposition. We generally found a stronger stimulation of substrate mass loss and microbial respiration, especially for cellulose, with simultaneous NP addition compared to a temporally separated N and P addition. However, litter types with a relatively high N to P availability responded more to initial P than N addition and vice versa. A third litter species showed no response to fertilization regardless of the sequence of addition, likely due to strong C limitation. Microbial community structure in the litter was strongly influenced by the fertilization sequence. In particular, the fungi to bacteria ratio increased following N addition alone, a shift that was reversed with complementary P addition. Opposite to the litter layer microorganisms, the soil microbial community structure was more strongly influenced by the identity of the decomposing substrate than by fertilization treatments, reinforcing the idea that C availability can strongly constrain decomposer communities

  4. Yeast culture supplement during nursing and transport affects immunity and intestinal microbial ecology of weanling pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Weaning and transport stress can have a negative impact on the piglet's immune system and intestinal microbiota. The objective of this study was to determine the influence of a yeast product on innate immunity and microbial ecology of the gastrointestinal tract following stress of weaning and trans...

  5. CO2 gradient affects on deep subsurface microbial ecology during carbon sequestration

    NASA Astrophysics Data System (ADS)

    Gulliver, D.; Gregory, K.

    2011-12-01

    Geological carbon sequestration is likely to be part of a comprehensive strategy to minimize the release of greenhouse gasses into the atmosphere. Reservoir storage capacities and long-term security of these deposits will be dependent on the trapping mechanisms and mineral transformation in the deep subsurface. Therefore, a critical need exists to understand the evolution of microbial populations that may influence the biogeochemistry in the reservoirs. As the CO2 front moves through the storage aquifer, microbial communities may preside in residual brine left behind in cracks, dead flow zones, and upstream to the front; this brine will have a gradient of dissolved CO2 in which microbial interaction may behave differently, depending on the distance from the CO2 front. The evolution of microbial ecology along this CO2 gradient was investigated using fluid-slurry samples obtained from the prospective carbon sequestration site, the Arbuckle saline aquifer at the Wellington oil field, KS. The native species of these samples were investigated with a series of batch reactors under constant temperature of 40 °C, constant total pressure of 2,000 psi, and varying CO2 partial pressures of 0 psi, 20 psi, 200 psi, and 2,000 psi. After 1 day, 7 days, and 56 days of exposure in the batch reactors, fluid samples were centrifuged and the resulting pellet was biologically analyzed. Clone libraries and quantitative PCR determined that the bacterial diversity and population of the native microbial community was dependant on both the duration of exposure and the CO2 partial pressure. For example, the microbial community of 0 psi CO2 and 20 psi CO2 was predominantly related to the families halomonadaceae and marinilabiaceae while at 2,000 psi CO2 the community was predominantly in the family psychromonadaceae. The population size at 2,000 psi CO2 was also found to decrease by 3 orders of magnitude after only 7 days of CO2 exposure. Although these experiments were relatively short

  6. The study of electrochemically active microbial biofilms on different carbon-based anode materials in microbial fuel cells.

    PubMed

    Liu, Ying; Harnisch, Falk; Fricke, Katja; Schröder, Uwe; Climent, Victor; Feliu, Juan Miguel

    2010-05-15

    In this communication we show that the achievable maximum current density for mature wastewater-based microbial biofilms is strongly dependent on the electrode material and the operation temperature. On graphite and polycrystalline carbon rods, the catalytic current of about 500 microA cm(-2) (projected surface area) at 30 degrees C was achieved. Carbon fiber veil or carbon-paper based materials, having a large microbially-accessible surface gave a projected current density approximately 40% higher than on graphite rod. In contrast, the biofilm cannot form well on graphite foil. Elevating the temperature from 30 to 40 degrees C increased current density by 80% on graphite rod anodes. Interestingly, the formal potential of the active site (-0.12 V (vs. standard hydrogen electrode (SHE))) is similar to all electrocatalytically active microbial biofilms and to that found for Geobacter sulfurreducens in previous studies. In addition, the real surface area values measured by BET surface area technique cannot provide a reasonable explanation for suitability of an electrode material for the formation of electrochemically active biofilm.

  7. Filtration properties of activated sludge in municipal MBR wastewater treatment plants are related to microbial community structure.

    PubMed

    Bugge, Thomas V; Larsen, Poul; Saunders, Aaron M; Kragelund, Caroline; Wybrandt, Lisbeth; Keiding, Kristian; Christensen, Morten L; Nielsen, Per H

    2013-11-01

    In the conventional activated sludge process, a number of important parameters determining the efficiency of settling and dewatering are often linked to specific groups of bacteria in the sludge--namely floc size, residual turbidity, shear sensitivity and composition of extracellular polymeric substances (EPS). In membrane bioreactors (MBRs) the nature of solids separation at the membrane has much in common with sludge dewaterability but less is known about the effect of specific microbial groups on the sludge characteristics that affect this process. In this study, six full-scale MBR plants were investigated to identify correlations between sludge filterability, sludge characteristics, and microbial community structure. The microbial community structure was described by quantitative fluorescence in situ hybridization and sludge filterability by a low-pressure filtration method. A strong correlation between the degree of flocculation (ratio between floc size and residual turbidity) and sludge filterability at low pressure was found. A good balance between EPS and cations in the sludge correlated with good flocculation, relatively large sludge flocs, and low amounts of small particles and single cells in the bulk phase (measured as residual turbidity), all leading to a good filterability. Floc properties could also be linked to the microbial community structure. Bacterial species forming strong microcolonies such as Nitrospira and Accumulibacter were present in plants with good flocculation and filtration properties, while few strong microcolonies and many filamentous bacteria in the plants correlated with poor flocculation and filtration problems. In conclusion this study extends the hitherto accepted perception that plant operation affects floc properties which affects fouling. Additionally, plant operation also affects species composition, which affects floc properties and in the end fouling propensity.

  8. Mutations affecting enzymatic activity in liver arginase

    SciTech Connect

    Vockley, J.G.; Tabor, D.E.; Goodman, B.K.

    1994-09-01

    The hydrolysis of arginine to ornithine and urea is catalyzed by arginase in the last step of the urea cycle. We examined a group of arginase deficient patients by PCR-SSCP analysis to characterize the molecular basis of this disorder. A heterogeneous population of nonsense mutations, microdeletions, and missense mutations has been identified in our cohort. Microdeletions which introduce premature stop codons downstream of the deletion and nonsense mutations result in no arginase activity. These mutations occur randomly along the gene. The majority of missense mutations identified appear to occur in regions of high cross-species homology. To test the effect of these missense mutations on arginase activity, site-directed mutagenesis was used to re-create the patient mutations for in vivo expression studies in a prokaryotic fusion-protein expression system. Of 4 different missense mutations identified in 6 individuals, only one was located outside of a conserved region. The three substitution mutations within the conserved regions had a significant effect on enzymatic activity (0-3.1 nmole/30min, normal is 1300-1400 nmoles/30min, as determined by in vitro arginase assay), while the fourth mutation, a T to S substitution, did not. In addition, site-directed mutagenesis was utilized to create mutations not in residues postulated to play a significant role in the enzymatic function or active site formation in manganese-binding proteins such as arginase. We have determined that the substitution of glycine for a histidine residue, located in a very highly conserved region of exon 3, and the substitution of a histidine and an aspartic acid residue within a similarly conserved region in exon 4, totally abolishes enzymatic activity. Mutations substituting glycine for an additional histidine and aspartic acid residue in exon 4 and two aspartic acid residues in exon 7 have also been created. We are currently in the process of characterizing these mutations.

  9. Molecular Signatures of Microbial Metabolism in an Actively Growing, Silicified, Microbial Structure from Yellowstone National Park

    NASA Astrophysics Data System (ADS)

    Ferreira, M.; Creveling, J.; Hilburn, I.; Karlsson, E.; Pepe-Ranney, C.; Spear, J.; Dawson, S.; Geobio2008, I.

    2008-12-01

    Silicified structures that exhibit a putative biologic component in their formation permeate the rock record as stromatolites. We have studied a silicified microbial structure from a hot spring in Yellowstone National Park using phenotypic, phylogenetic, and metagenomic analyses to determine microbial carbon metabolic pathways and the phylogenetic affiliations of microbes present in this unique structure. In this multi-faceted approach, dominant physiologies, specifically with regards to anaerobic and aerobic metabolisms, were inferred from 16S rRNA gene sequences and 454 sequencing data from bulk DNA samples of the structure. Carbon utilization as indicated by ECO Biolog plates showed abundant heterotrophy and heterotrophic diversity throughout the microbial structure. Microbes within the structure are able to utilize all tested sources of carbohydrates, lipids/fatty acids, and protein/amino acids as carbon sources. ECO plate testing of the hot spring water yielded considerable less carbohydrate consumption (only 4 out of 13 tested carbohydrates) and similar lipids/fatty acids and protein/amino acids consumption (2 out of 3 and 5 out of 5 tested sources respectively). Full length 16S rRNA gene sequences and metagenomic 454 pyrosequencing of community DNA showed limited diversity among primary producers. From the 16S data, the majority of the autotrophs are inferred to utilize the Calvin cycle for CO2 fixation, followed by 3-hydroxypropionate/4- hydroxybutyrate CO2 fixation. However, an analysis of the metagenomic data compared to the KEGG database does not show genes directly involved with Calvin cycle carbon fixation. Further BLAST searches of our data failed to find significant matches within our 6514 metagenomic sequences to known RuBisCo sequences taken from the NCBI database. This is likely due to a far under-sampled dataset of metagenomic sequences, and the low number (958) that had matches to the KEGG pathways database. Anaerobic versus aerobic physiology

  10. Characterization of autotrophic and heterotrophic soluble microbial product (SMP) fractions from activated sludge.

    PubMed

    Xie, Wen-Ming; Ni, Bing-Jie; Seviour, Thomas; Sheng, Guo-Ping; Yu, Han-Qing

    2012-12-01

    Soluble microbial products (SMP) generated by microbial populations can adversely affect the efficiency of biological wastewater treatment systems and secondary effluent quality. In this work, both experimental and modeling approaches were used to investigate the formation of SMP by both heterotrophic and autotrophic bacteria. Strategies to control and reduce SMP in activated sludge systems were thus evaluated. SMP produced by heterotrophs were found to account for more than 92% of total SMP. The SMP produced by autotrophs contributed to less than 8% of the total SMP, with 5% attributable to the ammonia-oxidizing bacteria (AOB) and 3% to the nitrite-oxidizing bacteria (NOB). When external organic substrate was present, the utilization-associated products (UAP) were the main component of SMP. When external organic substrate was completely consumed, biomass-associated products (BAP) from the hydrolysis of extracellular polymeric substances (EPS) dominated the SMP. The model developed in this study described the fractions and dynamics of UAP and BAP produced by heterotrophs, AOB and NOB. Solids retention time of the reactor had a significant effect on SMP production, while the effect of the hydraulic retention time was only minor. Decreasing the solids retention time from 15 to 0.5 d reduced SMP production in the reactor by 62%.

  11. Microbial Environment Affects Innate Immunity in Two Closely Related Earthworm Species Eisenia andrei and Eisenia fetida

    PubMed Central

    Dvořák, Jiří; Mančíková, Veronika; Pižl, Václav; Elhottová, Dana; Šilerová, Marcela; Roubalová, Radka; Škanta, František; Procházková, Petra; Bilej, Martin

    2013-01-01

    Survival of earthworms in the environment depends on their ability to recognize and eliminate potential pathogens. This work is aimed to compare the innate defense mechanisms of two closely related earthworm species, Eisenia andrei and Eisenia fetida, that inhabit substantially different ecological niches. While E. andrei lives in a compost and manure, E. fetida can be found in the litter layer in forests. Therefore, the influence of environment-specific microbiota on the immune response of both species was followed. Firstly, a reliable method to discern between E. andrei and E. fetida based on species-specific primers for cytochrome c oxidase I (COI) and stringent PCR conditions was developed. Secondly, to analyze the immunological profile in both earthworm species, the activity and expression of lysozyme, pattern recognition protein CCF, and antimicrobial proteins with hemolytic function, fetidin and lysenins, have been assessed. Whereas, CCF and lysozyme showed only slight differences in the expression and activity, fetidin/lysenins expression as well as the hemolytic activity was considerably higher in E. andrei as compared to E. fetida. The expression of fetidin/lysenins in E. fetida was not affected upon the challenge with compost microbiota, suggesting more substantial changes in the regulation of the gene expression. Genomic DNA analyses revealed significantly higher level of fetidin/lysenins (determined using universal primer pairs) in E. andrei compared to E. fetida. It can be hypothesized that E. andrei colonizing compost as a new habitat acquired an evolutionary selection advantage resulting in a higher expression of antimicrobial proteins. PMID:24223917

  12. Microbial environment affects innate immunity in two closely related earthworm species Eisenia andrei and Eisenia fetida.

    PubMed

    Dvořák, Jiří; Mančíková, Veronika; Pižl, Václav; Elhottová, Dana; Silerová, Marcela; Roubalová, Radka; Skanta, František; Procházková, Petra; Bilej, Martin

    2013-01-01

    Survival of earthworms in the environment depends on their ability to recognize and eliminate potential pathogens. This work is aimed to compare the innate defense mechanisms of two closely related earthworm species, Eisenia andrei and Eisenia fetida, that inhabit substantially different ecological niches. While E. andrei lives in a compost and manure, E. fetida can be found in the litter layer in forests. Therefore, the influence of environment-specific microbiota on the immune response of both species was followed. Firstly, a reliable method to discern between E. andrei and E. fetida based on species-specific primers for cytochrome c oxidase I (COI) and stringent PCR conditions was developed. Secondly, to analyze the immunological profile in both earthworm species, the activity and expression of lysozyme, pattern recognition protein CCF, and antimicrobial proteins with hemolytic function, fetidin and lysenins, have been assessed. Whereas, CCF and lysozyme showed only slight differences in the expression and activity, fetidin/lysenins expression as well as the hemolytic activity was considerably higher in E. andrei as compared to E. fetida. The expression of fetidin/lysenins in E. fetida was not affected upon the challenge with compost microbiota, suggesting more substantial changes in the regulation of the gene expression. Genomic DNA analyses revealed significantly higher level of fetidin/lysenins (determined using universal primer pairs) in E. andrei compared to E. fetida. It can be hypothesized that E. andrei colonizing compost as a new habitat acquired an evolutionary selection advantage resulting in a higher expression of antimicrobial proteins.

  13. Effects of fertilization and clipping on carbon, nitrogen storage, and soil microbial activity in a natural grassland in southern China.

    PubMed

    Du, Zhimin; Xie, Yan; Hu, Liqun; Hu, Longxing; Xu, Shendong; Li, Daoxin; Wang, Gongfang; Fu, Jinmin

    2014-01-01

    Grassland managements can affect carbon (C) and nitrogen (N) storage in grassland ecosystems with consequent feedbacks to climate change. We investigated the impacts of compound fertilization and clipping on grass biomass, plant and soil (0-20 cm depth) C, N storage, plant and soil C: N ratios, soil microbial activity and diversity, and C, N sequestration rates in grassland in situ in the National Dalaoling Forest Park of China beginning July, 2011. In July, 2012, the fertilization increased total biomass by 30.1%, plant C by 34.5%, plant N by 79.8%, soil C by 18.8% and soil N by 23.8% compared with the control, respectively. Whereas the clipping decreased total biomass, plant C and N, soil C and N by 24.9%, 30.3%, 39.3%, 18.5%, and 19.4%, respectively, when compared to the control. The plant C: N ratio was lower for the fertilization than for the control and the clipping treatments. The soil microbial activity and diversity indices were higher for the fertilization than for the control. The clipping generally exhibited a lower level of soil microbial activity and diversity compared to the control. The principal component analysis indicated that the soil microbial communities of the control, fertilization and clipping treatments formed three distinct groups. The plant C and N sequestration rates of the fertilization were significantly higher than the clipping treatment. Our results suggest that fertilization is an efficient management practice in improving the C and N storage of the grassland ecosystem via increasing the grass biomass and soil microbial activity and diversity.

  14. Impacts of Human Activity on the Microbial Communities of Devon Island, Canadian High Arctic

    NASA Astrophysics Data System (ADS)

    Bywaters, K. B.; Burton, A. S.; Wallace, S. L.; Glass, B. J.

    2016-09-01

    The impacts of human activities on microbial communities in arctic environments are poorly understood. This project compares the distribution of microbes at the HMP Mars analog site prior to and after human settlement.

  15. Dual active ionic liquids and organic salts for inhibition of microbially influenced corrosion.

    PubMed

    Seter, Marianne; Thomson, Melanie J; Stoimenovski, Jelena; MacFarlane, Douglas R; Forsyth, Maria

    2012-06-18

    We describe a series of novel compounds designed to combat the bacterial growth that leads to microbially induced corrosion on steel in the marine environment. A synergistic effect of the ionic components in these dual active organic salts is demonstrated.

  16. Microbial enzyme activities of peatland soils in south central Alaska lowlands

    EPA Science Inventory

    Microbial enzyme activities related to carbon and nutrient acquisition were measured on Alaskan peatland soils as indicators of nutrient limitation and biochemical sustainability. Peat decomposition is mediated by microorganisms and enzymes that in turn are limited by various ph...

  17. The influence of soil heavy metals pollution on soil microbial biomass, enzyme activity, and community composition near a copper smelter.

    PubMed

    Wang, YuanPeng; Shi, JiYan; Wang, Hui; Lin, Qi; Chen, XinCai; Chen, YingXu

    2007-05-01

    The environmental risk of heavy metal pollution is pronounced in soils adjacent to large industrial complexes. It is important to investigate the functioning of soil microorganisms in ecosystems exposed to long-term contamination by heavy metals. We studied the potential effects of heavy metals on microbial biomass, activity, and community composition in soil near a copper smelter in China. The results showed that microbial biomass C was negatively affected by the elevated metal levels and was closely correlated with heavy metal stress. Enzyme activity was greatly depressed by conditions in the heavy metal-contaminated sites. Good correlation was observed between enzyme activity and the distance from the smelter. Elevated metal loadings resulted in changes in the activity of the soil microbe, as indicated by changes in their metabolic profiles from correlation analysis. Significant decrease of soil phosphatase activities was found in the soils 200 m away from the smelter. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis demonstrated that heavy metals pollution had a significant impact on bacterial and actinomycetic community structure. There were negative correlations between soil microbial biomass, phosphatase activity, and NH(4)NO(3) extractable heavy metals. The soil microorganism activity and community composition could be predicted significantly using the availability of Cu and Zn. By combining different monitoring approaches from different viewpoints, the set of methods applied in this study were sensitive to site differences and contributed to a better understanding of heavy metals effects on the structure, size and activity of microbial communities in soils. The data presented demonstrate the role of heavy metals pollution in understanding the heavy metal toxicity to soil microorganism near a copper smelter in China.

  18. Main factors controlling microbial community structure, growth and activity after reclamation of a tailing pond with aided phytostabilization

    NASA Astrophysics Data System (ADS)

    Zornoza, Raúl; Acosta, José A.; Martínez-Martínez, Silvia; Faz, Ángel; Bååth, Erland

    2015-04-01

    Reclamation on bare tailing ponds has the potential to represent soil genesis in Technosols favoring the understanding of the changes of microbial communities and function. In this study we used phytostabilization aided with calcium carbonate and pig slurry/manure to reclaim an acidic bare tailing pond with the aim of investigating the effect of amending and different species on microbial community structure and function. We sampled after two years of amending and planting: unamended tailing soil (UTS), non-rhizospheric amended tailing soil (ATS), rhizospheric soil from four species, and non-rhizospheric native forest soil (NS), which acted as reference. The application of amendments increased pH up to neutrality, organic carbon (Corg), C/N and aggregate stability, while decreased salinity and heavy metals availability. No effect of rhizosphere was observed on physicochemical properties, metals immobilization and microbial community structure and function. To account for confounding effects due to soil organic matter, microbial properties were expressed per Corg. The high increments in pH and Corg have been the main factors driving changes in microbial community structure and function. Bacterial biomass was higher in UTS, without significant differences among the rest of soils. Fungal biomass followed the trend UTS < ATS = rhizospheric soils < NS. Bacterial growth increased and fungal growth decreased with increasing pH, despite the high availability of metals at low pH. Enzyme activities were lower in UTS, being β-glucosidase and β-glucosaminidase activities highly correlated with bacterial growth. Microbial activities were not correlated with the exchangeable fraction of heavy metals, indicating that microbial function is not strongly affected by these metals, likely due to the efficiency of the reclamation procedure to reduce metals toxicity. Changes in microbial community composition were largely explained by changes in pH, heavy metals availability and Corg

  19. Effect of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil.

    PubMed

    Kim, Seong-Hye; Han, Hyo-Yeol; Lee, You-Jin; Kim, Chul Woong; Yang, Ji-Won

    2010-07-15

    Electrokinetic remediation has been successfully used to remove organic contaminants and heavy metals within soil. The electrokinetic process changes basic soil properties, but little is known about the impact of this remediation technology on indigenous soil microbial activities. This study reports on the effects of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil. The main removal mechanism of diesel was electroosmosis and most of the bacteria were transported by electroosmosis. After 25 days of electrokinetic remediation (0.63 mA cm(-2)), soil pH developed from pH 3.5 near the anode to pH 10.8 near the cathode. The soil pH change by electrokinetics reduced microbial cell number and microbial diversity. Especially the number of culturable bacteria decreased significantly and only Bacillus and strains in Bacillales were found as culturable bacteria. The use of EDTA as an electrolyte seemed to have detrimental effects on the soil microbial activity, particularly in the soil near the cathode. On the other hand, the soil dehydrogenase activity was enhanced close to the anode and the analysis of microbial community structure showed the increase of several microbial populations after electrokinetics. It is thought that the main causes of changes in microbial activities were soil pH and direct electric current. The results described here suggest that the application of electrokinetics can be a promising soil remediation technology if soil parameters, electric current, and electrolyte are suitably controlled based on the understanding of interaction between electrokinetics, contaminants, and indigenous microbial community.

  20. Quantitative assessment of in situ microbial communities affecting nuclear waste disposal

    SciTech Connect

    White, D.C. |

    1996-05-01

    Microbes in the environments surrounding nuclear waste depositories pose several questions regarding the protection of the surrounding communities. microbes can facilitate microbially influenced corrosion (MIC), mobilize and facilitate the transport of nuclides as well as produce gaseous emissions which can compromise containment. We have developed an analysis of the extant microbiota that is independent of quantitative recovery and subsequent growth, based on signature biomarkers analysis (SBA).

  1. Promoting Uranium Immobilization by the Activities of Microbial Phosphatases

    SciTech Connect

    Robert J. Martinez; Melanie J. Beazley; Samuel M. Webb; Martial Taillefert; and Patricia A. Sobecky

    2007-04-19

    The overall objective of this project is to examine the activity of nonspecific phosphohydrolases present in naturally occurring subsurface microorganisms for the purpose of promoting the immobilization of radionuclides through the production of uranium [U(VI)] phosphate precipitates. Specifically, we hypothesize that the precipitation of U(VI) phosphate minerals may be promoted through the microbial release and/or accumulation of PO4 3- as a means to detoxify radionuclides and heavy metals. An experimental approach was designed to determine the extent of phosphatase activity in bacteria previously isolated from contaminated subsurface soils collected at the ERSP Field Research Center (FRC) in Oak Ridge, TN. Screening of 135 metal resistant isolates for phosphatase activity indicated the majority (75 of 135) exhibited a phosphatase-positive phenotype. During this phase of the project, a PCR based approach has also been designed to assay FRC isolates for the presence of one or more classes of the characterized non-specific acid phophastase (NSAP) genes likely to be involved in promoting U(VI) precipitation. Testing of a subset of Pb resistant (Pbr) Arthrobacter, Bacillus and Rahnella strains indicated 4 of the 9 Pbr isolates exhibited phosphatase phenotypes suggestive of the ability to bioprecipitate U(VI). Two FRC strains, a Rahnella sp. strain Y9602 and a Bacillus sp. strain Y9-2, were further characterized. The Rahnella sp. exhibited enhanced phosphatase activity relative to the Bacillus sp. Whole-cell enzyme assays identified a pH optimum of 5.5, and inorganic phosphate accumulated in pH 5.5 synthetic groundwater (designed to mimic FRC conditions) incubations of both strains in the presence of a model organophosphorus substrate provided as the sole C and P source. Kinetic experiments showed that these two organisms can grow in the presence of 200 μM dissolved uranium and that Rahnella is much more efficient in precipitating U(VI) than Bacillus sp. The

  2. Belowground carbon allocation by trees drives seasonal patterns of extracellular enzyme activities by altering microbial community composition in a beech forest soil.

    PubMed

    Kaiser, Christina; Koranda, Marianne; Kitzler, Barbara; Fuchslueger, Lucia; Schnecker, Jörg; Schweiger, Peter; Rasche, Frank; Zechmeister-Boltenstern, Sophie; Sessitsch, Angela; Richter, Andreas

    2010-08-01

    *Plant seasonal cycles alter carbon (C) and nitrogen (N) availability for soil microbes, which may affect microbial community composition and thus feed back on microbial decomposition of soil organic material and plant N availability. The temporal dynamics of these plant-soil interactions are, however, unclear. *Here, we experimentally manipulated the C and N availability in a beech forest through N fertilization or tree girdling and conducted a detailed analysis of the seasonal pattern of microbial community composition and decomposition processes over 2 yr. *We found a strong relationship between microbial community composition and enzyme activities over the seasonal course. Phenoloxidase and peroxidase activities were highest during late summer, whereas cellulase and protease peaked in late autumn. Girdling, and thus loss of mycorrhiza, resulted in an increase in soil organic matter-degrading enzymes and a decrease in cellulase and protease activity. *Temporal changes in enzyme activities suggest a switch of the main substrate for decomposition between summer (soil organic matter) and autumn (plant litter). Our results indicate that ectomycorrhizal fungi are possibly involved in autumn cellulase and protease activity. Our study shows that, through belowground C allocation, trees significantly alter soil microbial communities, which may affect seasonal patterns of decomposition processes.

  3. Biologically active extracts with kidney affections applications

    NASA Astrophysics Data System (ADS)

    Pascu (Neagu), Mihaela; Pascu, Daniela-Elena; Cozea, Andreea; Bunaciu, Andrei A.; Miron, Alexandra Raluca; Nechifor, Cristina Aurelia

    2015-12-01

    This paper is aimed to select plant materials rich in bioflavonoid compounds, made from herbs known for their application performances in the prevention and therapy of renal diseases, namely kidney stones and urinary infections (renal lithiasis, nephritis, urethritis, cystitis, etc.). This paper presents a comparative study of the medicinal plant extracts composition belonging to Ericaceae-Cranberry (fruit and leaves) - Vaccinium vitis-idaea L. and Bilberry (fruit) - Vaccinium myrtillus L. Concentrated extracts obtained from medicinal plants used in this work were analyzed from structural, morphological and compositional points of view using different techniques: chromatographic methods (HPLC), scanning electronic microscopy, infrared, and UV spectrophotometry, also by using kinetic model. Liquid chromatography was able to identify the specific compounds of the Ericaceae family, present in all three extracts, arbutosid, as well as specific components of each species, mostly from the class of polyphenols. The identification and quantitative determination of the active ingredients from these extracts can give information related to their therapeutic effects.

  4. Production of microbial glycolipid biosurfactants and their antimicrobial activity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microbial glycolipids produced by bacteria or yeast as secondary metabolites, such as sophorolipids (SLs), rhamnolipids (RLs) and mannosylerythritol lipids (MELs) are “green” biosurfactants desirable in a bioeconomy. High cost of production is a major hurdle toward widespread commercial use of bios...

  5. Evaluation of some biological tests as parameters for microbial activities in soils. II. Field investigations.

    PubMed

    Abd-El-Malek, Y; Monib, M; Rizk, S G; Shehata, S M

    1976-01-01

    Investigations were designed to study the effect of certain factors on the microbial activities in soil. The parameters, used as an index of the microbial activities, were total bacterial counts, dehydrogenase activity, oxidation of organic carbon, and CO2 evolved/7 days. Bahteem Farm clay soil was examined for determining the effects of depth, type of fertilization, and crop rotation on the microbial activities. It appears that the microbial activities, as indicated by the tested parameters, were more pronounced in the surface 15 cm-layer than in the subsurface layer (15-30 cm). Results of all the parameters tested showed markedly higher increases with farmyard manure than with nitrogenous fertilizer and in the control, without significant differences between the latter two. Moreover, the time of sampling had no effect on the results obtained for all parameters. Different types of rotations did not exert significant variation in total bacterial counts, though more than one crop per year increased the organic carbon content of soil and mostly the dehydrogenase activity, whereas the evolution of CO2 tended to decrease. At Gabal el-Asfar Farm, the effect of irrigation with sewage effluent, for long periods, on the microbial activities of sandy soil was investigated. Sewage water stimulated the total bacteria, raised the dehydrogenase activity, the organic carbon, and the production of CO2. In North El Tahreer and Mariut Sectors, the effect of both the type and age of cultivation on the microbial activities in the calcareous soils were examined. Cultivation raised the figures of all the tested parameters progressively with time of cultivation. It was also noticed that crops exerted more beneficial effects on microbial activities than orchards, and the dehydrogenase test was the most reliable parameter to reveal this fact.

  6. Microbial dynamics and enzyme activities in tropical Andosols depending on land use and nutrient inputs

    NASA Astrophysics Data System (ADS)

    Mganga, Kevin; Razavi, Bahar; Kuzyakov, Yakov

    2015-04-01

    Microbial decomposition of soil organic matter is mediated by enzymes and is a key source of terrestrial CO2 emissions. Microbial and enzyme activities are necessary to understand soil biochemical functioning and identify changes in soil quality. However, little is known about land use and nutrients availability effects on enzyme activities and microbial processes, especially in tropical soils of Africa. This study was conducted to examine how microbial and enzyme activities differ between different land uses and nutrient availability. As Andosols of Mt. Kilimanjaro are limited by nutrient concentrations, we hypothesize that N and P additions will stimulate enzyme activity. N and P were added to soil samples (0-20 cm) representing common land use types in East Africa: (1) savannah, (2) maize fields, (3) lower montane forest, (4) coffee plantation, (5) grasslands and (6) traditional Chagga homegardens. Total CO2 efflux from soil, microbial biomass and activities of β-glucosidase, cellobiohydrolase, chitinase and phosphatase involved in C, N and P cycling, respectively was monitored for 60 days. Total CO2 production, microbial biomass and enzyme activities varied in the order forest soils > grassland soils > arable soils. Increased β-glucosidase and cellobiohydrolase activities after N addition of grassland soils suggest that microorganisms increased N uptake and utilization to produce C-acquiring enzymes. Low N concentration in all soils inhibited chitinase activity. Depending on land use, N and P addition had an inhibitory or neutral effect on phosphatase activity. We attribute this to the high P retention of Andosols and low impact of N and P on the labile P fractions. Enhanced CO2 production after P addition suggests that increased P availability could stimulate soil organic matter biodegradation in Andosols. In conclusion, land use and nutrients influenced soil enzyme activities and microbial dynamics and demonstrated the decline in soil quality after landuse

  7. Effects of plastic film residues on occurrence of phthalates and microbial activity in soils.

    PubMed

    Wang, Jun; Lv, Shenghong; Zhang, Manyun; Chen, Gangcai; Zhu, Tongbin; Zhang, Shen; Teng, Ying; Christie, Peter; Luo, Yongming

    2016-05-01

    Plastic film mulching has played an important role in Chinese agriculture, especially in vegetable production, but large amounts of film residues can accumulate in the soil. The present study investigated the effects of plastic film residues on the occurrence of soil PAEs and microbial activities using a batch pot experiment. PAE concentrations increased with increasing plastic film residues but the soil microbial carbon and nitrogen, enzyme activities and microbial diversity decreased significantly. At the end of the experiment the PAE concentrations were 0-2.02 mg kg(-1) in the different treatments. Soil microbial C and N, enzyme activities, AWCD value, and Shannon-Weaver and Simpson indices declined by about 28.9-76.2%, 14.9-59.0%, 4.9-22.7%, 23.0-42.0% and 1.8-18.7%, respectively. Soil microbial activity was positively correlated with soil PAE concentration, and soil PAE concentrations were impacted by plastic color and residue volume. Correlations among, and molecular mechanisms of, plastic film residues, PAE occurrence and microbial activity require further study.

  8. Soil microbial biomass nitrogen and Beta-Glucosaminidase activity response to compaction, poultry litter application and cropping in a claypan soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Compaction-induced changes in soil physical properties may significantly affect soil microbial activity, especially nitrogen-cycling processes, in many agroecosystems. The objective of this study was to determine the effect of soil compaction on soil microbiological properties related to N in a clay...

  9. Biocidal and inhibitory activity screening of de novo synthesized surfactants against two eukaryotic and two prokaryotic microbial species.

    PubMed

    Tiecco, Matteo; Cardinali, Gianluigi; Roscini, Luca; Germani, Raimondo; Corte, Laura

    2013-11-01

    Thirty-six quaternary ammonium salts, of which 28 structurally different non-commercially available surfactants, were tested to screen their biocidal and inhibitory antimicrobial activity. Their activity was compared to commercially available amphiphiles as well as to non-amphiphilic quaternary ammonium salts. As target of these compounds four microbial species were employed of which two (Saccharomyces cerevisiae and Candida albicans) were important yeast in the food and clinical environment and the other two (Escherichia coli and Listeria innocua) represented the Gram negative and positive bacteria, respectively. The surfactants showed the ability to kill the microbial cells in water solution and to variably hamper their growth onto agar medium. The non-amphiphilic compounds (which represent analogues of some surfactants used in this study, since they have the same head group but no hydrophobic portion) had little effect in solution and no effect against the microbial growth on plate. Amphoteric and non-amphoteric zwitterionic surfactants showed reduced biocidal activity. The most active antimicrobial agent was N-tetradecyltropinium bromide (23S) surfactant. The presence of cells did not significantly affect the ability to form micelles, as demonstrated by comparative conductometric measurements.

  10. Dietary inclusion of feathers affects intestinal microbiota and microbial metabolites in growing Leghorn-type chickens.

    PubMed

    Meyer, B; Bessei, W; Bessei, A W; Vahjen, W; Zentek, J; Harlander-Matauschek, A

    2012-07-01

    Feather pecking in laying hens is a serious behavioral problem that is often associated with feather eating. The intake of feathers may influence the gut microbiota and its metabolism. The aim of this study was to determine the effect of 2 different diets, with or without 5% ground feathers, on the gut microbiota and the resulting microbial fermentation products and to identify keratin-degrading bacteria in chicken digesta. One-day-old Lohmann-Selected Leghorn chicks were divided into 3 feeding groups: group A (control), B (5% ground feathers in the diet), and C, in which the control diet was fed until wk 12 and then switched to the 5% feather diet to study the effect of time of first feather ingestion. The gut microbiota was analyzed by cultivation and denaturing gradient gel electrophoresis of ileum and cecum digesta. Short-chain fatty acids, ammonia, and lactate concentrations were measured as microbial metabolites. The concentration of keratinolytic bacteria increased after feather ingestion in the ileum (P < 0.001) and cecum (P = 0.033). Bacterial species that hydrolyzed keratin were identified as Enterococcus faecium, Lactobacillus crispatus, Lactobacillus reuteri-like species (97% sequence homology), and Lactobacillus salivarius-like species (97% sequence homology). Molecular analysis of cecal DNA extracts showed that the feather diet lowered the bacterial diversity indicated by a reduced richness (P < 0.001) and shannon (P = 0.012) index. The pattern of microbial metabolites indicated some changes, especially in the cecum. This study showed that feather intake induced an adaptation of the intestinal microbiota in chickens. It remains unclear to what extent the changed metabolism of the microbiota reflects the feather intake and could have an effect on the behavior of the hens.

  11. Pyrosequencing reveals highly diverse microbial communities in microbial electrolysis cells involved in enhanced H2 production from waste activated sludge.

    PubMed

    Lu, Lu; Xing, Defeng; Ren, Nanqi

    2012-05-01

    Renewable H(2) production from a plentiful biomass, waste activated sludge (WAS), can be achieved by fermentation, but the yields are low. The use of a microbial electrolysis cell (MEC) can increase the H(2) production yields to several times that of fermentation. We have proved that the enhancement of H(2) production was due to the ability of MECs to use a wider range of organic matter in WAS than in fermentation. To support this result strongly, we here investigated the microbial community structures of WAS and anode biofilms in WAS-fed MECs. A pyrosequencing analysis based on the bacterial 16S rRNA gene showed that dominant populations in MECs were more diverse than those in WAS (inoculum and substrate) after enrichment, and there was a clear distinction between MECs and WAS in microbial community structure. Diverse acid-producing bacteria and exoelectrogens (predominance of Geobacter) were detected in MECs but they were only rarely found in WAS. It has been reported that these acid-producing bacteria can ferment various sugars and amines with acetate, propionate, and butyrate as their major by-products. This was consistent with our chemical analyses. Detected exoelectrogens are known to use these organic acids (mainly acetate) and certain sugars to directly produce current for H(2) generation at the cathodes in the MECs. Using quantitative real-time PCR, we demonstrated that a consistent feed of alkaline-pretreated WAS containing large amounts of acetate led to a predominance of acetoclastic methanogens, while hydrogenotrophic methanogens were abundant in MECs fed both raw and alkaline-pretreated WAS. Syntrophic interactions between phylogenetically diverse microbial populations in anodophilic biofilms were found to drive the efficient cascade utilization of organic matter in WAS.

  12. Antioxidant, Immunomodulating, and Microbial-Modulating Activities of the Sustainable and Ecofriendly Spirulina.

    PubMed

    Finamore, Alberto; Palmery, Maura; Bensehaila, Sarra; Peluso, Ilaria

    2017-01-01

    The highly nutritional and ecofriendly Spirulina (Arthrospira platensis) has hypolipidemic, hypoglycemic, and antihypertensive properties. Spirulina contains functional compounds, such as phenolics, phycocyanins, and polysaccharides, with antioxidant, anti-inflammatory, and immunostimulating effects. Studies conducted on Spirulina suggest that it is safe in healthy subjects, but attitude to eating probably affects the acceptability of Spirulina containing foods. Although the antioxidant effect of Spirulina is confirmed by the intervention studies, the concerted modulation of antioxidant and inflammatory responses, suggested by in vitro and animal studies, requires more confirmation in humans. Spirulina supplements seem to affect more effectively the innate immunity, promoting the activity of natural killer cells. The effects on cytokines and on lymphocytes' proliferation depend on age, gender, and body weight differences. In this context, ageing and obesity are both associated with chronic low grade inflammation, immune impairment, and intestinal dysbiosis. Microbial-modulating activities have been reported in vitro, suggesting that the association of Spirulina and probiotics could represent a new strategy to improve the growth of beneficial intestinal microbiota. Although Spirulina might represent a functional food with potential beneficial effects on human health, the human interventions used only supplements. Therefore, the effect of food containing Spirulina should be evaluated in the future.

  13. Antioxidant, Immunomodulating, and Microbial-Modulating Activities of the Sustainable and Ecofriendly Spirulina

    PubMed Central

    Finamore, Alberto; Bensehaila, Sarra

    2017-01-01

    The highly nutritional and ecofriendly Spirulina (Arthrospira platensis) has hypolipidemic, hypoglycemic, and antihypertensive properties. Spirulina contains functional compounds, such as phenolics, phycocyanins, and polysaccharides, with antioxidant, anti-inflammatory, and immunostimulating effects. Studies conducted on Spirulina suggest that it is safe in healthy subjects, but attitude to eating probably affects the acceptability of Spirulina containing foods. Although the antioxidant effect of Spirulina is confirmed by the intervention studies, the concerted modulation of antioxidant and inflammatory responses, suggested by in vitro and animal studies, requires more confirmation in humans. Spirulina supplements seem to affect more effectively the innate immunity, promoting the activity of natural killer cells. The effects on cytokines and on lymphocytes' proliferation depend on age, gender, and body weight differences. In this context, ageing and obesity are both associated with chronic low grade inflammation, immune impairment, and intestinal dysbiosis. Microbial-modulating activities have been reported in vitro, suggesting that the association of Spirulina and probiotics could represent a new strategy to improve the growth of beneficial intestinal microbiota. Although Spirulina might represent a functional food with potential beneficial effects on human health, the human interventions used only supplements. Therefore, the effect of food containing Spirulina should be evaluated in the future. PMID:28182098

  14. Physical and Chemical Correlates of Microbial Activity and Biomass in Composting Municipal Sewage Sludge

    PubMed Central

    McKinley, Vicky L.; Vestal, J. Robie

    1985-01-01

    Various physical and chemical parameters were monitored to evaluate their influence on the microbial communities present in composting municipal sewage sludge. Temperature, moisture content, depth, pH, protein content, total nitrogen, total carbon, lipid phosphate biomass, and the rates of microbial incorporation of substrates into lipids were measured at several times throughout the 17- to 19-day composting runs. Temperature was found to have the most consistent and dramatic effect on microbial activity and biomass. When temperatures exceeded 55 to 60°C, microbial activity fell dramatically, usually by more than 1 order of magnitude. Microbial activity was generally greatest in samples taken from the 35 to 50°C areas of the composting piles. Changes in the composition of the compost over time included increased pH, increased protein content, and decreased total organic content. The changes in these parameters appeared to reflect the microbial activity and biomass present. The results of this study indicate that the rate of composting may best be optimized by controlling the composting temperatures, provided that the other parameters fall within reasonable limits in the starting material. PMID:16346940

  15. Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities.

    PubMed

    Abraham, Paul E; Giannone, Richard J; Xiong, Weili; Hettich, Robert L

    2014-06-17

    Contemporary microbial ecology studies usually employ one or more "omics" approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other "meta-omic" approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool.

  16. Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities

    SciTech Connect

    Abraham, Paul E; Giannone, Richard J; Xiong, Weili; Hettich, Robert {Bob} L

    2014-01-01

    Contemporary microbial ecology studies usually employ one or more omics approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other meta-omic approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool.

  17. Experimental factors affecting PCR-based estimates of microbial species richness and evenness

    SciTech Connect

    Engelbrektson, Anna; Kunin, Victor; Wrighton, Kelly C.; Zvenigorodsky, Natasha; Chen, Feng; Ochman, Howard; Hugenholtz, Philip

    2009-12-01

    Pyrosequencing of 16S rRNA gene amplicons for microbial community profiling can, for equivalent costs, yield greater than two orders of magnitude more sensitivity than traditional PCR-cloning and Sanger sequencing. With this increased sensitivity and the ability to analyze multiple samples in parallel, it has become possible to evaluate several technical aspects of PCRbased community structure profiling methods. We tested the effect of amplicon length and primer pair on estimates of species richness number of species and evenness relative abundance of species by assessing the potentially tractable microbial community residing in the termite hindgut. Two regions of the 16S rRNA gene were sequenced from one of two common priming sites, spanning the V1-V2 or V8 regions, using amplicons ranging n length from 352 to 1443 bp. Our results demonstrate that both amplicon length and primer pair markedly influence estimates of richness and evenness. However, estimates of species evenness are consistent among different primer pairs targeting the same region. These results highlight the importance of experimental methodology when comparing diversity estimates across communities.

  18. Experimental factors affecting PCR-based estimates of microbial species richness and evenness.

    PubMed

    Engelbrektson, Anna; Kunin, Victor; Wrighton, Kelly C; Zvenigorodsky, Natasha; Chen, Feng; Ochman, Howard; Hugenholtz, Philip

    2010-05-01

    Pyrosequencing of 16S rRNA gene amplicons for microbial community profiling can, for equivalent costs, yield more than two orders of magnitude more sensitivity than traditional PCR cloning and Sanger sequencing. With this increased sensitivity and the ability to analyze multiple samples in parallel, it has become possible to evaluate several technical aspects of PCR-based community structure profiling methods. We tested the effect of amplicon length and primer pair on estimates of species richness (number of species) and evenness (relative abundance of species) by assessing the potentially tractable microbial community residing in the termite hindgut. Two regions of the 16S rRNA gene were sequenced from one of two common priming sites, spanning the V1-V2 or V8 regions, using amplicons ranging in length from 352 to 1443 bp. Our results show that both amplicon length and primer pair markedly influence estimates of richness and evenness. However, estimates of species evenness are consistent among different primer pairs targeting the same region. These results highlight the importance of experimental methodology when comparing diversity estimates across communities.

  19. Soil Enzyme Activities, Microbial Communities and Carbon and Nitrogen Availability in Organic Agroecosystems Across an Intensively-Managed Agricultural Landscape

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Variability in the activity and composition of soil microbial communities may have important implications for the suite of microbially-derived ecosystem functions upon which agricultural systems rely, particularly organic agriculture. An on-farm approach was used to investigate microbial communitie...

  20. Coarse Woody Debris Increases Microbial Community Functional Diversity but not Enzyme Activities in Reclaimed Oil Sands Soils

    PubMed Central

    Kwak, Jin-Hyeob; Chang, Scott X.; Naeth, M. Anne; Schaaf, Wolfgang

    2015-01-01

    Forest floor mineral soil mix (FMM) and peat mineral soil mix (PMM) are cover soils commonly used for upland reclamation post open-pit oil sands mining in northern Alberta, Canada. Coarse woody debris (CWD) can be used to regulate soil temperature and water content, to increase organic matter content, and to create microsites for the establishment of microorganisms and vegetation in upland reclamation. We studied the effects of CWD on soil microbial community level physiological profile (CLPP) and soil enzyme activities in FMM and PMM in a reclaimed landscape in the oil sands. This experiment was conducted with a 2 (FMM vs PMM) × 2 (near CWD vs away from CWD) factorial design with 6 replications. The study plots were established with Populus tremuloides (trembling aspen) CWD placed on each plot between November 2007 and February 2008. Soil samples were collected within 5 cm from CWD and more than 100 cm away from CWD in July, August and September 2013 and 2014. Microbial biomass was greater (p<0.05) in FMM than in PMM, in July, and August 2013 and July 2014, and greater (p<0.05) near CWD than away from CWD in FMM in July and August samplings. Soil microbial CLPP differed between FMM and PMM (p<0.01) according to a principal component analysis and CWD changed microbial CLPP in FMM (p<0.05) but not in PMM. Coarse woody debris increased microbial community functional diversity (average well color development in Biolog Ecoplates) in both cover soils (p<0.05) in August and September 2014. Carbon degrading soil enzyme activities were greater in FMM than in PMM (p<0.05) regardless of distance from CWD but were not affected by CWD. Greater microbial biomass and enzyme activities in FMM than in PMM will increase organic matter decomposition and nutrient cycling, improving plant growth. Enhanced microbial community functional diversity by CWD application in upland reclamation has implications for accelerating upland reclamation after oil sands mining. PMID:26618605

  1. Biomineral formation as a biosignature for microbial activities Precambrian cherts

    NASA Astrophysics Data System (ADS)

    Rincón Tomás, Blanca; Mühlen, Dominik; Hoppert, Michael; Reitner, Joachim

    2015-04-01

    In recent anoxic sediments manganese(II)carbonate minerals (e.g., rhodochrosite, kutnohorite) derive mainly from the reduction of manganese(IV) compounds by microbial anaerobic respiration. Small particles of rhodochrosite in stromatolite-like features in the Dresser chert Fm (Pilbara supergroup, W-Australia), associated with small flakes of kerogen, account for biogenic formation of the mineral in this early Archaean setting. Contrastingly, the formation of huge manganese-rich (carbonate) deposits requires effective manganese redox cycling, also conducted by various microbial processes, mainly requiring conditions of the early and late Proterozoic (Kirschvink et al., 2000; Nealson and Saffrani 1994). However, putative anaerobic pathways like microbial nitrate-dependent manganese oxidation (Hulth et al., 1999), anoxygenic photosynthesis (Johnson et al., 2013) and oxidation in UV light may facilitate manganese cycling even in a reducing atmosphere. Thus manganese redox cycling might have been possible even before the onset of oxygenic photosynthesis. Hence, there are several ways how manganese carbonates could have been formed biogenically and deposited in Precambrian sediments. Thus, the minerals may be suitable biosignatures for microbial redox processes in many respects. The hyperthermophilic archaeon Pyrobaculum islandicum produces rhodochrosite during growth on hydrogen and organic compounds and may be a putative model organism for the reduction of Mn(IV). References Hulth S, Aller RC, Gilbert F. (1999) Geochim Cosmochim Acta, 63, 49-66. Johnson JE, Webb SM, Thomas K, Ono S, Kirschvink JL, Fischer WW. (2013) Proc Natl Acad Sci USA, 110, 11238-11243. Kirschvink JL, Gaidos EJ, Bertani LE, Beukes NJ, Gutzmer J, Maepa LN, Steinberger LE. (2000) Proc Natl Acad Sci USA, 97, 1400-1405. Nealson KH, Saffarini D. (1994). Annu Rev Microbiol, 48, 311-343.

  2. Multiple microbial activities for volatile organic compounds reduction by biofiltration.

    PubMed

    Civilini, Marcello

    2006-07-01

    In the northeast of Italy, high volatile organic carbon (VOC) emissions originate from small-medium companies producing furniture. In these conditions it is difficult to propose a single, efficient, and economic system to reduce pollution. Among the various choices, the biofiltration method could be a good solution, because microbial populations possess multiple VOC degradation potentials used to oxidize these compounds to CO2. Starting from the air emissions of a typical industrial wood-painting plant, a series of experiments studied in vitro microbial degradation of each individual VOC. Isolated strains were then added to a laboratory-scale biofiltration apparatus filled with an organic matrix, and the different VOC behavior demonstrated the potential of single and/or synergic microbial removal actions. When a single substrate was fed, the removal efficiency of a Pseudomonas aeruginosa inoculated reactor was 1.1, 1.17, and 0.33 g m(-3) hr(-1), respectively, for xylene, toluene, and ethoxy propyl acetate. A VOC mixture composed of butyl acetate, ethyl acetate, diacetin alcohol, ethoxy propanol acetate, methyl ethyl ketone, methyl isobutyl ketone, toluene, and xylene was then fed into a 2-m(3) reactor treating 100 m3 hr(-1) of contaminated air. The reactor was filled with the same mixture of organic matrix, enriched with all of the isolated strains together. During reactor study, different VOC loading rates were used, and the behavior was evaluated continuously. After a short acclimation period, the removal efficiency was > 65% at VOC load of 150-200 g m(-3) hr(-1). Quantification of removal efficiencies and VOC speciation confirmed the relationship among removal efficiencies, compound biodegradability, and the dynamic transport of each mixture component within the organic matrix. Samples of the fixed bed were withdrawn at different intervals and the heterogeneous microbial community evaluated for both total and differential compound counts.

  3. Changes in microbial activity of soils during the natural restoration of abandoned lands in central Russia

    NASA Astrophysics Data System (ADS)

    Ovsepyan, Lilit; Mostovaya, Anna; Lopes de Gerenyu, Valentin; Kurganova, Irina

    2015-04-01

    Most changes in land use affect significantly the amount of soil organic carbon (SOC) and alter the nutrition status of soil microbial community. The arable lands withdrawal induced usually the carbon sequestration in soil, the significant shifts in quality of soil organic matter and structure of microbial community. This study was aimed to determine the microbial activity of the abandoned lands in Central Russia due to the process of natural self-restoration. For the study, two representative chronosequences were selected in Central Russia: (1) deciduous forest area, DFA (Moscow region, 54o49N'; 37o34'E; Haplic Luvisols) and (2) forest steppe area, FSA (Belgorod region 50o36'N, 36o01'E Luvic Phaeozems). Each chronosequence included current arable, abandoned lands of different age, and forest plots. The total soil organic carbon (Corg, automatic CHNS analyzer), carbon immobilized in microbial biomass (Cmic, SIR method), and respiratory activity (RA) were determined in the topsoil (0-5, 5-10, 10-20 and 20-30 cm layers) for each plots. Relationships between Corg, Cmic, and RA were determined by liner regression method. Our results showed that the conversion of croplands to the permanent forest induced the progressive accumulation Corg, Cmic and acceleration of RA in the top 10-cm layer for both chronosequences. Carbon stock increased from 24.1 Mg C ha-1 in arable to 45.3 Mg C ha-1 in forest soil (Luvic Phaeozems, Belgorod region). In Haplic Luvisols (Moscow region), SOC build up was 2 time less: from 13.5 Mg C ha-1 in arable to 27.9 Mg C ha-1 in secondary forest. During post-agrogenic evolution, Cmic also increased significantly: from 0.34 to 1.43 g C kg-1 soil in Belgorod region and from 0.34 to 0.64 g C kg-1 soil in Moscow region. RA values varied widely in soils studied: from 0.54-0.63 mg C kg-1h-1 in arable plots to 2.02-3.4 mg C kg-1h-1 in forest ones. The close correlations between Cmic, RA and Corg in the top 0-5cm layer (R2 = 0.81-0.90; P<0.01-0.05) were

  4. Effect of fire on soil microbial composition and activity in a Pinus canariensis forest and over time recovery

    NASA Astrophysics Data System (ADS)

    Ramírez Rojas, Irene; Fernández Lugo, Silvia; Arévalo Sierra, Jose Ramon; Pérez Fernández, María

    2016-04-01

    Wildfires are recurrent disturbances to forest ecosystems of Pinus canariensis, but their effects on soil microbial communities are not well characterized and have not previously been compared directly. Effects of fires on soil biotic properties are strongly dependent on the intensity of the fire, as well as on the type of soil and vegetation cover. This study aims at developing a comprehensive picture of the soil and vegetation dynamics to natural fries in an experiment comprising prescribed burning. The study was conducted at sites with similar soil, climatic, and other properties in a Canary pine forest in the Canary Islands, Spain. Soil microbial communities were assessed following four treatments: control, burnt soil the day after the fire, burnt soil three months after the fire and burnt soil six months after the. Burn treatments were conducted by the stuff from Cabildo de Canarias (Spain) on the 4th and 5th of June 2014. As a general rule, the organic carbon and the microbial biomass tend to decrease in the surface horizon after the fire, but the system responds increasing microbial activities and restoring soil variables in the subsequent months after the burning. Microbial biomass carbon significantly decreased in the burnt soils with their maximum negative effect immediately after the fire and during autumn, six months after the fire. Microbial biomass nitrogen also decreased in the burnt site immediately after the fire but increased in the following months, probably because of microbial assimilation of the increased amounts of available NH4+ and NO3- due to burning. Bacterial community composition was analyzed by metagenomics analyses Illumina showing strong variations amongst horizons and burning treatment both in total numbers and their composition. Changes in plant community were also monitored at the level of germination and plant recovery. Although fire negatively affects germination, seedling survival improves by increased growth rates of seedlings

  5. Magnetic Fe3O4 nanoparticles induced effects on performance and microbial community of activated sludge from a sequencing batch reactor under long-term exposure.

    PubMed

    Ma, Bingrui; Wang, Sen; Li, Zhiwei; Gao, Mengchun; Li, Shanshan; Guo, Liang; She, Zonglian; Zhao, Yangguo; Zheng, Dong; Jin, Chunji; Wang, Xuejiao; Gao, Feng

    2017-02-01

    The performance and microbial community of activated sludge from a sequencing batch reactor (SBR) were investigated under long-term exposure of magnetic Fe3O4 nanoparticles (Fe3O4 NPs). The COD removal showed a slight decrease at 5-60mg/L Fe3O4 NPs compared to 0mg/L Fe3O4 NPs, whereas the NH4(+)-N removal had no obvious variation at 0-60mg/L Fe3O4 NPs. It was found that 10-60mg/L Fe3O4 NPs improved the denitrification process and phosphorus removal of activated sludge. The microbial enzymatic activities of activated sludge could be affected by Fe3O4 NPs, which had similar variation trends to the nitrogen and phosphorus removal rates of activated sludge. The reactive oxygen species (ROS) production and lactate dehydrogenase (LDH) release demonstrated that Fe3O4 NPs led to the toxicity to activated sludge and destroyed the integrity of microbial cytomembrane. High throughput sequencing indicated that Fe3O4 NPs could obviously affect the microbial richness and diversity of activated sludge.

  6. Litter Supply as a Driver of Microbial Activity and Community Structure on Decomposing Leaves: a Test in Experimental Streams

    PubMed Central

    Gerull, Linda; Mutz, Michael

    2013-01-01

    Succession of newly created landscapes induces profound changes in plant litter supplied to streams. Grasses dominate inputs into open-land streams, whereas tree litter is predominant in forested streams. We set out to elucidate whether the activity and structure of microbial communities on decomposing leaves are determined by litter quality (i.e., grass or tree leaves colonized) or whether changes during riparian succession affecting litter standing stocks on the stream bed play an overriding role. We used 15 outdoor experimental streams to simulate changes in litter supplies reflecting five stages of riparian succession: (i) a biofilm stage with no litter, (ii) an open-land stage characterized by grass litter inputs, (iii) a transitional stage with a mix of grass and tree litter, (iv) an early forested stage with tree litter, and (v) an advanced forested stage with 2.5 times the amount of tree litter. Microbial activities on tree (Betula pendula) and grass (Calamagrostis epigejos) litter were unaffected by either the quantity or type of litter supplied to the experimental streams (i.e., litter standing stock) but differed between the two litter types. This was in stark contrast with bacterial and fungal community structure, which markedly differed on grass and tree litter and, to a lesser extent, also among streams receiving different litter inputs. These patterns reveal distinct responses of microbial community structure and activity to the bulk litter available in streams but consistent responses to the litter type colonized. PMID:23770903

  7. Effects of surfactant and Zn (II) at various concentrations on microbial activity and ethylbenzene removal in biotricking filter.

    PubMed

    Wang, Lu; Yang, Chunping; Cheng, Yan; Huang, Jian; He, Huijun; Zeng, Guangming; Lu, Li

    2013-11-01

    The effects of Tween-20, a non-ionic surfactant, and Zn (II) on microbial activity and removal performance for ethylbenzene in a biotrickling filter (BTF) were evaluated. Batch experiments were conducted to evaluate the surfactant and Zn (II) at various concentrations for their toxicity to microorganisms, and results indicated that Tween-20 was beneficial to microbial activity at all the tested concentration, while Zn (II) affected adversely when the concentration overpassed 5.0mgL(-1). Then effects of the two additives on removal efficiency of ethylbenzene were evaluated in a BTF at an empty-bed retention time of 30s and an ethylbenzene concentration of 1100mgm(-3). Results showed that the optimal concentrations of Tween-20 and Zn (II) were about 12 and 1.0mgL(-1), respectively. Compared to the results when neither of the two additives was added, Tween-20 improved ethylbenzene removal efficiency from 67% to 86% at the optimal condition, while on that basis, Zn (II) just increased the removal efficiency from 86% to 90%. The promoting effects of the two additives on recovering microbial activity and removing excessive biomass were also observed in this article.

  8. Litter supply as a driver of microbial activity and community structure on decomposing leaves: a test in experimental streams.

    PubMed

    Frossard, Aline; Gerull, Linda; Mutz, Michael; Gessner, Mark O

    2013-08-01

    Succession of newly created landscapes induces profound changes in plant litter supplied to streams. Grasses dominate inputs into open-land streams, whereas tree litter is predominant in forested streams. We set out to elucidate whether the activity and structure of microbial communities on decomposing leaves are determined by litter quality (i.e., grass or tree leaves colonized) or whether changes during riparian succession affecting litter standing stocks on the stream bed play an overriding role. We used 15 outdoor experimental streams to simulate changes in litter supplies reflecting five stages of riparian succession: (i) a biofilm stage with no litter, (ii) an open-land stage characterized by grass litter inputs, (iii) a transitional stage with a mix of grass and tree litter, (iv) an early forested stage with tree litter, and (v) an advanced forested stage with 2.5 times the amount of tree litter. Microbial activities on tree (Betula pendula) and grass (Calamagrostis epigejos) litter were unaffected by either the quantity or type of litter supplied to the experimental streams (i.e., litter standing stock) but differed between the two litter types. This was in stark contrast with bacterial and fungal community structure, which markedly differed on grass and tree litter and, to a lesser extent, also among streams receiving different litter inputs. These patterns reveal distinct responses of microbial community structure and activity to the bulk litter available in streams but consistent responses to the litter type colonized.

  9. Effect of dry mycelium of Penicillium chrysogenum fertilizer on soil microbial community composition, enzyme activities and snap bean growth.

    PubMed

    Wang, Bing; Liu, Huiling; Cai, Chen; Thabit, Mohamed; Wang, Pu; Li, Guomin; Duan, Ziheng

    2016-10-01

    The dry mycelium fertilizer (DMF) was produced from penicillin fermentation fungi mycelium (PFFM) following an acid-heating pretreatment to degrade the residual penicillin. In this study, it was applied into soil as fertilizer to investigate its effects on soil properties, phytotoxicity, microbial community composition, enzyme activities, and growth of snap bean in greenhouse. As the results show, pH, total nitrogen, total phosphorus, total potassium, and organic matter of soil with DMF treatments were generally higher than CON treatment. In addition, the applied DMF did not cause heavy metal and residual drug pollution of the modified soil. The lowest GI values (<0.3) were recorded at DMF8 (36 kg DMF/plat) on the first days after applying the fertilizer, indicating that severe phytotoxicity appeared in the DMF8-modified soil. Results of microbial population and enzyme activities illustrated that DMF was rapidly decomposed and the decomposition process significantly affected microbial growth and enzyme activities. The DMF-modified soil phytotoxicity decreased at the late fertilization time. DMF1 was considered as the optimum amount of DMF dose based on principal component analysis scores. Plant height and plant yield of snap bean were remarkably enhanced with the optimum DMF dose.

  10. [Effects of bio-crust on soil microbial biomass and enzyme activities in copper mine tailings].

    PubMed

    Chen, Zheng; Yang, Gui-de; Sun, Qing-ye

    2009-09-01

    Bio-crust is the initial stage of natural primary succession in copper mine tailings. With the Yangshanchong and Tongguanshan copper mine tailings in Tongling City of Anhui Province as test objects, this paper studied the soil microbial biomass C and N and the activities of dehydrogenase, catalase, alkaline phosphatase, and urease under different types of bio-crust. The bio-crusts improved the soil microbial biomass and enzyme activities in the upper layer of the tailings markedly. Algal crust had the best effect in improving soil microbial biomass C and N, followed by moss-algal crust, and moss crust. Soil microflora also varied with the type of bio-crust. No'significant difference was observed in the soil enzyme activities under the three types of bio-crust. Soil alkaline phosphatase activity was significantly positively correlated with soil microbial biomass and dehydrogenase and urease activities, but negatively correlated with soil pH. In addition, moss rhizoid could markedly enhance the soil microbial biomass and enzyme activities in moss crust rhizoid.

  11. Microbial biomass and carbon mineralization in agricultural soils as affected by pesticide addition.

    PubMed

    Kumar, Anjani; Nayak, A K; Shukla, Arvind K; Panda, B B; Raja, R; Shahid, Mohammad; Tripathi, Rahul; Mohanty, Sangita; Rath, P C

    2012-04-01

    A laboratory study was conducted with four pesticides, viz. a fungicide (carbendazim), two insecticides (chlorpyrifos and cartap hydrochloride) and an herbicide (pretilachlor) applied to a sandy clay loam soil at a field rate to determine their effect on microbial biomass carbon (MBC) and carbon mineralization (C(min)). The MBC content of soil increased with time up to 30 days in cartap hydrochloride as well as chlorpyrifos treated soil. Thereafter, it decreased and reached close to the initial level by 90th day. However, in carbendazim treated soil, the MBC showed a decreasing trend up to 45 days and subsequently increased up to 90 days. In pretilachlor treated soil, MBC increased through the first 15 days, and thereafter decreased to the initial level. Application of carbendazim, chlorpyrifos and cartap hydrochloride decreased C(min) for the first 30 days and then increased afterwards, while pretilachlor treated soil showed an increasing trend.

  12. Evaluation of normalized energy recovery (NER) in microbial fuel cells affected by reactor dimensions and substrates.

    PubMed

    Xiao, Li; Ge, Zheng; Kelly, Patrick; Zhang, Fei; He, Zhen

    2014-04-01

    The objective of this study is to provide an initial evaluation of normalized energy recovery (NER - a new parameter for presenting energy performance) in microbial fuel cells (MFCs) through investigation of the effects of reactor dimensions and anode substrates. Although the larger-size MFCs generally have lower maximum power densities, their maximum NER is comparable to that of the smaller MFCs at the same anolyte flow rate. The mixed messages obtained from the MFC size tests suggest that MFCs can be further scaled up without decreasing energy recovery under certain conditions. The low-strength substrates seem to be more suitable for MFC treatment of wastewater, in terms of both energy recovery and organic removal. However, because the MFCs could not achieve the maximum NER and the maximum organic removal efficiency at the same time, one must determine a major goal for MFCs treating wastewater between energy recovery and contaminant removal.

  13. Does the essential oil of Lippia sidoides Cham. (pepper-rosmarin) affect its endophytic microbial community?

    PubMed Central

    2013-01-01

    Background Lippia sidoides Cham., also known as pepper-rosmarin, produces an essential oil in its leaves that is currently used by the pharmaceutical, perfumery and cosmetic industries for its antimicrobial and aromatic properties. Because of the antimicrobial compounds (mainly thymol and carvacrol) found in the essential oil, we believe that the endophytic microorganisms found in L. sidoides are selected to live in different parts of the plant. Results In this study, the endophytic microbial communities from the stems and leaves of four L. sidoides genotypes were determined using cultivation-dependent and cultivation-independent approaches. In total, 145 endophytic bacterial strains were isolated and further grouped using either ERIC-PCR or BOX-PCR, resulting in 76 groups composed of different genera predominantly belonging to the Gammaproteobacteria. The endophytic microbial diversity was also analyzed by PCR-DGGE using 16S rRNA-based universal and group-specific primers for total bacteria, Alphaproteobacteria, Betaproteobacteria and Actinobacteria and 18S rRNA-based primers for fungi. PCR-DGGE profile analysis and principal component analysis showed that the total bacteria, Alphaproteobacteria, Betaproteobacteria and fungi were influenced not only by the location within the plant (leaf vs. stem) but also by the presence of the main components of the L. sidoides essential oil (thymol and/or carvacrol) in the leaves. However, the same could not be observed within the Actinobacteria. Conclusion The data presented here are the first step to begin shedding light on the impact of the essential oil in the endophytic microorganisms in pepper-rosmarin. PMID:23387945

  14. The elevational pattern of microbial community and enzyme activity along the northern slop of Changbai Mountain

    NASA Astrophysics Data System (ADS)

    Xu, Zhiwei; Yu, Guirui; Zhang, Xinyu; Ge, Jianpin; He, Nianpeng; Wang, Qiufeng; Wang, Dan

    2014-05-01

    we present a comprehensive analysis of soil microbial community structure, enzyme activities and their role in soil organic matter mineralization along six elevations representing five typical vegetation types from forest to alpine tundra in Changbai Mountain, China. The results showed that the microbial PLFAs presented hump-shaped patterns along the elevation with the total microbial PLFAs highest in Ermans birch forest soil. The fungi to bacteria and gram positive to negative bacteria ratios increased along the elevation with the lowest values in Broad leaved forest and Dark-coniferous spruce-fir forest soil, respectively. The soil microbial community structures showed a biogeography distribution pattern in vertical direction with microbial community structures in Broad leaved forest and Mixed coniferous broad leaved forest different from other four sites. The soil enzyme activities in Broad leaved forest and Mixed coniferous broad leaved forest were significantly higher than in other four elevations. Principal component analysis (PCA) revealed substantial differences in soil microbial community composition among study sites, appeared to be driven primarily by MAT, MAP, soil temperature and content of silt & clay on the first principal component (PC1) which accounted for 87.1 % of the total sample variance. However, soil nutrients mainly responsible for the variation of soil enzyme activities. The soil organic matter mineralization rates tended to be highest in Ermans birch forest site and lowest in Dark-coniferous spruce-fir forest site and showed positive relationship with total microbial, bacterial and actinomycetes PLFAs. These findings could be used to facilitate interpretation of soil microbial community and ecological function in latitude forests ecosystem especially in volcanic forest ecosystem.

  15. Analytical applications of microbial fuel cells. Part II: Toxicity, microbial activity and quantification, single analyte detection and other uses.

    PubMed

    Abrevaya, Ximena C; Sacco, Natalia J; Bonetto, Maria C; Hilding-Ohlsson, Astrid; Cortón, Eduardo

    2015-01-15

    Microbial fuel cells were rediscovered twenty years ago and now are a very active research area. The reasons behind this new activity are the relatively recent discovery of electrogenic or electroactive bacteria and the vision of two important practical applications, as wastewater treatment coupled with clean energy production and power supply systems for isolated low-power sensor devices. Although some analytical applications of MFCs were proposed earlier (as biochemical oxygen demand sensing) only lately a myriad of new uses of this technology are being presented by research groups around the world, which combine both biological-microbiological and electroanalytical expertises. This is the second part of a review of MFC applications in the area of analytical sciences. In Part I a general introduction to biological-based analytical methods including bioassays, biosensors, MFCs design, operating principles, as well as, perhaps the main and earlier presented application, the use as a BOD sensor was reviewed. In Part II, other proposed uses are presented and discussed. As other microbially based analytical systems, MFCs are satisfactory systems to measure and integrate complex parameters that are difficult or impossible to measure otherwise, such as water toxicity (where the toxic effect to aquatic organisms needed to be integrated). We explore here the methods proposed to measure toxicity, microbial metabolism, and, being of special interest to space exploration, life sensors. Also, some methods with higher specificity, proposed to detect a single analyte, are presented. Different possibilities to increase selectivity and sensitivity, by using molecular biology or other modern techniques are also discussed here.

  16. Recent developments in production and biotechnological applications of cold-active microbial proteases.

    PubMed

    Kuddus, Mohammed; Ramteke, Pramod W

    2012-11-01

    Microbial proteases that occupy a pivotal position with respect to their commercial applications are most important hydrolytic enzymes and have been studied extensively since the advent of enzymology. Cold-adapted microorganisms are potential source of cold-active proteases and they have been isolated from the cold regions. Although there are many microbial sources available for producing proteases, only few are recognized as commercial producer. Cold-active proteases along with their producing microbes are of commercial value and find multiple applications in various industrial and biotechnological sectors such as additives in detergents, additives in food industries, environmental bioremediations, biotransformation and molecular biology applications. Therefore, cold-active proteases are the enzymes of choice for many biotechnologists, microbiologists, biochemists, environmentalists and biochemical engineers. In the present review, we discuss some novel sources along with recent developments in production and biotechnological applications of cold-active microbial proteases.

  17. Comparative toxicity of chlorpyrifos and its oxon derivatives to soil microbial activity by combined methods.

    PubMed

    Wang, Fei; Yao, Jun; Chen, Huilun; Chen, Ke; Trebse, Polonca; Zaray, Gyula

    2010-01-01

    The inhibitory effects of the pesticide Chlorpyrifos (CPF) and its oxon derivative (CPO) on soil microbial activity were evaluated through the measurement of metabolic parameters and the microbial urease enzyme. The thermodynamic parameters related to microbial activity were measured and recorded as power-time curves. Microbial growth rate constant k, total heat evolution Q(T), metabolic enthalpy DeltaH(met), mass specific heat rate J(Q/S), microbial biomass C and inhibitory ratio I were calculated. They showed the linear relationship with doses of CPF and CPO. Thereinto, the linear correlations, k versus biomass C and DeltaH(met) versus biomass C, elucidated that k and DeltaH(met) were growth yield dependent. In this work, 20% inhibitory ratio IC(20) was obtained with 9.8 microg g(-1) for CPF and 0.37 microg g(-1) CPO, meaning that the acute toxicity of CPO was 26 times that of CPF, since the CPO had more potent toxicity to living organism due to its active functional group. Comparing the change tendency of DeltaH(met) and other parameter, the values almost kept constant when exposure to CPF (<5.0 microg g(-1)). It illustrates that individual reacted to stress resulted from environment change by shifting resources from other biological activities (such as reproduction or growth) toward survival to some extent. Urease activity responses in relation to the CPF and CPO exposure were observed and consistent with above thermodynamic parameters.

  18. Natural oil slicks fuel surface water microbial activities in the northern Gulf of Mexico.

    PubMed

    Ziervogel, Kai; D'Souza, Nigel; Sweet, Julia; Yan, Beizhan; Passow, Uta

    2014-01-01

    We conducted a series of roller tank incubations with surface seawater from the Green Canyon oil reservoir, northern Gulf of Mexico, amended with either a natural oil slick (GCS-oil) or pristine oil. The goal was to test whether bacterial activities of natural surface water communities facilitate the formation of oil-rich marine snow (oil snow). Although oil snow did not form during any of our experiments, we found specific bacterial metabolic responses to the addition of GCS-oil that profoundly affected carbon cycling within our 4-days incubations. Peptidase and β-glucosidase activities indicative of bacterial enzymatic hydrolysis of peptides and carbohydrates, respectively, were suppressed upon the addition of GCS-oil relative to the non-oil treatment, suggesting that ascending oil and gas initially inhibits bacterial metabolism in surface water. Biodegradation of physically dispersed GCS-oil components, indicated by the degradation of lower molecular weight n-alkanes as well as the rapid transformation of particulate oil-carbon (C: N >40) into the DOC pool, led to the production of carbohydrate- and peptide-rich degradation byproducts and bacterial metabolites such as transparent exopolymer particles (TEP). TEP formation was highest at day 4 in the presence of GCS-oil; in contrast, TEP levels in the non-oil treatment already peaked at day 2. Cell-specific enzymatic activities closely followed TEP concentrations in the presence and absence of GCS-oil. These results demonstrate that the formation of oil slicks and activities of oil-degrading bacteria result in a temporal offset of microbial cycling of organic matter, affecting food web interactions and carbon cycling in surface waters over cold seeps.

  19. Natural oil slicks fuel surface water microbial activities in the northern Gulf of Mexico

    PubMed Central

    Ziervogel, Kai; D'souza, Nigel; Sweet, Julia; Yan, Beizhan; Passow, Uta

    2014-01-01

    We conducted a series of roller tank incubations with surface seawater from the Green Canyon oil reservoir, northern Gulf of Mexico, amended with either a natural oil slick (GCS-oil) or pristine oil. The goal was to test whether bacterial activities of natural surface water communities facilitate the formation of oil-rich marine snow (oil snow). Although oil snow did not form during any of our experiments, we found specific bacterial metabolic responses to the addition of GCS-oil that profoundly affected carbon cycling within our 4-days incubations. Peptidase and β-glucosidase activities indicative of bacterial enzymatic hydrolysis of peptides and carbohydrates, respectively, were suppressed upon the addition of GCS-oil relative to the non-oil treatment, suggesting that ascending oil and gas initially inhibits bacterial metabolism in surface water. Biodegradation of physically dispersed GCS-oil components, indicated by the degradation of lower molecular weight n-alkanes as well as the rapid transformation of particulate oil-carbon (C: N >40) into the DOC pool, led to the production of carbohydrate- and peptide-rich degradation byproducts and bacterial metabolites such as transparent exopolymer particles (TEP). TEP formation was highest at day 4 in the presence of GCS-oil; in contrast, TEP levels in the non-oil treatment already peaked at day 2. Cell-specific enzymatic activities closely followed TEP concentrations in the presence and absence of GCS-oil. These results demonstrate that the formation of oil slicks and activities of oil-degrading bacteria result in a temporal offset of microbial cycling of organic matter, affecting food web interactions and carbon cycling in surface waters over cold seeps. PMID:24847314

  20. Wheat bran extract alters colonic fermentation and microbial composition, but does not affect faecal water toxicity: a randomised controlled trial in healthy subjects.

    PubMed

    Windey, Karen; De Preter, Vicky; Huys, Geert; Broekaert, Willem F; Delcour, Jan A; Louat, Thierry; Herman, Jean; Verbeke, Kristin

    2015-01-28

    Wheat bran extract (WBE), containing arabinoxylan-oligosaccharides that are potential prebiotic substrates, has been shown to modify bacterial colonic fermentation in human subjects and to beneficially affect the development of colorectal cancer (CRC) in rats. However, it is unclear whether these changes in fermentation are able to reduce the risk of developing CRC in humans. The aim of the present study was to evaluate the effects of WBE on the markers of CRC risk in healthy volunteers, and to correlate these effects with colonic fermentation. A total of twenty healthy subjects were enrolled in a double-blind, cross-over, randomised, controlled trial in which the subjects ingested WBE (10 g/d) or placebo (maltodextrin, 10 g/d) for 3 weeks, separated by a 3-week washout period. At the end of each study period, colonic handling of NH3 was evaluated using the biomarker lactose[15N, 15N']ureide, colonic fermentation was characterised through a metabolomics approach, and the predominant microbial composition was analysed using denaturing gradient gel electrophoresis. As markers of CRC risk, faecal water genotoxicity was determined using the comet assay and faecal water cytotoxicity using a colorimetric cell viability assay. Intake of WBE induced a shift from urinary to faecal 15N excretion, indicating a stimulation of colonic bacterial activity and/or growth. Microbial analysis revealed a selective stimulation of Bifidobacterium adolescentis. In addition, WBE altered the colonic fermentation pattern and significantly reduced colonic protein fermentation compared with the run-in period. However, faecal water cytotoxicity and genotoxicity were not affected. Although intake of WBE clearly affected colonic fermentation and changed the composition of the microbiota, these changes were not associated with the changes in the markers of CRC risk.

  1. Pyrene biodegradation in an industrial soil exposed to simulated rhizodeposition: how does it affect functional microbial abundance?

    PubMed

    Meng, Liang; Zhu, Yong-Guan

    2011-02-15

    Rhizodeposition is an important biogeochemical process for the phytoremediation of contaminated substrates. This study investigated the effects of various rhizodeposition components from celery (Apium graveolens) on pyrene biodegradation and microbial abundance in a long-term contaminated soil. Batch microcosms simulating in situ contaminated soil were amended with lipophilic extract, water-soluble extract, or debris from celery root to mimic plant rhizodeposition within 70 days. Soil was intermittently analyzed for pyrene concentration and target gene abundance estimated by real-time PCR. Lipophilic extract was the major simulated rhizodeposit enhancing pyrene biodegradation, while water-soluble extract stimulated microbial growth most efficiently. The relative abundance of total polycyclic aromatic hydrocarbon (PAH) degraders was enhanced by lipophilic extract but inhibited by the other two rhizodeposits, indicating that these components exerted different selective pressures on PAH degrader community. Moreover, PAH catabolic pathway may involve in the pollutant detoxification and fatty acid metabolism by microorganisms, which were also affected by rhizodeposition. These results provide insights into plant-microbe interactions responsible for PAH biodegradation and offer opportunities to facilitate PAH phytoremediation in industrial sites.

  2. Gamma irradiation of sorghum flour: Effects on microbial inactivation, amylase activity, fermentability, viscosity and starch granule structure

    NASA Astrophysics Data System (ADS)

    Mukisa, Ivan M.; Muyanja, Charles M. B. K.; Byaruhanga, Yusuf B.; Schüller, Reidar B.; Langsrud, Thor; Narvhus, Judith A.

    2012-03-01

    Malted and un-malted sorghum ( Sorghum bicolor (L.) Moench) flour was gamma irradiated with a dose of 10 kGy and then re-irradiated with 25 kGy. The effects of irradiation on microbial decontamination, amylase activity, fermentability (using an amylolytic L. plantarum MNC 21 strain), starch granule structure and viscosity were determined. Standard methods were used during determinations. The 10 kGy dose had no effect on microbial load of un-malted flour but reduced that of malted flour by 3 log cycles. Re-irradiation resulted in complete decontamination. Irradiation of malt caused a significant ( p<0.05) reduction in alpha and beta amylase activity (22% and 32%, respectively). Irradiation of un-malted flour increased the rates of utilization of glucose and maltose by 53% and 100%, respectively, during fermentation. However, microbial growth, rate of lactic acid production, final lactic acid concentration and pH were not affected. Starch granules appeared normal externally even after re-irradiation, however, granules ruptured and dissolved easily after hydration and gelatinization. Production of high dry matter density porridge (200 g dry matter/L) with a viscosity of 3500 cP was achieved by irradiation of un-malted flout at 10 kGy. Gamma irradiation can be used to decontaminate flours and could be utilized to produce weaning porridge from sorghum.

  3. Response of microbial activities and diversity to PAHs contamination at coal tar contaminated land

    NASA Astrophysics Data System (ADS)

    Zhao, Xiaohui; Sun, Yujiao; Ding, Aizhong; Zhang, Dan; Zhang, Dayi

    2015-04-01

    Coal tar is one of the most hazardous and concerned organic pollutants and the main hazards are polycyclic aromatic hydrocarbons (PAHs). The indigenous microorganisms in soils are capable to degrade PAHs, with essential roles in biochemical process for PAHs natural attenuation. This study investigated 48 soil samples (from 8 depths of 6 boreholes) in Beijing coking and chemistry plant (China) and revealed the correlation between PAHs contamination, soil enzyme activities and microbial community structure, by 16S rRNA denaturing gradient gel electrophoresis (DGGE). At the site, the key contaminants were identified as naphthalene, acenaphthylene, acenaphthene, fluorene, phenanthrene and anthracene, and the total PAHs concentration ranged from 0.1 to 923.9 mg/kg dry soil. The total PAHs contamination level was positively correlated (p<0.05) with the bacteria count (0.9×107-14.2×107 CFU/mL), catalase activities (0.554-6.230 mL 0.02 M KMnO4/g•h) and dehydrogenase activities (1.9-30.4 TF μg/g•h soil), showing the significant response of microbial population and degrading functions to the organic contamination in soils. The PAHs contamination stimulated the PAHs degrading microbes and promoted their biochemical roles in situ. The positive relationship between bacteria count and dehydrogenase activities (p<0.05) suggested the dominancy of PAHs degrading bacteria in the microbial community. More interestingly, the microbial community deterioration was uncovered via the decline of microbial biodiversity (richness from 16S rRNA DGGE) against total PAHs concentration (p<0.05). Our research described the spatial profiles of PAHs contamination and soil microbial functions at the PAHs heavily contaminated sites, offering deeper understanding on the roles of indigenous microbial community in natural attenuation process.

  4. Minimum Energy Requirements for Sustained Microbial Activity in Anoxic Sediments

    NASA Technical Reports Server (NTRS)

    Hoehler, Tori M.; Alperin, Marc J.; Albert, Daniel B.; Martens, Christoper S.; DeVincenzi, Donald L. (Technical Monitor)

    2000-01-01

    Currently understood mechanisms of biochemical energy conservation dictate that, in order to be biologically useful, energy must be available to organisms in "quanta" equal to, at minimum one-third to one-fifth of the energy required to synthesize ATP in vivo. The existence of this biological energy quantum means that a significant fraction of the chemical amp on Earth cannot be used to drive biological productivity, and places a fundamental thermodynamic constraint on the origins, evolution, and distribution of life. We examined the energy requirements of intact microbial assemblages in anoxic sediments from Cape Lookout Bight, NC, USA, using dissolved hydrogen concentrations as a non-invasive probe. In this system, the thermodynamics of metabolic processes occurring inside microbial cells is reflected quantitatively by H2 concentrations measured outside those cells. We find that methanogenic archaea are supported by energy yields as small as 10 kJ per mol, about half the quantity calculated from studies of microorganisms in culture. This finding implies that a significantly broader range of geologic and chemical niches might be exploited by microorganisms than would otherwise be expected.

  5. Monitoring the Perturbation of Soil and Groundwater Microbial Communities Due to Pig Production Activities

    PubMed Central

    Hong, Pei-Ying; Yannarell, Anthony C.; Dai, Qinghua; Ekizoglu, Melike

    2013-01-01

    This study aimed to determine if biotic contaminants originating from pig production farms are disseminated into soil and groundwater microbial communities. A spatial and temporal sampling of soil and groundwater in proximity to pig production farms was conducted, and quantitative PCR (Q-PCR) was utilized to determine the abundances of tetracycline resistance genes (i.e., tetQ and tetZ) and integrase genes (i.e., intI1 and intI2). We observed that the abundances of tetZ, tetQ, intI1, and intI2 in the soils increased at least 6-fold after manure application, and their abundances remained elevated above the background for up to 16 months. Q-PCR further determined total abundances of up to 5.88 × 109 copies/ng DNA for tetZ, tetQ, intI1, and intI2 in some of the groundwater wells that were situated next to the manure lagoon and in the facility well used to supply water for one of the farms. We further utilized 16S rRNA-based pyrosequencing to assess the microbial communities, and our comparative analyses suggest that most of the soil samples collected before and after manure application did not change significantly, sharing a high Bray-Curtis similarity of 78.5%. In contrast, an increase in Bacteroidetes and sulfur-oxidizing bacterial populations was observed in the groundwaters collected from lagoon-associated groundwater wells. Genera associated with opportunistic human and animal pathogens, such as Acinetobacter, Arcobacter, Yersinia, and Coxiella, were detected in some of the manure-treated soils and affected groundwater wells. Feces-associated bacteria such as Streptococcus, Erysipelothrix, and Bacteroides were detected in the manure, soil, and groundwater ecosystems, suggesting a perturbation of the soil and groundwater environments by invader species from pig production activities. PMID:23396341

  6. Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells.

    PubMed

    Berry, David; Mader, Esther; Lee, Tae Kwon; Woebken, Dagmar; Wang, Yun; Zhu, Di; Palatinszky, Marton; Schintlmeister, Arno; Schmid, Markus C; Hanson, Buck T; Shterzer, Naama; Mizrahi, Itzhak; Rauch, Isabella; Decker, Thomas; Bocklitz, Thomas; Popp, Jürgen; Gibson, Christopher M; Fowler, Patrick W; Huang, Wei E; Wagner, Michael

    2015-01-13

    Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D2O) combined with Raman microspectroscopy. Incorporation of D2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics.

  7. Key design factors affecting microbial community composition and pathogenic organism removal in horizontal subsurface flow constructed wetlands.

    PubMed

    Morató, Jordi; Codony, Francesc; Sánchez, Olga; Pérez, Leonardo Martín; García, Joan; Mas, Jordi

    2014-05-15

    Constructed wetlands constitute an interesting option for wastewater reuse since high concentrations of contaminants and pathogenic microorganisms can be removed with these natural treatment systems. In this work, the role of key design factors which could affect microbial removal and wetland performance, such as granular media, water depth and season effect was evaluated in a pilot system consisting of eight parallel horizontal subsurface flow (HSSF) constructed wetlands treating urban wastewater from Les Franqueses del Vallès (Barcelona, Spain). Gravel biofilm as well as influent and effluent water samples of these systems were taken in order to detect the presence of bacterial indicators such as total coliforms (TC), Escherichia coli, fecal enterococci (FE), Clostridium perfringens, and other microbial groups such as Pseudomonas and Aeromonas. The overall microbial inactivation ratio ranged between 1.4 and 2.9 log-units for heterotrophic plate counts (HPC), from 1.2 to 2.2 log units for total coliforms (TC) and from 1.4 to 2.3 log units for E. coli. The presence of fine granulometry strongly influenced the removal of all the bacterial groups analyzed. This effect was significant for TC (p=0.009), E. coli (p=0.004), and FE (p=0.012). Shallow HSSF constructed wetlands were more effective for removing Clostridium spores (p=0.039), and were also more efficient for removing TC (p=0.011) and E. coli (p=0.013) when fine granulometry was used. On the other hand, changes in the total bacterial community from gravel biofilm were examined by using denaturing gradient gel electrophoresis (DGGE) and sequencing of polymerase chain reaction (PCR)-amplified fragments of the 16S rRNA gene recovered from DGGE bands. Cluster analysis of the DGGE banding pattern from the different wetlands showed that microbial assemblages separated according to water depth, and sequences of different phylogenetic groups, such as Alpha, Beta and Delta-Proteobacteria, Nitrospirae, Bacteroidetes

  8. Microbial colonization affects the efficiency of photovoltaic panels in a tropical environment.

    PubMed

    Shirakawa, Marcia A; Zilles, Roberto; Mocelin, Andre; Gaylarde, Christine C; Gorbushina, Anna; Heidrich, Gabriele; Giudice, Mauro C; Del Negro, Gilda M B; John, Vanderley M

    2015-07-01

    Sub-aerial biofilm (SAB) development on solar panels was studied in São Paulo. After 6, 12 and 18 months' exposure, photovoltaic panels were covered by increasing proportions of organic matter (42%, 53% and 58%, respectively). Fungi were an important component of these biofilms; very few phototrophs were found. Major microorganisms detected were melanised meristematic ascomycetes and pigmented bacterial genera Arthrobacter and Tetracoccus. While diverse algae, cyanobacteria and bacteria were identified in biofilms at 6 and 12 months, diversity at a later stage was reduced to that typical for SAB: the only fungal group detected in 18 month biofilm was the meristematic Dothideomycetes and the only phototrophs Ulothrix and Chlorella. Photovoltaic modules showed significant power reductions after 6, 12 (both 7%) and 18 (11%) months. The lack of difference in power reduction between 6 and 12 months reflects the dual nature of soiling, which can result from the deposition of particulates as well as from SAB fouling. Although 12-month old SAB demonstrated an almost 10-fold increase in fungal colonization and a higher organic content, the larger non-microbial particles (above 10 μm), which were important for efficiency reduction of lightly-biofilmed panels, were removed by high rainfall just before the 12-month sampling.

  9. The Dynamic Arctic Snow Pack: An Unexplored Environment for Microbial Diversity and Activity

    PubMed Central

    Larose, Catherine; Dommergue, Aurélien; Vogel, Timothy M.

    2013-01-01

    The Arctic environment is undergoing changes due to climate shifts, receiving contaminants from distant sources and experiencing increased human activity. Climate change may alter microbial functioning by increasing growth rates and substrate use due to increased temperature. This may lead to changes of process rates and shifts in the structure of microbial communities. Biodiversity may increase as the Arctic warms and population shifts occur as psychrophilic/psychrotolerant species disappear in favor of more mesophylic ones. In order to predict how ecological processes will evolve as a function of global change, it is essential to identify which populations participate in each process, how they vary physiologically, and how the relative abundance, activity and community structure will change under altered environmental conditions. This review covers aspects of the importance and implication of snowpack in microbial ecology emphasizing the diversity and activity of these critical members of cold zone ecosystems. PMID:24832663

  10. Antibacterial and enzymatic activity of microbial community during wastewater treatment by pilot scale vermifiltration system.

    PubMed

    Arora, Sudipti; Rajpal, Ankur; Bhargava, Renu; Pruthi, Vikas; Bhatia, Akansha; Kazmi, A A

    2014-08-01

    The present study investigated microbial community diversity and antibacterial and enzymatic properties of microorganisms in a pilot-scale vermifiltration system during domestic wastewater treatment. The study included isolation and identification of diverse microbial community by culture-dependent method from a vermifilter (VF) with earthworms and a conventional geofilter (GF) without earthworms. The results of the four months study revealed that presence of earthworms in VF could efficiently remove biochemical oxygen demand (BOD), chemical oxygen demand (COD), total and fecal coliforms, fecal streptococci and other pathogens. Furthermore, the burrowing activity of earthworms promoted the aeration conditions in VF which led to the predominance of the aerobic microorganisms, accounting for complex microbial community diversity. Antibacterial activity of the isolated microorganisms revealed the mechanism behind the removal of pathogens, which is reported for the first time. Specifically, cellulase, amylase and protease activity is responsible for biodegradation and stabilization of organic matter.

  11. Microbial Community Dynamics and Activity Link to Indigo Production from Indole in Bioaugmented Activated Sludge Systems

    PubMed Central

    Deng, Jie; Deng, Ye; Van Nostrand, Joy D.; Wu, Liyou; He, Zhili; Qin, Yujia; Zhou, Jiti; Zhou, Jizhong

    2015-01-01

    Biosynthesis of the popular dyestuff indigo from indole has been comprehensively studied using pure cultures, but less has been done to characterize the indigo production by microbial communities. In our previous studies, a wild strain Comamonas sp. MQ was isolated from activated sludge and the recombinant Escherichia coli nagAc carrying the naphthalene dioxygenase gene (nag) from strain MQ was constructed, both of which were capable of producing indigo from indole. Herein, three activated sludge systems, G1 (non-augmented control), G2 (augmented with Comamonas sp. MQ), and G3 (augmented with recombinant E. coli nagAc), were constructed to investigate indigo production. After 132-day operation, G3 produced the highest yields of indigo (99.5 ± 3.0 mg/l), followed by G2 (27.3 ± 1.3 mg/l) and G1 (19.2 ± 1.2 mg/l). The microbial community dynamics and activities associated with indigo production were analyzed by Illumina Miseq sequencing of 16S rRNA gene amplicons. The inoculated strain MQ survived for at least 30 days, whereas E. coli nagAc was undetectable shortly after inoculation. Quantitative real-time PCR analysis suggested the abundance of naphthalene dioxygenase gene (nagAc) from both inoculated strains was strongly correlated with indigo yields in early stages (0–30 days) (P < 0.001) but not in later stages (30–132 days) (P > 0.10) of operation. Based on detrended correspondence analysis (DCA) and dissimilarity test results, the communities underwent a noticeable shift during the operation. Among the four major genera (> 1% on average), the commonly reported indigo-producing populations Comamonas and Pseudomonas showed no positive relationship with indigo yields (P > 0.05) based on Pearson correlation test, while Alcaligenes and Aquamicrobium, rarely reported for indigo production, were positively correlated with indigo yields (P < 0.05). This study should provide new insights into our understanding of indigo bio-production by microbial communities

  12. Soluble microbial products (SMPs) release in activated sludge systems: a review

    PubMed Central

    2012-01-01

    This review discusses the characterization, production and implications of soluble microbial products (SMPs) in biological wastewater treatment. The precise definition of SMPs is open to talk about, but is currently regarded as “the pool of organic compounds that are released into solution from substrate metabolism and biomass decay”'. Some of the SMPs have been identified as humic acids, polysaccharides, proteins, amino acids, antibiotics, extracellular enzymes and structural components of cells and products of energy metabolism. They adversely affect the kinetic activity, flocculating and settling properties of sludge. This review outlines some important findings with regard to biodegradability and treatability of SMPs and also the effect of process parameters on their production. As SMPs are produced during biological treatment process, their trace amounts normally remain in the effluent that defines the highest COD removal efficiency. Their presence in effluent represents a high potential risk of toxic by-product formation during chlorine disinfection. Studies have indicated that among all wastewater post-treatment processes, the adsorption by granular activated carbon combined with biologically induced degradation is the most effective method for removal of SMPs. However, it may be concludes that the knowledge regarding SMPs is still under progress and more work is required to fully understand their contribution to the treatment process. PMID:23369231

  13. Soluble microbial products (SMPs) release in activated sludge systems: a review.

    PubMed

    Azami, Hamed; Sarrafzadeh, Mohammad Hossein; Mehrnia, Mohammad Reza

    2012-12-18

    This review discusses the characterization, production and implications of soluble microbial products (SMPs) in biological wastewater treatment. The precise definition of SMPs is open to talk about, but is currently regarded as "the pool of organic compounds that are released into solution from substrate metabolism and biomass decay"'. Some of the SMPs have been identified as humic acids, polysaccharides, proteins, amino acids, antibiotics, extracellular enzymes and structural components of cells and products of energy metabolism. They adversely affect the kinetic activity, flocculating and settling properties of sludge. This review outlines some important findings with regard to biodegradability and treatability of SMPs and also the effect of process parameters on their production. As SMPs are produced during biological treatment process, their trace amounts normally remain in the effluent that defines the highest COD removal efficiency. Their presence in effluent represents a high potential risk of toxic by-product formation during chlorine disinfection. Studies have indicated that among all wastewater post-treatment processes, the adsorption by granular activated carbon combined with biologically induced degradation is the most effective method for removal of SMPs. However, it may be concludes that the knowledge regarding SMPs is still under progress and more work is required to fully understand their contribution to the treatment process.

  14. Promoting Uranium Immobilization by the Activities of Microbial Phosphatases

    SciTech Connect

    Martinez, Robert J.; Beazley, Melanie J.; Wilson, Jarad J.; Taillefert, Martial; Sobecky, Patricia A.

    2005-04-05

    The overall goal of this project is to examine the role of nonspecific phosphohydrolases present in naturally occurring subsurface microorganisms for the purpose of promoting the immobilization of radionuclides through the production of uranium [U(VI)] phosphate precipitates. Specifically, we hypothesize that the precipitation of U(VI) phosphate minerals may be promoted through the microbial release and/or accumulation of PO{sub 4}{sup 3-}. During this phase of the project we have been conducting assays to determine the effects of pH, inorganic anions and organic ligands on U(VI) mineral formation and precipitation when FRC bacterial isolates were grown in simulated groundwater medium. The molecular characterization of FRC isolates has also been undertaken during this phase of the project. Analysis of a subset of gram-positive FRC isolates cultured from FRC soils (Areas 1, 2 and 3) and background sediments have indicated a higher percentage of isolates exhibiting phosphatase phenotypes (i.e., in particular those surmised to be PO{sub 4}{sup 3-}-irrepressible) relative to isolates from the reference site. A high percentage of strains that exhibited such putatively PO{sub 4}{sup 3-}-irrepressible phosphatase phenotypes were also resistant to the heavy metals lead and cadmium. Previous work on FRC strains, including Arthrobacter, Bacillus and Rahnella spp., has demonstrated differences in tolerance to U(VI) toxicity (200 {micro}M) in the absence of organophosphate substrates. For example, Arthrobacter spp. exhibited the greatest tolerance to U(VI) while the Rahnella spp. have been shown to facilitate the precipitation of U(VI) from solution and the Bacillus spp. demonstrate the greatest sensitivity to acidic conditions and high concentrations of U(VI). PCR-based detection of FRC strains are being conducted to determine if non-specific acid phosphatases of the known molecular classes [i.e., classes A, B and C] are present in these FRC isolates. Additionally, these

  15. Influence of Deep Ocean Sewage Outfalls on the Microbial Activity of the Surrounding Sediment

    PubMed Central

    Novitsky, James A.; Karl, David M.

    1985-01-01

    The microbial activity near two deep ocean sewage outfalls off the coast of the island of Oahu, Hawaii, was characterized. Water samples and sediment samples to a depth of 4.5 cm were analyzed from an area of approximately 4.5 × 104 m2 surrounding the outfalls. Although the effluent water at both sites exhibited heterotrophic activity that was 2 orders of magnitude greater than water from a control site, ambient water samples taken within 1 m of the discharge ports exhibited activity only twice that of the control water. The heterotrophic activity of the outfall sediment was only elevated above that of the control site for surface samples collected within 10 m of the outfall. Likewise, the rates of microbial nucleic acid synthesis and carbon production in the sediment were only elevated immediately adjacent to the outfalls. Total microbial biomass, as determined by the ATP content of the sediment, varied spatially but was generally elevated at the outfall sites. The specific growth rates calculated for the sediment microbial populations, however, were not greater at the outfall sites. At one site the rocks surrounding the diffuser pipe were covered with copious amounts of slime that appeared to be composed entirely of microbial cells and filaments. This microbial mat was extremely active with respect to heterotrophic activity and biomass production. Overall, it appears that the impact of the sewage discharge on the ambient seawater microbiota is slight and that the effect on the sediment microbiota is confined to an area immediately adjacent to the diffuser ports. In the sand itself, the effect is limited to the upper 2 cm at most. PMID:16346944

  16. Methods for determining the abundance, diversity and activity of soil microbial communities

    NASA Astrophysics Data System (ADS)

    Pereg, Lily

    2014-05-01

    The diversity and abundance of soil microbial communities play important roles in determining soil structure, quality and productivity. The past decade has seen an increase in the number and efficiency of methods for determining microbial diversity, abundance and function. Recognising that only a very small proportion of the soil microbial community can be cultured, most current studies use molecular techniques based on the 16S and 18S rRNA encoding sequences (DGGE, TRFLP, OFRG, ARISA, SSCP) as well as techniques based on the cellular composition of the microbes (PLFA composition). Recent developments include high-throughput sequencing and microarrays, representing major advances in microbial community analysis. While the diversity of microbes can be determined using DNA-based techniques, microbial activity changes under various conditions. Therefore, the analysis of soil function at any given time requires the analysis of gene expression using RNA-based techniques. Molecular techniques have tremendously advanced our knowledge in the field of soil microbiology, however, the limitations should not be underestimated. This presentation will critically review both the advantages and the limitations of techniques used in soil microbial analysis.

  17. Effects of soil type and farm management on soil ecological functional genes and microbial activities

    SciTech Connect

    Reeve, Jennifer; Schadt, Christopher Warren; Carpenter-Boggs, Lynne; Kang, S.; Zhou, Jizhong; Reganold, John P.

    2010-01-01

    Relationships between soil microbial diversity and soil function are the subject of much debate. Process-level analyses have shown that microbial function varies with soil type and responds to soil management. However, such measurements cannot determine the role of community structure and diversity in soil function. The goal of this study was to investigate the role of gene frequency and diversity, measured by microarray analysis, on soil processes. The study was conducted in an agro-ecosystem characterized by contrasting management practices and soil types. Eight pairs of adjacent commercial organic and conventional strawberry fields were matched for soil type, strawberry variety, and all other environmental conditions. Soil physical, chemical and biological analyses were conducted including functional gene microarrays (FGA). Soil physical and chemical characteristics were primarily determined by soil textural type (coarse vs fine-textured), but biological and FGA measures were more influenced by management (organic vs conventional). Organically managed soils consistently showed greater functional activity as well as FGA signal intensity (SI) and diversity. Overall FGA SI and diversity were correlated to total soil microbial biomass. Functional gene group SI and/or diversity were correlated to related soil chemical and biological measures such as microbial biomass, cellulose, dehydrogenase, ammonium and sulfur. Management was the dominant determinant of soil biology as measured by microbial gene frequency and diversity, which paralleled measured microbial processes.

  18. Formation of Hydrothermal nontronite associated with microbial activity at the South Atlantic Ridge

    NASA Astrophysics Data System (ADS)

    Ta, Kaiwen; Peng, Xiaotong; Chen, Shun; Xu, Hengchao; Li, Jiwei; Jiang, Lei; Du, Mengran

    2015-04-01

    Nontronite is an ubiquitous clay minerals in marine sediments, microbial mediation of hydrothermal nontronite have been increasing. The deposits collected from Southern Atlantic Ridge were very friable with an obvious laminated to stromatolitic to highly porous structure, varying from red, black to light yellow indicate redox condition may undergo range from micro-oxidizing to reducing. Although microbial activity are revealed to play an important role in the formation of clay minerals in sediment, little is currently known about microbial communities that reside in nontronite associated with hydrothermal activity. Here, we used Scanning electron microscopy (SEM), high-resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD), nano secondary ion mass spectrometer (nanoSIMS) and molecular techniques to focus on potential mediation role of microbial in the nontronite formation of low-temperature hydrothermal deposits in South Atlantic Mid-ocean ridge. Our data suggest that the presences of abundant lamellar nontronite structures, as well as microbe-like mineralized morphologies similar to consistent with a biogenic origin. Nontronite in the lower zone of Fe-Mn oxyhydroxides are inferred to have been suboxic environment and their formation appear to be significantly controlled by the locus of redox conditions. Keywords: Nontronite, Microbial activity, Hydrothermal deposits, Biogenic origin.

  19. Experimental evidence that microbial activity lowers the albedo of glacier surfaces: the cryoconite casserole experiment.

    NASA Astrophysics Data System (ADS)

    Musilova, M.; Tranter, M.; Takeuchi, N.; Anesio, A. M.

    2014-12-01

    Darkened glacier and ice sheet surfaces have lower albedos, absorb more solar radiation and consequently melt more rapidly. The increase in glacier surface darkening is an important positive feedback to warming global temperatures, leading to ever growing world-wide ice mass loss. Most studies focus primarily on glacial albedo darkening caused by the physical properties of snow and ice surfaces, and the deposition of dark impurities on glaciers. To date, however, the important effects of biological activity have not been included in most albedo reduction models. This study provides the first experimental evidence that microbial activity can significantly decrease the albedo of glacier surfaces. An original laboratory experiment, the cryoconite casserole, was designed to test the microbial darkening of glacier surface debris (cryoconite) under simulated Greenlandic summer conditions. It was found that minor fertilisation of the cryoconite (at nutrient concentrations typical of glacial ice melt) stimulated extensive microbial activity. Microbes intensified their organic carbon fixation and even mined phosphorous out of the glacier surface sediment. Furthermore, the microbial organic carbon production, accumulation and transformation caused the glacial debris to darken further by 17.3% reflectivity (albedo analogue). These experiments are consistent with the hypothesis that enhanced fertilisation by anthropogenic inputs results in substantial amounts of organic carbon fixation, debris darkening and ultimately to a considerable decrease in the ice albedo of glacier surfaces on global scales. The sizeable amounts of microbially produced glacier surface organic matter and nutrients can thus be a vital source of bioavailable nutrients for subglacial and downstream environments.

  20. Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor.

    PubMed

    Yanagawa, Katsunori; Ijiri, Akira; Breuker, Anja; Sakai, Sanae; Miyoshi, Youko; Kawagucci, Shinsuke; Noguchi, Takuroh; Hirai, Miho; Schippers, Axel; Ishibashi, Jun-Ichiro; Takaki, Yoshihiro; Sunamura, Michinari; Urabe, Tetsuro; Nunoura, Takuro; Takai, Ken

    2017-02-01

    Subseafloor microbes beneath active hydrothermal vents are thought to live near the upper temperature limit for life on Earth. We drilled and cored the Iheya North hydrothermal field in the Mid-Okinawa Trough, and examined the phylogenetic compositions and the products of metabolic functions of sub-vent microbial communities. We detected microbial cells, metabolic activities and molecular signatures only in the shallow sediments down to 15.8 m below the seafloor at a moderately distant drilling site from the active hydrothermal vents (450 m). At the drilling site, the profiles of methane and sulfate concentrations and the δ(13)C and δD isotopic compositions of methane suggested the laterally flowing hydrothermal fluids and the in situ microbial anaerobic methane oxidation. In situ measurements during the drilling constrain the current bottom temperature of the microbially habitable zone to ~45 °C. However, in the past, higher temperatures of 106-198 °C were possible at the depth, as estimated from geochemical thermometry on hydrothermally altered clay minerals. The 16S rRNA gene phylotypes found in the deepest habitable zone are related to those of thermophiles, although sequences typical of known hyperthermophilic microbes were absent from the entire core. Overall our results shed new light on the distribution and composition of the boundary microbial community close to the high-temperature limit for habitability in the subseafloor environment of a hydrothermal field.

  1. Nematicidal activity of microbial pigment from Serratia marcescens.

    PubMed

    Rahul, Suryawanshi; Chandrashekhar, Patil; Hemant, Borase; Chandrakant, Narkhede; Laxmikant, Shinde; Satish, Patil

    2014-01-01

    Ineffectiveness of available nematicides and the high damage caused by plant-parasitic nematodes result in the urgent need to find some natural remedy for their control. Bioactivity of the pigment extracted from Serratia marcescens was screened for controlling nematodes at their juvenile stage. Test pigment was found effective against juvenile stages of Radopholus similis and Meloidogyne javanica at low concentrations (LC50 values, 83 and 79 μg/mL, respectively) as compared with positive control of copper sulphate (LC50 values, 380 and 280 μg/mL, respectively). The pigment also exhibited inhibition on nematode egg-hatching ability. Characterisation of extracted pigment with TLC, FTIR, HPLC, HPTLC and spectroscopic analysis confirmed the presence of prodigiosin as a bioactive metabolite. Considering the sensory mechanism of pathogen recognition by nematodes, the use of microbial secondary metabolites can be effective for nematode control rather than using whole organism.

  2. Carbonate Precipitation through Microbial Activities in Natural Environment, and Their Potential in Biotechnology: A Review

    PubMed Central

    Zhu, Tingting; Dittrich, Maria

    2016-01-01

    Calcium carbonate represents a large portion of carbon reservoir and is used commercially for a variety of applications. Microbial carbonate precipitation, a by-product of microbial activities, plays an important metal coprecipitation and cementation role in natural systems. This natural process occurring in various geological settings can be mimicked and used for a number of biotechnologies, such as metal remediation, carbon sequestration, enhanced oil recovery, and construction restoration. In this study, different metabolic activities leading to calcium carbonate precipitation, their native environment, and potential applications and challenges are reviewed. PMID:26835451

  3. Arctic Gypsum Endoliths: a biogeochemical characterization of a viable and active microbial community

    NASA Astrophysics Data System (ADS)

    Ziolkowski, L. A.; Mykytczuk, N. C. S.; Omelon, C. R.; Johnson, H.; Whyte, L. G.; Slater, G. F.

    2013-02-01

    evidence of microbial-mineral interaction, an alternative hypothesis is that the soluble and friable nature of the gypsum and harsh conditions lead to elevated erosion rates, limiting microbial residence times in this habitat. Regardless, this endolithic community represents a microbial system that does not rely on a nutrient pool from the host gypsum cap rock, instead receiving these elements from allochthonous debris to maintain a more diverse and active community than might have been predicted in the polar desert of the Canadian high Arctic.

  4. [Microbial activity and functional diversity in rhizosphere of cucumber under different subsurface drip irrigation scheduling].

    PubMed

    Li, Hua; He, Hong-Jun; Li, Teng-Fei; Zhang, Zi-Kun

    2014-08-01

    The effects of subsurface drip irrigation scheduling on microbial activity and functional diversity in rhizosphere of cucumber in solar greenhouse were studied in this paper. The results showed that the soil microbial biomass C and N, basal respiration, metabolic quotient and values of AWCD, Shannon and McIntosh indexes were increased at first and then decreased with the increase of irrigation water amount. The values of microbial C and N, basal respiration and metabolic quotient in I2 treatments were significantly higher than those in I1 treatments at the 0.8E(p) irrigation level. The numbers of bacteria, actinomyces and nitrogen-fixing bacteria, and the activities of urease, phosphatase, sucrase, catalase and polyhenoloxidase were significantly higher in the 0.8E(p) treatment than in the other treatments. The numbers of bacteria and nitrogen-fixing bacteria, the activities of urease, phosphatase and sucrase in I2 treatments were significantly higher than in I1 treatment, the actinomyces number and activities of catalase and polyhenoloxidase had no significant difference between I1 and I2 treatments, however, the fungi number in I2 treatments were significantly lower than in I2 treaments at the 0.8E(p) irrigation level. The microbial activity and functional diversity in rhizosphere of cucumber were strengthened in the I20.8E(p) treatment, meanwhile, the soil microflora was improved and the soil enzymes activities were enhanced, therefore, the cucumber growth was promoted as well.

  5. Response of oxidative enzyme activities to nitrogen deposition affects soil concentrations of dissolved organic carbon

    USGS Publications Warehouse

    Waldrop, M.P.; Zak, D.R.

    2006-01-01

    Recent evidence suggests that atmospheric nitrate (NO3- ) deposition can alter soil carbon (C) storage by directly affecting the activity of lignin-degrading soil fungi. In a laboratory experiment, we studied the direct influence of increasing soil NO 3- concentration on microbial C cycling in three different ecosystems: black oak-white oak (BOWO), sugar maple-red oak (SMRO), and sugar maple-basswood (SMBW). These ecosystems span a broad range of litter biochemistry and recalcitrance; the BOWO ecosystem contains the highest litter lignin content, SMRO had intermediate lignin content, and SMBW leaf litter has the lowest lignin content. We hypothesized that increasing soil solution NO 3- would reduce lignolytic activity in the BOWO ecosystem, due to a high abundance of white-rot fungi and lignin-rich leaf litter. Due to the low lignin content of litter in the SMBW, we further reasoned that the NO3- repression of lignolytic activity would be less dramatic due to a lower relative abundance of white-rot basidiomycetes; the response in the SMRO ecosystem should be intermediate. We increased soil solution NO3- concentrations in a 73-day laboratory incubation and measured microbial respiration and soil solution dissolved organic carbon (DOC) and phenolics concentrations. At the end of the incubation, we measured the activity of ??-glucosidase, N-acetyl-glucosaminidase, phenol oxidase, and peroxidase, which are extracellular enzymes involved with cellulose and lignin degradation. We quantified the fungal biomass, and we also used fungal ribosomal intergenic spacer analysis (RISA) to gain insight into fungal community composition. In the BOWO ecosystem, increasing NO 3- significantly decreased oxidative enzyme activities (-30% to -54%) and increased DOC (+32% upper limit) and phenolic (+77% upper limit) concentrations. In the SMRO ecosystem, we observed a significant decrease in phenol oxidase activity (-73% lower limit) and an increase in soluble phenolic concentrations

  6. Site-specific microbial communities in three PCB-impacted sediments are associated with different in situ dechlorinating activities.

    PubMed

    Kjellerup, Birthe V; Sun, Xueli; Ghosh, Upal; May, Harold D; Sowers, Kevin R

    2008-05-01

    Competitive PCR and denaturing HPLC analyses together with an assay detecting potential polychlorinated biphenyl (PCB) dechlorinating activities were combined with physical-chemical site characterizations to identify factors affecting the reductive dechlorination of PCBs in the three historically impacted sediments: Grasse and Buffalo Rivers, NY and Anacostia River, DC. In Grasse River sediment an in situ enriched population of Dehalococcoides phylotypes was abundant in high numbers together with a relatively high dechlorination activity and a high concentration of congeners containing unflanked chlorine substitutions. In contrast microbial communities in Anacostia and Buffalo Rivers sediments consisted of similar total numbers of putative dechlorinating bacteria, but the populations consisted of more diverse putative dechlorinating phylotypes and were associated with lower dechlorination activities and higher concentrations of flanked congeners. Differences observed in the PCB dechlorination activity were not influenced by the chemical PCB availability in spiked sediment or physical sediment characteristics, but were consistent with the concentration of PCBs and total organic carbon in the native sediment. Application of molecular methods for selective detection of indigenous microbial dechlorinating communities combined with assessment of the dechlorinating activity and analysis of the in situ congener profiles provided a comprehensive approach for characterization and identification of sites that are amenable to bioremediation, which is essential for the development of in situ treatment strategies.

  7. Microbial catabolic activities are naturally selected by metabolic energy harvest rate

    PubMed Central

    González-Cabaleiro, Rebeca; Ofiţeru, Irina D; Lema, Juan M; Rodríguez, Jorge

    2015-01-01

    The fundamental trade-off between yield and rate of energy harvest per unit of substrate has been largely discussed as a main characteristic for microbial established cooperation or competition. In this study, this point is addressed by developing a generalized model that simulates competition between existing and not experimentally reported microbial catabolic activities defined only based on well-known biochemical pathways. No specific microbial physiological adaptations are considered, growth yield is calculated coupled to catabolism energetics and a common maximum biomass-specific catabolism rate (expressed as electron transfer rate) is assumed for all microbial groups. Under this approach, successful microbial metabolisms are predicted in line with experimental observations under the hypothesis of maximum energy harvest rate. Two microbial ecosystems, typically found in wastewater treatment plants, are simulated, namely: (i) the anaerobic fermentation of glucose and (ii) the oxidation and reduction of nitrogen under aerobic autotrophic (nitrification) and anoxic heterotrophic and autotrophic (denitrification) conditions. The experimentally observed cross feeding in glucose fermentation, through multiple intermediate fermentation pathways, towards ultimately methane and carbon dioxide is predicted. Analogously, two-stage nitrification (by ammonium and nitrite oxidizers) is predicted as prevailing over nitrification in one stage. Conversely, denitrification is predicted in one stage (by denitrifiers) as well as anammox (anaerobic ammonium oxidation). The model results suggest that these observations are a direct consequence of the different energy yields per electron transferred at the different steps of the pathways. Overall, our results theoretically support the hypothesis that successful microbial catabolic activities are selected by an overall maximum energy harvest rate. PMID:26161636

  8. Sub-soil microbial activity under rotational cotton crops in Australia

    NASA Astrophysics Data System (ADS)

    Polain, Katherine; Knox, Oliver; Wilson, Brian; Pereg, Lily

    2016-04-01

    Soil microbial communities contribute significantly to soil organic matter formation, stabilisation and destabilisation, through nutrient cycling and biodegradation. The majority of soil microbial research examines the processes occurring in the top 0 cm to 30 cm of the soil, where organic nutrients are easily accessible. In soils such as Vertosols, the high clay content causes swelling and cracking. When soil cracking is coupled with rain or an irrigation event, a flush of organic nutrients can move down the soil profile, becoming available for subsoil microbial community use and potentially making a significant contribution to nutrient cycling and biodegradation in soils. At present, the mechanisms and rates of soil nutrient turnover (such as carbon and nitrogen) at depth under cotton rotations are mostly speculative and the process-response relationships remain unclear, although they are undoubtedly underpinned by microbial activity. Our research aims to determine the contribution and role of soil microbiota to the accumulation, cycling and mineralisation of carbon and nitrogen through the whole root profile under continuous cotton (Gossypium hirsutum) and cotton-maize rotations in regional New South Wales, Australia. Through seasonal work, we have established both baseline and potential microbial activity rates from 0 cm to 100 cm down the Vertosol profile, using respiration and colourimetric methods. Further whole soil profile analyses will include determination of microbial biomass and isotopic carbon signatures using phospholipid fatty acid (PLFA) methodology, identification of microbial communities (sequencing) and novel experiments to investigate potential rates of nitrogen mineralisation and quantification of associated genes. Our preliminary observations and the hypotheses tested in this three-year study will be presented.

  9. Combined effects of bacterial-feeding nematodes and prometryne on the soil microbial activity.

    PubMed

    Zhou, Jihai; Li, Xuechao; Jiang, Ying; Wu, Yue; Chen, Jiandong; Hu, Feng; Li, Huixin

    2011-09-15

    Microcosm experiments were carried out to study the effects of bacterial-feeding nematodes and indigenous microbes and their interactions on the degradation of prometryne and soil microbial activity in contaminated soil. The results showed that soil indigenous microbes could degrade prometryne up to 59.6-67.9%; bacterial-feeding nematodes accelerated the degradation of prometryne in contaminated soil, and prometryne degradation was raised by 8.36-10.69%. Soil microbial biomass C (C(mic)), basal soil respiration (BSR), and respiratory quotient (qCO(2)) increased in the beginning of the experiment and decreased in the later stage of the experiment. Nematodes grew and reproduced quite fast, and did increase the growth of soil microbes and enhance soil microbial activity in prometryne contaminated soil during the incubation period.

  10. Earthworms facilitate the stabilization of pelletized dewatered sludge through shaping microbial biomass and activity and community.

    PubMed

    Fu, Xiaoyong; Cui, Guangyu; Huang, Kui; Chen, Xuemin; Li, Fusheng; Zhang, Xiaoyu; Li, Fei

    2016-03-01

    In this study, the effect of earthworms on microbial features during vermicomposting of pelletized dewatered sludge (PDS) was investigated through comparing two degradation systems with and without earthworm E isenia fetida involvement. After 60 days of experimentation, a relatively stable product with low organic matter and high nitrate and phosphorous was harvested when the earthworms were involved. During the process, earthworms could enhance microbial activity and biomass at the initial stage and thus accelerating the rapid decomposition of PDS. The end products of vermicomposting allowed the lower values of bacterial and eukaryotic densities comparison with those of no earthworm addition. In addition, the presence of earthworms modified the bacterial and fungal diversity, making the disappearances of some pathogens and specific decomposing bacteria of recalcitrant substrates in the vermicomposting process. This study evidences that earthworms can facilitate the stabilization of PDS through modifying microbial activity and number and community during vermicomposting.

  11. The effect of malathion on the activity, performance, and microbial ecology of activated sludge.

    PubMed

    Rauglas, Erik; Martin, Seth; Bailey, Kandace; Magnuson, Matthew; Phillips, Rebecca; Harper, Willie F

    2016-12-01

    This study evaluated the effect of a VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothioate) surrogate (malathion) on the activity, performance, and ecology of activated sludge bioreactors. In the presence of malathion, the maximum observed respiration rates varied between 43 and 53 μg/O2 min, generally similar to the 49 μg O2/min rates observed in controls. Malathion did not alter the respiration ratio of O2 consumed-to-CO2 produced nor did it impact the shape of the oxygen consumption curves during respirometry. Shorter term (12 h) batch tests showed that both chemical oxygen demand (COD) and ammonia removal were not negatively impacted by the presence of 0.1-3 mg/L malathion. Longer term continuous addition (i.e. 40 days) of 0.1 mg/L of malathion also had no effect on COD and ammonia removal. In contrast to shorter term exposures, longer term continuous addition of 3 mg/L of malathion negatively impacted both COD and nitrogen removal and was associated with shifts in the abundance of species that are common to activated sludge. These results illustrate the impact that chemicals like malathion may have on COD removal, and nitrification, as well as the robustness of activated sludge microbial communities.

  12. Factors affecting the performance of a single-chamber microbial fuel cell-type biological oxygen demand sensor.

    PubMed

    Yang, Gai-Xiu; Sun, Yong-Ming; Kong, Xiao-Ying; Zhen, Feng; Li, Ying; Li, Lian-Hua; Lei, Ting-Zhou; Yuan, Zhen-Hong; Chen, Guan-Yi

    2013-01-01

    Microbial fuel cells (MFCs) are devices that exploit microorganisms as biocatalysts to degrade organic matter or sludge present in wastewater (WW), and thereby generate electricity. We developed a simple, low-cost single-chamber microbial fuel cell (SCMFC)-type biochemical oxygen demand (BOD) sensor using carbon felt (anode) and activated sludge, and demonstrated its feasibility in the construction of a real-time BOD measurement system. Further, the effects of anodic pH and organic concentration on SCMFC performance were examined, and the correlation between BOD concentration and its response time was analyzed. Our results demonstrated that the SCMFC exhibited a stable voltage after 132 min following the addition of synthetic WW (BOD concentration: 200 mg/L). Notably, the response signal increased with an increase in BOD concentration (range: 5-200 mg/L) and was found to be directly proportional to the substrate concentration. However, at higher BOD concentrations (>120 mg/L) the response signal remained unaltered. Furthermore, we optimized the SCMFC using synthetic WW, and tested it with real WW. Upon feeding real WW, the BOD values exhibited a standard deviation from 2.08 to 8.3% when compared to the standard BOD5 method, thus demonstrating the practical applicability of the developed system to real treatment effluents.

  13. Microbial life in cold, hydrologically active oceanic crustal fluids

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  14. Effect of land use on microbial biomass and enzyme activities in tropical soil

    NASA Astrophysics Data System (ADS)

    Maharjan, Menuka; Sanaullah, Muhammad; Kuzyakov, Yakov

    2016-04-01

    Land use change especially from forest to intensive agriculture for sustaining livelihood causing severe consequence on soil quality. Soil microbial biomass and enzyme activities are very sensitive to change in environment. The objective was to assess effects of three land uses i.e. forest, organic and conventional farming on microbial biomass C and N and enzymes involved in C-cycle (β-glucosidase), N-cycle (leucine-aminopeptidase), P-cycle (Phosphatase) and S-cycle (Sulphatase) at different depth (0-100 cm with 10 cm in interval) of soil in Chitwan, Nepal. The result showed that both carbon and nitrogen content (%) was significantly higher in organic farming than conventional farming and forest. However, the trend decreased in lower depth. Significantly high microbial biomass C and N (μg C and N g-1 soil) were found in organic farming than conventional farming and forest at 0-10 cm but the trend was inconsistent in lower depth. β-glucosidase, leucine-aminopeptidase and sulphatase (nmol g-1 soil) activities were higher in organic and conventional farming compared to forest at 0-20 cm. Phosphatase activity was higher in conventional farming than forest and organic farming at 0-20cm. The activities were inconsistent below 20 cm. Application of farmyard manure and organic matter from the vegetation contributes the higher microbial biomass and enzyme activities in organic farming.

  15. Corrugator activity confirms immediate negative affect in surprise

    PubMed Central

    Topolinski, Sascha; Strack, Fritz

    2015-01-01

    The emotion of surprise entails a complex of immediate responses, such as cognitive interruption, attention allocation to, and more systematic processing of the surprising stimulus. All these processes serve the ultimate function to increase processing depth and thus cognitively master the surprising stimulus. The present account introduces phasic negative affect as the underlying mechanism responsible for this switch in operating mode. Surprising stimuli are schema-discrepant and thus entail cognitive disfluency, which elicits immediate negative affect. This affect in turn works like a phasic cognitive tuning switching the current processing mode from more automatic and heuristic to more systematic and reflective processing. Directly testing the initial elicitation of negative affect by surprising events, the present experiment presented high and low surprising neutral trivia statements to N = 28 participants while assessing their spontaneous facial expressions via facial electromyography. High compared to low surprising trivia elicited higher corrugator activity, indicative of negative affect and mental effort, while leaving zygomaticus (positive affect) and frontalis (cultural surprise expression) activity unaffected. Future research shall investigate the mediating role of negative affect in eliciting surprise-related outcomes. PMID:25762956

  16. Alteration of rare earth element distribution as a result of microbial activity and empirical methane injection

    NASA Astrophysics Data System (ADS)

    Castillo, D. J.; Davies, N. W.; Thurber, A. R.; Haley, B. A.; Colwell, F. S.

    2014-12-01

    As a result of warming, methane is being released into the marine environment in areas that have not historically experienced methane input. While methane is a potent greenhouse gas, microbial oxidation of methane within the sediment greatly limits the role of marine methane sources on atmospheric forcing. However, in these areas of new methane release, consumption of methane prior to its release into the atmosphere is a result of the response of the microbial community to this new input of methane. Further, rare earth elements (REEs) are not currently thought to be involved with microbial activity, but this assumption has not been rigorously tested. Here we test that: (1) microbial communities will rapidly respond to the onset of methane emission, and (2) the microbial response to this methane input will impact the distribution of REEs within the sediment. Undisturbed cores sampled from a tidal flat at Yaquina Bay, OR, were brought back to a lab and injected with anoxic seawater (as a control) or anoxic sea water saturated with methane gas for a total of 2 weeks. Aerobic methanotrophs proliferated over this short time period, becoming an abundant member of the microbial community as identified using fatty acid biomarkers. Excitingly, the experimental injection of methane also shifted the distribution of REEs within the sediment, a trend that appeared to follow the microbial response and that was different from the control cores. Further, the lightest REEs appeared to be used more than the heavier ones, supporting that the REEs are being actively used by the microbes. While we focused on identifying the response of those microbes responsible in methane-cycling, we also identified how the entire microbial community shifts as a result of methane input, and correlating with shifts in REE distribution. Here we have empirically demonstrated the rapid response of methanotrophs to the onset of methane emission and that REE distribution within the sediment is likely

  17. Microbial diversity and autotrophic activity in Kamchatka hot springs.

    PubMed

    Merkel, Alexander Yu; Pimenov, Nikolay V; Rusanov, Igor I; Slobodkin, Alexander I; Slobodkina, Galina B; Tarnovetckii, Ivan Yu; Frolov, Evgeny N; Dubin, Arseny V; Perevalova, Anna A; Bonch-Osmolovskaya, Elizaveta A

    2017-03-01

    Microbial communities of Kamchatka Peninsula terrestrial hot springs were studied using molecular, radioisotopic and cultural approaches. Analysis of 16S rRNA gene fragments performed by means of high-throughput sequencing revealed that aerobic autotrophic sulfur-oxidizing bacteria of the genus Sulfurihydrogenibium (phylum Aquificae) dominated in a majority of streamers. Another widely distributed and abundant group was that of anaerobic bacteria of the genus Caldimicrobium (phylum Thermodesulfobacteria). Archaea of the genus Vulcanisaeta were abundant in a high-temperature, slightly acidic hot spring, where they were accompanied by numerous Nanoarchaeota, while the domination of uncultured Thermoplasmataceae A10 was characteristic for moderately thermophilic acidic habitats. The highest rates of inorganic carbon assimilation determined by the in situ incubation of samples in the presence of (14)C-labeled bicarbonate were found in oxygen-dependent streamers; in two sediment samples taken from the hottest springs this process, though much weaker, was found to be not dependent on oxygen. The isolation of anaerobic lithoautotrophic prokaryotes from Kamchatka hot springs revealed a wide distribution of the ability for sulfur disproportionation, a new lithoautotrophic process capable to fuel autonomous anaerobic ecosystems.

  18. Changes of soil organic matter and microbial activity in irrigated and non irrigated olive groves

    NASA Astrophysics Data System (ADS)

    Kavvadias, Victor; Papadopoulou, Maria; Theocharopoulos, Sideris; Vavoulidou, Evagelia; Doula, Maria; Reppas, Spiros

    2014-05-01

    The implementation of olive cultivation techniques in Greece has not been systematically tested under the prevailing Mediterranean conditions. A LIFE+ project was initiated (oLIVE-CLIMA; LIFE 11/ENV/000942) aiming to introduce new management practices in olive tree crops that lead to increased carbon dioxide uptake by plants as well as carbon sequestration from the atmosphere and reverse the trend of soil organic matter decline, erosion and desertification. This paper presents data on soil organic matter and microbial activity from a soil campaign in a pilot region in Greece, and particularly in the area of Chora, prefecture of Messinia, South west Peloponnese. The soil campaign took place during the period December 2012-February 2013. Twelve soil parcels of olive groves were selected (6 irrigated and 6 rainfed) and in each soil parcel six composite soil samples were taken from 0-10 cm depth at equal intervals along a straight line of the trunk of the tree to the middle of the distance from the nearest tree of the next tree series. The first three samples were under olive tree canopy. An additional composite sample was taken at depth of 10-40 cm. Soil samples were analyzed for soil physicochemical and biological properties. In this study results for total organic carbon (TOC), soil basal microbial respiration (BR), microbial biomass C (MB-C) from the region of Messinia, are presented. Organic matter was determined by dichromate oxidation. The microbial activity was measured by the amount of CO2 evolution, while microbial biomass C was determined by substrate-induced respiration, after the addition of glucose. The results showed considerable differences in TOC, BR and MB-C associated with the sampling position and soil depth. The higher TOC, BR and MB-C values, in most cases, were determined in samples taken from points under the canopy, but not close to the tree trunk compared to the sampling points outside the canopy. This indicates the positive effect of

  19. The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon

    PubMed Central

    Xu, Weihui; Wang, Zhigang; Wu, Fengzhi

    2015-01-01

    The growth of watermelon is often threatened by Fusarium oxysporum f. sp. niveum (Fon) in successively monocultured soil, which results in economic loss. The objective of this study was to investigate the effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon and to explore the relationship between the effect and the incidence of wilt caused by Fon. The results showed that the activities of soil polyphenol oxidase, urease and invertase were increased, the microbial biomass nitrogen (MBN) and microbial biomass phosphorus (MBP) were significantly increased, and the ratio of MBC/MBN was decreased (P < 0.05). Real-time PCR analysis showed that the Fon population declined significantly in the watermelon/wheat companion system compared with the monoculture system (P < 0.05). The analysis of microbial communities showed that the relative abundance of microbial communities was changed in the rhizosphere of watermelon. Compared with the monoculture system, the relative abundances of Alphaproteobacteria, Actinobacteria, Gemmatimonadetes and Sordariomycetes were increased, and the relative abundances of Gammaproteobacteria, Sphingobacteria, Cytophagia, Pezizomycetes, and Eurotiomycetes were decreased in the rhizosphere of watermelon in the watermelon/wheat companion system; importantly, the incidence of Fusarium wilt was also decreased in the watermelon/wheat companion system. In conclusion, this study indicated that D123 wheat as a companion crop increased soil enzyme activities and microbial biomass, decreased the Fon population, and changed the relative abundance of microbial communities in the rhizosphere of watermelon, which may be related to the reduction of Fusarium wilt in the watermelon/wheat companion system. PMID:26388851

  20. Arctic gypsum endoliths: a biogeochemical characterization of a viable and active microbial community

    NASA Astrophysics Data System (ADS)

    Ziolkowski, L. A.; Mykytczuk, N. C. S.; Omelon, C. R.; Johnson, H.; Whyte, L. G.; Slater, G. F.

    2013-11-01

    , which contrasts with other endolithic habitats. While it is possible that these communities turn over carbon quickly and leave little evidence of microbe-mineral interaction, an alternative hypothesis is that the soluble and friable nature of gypsum and harsh conditions lead to elevated erosion rates, limiting microbial residence times in this habitat. Regardless, this endolithic community represents a microbial system that does not rely on a nutrient pool from the host gypsum cap rock, instead receiving these elements from allochthonous debris to maintain a more diverse and active community than might have been predicted in the polar desert of the Canadian high Arctic.

  1. Effects of Environmental Toxicants on Metabolic Activity of Natural Microbial Communities

    PubMed Central

    Barnhart, Carole L. H.; Vestal, J. Robie

    1983-01-01

    Two methods of measuring microbial activity were used to study the effects of toxicants on natural microbial communities. The methods were compared for suitability for toxicity testing, sensitivity, and adaptability to field applications. This study included measurements of the incorporation of 14C-labeled acetate into microbial lipids and microbial glucosidase activity. Activities were measured per unit biomass, determined as lipid phosphate. The effects of various organic and inorganic toxicants on various natural microbial communities were studied. Both methods were useful in detecting toxicity, and their comparative sensitivities varied with the system studied. In one system, the methods showed approximately the same sensitivities in testing the effects of metals, but the acetate incorporation method was more sensitive in detecting the toxicity of organic compounds. The incorporation method was used to study the effects of a point source of pollution on the microbiota of a receiving stream. Toxic doses were found to be two orders of magnitude higher in sediments than in water taken from the same site, indicating chelation or adsorption of the toxicant by the sediment. The microbiota taken from below a point source outfall was 2 to 100 times more resistant to the toxicants tested than was that taken from above the outfall. Downstream filtrates in most cases had an inhibitory effect on the natural microbiota taken from above the pollution source. The microbial methods were compared with commonly used bioassay methods, using higher organisms, and were found to be similar in ability to detect comparative toxicities of compounds, but were less sensitive than methods which use standard media because of the influences of environmental factors. PMID:16346432

  2. Soil microbial activity and structure in mineralized terranes of the Western US

    NASA Astrophysics Data System (ADS)

    Blecker, S. W.; Stillings, L. L.; Decrappeo, N.; Ippolito, J.

    2009-12-01

    Mineralized terranes (areas enriched in metal-bearing minerals) occur throughout the Western US, and are characterized by highly variable soil trace metal concentrations across small spatial scales. Assuming that non-lithologic (extrinsic) soil forming factors are relatively constant between mineralized and unmineralized zones, these mineralized areas allowed us to evaluate the effect of lithology on soil microbial activity. We established the following study sites: 1) sage-grassland on a Mo/Cu deposit (Battle Mountain, NV); 2) pine-chaparral on Ni/Cr bearing rocks (Chinese Camp, CA); and 3) two pine woodland sites on acid-sulfate altered rocks (Reno, NV; Bridgeport, CA). Microbial, physical and chemical measurements were performed on soils from undisturbed mineralized areas and adjacent unmineralized areas to determine baseline conditions for comparison to sites disturbed by mining. A host of abiotic soil parameters, along with bioavailable (diethylenetriaminepentaacetic acid (DTPA)-extractable) and total metals, were measured to examine their correlation with the following measures of microbial activity: enzyme assays (arylsulfatase, phosphatase, fluorescein diacetate hydrolysis), C/N mineralization potential, C substrate utilization (Biolog Ecoplate), and microbial biomass and community structure (phospholipid fatty acid analysis). Within the Battle Mountain study area, both microbial activity and structure were statistically similar between mineralized and unmineralized soils. Nutrient and metal concentrations were also similar; the only differences being higher Cu and lower P in the mineralized soils. Within the Chinese Camp study area, soil organic carbon and total nitrogen concentrations were similar between the serpentine (Ni/Cr bearing) and adjacent andesite soils, while differences were noted for other nutrients (S, P, Ca, Mg). For the serpentine soils, Co, Fe, Mn, and Ni showed the strongest correlations with microbial activity, where Cr, Mn showed the

  3. Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments

    PubMed Central

    Franzetti, Andrea; Lundin, Daniel; Sjöling, Sara

    2016-01-01

    Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic areas in the world. High nutrient input and low water exchange result in eutrophication and oxygen depletion below the halocline. As a consequence at Landsort Deep, the deepest point of the Baltic Sea, anoxia in the sediments has been a persistent condition over the past decades. Given that microbial communities are drivers of essential ecosystem functions we investigated the microbial community metabolisms and functions of oxygen depleted Landsort Deep sediments by metatranscriptomics. Results show substantial expression of genes involved in protein metabolism demonstrating that the Landsort Deep sediment microbial community is active. Identified expressed gene suites of metabolic pathways with importance for carbon transformation including fermentation, dissimilatory sulphate reduction and methanogenesis were identified. The presence of transcripts for these metabolic processes suggests a potential for heterotrophic-autotrophic community synergism and indicates active mineralisation of the organic matter deposited at the sediment as a consequence of the eutrophication process. Furthermore, cyanobacteria, probably deposited from the water column, are transcriptionally active in the anoxic sediment at this depth. Results also reveal high abundance of transcripts encoding integron integrases. These results provide insight into the activity of the microbial community of the anoxic sediment at the deepest point of the Baltic Sea and its possible role in ecosystem functioning. PMID:26823996

  4. Chlorpromazine as permeabilizer and reagent for detection of microbial peroxidase and peroxidaselike activities.

    PubMed Central

    Galeazzi, L; Turchetti, G; Grilli, G; Groppa, G; Giunta, S

    1986-01-01

    Chlorpromazine was used to perform a test for the detection of microbial peroxidase activities. The compound acts as both a cell permeabilizer and a reagent in the procedure developed which allows the detection of peroxidase and peroxidase like reactions both semiquantitatively in whole cell determinations and quantitatively in cell-free supernatants. PMID:3539020

  5. Imidazolium tagged acridines: Synthesis, characterization and applications in DNA binding and anti-microbial activities

    NASA Astrophysics Data System (ADS)

    Raju, Gembali; Vishwanath, S.; Prasad, Archana; Patel, Basant K.; Prabusankar, Ganesan

    2016-03-01

    New water soluble 4,5-bis imidazolium tagged acridines have been synthesized and structurally characterized by multinuclear NMR and single crystal X-ray diffraction techniques. The DNA binding and anti-microbial activities of these acridine derivatives were investigated by fluorescence and far-UV circular dichroism studies.

  6. Microbial respiration and extracellular enzyme activity in sediments from the Gulf of Mexico hypoxic zone

    EPA Science Inventory

    This study explores the relationship between sediment chemistry (TC, TN, TP) and microbial respiration (DHA) and extracellular enzyme activity (EEA) across the Gulf of Mexico (GOM) hypoxic zone. TC, TN, and TP were all positively correlated with each other (r=0.19-0.68). DHA was ...

  7. A Qualitative Experiment to Analyze Microbial Activity in Topsoil Using Paper and a Handmade Reflection Photometer

    ERIC Educational Resources Information Center

    Agbeko, Julius Kofi; Kita, Masakazu

    2007-01-01

    This article describes a novel, hands-on method to qualitatively determine the extent of microbial activity in topsoil using ordinary blank paper. Appropriate and scalable for the high school and college level, these experiments expose students to some of the challenges facing environmental researchers and also contribute to curriculum development…

  8. Factors affecting the microbial degradation of phenanthrene in soil. (Reannouncement with new availability information)

    SciTech Connect

    Manilal, V.B.; Alexander, M.

    1991-12-31

    Because phenanthrene was mineralized more slowly in soils than in liquid media, a study was conducted to determine the environmental factors that may account for the slow biodegradation in soil. Mineralization was enhanced by additions of phosphate but not potassium, and it was reduced by additions of nitrate. Aeration or amending the soil with glucose affected the rate of mineralization, although not markedly. Phenanthrene was sorbed to soil constituents, the extent of sorption being directly related to the percentage of organic matter in the soil. Soluble phenanthrene was not detected after addition of the compound to a muck soil. The rate of mineralization was slow in the organic soil and higher in mineral soils with lower percentages of organic matter. We suggest that sorption by soil organic matter slows the biodegradation of polycyclic aromatic hydrocarbons that are otherwise readily metabolized.

  9. Microbial Content of Nonsterile Therapeutic Agents Containing Natural or Seminatural Active Ingredients

    PubMed Central

    Schiller, I.; Kuntscher, H.; Wolff, A.; Nekola, M.

    1968-01-01

    The relationship was investigated between various chemical or pharmaceutical production processes and the extent of microbial contamination, of natural origin, of the resulting products. The products contained active ingredients of vegetable, enzymatic, or animal origin. It was concluded that (i) vegetable products practically free from microbes can be produced if the proper manufacturing steps are taken; (ii) sterilization of the media used to manufacture antibiotics, etc., produces products with little contamination; and (iii) products containing extracts of animal organs require careful refrigeration and addition of preservatives to produce acceptable levels of microbial contamination. PMID:5726165

  10. Microbial Community Composition, Functions, and Activities in the Gulf of Mexico 1 Year after the Deepwater Horizon Accident.

    PubMed

    Yergeau, Etienne; Maynard, Christine; Sanschagrin, Sylvie; Champagne, Julie; Juck, David; Lee, Kenneth; Greer, Charles W

    2015-09-01

    Several studies have assessed the effects of the released oil on microbes, either during or immediately after the Deepwater Horizon accident. However, little is known about the potential longer-term persistent effects on microbial communities and their functions. In this study, one water column station near the wellhead (3.78 km southwest of the wellhead), one water column reference station outside the affected area (37.77 km southeast of the wellhead), and deep-sea sediments near the wellhead (3.66 km southeast of the wellhead) were sampled 1 year after the capping of the well. In order to analyze microbial community composition, function, and activity, we used metagenomics, metatranscriptomics, and mineralization assays. Mineralization of hexadecane was significantly higher at the wellhead station at a depth of ∼1,200 m than at the reference station. Community composition based on taxonomical or functional data showed that the samples taken at a depth of ∼1,200 m were significantly more dissimilar between the stations than at other depths (surface, 100 m, 750 m, and >1,500 m). Both Bacteria and Archaea showed reduced activity at depths of ∼1,200 m when the wellhead station was compared to the reference station, and their activity was significantly higher in surficial sediments than in 10-cm sediments. Surficial sediments also harbored significantly different active genera than did 5- and 10-cm sediments. For the remaining microbial parameters assessed, no significant differences could be observed between the wellhead and reference stations and between surface and 5- to 10-cm-deep sediments.

  11. Microbial Community Composition, Functions, and Activities in the Gulf of Mexico 1 Year after the Deepwater Horizon Accident

    PubMed Central

    Yergeau, Etienne; Maynard, Christine; Sanschagrin, Sylvie; Champagne, Julie; Juck, David; Lee, Kenneth

    2015-01-01

    Several studies have assessed the effects of the released oil on microbes, either during or immediately after the Deepwater Horizon accident. However, little is known about the potential longer-term persistent effects on microbial communities and their functions. In this study, one water column station near the wellhead (3.78 km southwest of the wellhead), one water column reference station outside the affected area (37.77 km southeast of the wellhead), and deep-sea sediments near the wellhead (3.66 km southeast of the wellhead) were sampled 1 year after the capping of the well. In order to analyze microbial community composition, function, and activity, we used metagenomics, metatranscriptomics, and mineralization assays. Mineralization of hexadecane was significantly higher at the wellhead station at a depth of ∼1,200 m than at the reference station. Community composition based on taxonomical or functional data showed that the samples taken at a depth of ∼1,200 m were significantly more dissimilar between the stations than at other depths (surface, 100 m, 750 m, and >1,500 m). Both Bacteria and Archaea showed reduced activity at depths of ∼1,200 m when the wellhead station was compared to the reference station, and their activity was significantly higher in surficial sediments than in 10-cm sediments. Surficial sediments also harbored significantly different active genera than did 5- and 10-cm sediments. For the remaining microbial parameters assessed, no significant differences could be observed between the wellhead and reference stations and between surface and 5- to 10-cm-deep sediments. PMID:26092461

  12. MICROBIAL ACTIVITIES FOR THE REMEDIATION OF MERCURY CONTAMINATION

    EPA Science Inventory

    Methylmercury (MeHg) accumulation by aquatic biota could be reduced by stimulating bacterial degradation of MeHg and the reduction of Hg(II) to volatile Hg to zero power. Reduction of Hg(II) affects MeHg production by substrate limitation. The potential of bacterial reduction of ...

  13. A model of microbial activity in lake sediments in response to periodic water-column mixing.

    PubMed

    Gantzer, Charles J; Stefan, Heinz G

    2003-07-01

    Under stagnant conditions, the mass transport of a soluble substrate from a lake's water column to the sediment/water interface is limited by molecular diffusion. Stagnant conditions coupled with a continuing sediment biological demand create a substrate depletion zone above the sediment/water interface. The frequency at which the substrate depletion zone is destroyed by internal seiches and other intermittent flow phenomena influences the time-averaged substrate concentration at the sediment/water interface. A more frequent mixing results in a greater time-averaged interface concentration and consequently affects the amount of microbial biomass that can be supported in the lake sediments and the flux of the substrate into the sediment. A one-dimensional, two-substrate model is used to examine the impact of mixing frequency on the activity of sulfate-reducing bacteria (SRB) in lake sediments. In the model, sulfate is supplied from the water column, while acetate is generated within the sediments. Mass transport to and within the sediments is by molecular diffusion except for instantaneous mixing events. Between mixing events, sulfate concentration gradients form above the sediment/water interface in the diffusive boundary layer. Sulfate depletion zones can be centimeters thick. When typical biological rate and diffusion coefficients for sulfate and acetate are used as inputs, the model indicates that a more frequent water-column mixing results in greater SRB concentrations. For an assumed bulk water-column sulfate concentration of 4.8 mg x l(-1), the sediment SRB concentrations for the modeled hourly, 6-hourly, daily, and weekly mixing frequencies were 175, 136, 91, and 30 mg x m(-2), respectively. The model also predicts higher time-averaged sulfate flux rates at more frequent water-column mixing. The time-averaged sulfate flux rates for the hourly, 6-hourly, daily, and weekly mixing frequencies were 1.26, 1.13, 0.78, and 0.30 mg x m(-2)h(-1), respectively. Thus

  14. [Microbial composition of the activated sludges of the Moscow wastewater treatment plants].

    PubMed

    Kallistova, A Iu; Pimenov, N V; Kozlov, M N; Nikolaev, Iu A; Dorofeev, A G; Aseeva, V G; Grachev, V A; Men'ko, E V; Berestovskaia, Iu Iu; Nozhevnikova, A N; Kevbrina, M V

    2014-01-01

    The contribution of the major technologically important microbial groups (ammonium- and nitrite-oxidizing, phosphate-accumulating, foam-inducing, and anammox bacteria, as well as planctomycetes and methanogenic archaea) was characterized for the aeration tanks of the Moscow wastewater treatment facilities. FISH investigation revealed that aerobic sludges were eubacterial communities; the metabolically active archaea contributed insignificantly. Stage II nitrifying microorganisms and planctomycetes were significant constituents of the bacterial component of activated sludge, with Nitrobacter spp. being the dominant nitrifier. No metabolically active anammox bacteria were revealed in the sludge from aeration tanks. The sludge from the aeration tanks using different wastewater treatment technologies were found to differ in characteristics. Abundance of the nitrifying and phosphate-accumulating bacteria in the sludges generally correlated with microbial activity, in microcosms and with efficiency of nitrogen and phosphorus removal from wastewater. The highest microbial numbers and activity were found in the sludges of the tanks operating according to the technologies developed in the universities of Hanover and Cape Town. The activated sludge from the Novokur yanovo facilities, where abundant growth of filamentous bacteria resulted in foam formation, exhibited the lowest activity The group of foaming bacteria included Gordonia spp. and Acinetobacter spp., utilizing petroleum and motor oils, Sphaerotilus spp. utilizing unsaturated fatty acids, and Candidatus 'Microthrix parvicella'. Thus, the data on abundance and composition of metabolically active microorganisms obtained by FISH may be used for the technological control of wastewater treatment.

  15. Comparison of microbial activity in anaerobic and microaerobic digesters.

    PubMed

    Jenicek, P; Celis, C A; Koubova, J; Pokorna, D

    2011-01-01

    Microaerobic alternative of anaerobic digestion offers many advantages especially when sulfide concentration in the digester is high. For better understanding of the microaerobic technology more detailed characterization of biomass activity is needed. Two equal digesters were operated under the same condition except of microaeration in one of them. During long term operation of anaerobic and microaerobic digesters the sludge quality and the biomass activity was monitored. The activity of sulfide oxidizing bacteria of microaerobic biomass was significantly higher in comparison with anaerobic biomass. The activity of sulfate reducing bacteria was comparable. The activity of methanogenic bacteria activity depended on sulfide concentration more than on microaeration. The extent of foaming problems was lower in the microaerobic than in the anaerobic digester.

  16. Aboveground and belowground plant traits as drivers of microbial abundance and activity.

    NASA Astrophysics Data System (ADS)

    Baxendale, Catherine; Lavorel, Sandra; Grigulis, Karl; Legay, Nicolas; Krainer, Ute; Bahn, Michael; Kastl, Eva; Pommier, Thomas; Bardgett, Richard

    2013-04-01

    Although there is growing awareness of the roles that plant-soil interactions play in regulating ecosystem processes, our understanding of the role that specific aboveground and belowground plant traits play in defining them is limited. In this study, we aimed to develop a conceptual model linking plant functional trait impacts on soil microbial functional diversity and their coupled effects on ecosystem processes. This was done by replicating three mesocosm studies, based on model sub-alpine grasslands, across three sites in different parts of Europe as part of the pan-European project, VITAL. We manipulated community plant traits by planting communities of varying abundance and dominance of 4 common grassland species. After 1.5 years, we then measured aboveground traits (specific leaf area, leaf dry matter content, leaf nitrogen and carbon content and leaf C:N ratio), belowground traits (specific root length, average diameter, root dry matter content, root nitrogen and carbon content and root C:N ratio) microbial community abundance (using phospholipid fatty acid (PLFA) analysis and gene abundance of nitrifier and denitrifier communities), and microbial activity (via potential nitrification and denitrification rates). We present links between manipulated community traits, microbial properties and ecosystem processes, supporting the role of plant traits in driving microbial properties.

  17. Impacts of Activated Carbon Amendment on Hg Methylation, Demethylation and Microbial Activity in Marsh Soils

    NASA Astrophysics Data System (ADS)

    Gilmour, C. C.; Ghosh, U.; Santillan, E. F. U.; Soren, A.; Bell, J. T.; Butera, D.; McBurney, A. W.; Brown, S.; Henry, E.; Vlassopoulos, D.

    2015-12-01

    In-situ sorbent amendments are a low-impact approach for remediation of contaminants in sediments, particular in habitats like wetlands that provide important ecosystem services. Laboratory microcosm trials (Gilmour et al. 2013) and early field trials show that activated carbon (AC) can effectively increase partitioning of both inorganic Hg and methylmercury to the solid phase. Sediment-water partitioning can serve as a proxy for Hg and MeHg bioavailability in soils. One consideration in using AC in remediation is its potential impact on organisms. For mercury, a critical consideration is the potential impact on net MeHg accumulation and bioavailability. In this study, we specifically evaluated the impact of AC on rates of methylmercury production and degradation, and on overall microbial activity, in 4 different Hg-contaminated salt marsh soils. The study was done over 28 days in anaerobic, sulfate-reducing slurries. A double label of enriched mercury isotopes (Me199Hg and inorganic 201Hg) was used to separately follow de novo Me201Hg production and Me199Hg degradation. AC amendments decreased both methylation and demethylation rate constants relative to un-amended controls, but the impact on demethylation was stronger. The addition of 5% (dry weight) regenerated AC to soil slurries drove demethylation rate constants to nearly zero; i.e. MeHg sorption to AC almost totally blocked its degradation. The net impact was increased solid phase MeHg concentrations in some of the soil slurries with the highest methylation rate constants. However, the net impact of AC amendments was to increase MeHg (and inorganic Hg) partitioning to the soil phase and decrease concentrations in the aqueous phase. AC significantly decreased aqueous phase inorganic Hg and MeHg concentrations after 28 days. Overall, the efficacy of AC in reducing aqueous MeHg was highest in the soils with the highest MeHg concentrations. The AC addition did not significantly impact microbial activity, as

  18. [Effects of growing time on Panax ginseng rhizosphere soil microbial activity and biomass].

    PubMed

    Xiao, Chun-ping; Yang, Li-min; Ma, Feng-min

    2014-12-01

    Using the field sampling and indoor soil cultivation methods, the dynamic of ginseng rhizosphere soil microbial activity and biomass with three cultivated ages was studied to provide a theory basis for illustrating mechanism of continuous cropping obstacles of ginseng. The results showed that ginseng rhizosphere soil microbial activity and biomass accumulation were inhibited observably by growing time. The soil respiration, soil cellulose decomposition and soil nitrification of ginseng rhizosphere soil microorganism were inhibited significantly (P <0.05), in contrast to the control soil uncultivated ginseng (R0). And the inhibition was gradual augmentation with the number of growing years. The soil microbial activity of 3a ginseng soil (R3) was the lowest, and its activity of soil respiration, soil cellulose decomposition, soil ammonification and soil nitrification was lower than that in R0 with 56.31%, 86.71% and 90. 53% , respectively. The soil ammonification of ginseng rhizosphere soil microbial was significantly promoted compared with R0. The promotion was improved during the early growing time, while the promotion was decreased with the number of growing years. The soil ammonification of R1, R2 and R3 were lower than that in R0 with 32.43%, 80.54% and 66.64% separately. The SMB-C and SMB-N in ginseng rhizosphere soil had a decreased tendency with the number of growing years. The SMB-C difference among 3 cultivated ages was significant, while the SMB-N was not. The SMB of R3 was the lowest. Compared with R0, the SMB-C and the SMB-N were significantly reduced 77.30% and 69.36%. It was considered by integrated analysis that the leading factor of continuous cropping obstacle in ginseng was the changes of the rhizosphere soil microbial species, number and activity as well as the micro-ecological imbalance of rhizosphere soil caused by the accumulation of ginseng rhizosphere secretions.

  19. Response of soil microbial activity and biodiversity in soils polluted with different concentrations of cypermethrin insecticide.

    PubMed

    Tejada, Manuel; García, Carlos; Hernández, Teresa; Gómez, Isidoro

    2015-07-01

    We performed a laboratory study into the effect of cypermethrin insecticide applied to different concentrations on biological properties in two soils [Typic Xerofluvent (soil A) and Xerollic Calciorthid (soil B)]. Two kg of each soil were polluted with cypermethrin at a rate of 60, 300, 600, and 1,200 g ha(-1) (C1, C2, C3, and C4 treatments). A nonpolluted soil was used as a control (C0 treatment). For all treatments and each experimental soil, soil dehydrogenase, urease, β-glucosidase, phosphatase, and arylsulphatase activities and soil microbial community were analysed by phospholipid fatty acids, which were measured at six incubation times (3, 7, 15, 30, 60, and 90 days). The behavior of the enzymatic activities and microbial population were dependent on the dose of insecticide applied to the soil. Compared with the C0 treatment, in soil A, the maximum inhibition of the enzymatic activities was at 15, 30, 45, and 90 days for the C1, C2, C3, and C4 treatments, respectively. However, in soil B, the maximum inhibition occurred at 7, 15, 30, and 45 days for the C1, C2, C3, and C4 treatments, respectively. These results suggest that the cypermethrin insecticide caused a negative effect on soil enzymatic activities and microbial diversity. This negative impact was greater when a greater dose of insecticide was used; this impact was also greater in soil with lower organic matter content. For both soils, and from these respective days onward, the enzymatic activities and microbial populations progressively increased by the end of the experimental period. This is possibly due to the fact that the insecticide or its breakdown products and killed microbial cells, subsequently killed by the insecticide, are being used as a source of energy or as a carbon source for the surviving microorganisms for cell proliferation.

  20. 16 CFR 801.3 - Activities in or affecting commerce.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 16 Commercial Practices 1 2014-01-01 2014-01-01 false Activities in or affecting commerce. 801.3 Section 801.3 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENTS AND INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF 1976 COVERAGE RULES § 801.3...

  1. 16 CFR 801.3 - Activities in or affecting commerce.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 16 Commercial Practices 1 2012-01-01 2012-01-01 false Activities in or affecting commerce. 801.3 Section 801.3 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENTS AND INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF 1976 COVERAGE RULES § 801.3...

  2. 16 CFR 801.3 - Activities in or affecting commerce.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 16 Commercial Practices 1 2010-01-01 2010-01-01 false Activities in or affecting commerce. 801.3 Section 801.3 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENTS AND INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF 1976 COVERAGE RULES § 801.3...

  3. 16 CFR 801.3 - Activities in or affecting commerce.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 16 Commercial Practices 1 2013-01-01 2013-01-01 false Activities in or affecting commerce. 801.3 Section 801.3 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENTS AND INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF 1976 COVERAGE RULES § 801.3...

  4. 16 CFR 801.3 - Activities in or affecting commerce.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 16 Commercial Practices 1 2011-01-01 2011-01-01 false Activities in or affecting commerce. 801.3 Section 801.3 Commercial Practices FEDERAL TRADE COMMISSION RULES, REGULATIONS, STATEMENTS AND INTERPRETATIONS UNDER THE HART-SCOTT-RODINO ANTITRUST IMPROVEMENTS ACT OF 1976 COVERAGE RULES § 801.3...

  5. Monitoring Affect States during Effortful Problem Solving Activities

    ERIC Educational Resources Information Center

    D'Mello, Sidney K.; Lehman, Blair; Person, Natalie

    2010-01-01

    We explored the affective states that students experienced during effortful problem solving activities. We conducted a study where 41 students solved difficult analytical reasoning problems from the Law School Admission Test. Students viewed videos of their faces and screen captures and judged their emotions from a set of 14 states (basic…

  6. Growth of salmonellae on sprouting alfalfa seeds as affected by the inoculum size, native microbial load, and Pseudomonas fluorescens 2-79

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The incidence of human illness associated with the consumption of fresh sprouts has increased very sharply during the past decade. The objective of this study was to investigate the growth dynamics of salmonellae on sprouting alfalfa seeds as affected by the inoculum size, native microbial load, an...

  7. Diclofop-methyl affects microbial rhizosphere community and induces systemic acquired resistance in rice.

    PubMed

    Chen, Si; Li, Xingxing; Lavoie, Michel; Jin, Yujian; Xu, Jiahui; Fu, Zhengwei; Qian, Haifeng

    2017-01-01

    Diclofop-methyl (DM), a widely used herbicide in food crops, may partly contaminate the soil surface of natural ecosystems in agricultural area and exert toxic effects at low dose to nontarget plants. Even though rhizosphere microorganisms strongly interact with root cells, little is known regarding their potential modulating effect on herbicide toxicity in plants. Here we exposed rice seedlings (Xiushui 63) to 100μg/L DM for 2 to 8days and studied the effects of DM on rice rhizosphere microorganisms, rice systemic acquired resistance (SAR) and rice-microorganisms interactions. The results of metagenomic 16S rDNA Illumina tags show that DM increases bacterial biomass and affects their community structure in the rice rhizosphere. After DM treatment, the relative abundance of the bacterium genera Massilia and Anderseniella increased the most relative to the control. In parallel, malate and oxalate exudation by rice roots increased, potentially acting as a carbon source for several rhizosphere bacteria. Transcriptomic analyses suggest that DM induced SAR in rice seedlings through the salicylic acid (but not the jasmonic acid) signal pathway. This response to DM stress conferred resistance to infection by a pathogenic bacterium, but was not influenced by the presence of bacteria in the rhizosphere since SAR transcripts did not change significantly in xenic and axenic plant roots exposed to DM. The present study provides new insights on the response of rice and its associated microorganisms to DM stress.

  8. Metaproteogenomics reveals the soil microbial communities active in nutrient cycling processes under different tree species

    NASA Astrophysics Data System (ADS)

    Keiblinger, Katharina Maria; Masse, Jacynthe; Zühlke, Daniela; Riedel, Katharina; Zechmeister-Boltenstern, Sophie; Prescott, Cindy E.; Grayston, Sue

    2016-04-01

    Tree species exert strong effects on microbial communities in litter and soil and may alter rates of soil processes fundamental to nutrient cycling and carbon fluxes (Prescott and Grayston 2013). However, the influence of tree species on decomposition processes are still contradictory and poorly understood. An understanding of the mechanisms underlying plant influences on soil processes is important for our ability to predict ecosystem response to altered global/environmental conditions. In order to link microbial community structure and function to forest-floor nutrient cycling processes, we sampled forest floors under western redcedar (Thuja plicata), Douglas-fir (Pseudotsuga menziesii) and Sitka spruce (Picea sitchensis) grown in nutrient-poor sites in common garden experiments on Vancouver island (Canada). We measured forest-floor total N, total C, initial NH4+ and NO3- concentrations, DOC, Cmic and Nmic. Gross rates of ammonification and NH4+ consumption were measured using the 15N pool-dilution method. Organic carbon quality was assessed through FTIR analyses. Microbial community structure was analysed by a metaproteogenomic approach using 16S and ITS amplification and sequencing with MiSeq platform. Proteins were extracted and peptides characterized via LC-MS/MS on a Velos Orbitrap to assess the active microbial community. Different microbial communities were active under the three tree species and variation in process rates were observed and will be discussed. This research provides new insights on microbial processes during organic matter decomposition. The metaproteogenomic approach enables us to investigate these changes with respect to possible effects on soil C-storage at even finer taxonomic resolution.

  9. Microbial Community Structure of Activated Sludge for Biosolubilization of Two Different Rock Phosphates.

    PubMed

    Xiao, Chunqiao; Wu, Xiaoyan; Liu, Tingting; Xu, Guang; Chi, Ruan

    2016-12-16

    A microbial consortium was directly taken from activated sludge and was used to solubilize rock phosphates (RPs) in a lab-scale bioreactor in this study. Results showed that the microbial consortium could efficiently release soluble phosphorus (P) from the RPs, and during 30-day incubation, it grew well in the bioreactor and reduced the pH of the solutions. The biosolubilization process was also illustrated by the observation of scanning electron microscopy combined with an energy dispersive X-ray spectroscopy (SEM-EDX), which showed an obvious corrosion on the ore surfaces, and most elements were removed from the ore samples. The analysis of microbial community structure by Illumina 16S ribosomal RNA (rRNA) gene and 18S rRNA gene MiSeq sequencing reflected different microbial diversity and richness in the solutions added with different ore samples. A lower richness and diversity of bacteria but a higher richness and diversity of fungi occurred in the solution added with ore sample 1 compared to that of in the solution added with ore sample 2. Alphaproteobacteria and Saccharomycetes were the dominating bacterial and fungal group, respectively, both in the solutions added with ore samples 1 and 2 at the class level. However, their abundances in the solution added with ore sample 1 were obviously lower than that in the solution added with ore sample 2. This study provides new insights into our understanding of the microbial community structure in the biosolubilization of RPs by a microbial consortium directly taken from activated sludge.

  10. Effects of petroleum contamination on soil microbial numbers, metabolic activity and urease activity.

    PubMed

    Guo, Huan; Yao, Jun; Cai, Minmin; Qian, Yiguang; Guo, Yue; Richnow, Hans H; Blake, Ruth E; Doni, Serena; Ceccanti, Brunello

    2012-06-01

    The influence of petroleum contamination on soil microbial activities was investigated in 13 soil samples from sites around an injection water well (Iw-1, 2, 3, 4) (total petroleum hydrocarbons (TPH): 7.5-78 mg kg(-1)), an oil production well (Op-1, 2, 3, 4, 5) (TPH: 149-1110 mg kg(-1)), and an oil spill accident well (Os-1, 2, 3, 4) (TPH: 4500-34600 mg kg(-1)). The growth rate constant (μ) of glucose stimulated organisms, determined by microcalorimetry, was higher in Iw soil samples than in Op and Os samples. Total cultivable bacteria and fungi and urease activity also decreased with increasing concentration of TPH. Total heat produced demonstrated that TPH at concentrations less than about 1 g kg(-1) soil stimulated anaerobic respiration. A positive correlation between TPH and soil organic matter (OM) and stimulation of fungi-bacteria-urease at low TPH doses suggested that TPH is bound to soil OM and slowly metabolized in Iw soils during OM consumption. These methods can be used to evaluate the potential of polluted soils to carry out self-bioremediation by metabolizing TPH.

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

    PubMed

    Wang, Qiongshan; He, Mengchang; Wang, Ying

    2011-01-01

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

  12. Microbial diversity and activity through a permafrost/ground ice core profile from the Canadian high Arctic.

    PubMed

    Steven, Blaire; Pollard, Wayne H; Greer, Charles W; Whyte, Lyle G

    2008-12-01

    Culture-dependent and culture-independent methods were used in an investigation of the microbial diversity in a permafrost/massive ground ice core from the Canadian high Arctic. Denaturing gradient gel electrophoresis as well as Bacteria and Archaea 16S rRNA gene clone libraries showed differences in the composition of the microbial communities in the distinct core horizons. Microbial diversity was similar in the active layer (surface) soil, permafrost table and permafrost horizons while the ground ice microbial community showed low diversity. Bacteria and Archaea sequences related to the Actinobacteria (54%) and Crenarchaeota (100%) respectively were predominant in the active layer while the majority of sequences in the permafrost were related to the Proteobacteria (57%) and Euryarchaeota (76%). The most abundant phyla in the ground ice clone libraries were the Firmicutes (59%) and Crenarchaeota (82%). Isolates from the permafrost were both less abundant and diverse than in the active layer soil, while no culturable cells were recovered from the ground ice. Mineralization of [1-(14)C] acetic acid and [2-(14)C] glucose was used to detect microbial activity in the different horizons in the core. Mineralization was detected at near ambient permafrost temperatures (-15 degrees C), indicating that permafrost may harbour an active microbial population, while the low microbial diversity, abundance and activity in ground ice suggests a less hospitable microbial habitat.

  13. Effects of Cu on metabolisms and enzyme activities of microbial communities in the process of composting.

    PubMed

    Guo, Xingliang; Gu, Jie; Gao, Hua; Qin, Qingjun; Chen, Zhixue; Shao, Li; Chen, Lin; Li, Hailong; Zhang, Weijuan; Chen, Shengnan; Liu, Jiang

    2012-03-01

    With the compost matrix of pig manure, wheat straw, and spent mushroom substrate, and then inoculated with the Compound Microbe Preparation, the study investigated the effects of the heavy metal Cu on the process of composting. Biolog EcoPlate™ test revealed that at a low content, Cu could improve the capacities of microbial communities to transform and exploit carbon sources in the form of polymer, thus speeding up the decomposition of agricultural wastes, and at a high content, Cu presented inhibiting effect on microbial communities to exploit complex macromolecular carbon sources, thus extending the decomposition of agricultural wastes. Enzyme activity testing showed that at a low content, Cu presented enzyme activity-activating effect at the early period of composting and inhibiting effect in the late period of composting, and at a high content, Cu presented enzyme activity-inhibiting effects through the process of composting.

  14. Climate change in winter versus the growing-season leads to different effects on soil microbial activity in northern hardwood forests

    NASA Astrophysics Data System (ADS)

    Sorensen, P. O.; Templer, P. H.; Finzi, A.

    2014-12-01

    Mean winter air temperatures have risen by approximately 2.5˚ C per decade over the last fifty years in the northeastern U.S., reducing the maximum depth of winter snowpack by approximately 26 cm over this period and the duration of winter snow cover by 3.6 to 4.2 days per decade. Forest soils in this region are projected to experience a greater number of freeze-thaw cycles and lower minimum winter soil temperatures as the depth and duration of winter snow cover declines in the next century. Climate change is likely to result not only in lower soil temperatures during winter, but also higher soil temperatures during the growing-season. We conducted two complementary experiments to determine how colder soils in winter and warmer soils in the growing-season affect microbial activity in hardwood forests at Harvard Forest, MA and Hubbard Brook Experimental Forest, NH. A combination of removing snow via shoveling and buried heating cables were used to induce freeze-thaw events during winter and to warm soils 5˚C above ambient temperatures during the growing-season. Increasing the depth and duration of soil frost via snow-removal resulted in short-term reductions in soil nitrogen (N) production via microbial proteolytic enzyme activity and net N mineralization following snowmelt, prior to tree leaf-out. Declining mass specific rates of carbon (C) and N mineralization associated with five years of snow removal at Hubbard Brook Experimental Forest may be an indication of microbial physiological adaptation to winter climate change. Freeze-thaw cycles during winter reduced microbial extracellular enzyme activity and the temperature sensitivity of microbial C and N mineralization during the growing-season, potentially offsetting nutrient and soil C losses due to soil warming in the growing-season. Our multiple experimental approaches show that winter climate change is likely to contribute to reduced microbial activity in northern hardwood forests.

  15. Response of soil microbial activity and community structure to land use changes in a mountain rainforest region of Southern Ecuador

    NASA Astrophysics Data System (ADS)

    Potthast, Karin; Hamer, Ute; Makeschin, Franz

    2010-05-01

    (DOC_KCl) and nitrogen (TDN_KCl). Thereby, the highest amounts of DOC_KCl and TDN_KCl were associated with high carbon and nitrogen mineralization rates which resulted from the supply of fresh organic substrate from the litter in the forest as well as from easily degradable organic substrate from root exudates of the dense fine-root system of the Setaria grass. Comparing 0 to 5 cm depth, the active pasture showed the highest carbon mineralization, gross N mineralization and ammonium consumption rates which corresponded to the lowest net N mineralization rates indicating an active microbial immobilization of inorganic N. Furthermore, this was associated with the lowest Cmic:Nmic ratio compared to the other land uses. The metabolic quotient of 0 to 5 cm depth increased from 1.1 (forest) to 1.8 (pasture) to 2.7 mg CO2-C g-1 Cmic h-1 (abandoned pasture) indicating the lowest substrate use efficiency after the invasion of bracken due to a higher C:N ratio and lignin content of the bracken residues (Potthast et al., 2010). Mineralization rates of all three land use types were affected by the amount of organic matter susceptible to decomposition. Thereby, the land use change from an active to an abandoned pasture showed an impact on nutrient transfer and on the amount of soil N supplied to plants. Potthast, K., Hamer, U., Makeschin, F., 2010. Impact of litter quality on mineralization processes in managed and abandoned pasture soils in Southern Ecuador. Soil Biology and Biochemistry 42, 56-64.

  16. Rhizosphere bacterial community composition responds to arbuscular mycorrhiza, but not to reductions in microbial activity induced by foliar cutting.

    PubMed

    Vestergård, Mette; Henry, Frédéric; Rangel-Castro, Juan Ignacio; Michelsen, Anders; Prosser, James I; Christensen, Søren

    2008-04-01

    Differences in bacterial community composition (BCC) between bulk and rhizosphere soil and between rhizospheres of different plant species are assumed to be strongly governed by quantitative and qualitative rhizodeposit differences. However, data on the relationship between rhizodeposit amounts and BCC are lacking. Other soil microorganisms, e.g. arbuscular mycorrhizal fungi (AMF), may also influence BCC. We simulated foliar herbivory (cutting) to reduce belowground carbon allocation and rhizodeposition of pea plants grown either with or without AMF. This reduced soil respiration, rhizosphere microbial biomass and bacteriovorous protozoan abundance, whereas none of these were affected by AMF. After labelling plants with (13)CO(2), root and rhizosphere soil (13)C enrichment of cut plants were reduced to a higher extent (24-46%) than shoot (13)C enrichment (10-24%). AMF did not affect (13)C enrichment. Despite these clear indications of reduced rhizosphere carbon-input, denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes PCR-amplified targeting DNA and RNA from rhizosphere soil did not reveal any effects of cutting on banding patterns. In contrast, AMF induced consistent differences in both DNA- and RNA-based DGGE profiles. These results show that a reduction in rhizosphere microbial activity is not necessarily accompanied by changes in BCC, whereas AMF presence inhibits proliferation of some bacterial taxa while stimulating others.

  17. Tracking Dynamics of Plant Biomass Composting by Changes in Substrate Structure, Microbial Community, and Enzyme Activity

    SciTech Connect

    Wei, H.; Tucker, M. P.; Baker, J. O.; Harris, M.; Luo, Y. H.; Xu, Q.; Himmel, M. E.; Ding, S. Y.

    2012-04-01

    Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars. However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as a model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels.

  18. Formation of recent Pb-Ag-Au mineralization by potential sub-surface microbial activity

    NASA Astrophysics Data System (ADS)

    Tornos, Fernando; Velasco, Francisco; Menor-Salván, César; Delgado, Antonio; Slack, John F.; Escobar, Juan Manuel

    2014-08-01

    Las Cruces is a base-metal deposit in the Iberian Pyrite Belt, one of the world’s best-known ore provinces. Here we report the occurrence of major Pb-Ag-Au mineralization resulting from recent sub-surface replacement of supergene oxyhydroxides by carbonate and sulphide minerals. This is probably the largest documented occurrence of recent microbial activity producing an ore assemblage previously unknown in supergene mineralizing environments. The presence of microbial features in the sulphides suggests that these may be the first-described natural bacteriomorphs of galena. The low δ13C values of the carbonate minerals indicate formation by deep anaerobic microbial processes. Sulphur isotope values of sulphides are interpreted here as reflecting microbial reduction in a system impoverished in sulphate. We suggest that biogenic activity has produced around 3.1 × 109 moles of reduced sulphur and 1010 moles of CO2, promoting the formation of ca. 1.19 Mt of carbonates, 114,000 t of galena, 638 t of silver sulphides and 6.5 t of gold.

  19. Discovery of New Compounds Active against Plasmodium falciparum by High Throughput Screening of Microbial Natural Products.

    PubMed

    Pérez-Moreno, Guiomar; Cantizani, Juan; Sánchez-Carrasco, Paula; Ruiz-Pérez, Luis Miguel; Martín, Jesús; El Aouad, Noureddine; Pérez-Victoria, Ignacio; Tormo, José Rubén; González-Menendez, Víctor; González, Ignacio; de Pedro, Nuria; Reyes, Fernando; Genilloud, Olga; Vicente, Francisca; González-Pacanowska, Dolores

    2016-01-01

    Due to the low structural diversity within the set of antimalarial drugs currently available in the clinic and the increasing number of cases of resistance, there is an urgent need to find new compounds with novel modes of action to treat the disease. Microbial natural products are characterized by their large diversity provided in terms of the chemical complexity of the compounds and the novelty of structures. Microbial natural products extracts have been underexplored in the search for new antiparasitic drugs and even more so in the discovery of new antimalarials. Our objective was to find new druggable natural products with antimalarial properties from the MEDINA natural products collection, one of the largest natural product libraries harboring more than 130,000 microbial extracts. In this work, we describe the optimization process and the results of a phenotypic high throughput screen (HTS) based on measurements of Plasmodium lactate dehydrogenase. A subset of more than 20,000 extracts from the MEDINA microbial products collection has been explored, leading to the discovery of 3 new compounds with antimalarial activity. In addition, we report on the novel antiplasmodial activity of 4 previously described natural products.

  20. Microbial Activation of Wooden Vats Used for Traditional Cheese Production and Evolution of Neoformed Biofilms.

    PubMed

    Gaglio, Raimondo; Cruciata, Margherita; Di Gerlando, Rosalia; Scatassa, Maria Luisa; Cardamone, Cinzia; Mancuso, Isabella; Sardina, Maria Teresa; Moschetti, Giancarlo; Portolano, Baldassare; Settanni, Luca

    2015-11-06

    Three Lactococcus lactis subsp. cremoris strains were used to develop ad hoc biofilms on the surfaces of virgin wooden vats used for cheese production. Two vats (TZ) were tested under controlled conditions (pilot plant), and two vats (TA) were tested under uncontrolled conditions (industrial plant). In each plant, one vat (TA1 and TZ1) was used for the control, traditional production of PDO Vastedda della Valle del Belìce (Vastedda) cheese, and one (TA2 and TZ2) was used for experimental production performed after lactococcal biofilm activation and the daily addition of a natural whey starter culture (NWSC). Microbiological and scanning electron microscopy analyses showed differences in terms of microbial levels and composition of the neoformed biofilms. The levels of the microbial groups investigated during cheese production showed significant differences between the control trials and between the control and experimental trials, but the differences were not particularly marked between the TA2 and TZ2 productions, which showed the largest numbers of mesophilic lactic acid bacterium (LAB) cocci. LAB populations were characterized phenotypically and genotypically, and 44 dominant strains belonging to 10 species were identified. Direct comparison of the polymorphic profiles of the LAB collected during cheese making showed that the addition of the NWSC reduced their biodiversity. Sensory evaluation showed that the microbial activation of the wooden vats with the multistrain Lactococcus culture generated cheeses with sensory attributes comparable to those of commercial cheese. Thus, neoformed biofilms enable a reduction of microbial variability and stabilize the sensorial attributes of Vastedda cheese.

  1. Formation of recent Pb-Ag-Au mineralization by potential sub-surface microbial activity.

    PubMed

    Tornos, Fernando; Velasco, Francisco; Menor-Salván, César; Delgado, Antonio; Slack, John F; Escobar, Juan Manuel

    2014-08-06

    Las Cruces is a base-metal deposit in the Iberian Pyrite Belt, one of the world's best-known ore provinces. Here we report the occurrence of major Pb-Ag-Au mineralization resulting from recent sub-surface replacement of supergene oxyhydroxides by carbonate and sulphide minerals. This is probably the largest documented occurrence of recent microbial activity producing an ore assemblage previously unknown in supergene mineralizing environments. The presence of microbial features in the sulphides suggests that these may be the first-described natural bacteriomorphs of galena. The low δ(13)C values of the carbonate minerals indicate formation by deep anaerobic microbial processes. Sulphur isotope values of sulphides are interpreted here as reflecting microbial reduction in a system impoverished in sulphate. We suggest that biogenic activity has produced around 3.1 × 10(9) moles of reduced sulphur and 10(10) moles of CO2, promoting the formation of ca. 1.19 Mt of carbonates, 114,000 t of galena, 638 t of silver sulphides and 6.5 t of gold.

  2. Tracking dynamics of plant biomass composting by changes in substrate structure, microbial community, and enzyme activity

    PubMed Central

    2012-01-01

    Background Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars. However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. Results In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as a model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. Conclusion The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels. PMID:22490508

  3. Microbial metabolic activity in soil as measured by dehydrogenase determinations

    NASA Technical Reports Server (NTRS)

    Casida, L. E., Jr.

    1977-01-01

    The dehydrogenase technique for measuring the metabolic activity of microorganisms in soil was modified to use a 6-h, 37 C incubation with either glucose or yeast extract as the electron-donating substrate. The rate of formazan production remained constant during this time interval, and cellular multiplication apparently did not occur. The technique was used to follow changes in the overall metabolic activities of microorganisms in soil undergoing incubation with a limiting concentration of added nutrient. The sequence of events was similar to that obtained by using the Warburg respirometer to measure O2 consumption. However, the major peaks of activity occurred earlier with the respirometer. This possibly is due to the lack of atmospheric CO2 during the O2 consumption measurements.

  4. Seasonal Variation in Soil Microbial Biomass, Bacterial Community Composition and Extracellular Enzyme Activity in Relation to Soil Respiration in a Northern Great Plains Grassland

    NASA Astrophysics Data System (ADS)

    Wilton, E.; Flanagan, L. B.

    2014-12-01

    Soil respiration rate is affected by seasonal changes in temperature and moisture, but is this a direct effect on soil metabolism or an indirect effect caused by changes in microbial biomass, bacterial community composition and substrate availability? In order to address this question, we compared continuous measurements of soil and plant CO2 exchange made with an automatic chamber system to analyses conducted on replicate soil samples collected on four dates during June-August. Microbial biomass was estimated from substrate-induced respiration rate, bacterial community composition was determined by 16S rRNA amplicon pyrosequencing, and β-1,4-N-acetylglucosaminidase (NAGase) and phenol oxidase enzyme activities were assayed fluorometrically or by absorbance measurements, respectively. Soil microbial biomass declined from June to August in strong correlation with a progressive decline in soil moisture during this time period. Soil bacterial species richness and alpha diversity showed no significant seasonal change. However, bacterial community composition showed a progressive shift over time as measured by Bray-Curtis dissimilarity. In particular, the change in community composition was associated with increasing relative abundance in the alpha and delta classes, and declining abundance of the beta and gamma classes of the Proteobacteria phylum during June-August. NAGase showed a progressive seasonal decline in potential activity that was correlated with microbial biomass and seasonal changes in soil moisture. In contrast, phenol oxidase showed highest potential activity in mid-July near the time of peak soil respiration and ecosystem photosynthesis, which may represent a time of high input of carbon exudates into the soil from plant roots. This input of exudates may stimulate the activity of phenol oxidase, a lignolytic enzyme involved in the breakdown of soil organic matter. These analyses indicated that seasonal change in soil respiration is a complex

  5. Effects of selected surfactants on soil microbial activity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Surfactants (surface-active agents) facilitate and accentuate the emulsifying, dispersing, spreading, and wetting properties of liquids. Surfactants are used in industry to reduce the surface tension of liquid and to solubilize compounds. For agricultural pest management, surfactants are an import...

  6. Microbial Enzyme Activity and Carbon Cycling in Grassland Soil Fractions

    NASA Astrophysics Data System (ADS)

    Allison, S. D.; Jastrow, J. D.

    2004-12-01

    Extracellular enzymes are necessary to degrade complex organic compounds present in soils. Using physical fractionation procedures, we tested whether old soil carbon is spatially isolated from degradative enzymes across a prairie restoration chronosequence in Illinois, USA. We found that carbon-degrading enzymes were abundant in all soil fractions, including macroaggregates, microaggregates, and the clay fraction, which contains carbon with a mean residence time of ~200 years. The activities of two cellulose-degrading enzymes and a chitin-degrading enzyme were 2-10 times greater in organic matter fractions than in bulk soil, consistent with the rapid turnover of these fractions. Polyphenol oxidase activity was 3 times greater in the clay fraction than in the bulk soil, despite very slow carbon turnover in this fraction. Changes in enzyme activity across the restoration chronosequence were small once adjusted for increases in soil carbon concentration, although polyphenol oxidase activity per unit carbon declined by 50% in native prairie versus cultivated soil. These results are consistent with a `two-pool' model of enzyme and carbon turnover in grassland soils. In light organic matter fractions, enzyme production and carbon turnover both occur rapidly. However, in mineral-dominated fractions, both enzymes and their carbon substrates are immobilized on mineral surfaces, leading to slow turnover. Soil carbon accumulation in the clay fraction and across the prairie restoration chronosequence probably reflects increasing physical isolation of enzymes and substrates on the molecular scale, rather than the micron to millimeter scale.

  7. Soil Rhizosphere Microbial Communities and Enzyme Activities under Organic Farming

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study investigated the activities of ß-glucosidase (C cycling, ß-glucosaminidase (C and N cycling), acid phosphatase (P cycling) and arylsulfatase (S cycling) under lettuce (Lactuca sativa), potato (Solanum Tuberosum), onion (Allium cepa L), broccoli (Brassica oleracea var. botrytis) and Tall f...

  8. Analysis of matrix effects critical to microbial transport in organic waste-affected soils across laboratory and field scales

    NASA Astrophysics Data System (ADS)

    Unc, Adrian; Goss, Michael J.; Cook, Simon; Li, Xunde; Atwill, Edward R.; Harter, Thomas

    2012-06-01

    Organic waste applications to soil (manure, various wastewaters, and biosolids) are among the most significant sources of bacterial contamination in surface and groundwater. Transport of bacteria through the vadose zone depends on flow path geometry and stability and is mitigated by interaction between soil, soil solution, air-water interfaces, and characteristics of microbial surfaces. After initial entry, the transport through soil depends on continued entrainment of bacteria and resuspension of those retained in the porous structure. We evaluated the retention of bacteria-sized artificial microspheres, varying in diameter and surface charge and applied in different suspending solutions, by a range of sieved soils contained in minicolumns, the transport of hydrophobic bacteria-sized microspheres through undisturbed soil columns as affected by waste type under simulated rainfall, and the field-scale transport of Enterococcus spp. to an unconfined sandy aquifer after the application of liquid manure. Microsphere retention reflected microsphere properties. The soil type and suspending solution affected retention of hydrophilic but not hydrophobic particles. Retention was not necessarily facilitated by manure-microsphere-soil interactions but by manure-soil interactions. Undisturbed column studies confirmed the governing role of waste type on vadose-zone microsphere transport. Filtration theory applied as an integrated analysis of transport across length scales showed that effective collision efficiency depended on the distance of travel. It followed a power law behavior with the power coefficient varying from ˜0.4 over short distances to >0.9 over 1 m (i.e., very little filtration for a finite fraction of biocolloids), consistent with reduced influence of soil solution and biocolloid properties at longer travel distances.

  9. High Ozone (O3) Affects the Fitness Associated with the Microbial Composition and Abundance of Q Biotype Bemisia tabaci

    PubMed Central

    Hong, Yanyun; Yi, Tuyong; Tan, Xiaoling; Zhao, Zihua; Ge, Feng

    2016-01-01

    Ozone (O3) affects the fitness of an insect, such as its development, reproduction and protection against fungal pathogens, but the mechanism by which it does so remains unclear. Here, we compared the fitness (i.e., the growth and development time, reproduction and protection against Beauveria bassiana (B. bassiana) of Q biotype whiteflies fumigated under hO3 (280 ± 20 ppb) and control O3 (50 ± 10 ppb) concentrations. Moreover, we determined that gene expression was related to development, reproduction and immunity to B. bassiana and examined the abundance and composition of bacteria and fungi inside of the body and on the surface of the Q biotype whitefly. We observed a significantly enhanced number of eggs that were laid by a female, shortened developmental time, prolonged adult lifespan, decreased weight of one eclosion, and reduced immunity to B. bassiana in whiteflies under hO3, but hO3 did not significantly affect the expression of genes related to development, reproduction and immunity. However, hO3 obviously changed the composition of the bacterial communities inside of the body and on the surface of the whiteflies, significantly reducing Rickettsia and enhancing Candidatus_Cardinium. Similarly, hO3 significantly enhanced Thysanophora penicillioides from the Trichocomaceae family and reduced Dothideomycetes (at the class level) inside of the body. Furthermore, positive correlations were found between the abundance of Candidatus_Cardinium and the female whitefly ratio and the fecundity of a single female, and positive correlations were found between the abundance of Rickettsia and the weight of adult whiteflies just after eclosion and immunity to B. bassiana. We conclude that hO3 enhances whitefly development and reproduction but impairs immunity to B. bassiana, and our results also suggest that the changes to the microbial environments inside of the body and on the surface could be crucial factors that alter whitefly fitness under hO3. PMID:27799921

  10. Asymmetric frontal cortical activity and negative affective responses to ostracism.

    PubMed

    Peterson, Carly K; Gravens, Laura C; Harmon-Jones, Eddie

    2011-06-01

    Ostracism arouses negative affect. However, little is known about variables that influence the intensity of these negative affective responses. Two studies fill this void by incorporating work on approach- and withdrawal-related emotional states and their associated cortical activations. Study 1 found that following ostracism anger related directly to relative left frontal cortical activation. Study 2 used unilateral hand contractions to manipulate frontal cortical activity prior to an ostracizing event. Right-hand contractions, compared to left-hand contractions, caused greater relative left frontal cortical activation during the hand contractions as well as ostracism. Also, right-hand contractions caused more self-reported anger in response to being ostracized. Within-condition correlations revealed patterns of associations between ostracism-induced frontal asymmetry and emotive responses to ostracism consistent with Study 1. Taken together, these results suggest that asymmetrical frontal cortical activity is related to angry responses to ostracism, with greater relative left frontal cortical activity being associated with increased anger.

  11. Functional Diversity and Microbial Activity of Forest Soils that Are Heavily Contaminated by Lead and Zinc.

    PubMed

    Pająk, Marek; Błońska, Ewa; Frąc, Magdalena; Oszust, Karolina

    The objective of this study was to assess the impact of metal contamination on microbial functional diversity and enzyme activity in forest soils. This study involved the evaluation of the influence of the texture, carbon content and distance to the source of contamination on the change in soil microbial activity, which did not investigate in previous studies. The study area is located in southern Poland near the city of Olkusz around the flotation sedimentation pond of lead and zinc at the Mining and Metallurgical Company "ZGH Bolesław, Inc.". The central point of the study area was selected as the middle part of the sedimentation pond. The experiment was conducted over a regular 500 × 500-m grid, where 33 sampling points were established. Contents of organic carbon and trace elements (Zn, Pb and Cd), pH and soil texture were investigated. The study included the determination of dehydrogenase and urease activities and microbial functional diversity evaluation based on the community-level physiological profiling approach by Biolog EcoPlate. The greatest reduction in the dehydrogenase and urease activities was observed in light sandy soils with Zn content >220 mg · kg(-1) and a Pb content > 100 mg · kg(-1). Soils with a higher concentration of fine fraction, despite having the greatest concentrations of metals, were characterized by high rates of Biolog®-derived parameters and a lower reduction of enzyme activity.

  12. Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities.

    PubMed

    Li, Jun-Min; Jin, Ze-Xin; Hagedorn, Frank; Li, Mai-He

    2014-11-04

    Native parasitic plants may be used to infect and control invasive plants. We established microcosms with invasive Mikania micrantha and native Coix lacryma-jobi growing in mixture on native soils, with M. micrantha being infected by parasitic Cuscuta campestris at four intensity levels for seven weeks to estimate the top-down effects of plant parasitism on the biomass and functional diversity of soil microbial communities. Parasitism significantly decreased root biomass and altered soil microbial communities. Soil microbial biomass decreased, but soil respiration increased at the two higher infection levels, indicating a strong stimulation of soil microbial metabolic activity (+180%). Moreover, a Biolog assay showed that the infection resulted in a significant change in the functional diversity indices of soil microbial communities. Pearson correlation analysis indicated that microbial biomass declined significantly with decreasing root biomass, particularly of the invasive M. micrantha. Also, the functional diversity indices of soil microbial communities were positively correlated with soil microbial biomass. Therefore, the negative effects on the biomass, activity and functional diversity of soil microbial community by the seven week long plant parasitism was very likely caused by decreased root biomass and root exudation of the invasive M. micrantha.

  13. Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities

    PubMed Central

    Li, Jun-Min; Jin, Ze-Xin; Hagedorn, Frank; Li, Mai-He

    2014-01-01

    Native parasitic plants may be used to infect and control invasive plants. We established microcosms with invasive Mikania micrantha and native Coix lacryma-jobi growing in mixture on native soils, with M. micrantha being infected by parasitic Cuscuta campestris at four intensity levels for seven weeks to estimate the top-down effects of plant parasitism on the biomass and functional diversity of soil microbial communities. Parasitism significantly decreased root biomass and altered soil microbial communities. Soil microbial biomass decreased, but soil respiration increased at the two higher infection levels, indicating a strong stimulation of soil microbial metabolic activity (+180%). Moreover, a Biolog assay showed that the infection resulted in a significant change in the functional diversity indices of soil microbial communities. Pearson correlation analysis indicated that microbial biomass declined significantly with decreasing root biomass, particularly of the invasive M. micrantha. Also, the functional diversity indices of soil microbial communities were positively correlated with soil microbial biomass. Therefore, the negative effects on the biomass, activity and functional diversity of soil microbial community by the seven week long plant parasitism was very likely caused by decreased root biomass and root exudation of the invasive M. micrantha. PMID:25367357

  14. Effects of harvester ant (Messor spp.) activity on soil properties and microbial communities in a Negev Desert ecosystem

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Harvester ants (Messor spp.) function as an essential link between aboveground resources and belowground biota such as the microbial community. We examined changes in soil microbial biomass and functional diversity resulting from harvester ant (Messor spp.) activity in the Negev Desert, Israel. Abi...

  15. Milk kefir: composition, microbial cultures, biological activities, and related products

    PubMed Central

    Prado, Maria R.; Blandón, Lina Marcela; Vandenberghe, Luciana P. S.; Rodrigues, Cristine; Castro, Guillermo R.; Thomaz-Soccol, Vanete; Soccol, Carlos R.

    2015-01-01

    In recent years, there has been a strong focus on beneficial foods with probiotic microorganisms and functional organic substances. In this context, there is an increasing interest in the commercial use of kefir, since it can be marketed as a natural beverage that has health promoting bacteria. There are numerous commercially available kefir based-products. Kefir may act as a matrix in the effective delivery of probiotic microorganisms in different types of products. Also, the presence of kefir’s exopolysaccharides, known as kefiran, which has biological activity, certainly adds value to products. Kefiran can also be used separately in other food products and as a coating film for various food and pharmaceutical products. This article aims to update the information about kefir and its microbiological composition, biological activity of the kefir’s microflora and the importance of kefiran as a beneficial health substance. PMID:26579086

  16. How does the anthropogenic activity affect the spring discharge?

    NASA Astrophysics Data System (ADS)

    Hao, Yonghong; Zhang, Juan; Wang, Jiaojiao; Li, Ruifang; Hao, Pengmei; Zhan, Hongbin

    2016-09-01

    Karst hydrological process has largely been altered by climate change and human activity. In many places throughout the world, human activity (e.g. groundwater pumping and dewatering from mining) has intensified and surpassed climate change, where human activity becomes the primary factor that affects groundwater system. But it is still largely unclear how the human activity affects spring discharge in magnitude and periodicity. This study investigates the effects of anthropogenic activity on spring discharge, using the Xin'an Springs of China as an example. The Xin'an Spring discharge were divided into two time periods: the pre-development period from 1956 to 1971 and the post-development period from 1972 to 2013. We confirm the dividing time (i.e. 1971) of these two periods using the Wilcoxon rank-sum test. Then the wavelet transform and wavelet coherence were used to analyze the karst hydrological processes for the two periods respectively. We analyze the correlations of precipitation and the Xin'an spring discharge with the monsoons including the Indian Summer Monsoon (ISM) and the West North Pacific Monsoon (WNPM) and the climate teleconnections including El Niño Southern Oscillation (ENSO) and Pacific Decadal Oscillation (PDO), respectively. The results indicated that the spring discharge was attenuated about 19.63% under the influence of human activity in the Xin'an Springs basin. However, human activity did not alter the size of the resonance frequencies between the spring discharge and the monsoons. In contrast, it reinforced the periodicities of the monsoons-driven spring discharge. It suggested that human has adapted to the major climate periodicities, and human activity had the same rhyme with the primary climate periodicity. In return, human activity enhances the correlation between the monsoons and the spring discharge.

  17. The dissipation of three fungicides in a biobed organic substrate and their impact on the structure and activity of the microbial community.

    PubMed

    Marinozzi, Maria; Coppola, Laura; Monaci, Elga; Karpouzas, Dimitrios G; Papadopoulou, Evangelia; Menkissoglu-Spiroudi, Urania; Vischetti, Costantino

    2013-04-01

    Biopurification systems (BPS) have been introduced to minimise the risk for point source contamination of natural water resources by pesticides. Their depuration efficiency relies mostly on the high biodegradation of their packing substrate (biomixture). Despite that, little is known regarding the interactions between biomixture microflora and pesticides, especially fungicides which are expected to have a higher impact on the microbial community. This study reports the dissipation of the fungicides azoxystrobin (AZX), fludioxonil (FL) and penconazole (PC), commonly used in vineyards, in a biomixture composed of pruning residues and straw used in vineyard BPS. The impact of fungicides on the microbial community was also studied via microbial biomass carbon, basal respiration and phospholipid fatty acid analysis. AZX dissipated faster (t1/2 = 30.1 days) than PC (t1/2 = 99.0 days) and FL (t1/2 = 115.5 days). Fungicides differently affected the microbial community. PC showed the highest adverse effect on both the size and the activity of the biomixture microflora. A significant change in the structure of the microbial community was noted for PC and FL, and it was attributed to a rapid inhibition of the fungal fraction while bacteria showed a delayed response which was attributed to indirect effects by the late proliferation of fungi. All effects observed were transitory and a full recovery of microbial indices was observed 60 days post-application. Overall, no clear link between pesticide persistence and microbial responses was observed stressing the complex nature of interactions between pesticides in microflora in BPS.

  18. Microbial Activity in Active and Upper Permafrost Layers in Axel Heiberg Island

    NASA Astrophysics Data System (ADS)

    Vishnivetskaya, T. A.; Allan, J.; Cheng, K.; Chourey, K.; Hettich, R. L.; Layton, A.; Liu, X.; Murphy, J.; Mykytczuk, N. C.; Phelps, T. J.; Pfiffner, S. M.; Saarunya, G.; Stackhouse, B. T.; Whyte, L.; Onstott, T. C.

    2011-12-01

    Data on microbial communities and their metabolic activity in Arctic wetlands and underlying permafrost sediments is lacking. Samples were collected from different depths of a cryosol (D1, D2) and upper permafrost (D3) at the Axel Heiberg Island in July 2009. Upper cryosol has lower H2O but higher C and N content when compared to deeper horizons including upper permafrost layer. Deep cryosol and upper permafrost contained SO42- (155 and 132 ppm) and NO3- (0.12 and 0.10 ppm), respectively. The phylogenetic analyses of the environmental 16S rRNA genes showed the putative SRB were more abundant in permafrost (8%) than in cryosols, D1 (0.2%) and D2 (1.1%). Putative denitrifying bacteria varied along depth with near 0.1% in D1 and a significant increase in D2 (2.7%) and D3 (2.2%). Methanogens were not detected; methanotrophs were present at low levels in D3 (1%). Two sets of microcosms were set up. Firstly, anaerobic microcosms, amended with 10 mM glucose, sulfate or nitrate, were cultivated at varying temperatures (15o, 6o, and 0o C) for 10 months. Metabolic activity was monitored by measuring CO2 and CH4 every 3 months. A total of 89.5% of the D3-originated microcosms showed higher activity in comparison to cryosols in first 3 months. CH4 was not detected in these microcosms, whereas CO2 production was higher at 15o C or with glucose. Metaproteomics analyses of microcosms with higher levels of CO2 production indicated the presence of stress responsive proteins (e.g. DnaK, GroEL) and proteins essential for energy production and survival under carbon starvation (e.g. F0F1 ATP synthase, acyl-CoA dehydrogenase). These proteins have been previously shown to be up-regulated at low temperatures by permafrost bacteria. Metaproteomics data based on the draft sequences indicated the presence of proteins from the genera Bradyrhizobium, Sphingomonas, Lysinibacillus and Methylophilaceae and these bacteria were also detected by pyrosequencing. Secondly, a duplicate set of anaerobic

  19. Effects of soil organic matter properties and microbial community composition on enzyme activities in cryoturbated arctic soils.

    PubMed

    Schnecker, Jörg; Wild, Birgit; Hofhansl, Florian; Eloy Alves, Ricardo J; Bárta, Jiří; Capek, Petr; Fuchslueger, Lucia; Gentsch, Norman; Gittel, Antje; Guggenberger, Georg; Hofer, Angelika; Kienzl, Sandra; Knoltsch, Anna; Lashchinskiy, Nikolay; Mikutta, Robert; Santrůčková, Hana; Shibistova, Olga; Takriti, Mounir; Urich, Tim; Weltin, Georg; Richter, Andreas

    2014-01-01

    Enzyme-mediated decomposition of soil organic matter (SOM) is controlled, amongst other factors, by organic matter properties and by the microbial decomposer community present. Since microbial community composition and SOM properties are often interrelated and both change with soil depth, the drivers of enzymatic decomposition are hard to dissect. We investigated soils from three regions in the Siberian Arctic, where carbon rich topsoil material has been incorporated into the subsoil (cryoturbation). We took advantage of this subduction to test if SOM properties shape microbial community composition, and to identify controls of both on enzyme activities. We found that microbial community composition (estimated by phospholipid fatty acid analysis), was similar in cryoturbated material and in surrounding subsoil, although carbon and nitrogen contents were similar in cryoturbated material and topsoils. This suggests that the microbial community in cryoturbated material was not well adapted to SOM properties. We also measured three potential enzyme activities (cellobiohydrolase, leucine-amino-peptidase and phenoloxidase) and used structural equation models (SEMs) to identify direct and indirect drivers of the three enzyme activities. The models included microbial community composition, carbon and nitrogen contents, clay content, water content, and pH. Models for regular horizons, excluding cryoturbated material, showed that all enzyme activities were mainly controlled by carbon or nitrogen. Microbial community composition had no effect. In contrast, models for cryoturbated material showed that enzyme activities were also related to microbial community composition. The additional control of microbial community composition could have restrained enzyme activities and furthermore decomposition in general. The functional decoupling of SOM properties and microbial community composition might thus be one of the reasons for low decomposition rates and the persistence of 400 Gt

  20. Characterization of methane production and microbial community shifts during waste activated sludge degradation in microbial electrolysis cells.

    PubMed

    Sun, Rui; Zhou, Aijuan; Jia, Jianna; Liang, Qing; Liu, Qian; Xing, Defeng; Ren, Nanqi

    2015-01-01

    Microbial electrolysis cell (MECs) were investigated as a promising technology to manage waste activated sludge (WAS) reduction and bio-methane generation. The effect of WAS concentration on the MECs performance was discussed. At the optimal concentration of 15gCOD/L, maximum methane yield of MECs fed with alkaline pretreated WAS (A-WAS) were achieved with the value of 77.13±2.52LCH4/kg-COD on Day 3, which had been improved by 1.5-fold compared with MECs fed with raw WAS (R-WAS), while that was negligible in open circuit controls. Efficient sludge reduction was also obtained in terms of TCOD, total protein, TSS and VSS removal. Pyrosequencing revealed the dominance of exoelectrogen Geobacter and hydrogen-producing bacteria Petrimonas in MECs fed with WAS. Methanocorpusculum with the capacity of methane generation using CO2 and H2 also showed overwhelming dominance (96.01%). The large proportions of Petrimonas and Methanocorpusculum indicated the occurrence of hydrogenotrophic methanogenesis in our methane-producing MECs.

  1. Factors affecting farm noise during common agricultural activities.

    PubMed

    Franklin, R C; Depczynski, J; Challinor, K; Williams, W; Fragar, L J

    2006-05-01

    Hearing injury due to exposure to excessive noise during common farming activities is a significant problem for farmers. The aim of this study was to investigate factors that affect the level of risk to hearing caused by common farming activities. Noise levels on farms were measured across a range of activities and producer groups, and situational factors that effect noise levels were also investigated. Older tractors were found to be 6 dB louder than newer tractors. Cabs reduced noise to the operator by 16 dB, which was halved to 8 dB if a door was open. Radios added between 3 and 5 dB to the noise in the cab. These variables significantly affect the noise level at the ear of operators and others in the workplace, and affect the subsequent exposure limits that are considered safe. Situational factors need to be considered in assessing the level of risk to farmers' hearing and in choosing noise management strategies on the farm. This information has been incorporated into material about hearing and discussions with farmers who participated in field day hearing screening programs in Australia.

  2. 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

  3. Organic layer serves as a hotspot of microbial activity and abundance in Arctic tundra soils.

    PubMed

    Lee, Seung-Hoon; Jang, Inyoung; Chae, Namyi; Choi, Taejin; Kang, Hojeong

    2013-02-01

    Tundra ecosystem is of importance for its high accumulation of organic carbon and vulnerability to future climate change. Microorganisms play a key role in carbon dynamics of the tundra ecosystem by mineralizing organic carbon. We assessed both ecosystem process rates and community structure of Bacteria, Archaea, and Fungi in different soil layers (surface organic layer and subsurface mineral soil) in an Arctic soil ecosystem located at Spitsbergen, Svalbard during the summer of 2008 by using biochemical and molecular analyses, such as enzymatic assay, terminal restriction fragment length polymorphism (T-RFLP), quantitative polymerase chain reaction (qPCR), and pyrosequencing. Activity of hydrolytic enzymes showed difference according to soil type. For all three microbial communities, the average gene copy number did not significantly differ between soil types. However, archaeal diversities appeared to differ according to soil type, whereas bacterial and fungal diversity indices did not show any variation. Correlation analysis between biogeochemical and microbial parameters exhibited a discriminating pattern according to microbial or soil types. Analysis of the microbial community structure showed that bacterial and archaeal communities have different profiles with unique phylotypes in terms of soil types. Water content and hydrolytic enzymes were found to be related with the structure of bacterial and archaeal communities, whereas soil organic matter (SOM) and total organic carbon (TOC) were related with bacterial communities. The overall results of this study indicate that microbial enzyme activity were generally higher in the organic layer than in mineral soils and that bacterial and archaeal communities differed between the organic layer and mineral soils in the Arctic region. Compared to mineral soil, peat-covered organic layer may represent a hotspot for secondary productivity and nutrient cycling in this ecosystem.

  4. Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

    PubMed Central

    Mukherjee, Shinjini; Juottonen, Heli; Siivonen, Pauli; Lloret Quesada, Cosme; Tuomi, Pirjo; Pulkkinen, Pertti; Yrjälä, Kim

    2014-01-01

    Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites. PMID:25105905

  5. Effects of treated wastewater irrigation on contents and dynamics of soil organic carbon and microbial activity

    NASA Astrophysics Data System (ADS)

    Jüschke, E.; Marschner, B.; Chen, Y.; Tarchitzky, J.

    2009-04-01

    In many arid and semi-arid regions, the demand for freshwater as drinking water and other domestic uses is constantly growing due to demographic growth and increasing standard of living. Therefore, less freshwater is available for agricultural irrigation and new water sources are needed. Treated wastewater (TWW) already serves as an important water source in Jordan, the Palestinian Territories and Israel. Related to its high loads with nutrients, salts and organic materials within its use as irrigation water major effects on the soil physical and chemical properties can occur, in the worst case leading to soil degradation. In an ongoing study we are investigated in the effects of TWW irrigation on agricultural soils in the region. Here we present results from analyses of total soil carbon contents and qualities in soils irrigated with freshwater and TWW. Furthermore microbiological parameters were investigated as microbial biomass, microbial activities and enzyme activities. In several sites, subsoils (50-160 cm) from TWW irrigated plots were depleted in soil organic matter with the largest differences occurring in sites with the longest TWW irrigation history. Laboratory incubation experiments with additions of 14C-labelled compounds to the soils showed that microbial activity in freshwater irrigated soils was much more stimulated by sugars or amino acids than in TWW irrigated soils. The lack of such "priming effects" (Hamer & Marschner 2005) in the TWW irrigated soils indicates that here the microorganisms are already operating at their optimal metabolic activity due to the continuous substrate inputs with soluble organic compounds from the TWW. Apparently, this higher microbial activity is causing an increased depletion of soil organic matter, which may have negative long-term effects on soil quality.

  6. Traces of microbial activity in the deep sediment of the Dead Sea: How is life influencing the sedimentary record of this hypersaline lake ?

    NASA Astrophysics Data System (ADS)

    Thomas, Camille; Ebert, Yael; Kiro, Yael; Stein, Mordechai; Ariztegui, Daniel

    2016-04-01

    As part of the ICDP-sponsored Dead Sea Deep Drilling Project (DSDDP), a multi-disciplinary study has been carried out to understand the influence that microbial communities can have on the Dead Sea sedimentary record. Organic matter (lipids) and DNA extraction have been performed along the main core retrieved from the center of the modern Dead Sea. They revealed different associations of microbial communities, influenced by changing climatic and limnological regimes during sedimentation. Moreover, imaging and chemical characterization of authigenic iron-sulfur minerals have revealed the unexpected presence of an active sulfur cycle in the sediment. In particular, their morphology and Fe/S ratios are coherent with incomplete sulfate reduction, limited by sulfur reduction, and often resulting in the preservation of greigite. In glacial period intervals, pyritization may be complete, indicating full sulfate reduction probably allowed by significant accumulation of organic matter in the alternating aragonite and detritus (aad) facies. The DSDDP core provides a unique opportunity to investigate deep diagenetic processes and to assess the role of microbial activity in the Dead Sea hypersaline sediment. Our study shows that this microbial activity influences the carbon and sulfur phases, as well as magnetic fractions, potentially affecting proxies used for paleoenvironmental and paleoclimatic reconstructions.

  7. Effect of three typical sulfide mineral flotation collectors on soil microbial activity.

    PubMed

    Guo, Zunwei; Yao, Jun; Wang, Fei; Yuan, Zhimin; Bararunyeretse, P; Zhao, Yue

    2016-04-01

    The sulfide mineral flotation collectors are wildly used in China, whereas their toxic effect on soil microbial