Heavy metal levels, physicochemical properties and microbial ...

African Journals Online (AJOL)

Journal of Applied Sciences and Environmental Management ... out to assess the microbial, physicochemical and heavy metal characteristics of soil samples from five different waste collection sites within the University of Benin, Benin City and evaluated using standard analytical and classical microbiological methods.

Responses of microbial tolerance to heavy metals along a century-old metal ore pollution gradient in a subarctic birch forest.

Science.gov (United States)

Rousk, Johannes; Rousk, Kathrin

2018-05-07

Heavy metals are some of the most persistent and potent anthropogenic environmental contaminants. Although heavy metals may compromise microbial communities and soil fertility, it is challenging to causally link microbial responses to heavy metals due to various confounding factors, including correlated soil physicochemistry or nutrient availability. A solution is to investigate whether tolerance to the pollutant has been induced, called Pollution Induced Community Tolerance (PICT). In this study, we investigated soil microbial responses to a century-old gradient of metal ore pollution in an otherwise pristine subarctic birch forest generated by a railway source of iron ore transportation. To do this, we determined microbial biomass, growth, and respiration rates, and bacterial tolerance to Zn and Cu in replicated distance transects (1 m-4 km) perpendicular to the railway. Microbial biomass, growth and respiration rates were stable across the pollution gradient. The microbial community structure could be distinguished between sampled distances, but most of the variation was explained by soil pH differences, and it did not align with distance from the railroad pollution source. Bacterial tolerance to Zn and Cu started from background levels at 4 km distance from the pollution source, and remained at background levels for Cu throughout the gradient. Yet, bacterial tolerance to Zn increased 10-fold 100 m from the railway source. Our results show that the microbial community structure, size and performance remained unaffected by the metal ore exposure, suggesting no impact on ecosystem functioning. Copyright © 2018 Elsevier Ltd. All rights reserved.

Anoxia stimulates microbially catalyzed metal release from Animas River sediments.

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Saup, Casey M; Williams, Kenneth H; Rodríguez-Freire, Lucía; Cerrato, José M; Johnston, Michael D; Wilkins, Michael J

2017-04-19

The Gold King Mine spill in August 2015 released 11 million liters of metal-rich mine waste to the Animas River watershed, an area that has been previously exposed to historical mining activity spanning more than a century. Although adsorption onto fluvial sediments was responsible for rapid immobilization of a significant fraction of the spill-associated metals, patterns of longer-term mobility are poorly constrained. Metals associated with river sediments collected downstream of the Gold King Mine in August 2015 exhibited distinct presence and abundance patterns linked to location and mineralogy. Simulating riverbed burial and development of anoxic conditions, sediment microcosm experiments amended with Animas River dissolved organic carbon revealed the release of specific metal pools coupled to microbial Fe- and SO 4 2- -reduction. Results suggest that future sedimentation and burial of riverbed materials may drive longer-term changes in patterns of metal remobilization linked to anaerobic microbial metabolism, potentially driving decreases in downstream water quality. Such patterns emphasize the need for long-term water monitoring efforts in metal-impacted watersheds.

Anoxia stimulates microbially catalyzed metal release from Animas River sediments

International Nuclear Information System (INIS)

Saup, Casey M.; Williams, Kenneth H.; Rodríguez-Freire, Lucía; Cerrato, José M.; Johnston, Michael D.; Wilkins, Michael J.

2017-01-01

The Gold King Mine spill in August 2015 released 11 million liters of metal-rich mine waste to the Animas River watershed, an area that has been previously exposed to historical mining activity spanning more than a century. Although adsorption onto fluvial sediments was responsible for rapid immobilization of a significant fraction of the spill-associated metals, patterns of longer-term mobility are poorly constrained. Metals associated with river sediments collected downstream of the Gold King Mine in August 2015 exhibited distinct presence and abundance patterns linked to location and mineralogy. Simulating riverbed burial and development of anoxic conditions, sediment microcosm experiments amended with Animas River dissolved organic carbon revealed the release of specific metal pools coupled to microbial Fe- and SO 4 2- reduction. Results suggest that future sedimentation and burial of riverbed materials may drive longer-term changes in patterns of metal remobilization linked to anaerobic microbial metabolism, potentially driving decreases in downstream water quality. Such patterns emphasize the need for long-term water monitoring efforts in metal-impacted watersheds.

Short-time effect of heavy metals upon microbial community activity

International Nuclear Information System (INIS)

Wang Fei; Yao Jun; Si Yang; Chen Huilun; Russel, Mohammad; Chen Ke; Qian Yiguang; Zaray, Gyula; Bramanti, Emilia

2010-01-01

Microcalorimetry was applied to assess and compare the toxic effect of heavy metals, such as As, Cu, Cd, Cr, Co, Pb and Zn, on the soil microbial activities and community. About 1.0 g soil spiked 5.0 mg glucose and 5.0 mg ammonium sulfate, the microbial activities were recorded as power-time curves, and their indices, microbial growth rate constant k, total heat evolution Q T , metabolic enthalpy ΔH met and mass specific heat rate J Q/S , were calculated. Comparing these thermodynamic parameters associated with growth yield, a general order of toxicity to the soil was found to be Cr > Pb > As > Co > Zn > Cd > Cu. When soil was exposed to heavy metals, the amount of bacteria and fungi decreased with the incubation time, and the bacterial number diminished sharply. It illustrates that fungi are more tolerant, and bacteria-fungi ratio would be altered under metal stress. To determine the status of the glucose consumed, a glucose biosensor with eggshell membrane was used to measure the remaining glucose in soil sample. Results showed that the time at which glucose was consumed completely was agreed with the microcalorimetric time to a large extent, and depended on the toxicity of heavy metals as well.

Short-time effect of heavy metals upon microbial community activity.

Science.gov (United States)

Wang, Fei; Yao, Jun; Si, Yang; Chen, Huilun; Russel, Mohammad; Chen, Ke; Qian, Yiguang; Zaray, Gyula; Bramanti, Emilia

2010-01-15

Microcalorimetry was applied to assess and compare the toxic effect of heavy metals, such as As, Cu, Cd, Cr, Co, Pb and Zn, on the soil microbial activities and community. About 1.0 g soil spiked 5.0mg glucose and 5.0mg ammonium sulfate, the microbial activities were recorded as power-time curves, and their indices, microbial growth rate constant k, total heat evolution Q(T), metabolic enthalpy Delta H(met) and mass specific heat rate J(Q/S), were calculated. Comparing these thermodynamic parameters associated with growth yield, a general order of toxicity to the soil was found to be Cr>Pb>As>Co>Zn>Cd>Cu. When soil was exposed to heavy metals, the amount of bacteria and fungi decreased with the incubation time, and the bacterial number diminished sharply. It illustrates that fungi are more tolerant, and bacteria-fungi ratio would be altered under metal stress. To determine the status of the glucose consumed, a glucose biosensor with eggshell membrane was used to measure the remaining glucose in soil sample. Results showed that the time at which glucose was consumed completely was agreed with the microcalorimetric time to a large extent, and depended on the toxicity of heavy metals as well.

Short-time effect of heavy metals upon microbial community activity

Energy Technology Data Exchange (ETDEWEB)

Wang Fei [Key Laboratory of Biogeology and Environmental Geology of Chinese Ministry of Education and Sino-Hungarian Joint Laboratory of Environmental Science and Health and School of Environmental Sciences, China University of Geosciences, 430074 Wuhan (China); Yao Jun, E-mail: yaojun@cug.edu.cn [Key Laboratory of Biogeology and Environmental Geology of Chinese Ministry of Education and Sino-Hungarian Joint Laboratory of Environmental Science and Health and School of Environmental Sciences, China University of Geosciences, 430074 Wuhan (China); Si Yang; Chen Huilun; Russel, Mohammad; Chen Ke; Qian Yiguang [Key Laboratory of Biogeology and Environmental Geology of Chinese Ministry of Education and Sino-Hungarian Joint Laboratory of Environmental Science and Health and School of Environmental Sciences, China University of Geosciences, 430074 Wuhan (China); Zaray, Gyula [Department of Chemical Technology and Environmental Chemistry, Eoetvoes University, H-1518 Budapest, P.O. Box 32 (Hungary); Bramanti, Emilia [Laboratory of Instrumental Analytical Chemistry, Institute for Chemical and Physical Processes, Area di Ricerca, Via G. Moruzzi 1, 56124 Pisa (Italy)

2010-01-15

Microcalorimetry was applied to assess and compare the toxic effect of heavy metals, such as As, Cu, Cd, Cr, Co, Pb and Zn, on the soil microbial activities and community. About 1.0 g soil spiked 5.0 mg glucose and 5.0 mg ammonium sulfate, the microbial activities were recorded as power-time curves, and their indices, microbial growth rate constant k, total heat evolution Q{sub T}, metabolic enthalpy {Delta}H{sub met} and mass specific heat rate J{sub Q/S}, were calculated. Comparing these thermodynamic parameters associated with growth yield, a general order of toxicity to the soil was found to be Cr > Pb > As > Co > Zn > Cd > Cu. When soil was exposed to heavy metals, the amount of bacteria and fungi decreased with the incubation time, and the bacterial number diminished sharply. It illustrates that fungi are more tolerant, and bacteria-fungi ratio would be altered under metal stress. To determine the status of the glucose consumed, a glucose biosensor with eggshell membrane was used to measure the remaining glucose in soil sample. Results showed that the time at which glucose was consumed completely was agreed with the microcalorimetric time to a large extent, and depended on the toxicity of heavy metals as well.

Recovery of valuable metals from polymetallic mine tailings by natural microbial consortium.

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Vardanyan, Narine; Sevoyan, Garegin; Navasardyan, Taron; Vardanyan, Arevik

2018-05-28

Possibilities for the recovery of non-ferrous and precious metals from Kapan polymetallic mine tailings (Armenia) were studied. The aim of this paper was to study the possibilities of bioleaching of samples of concentrated tailings by the natural microbial consortium of drainage water. The extent of extraction of metals from the samples of concentrated tailings by natural microbial consortium reached 41-55% and 53-73% for copper and zinc, respectively. Metal leaching efficiencies of pure culture Leptospirillum ferrooxidans Teg were higher, namely 47-93% and 73-81% for copper and zinc, respectively. The content of gold in solid phase of tailings increased about 7-16% and 2-9% after bio-oxidation process by L. ferrooxidans Teg and natural microbial consortium, respectively. It was shown that bioleaching of the samples of tailings could be performed using the natural consortium of drainage water. However, to increase the intensity of the recovery of valuable metals, natural consortium of drainage water combined with iron-oxidizing L. ferrooxidans Teg has been proposed.

Stability of U(VI) and Tc(VII) Reducing Microbial Communities to EnvironmentalPerturbation: Development and Testing of a Thermodynamic Network Model. Technical Report

International Nuclear Information System (INIS)

Jonathan D. Istok

2008-01-01

'Bioimmobilization' of redox-sensitive metals and radionuclides is being investigated as a way to remediate contaminated groundwater and sediments. In this approach, growth-limiting substrates are added to stimulate the activity of targeted groups of indigenous microorganisms and create conditions favorable for the microbially-mediated precipitation ('bioimmobilization') of targeted contaminants. This project investigated a fundamentally new approach for modeling this process that couples thermodynamic descriptions for microbial growth with associated geochemical reactions. In this approach, a synthetic microbial community is defined as a collection of defined microbial groups; each with a growth equation derived from bioenergetic principles. The growth equations and standard-state free energy yields are appended to a thermodynamic database for geochemical reactions and the combined equations are solved simultaneously to predict the effect of added substrates on microbial biomass, community composition, and system geochemistry. This approach, with a single set of thermodynamic parameters (one for each growth equation), was used to predict the results of laboratory and field bioimmobilization experiments at two geochemically diverse research sites. Predicted effects of ethanol or acetate addition on uranium and technetium solubility, major ion geochemistry, mineralogy, microbial biomass and community composition were in general agreement with experimental observations although the available experimental data precluded rigorous model testing. Model simulations provide insight into the long-standing difficulty in transferring experimental results from the laboratory to the field and from one field site to the next, especially if the form, concentration, or delivery of growth substrate is varied from one experiment to the next. Although originally developed for use in better understanding bioimmobilization of uranium and technetium via reductive precipitation, the

Bioassessment of heavy metal toxicity and enhancement of heavy metal removal by sulfate-reducing bacteria in the presence of zero valent iron.

Science.gov (United States)

Guo, Jing; Kang, Yong; Feng, Ying

2017-12-01

A simple and valid toxicity evaluation of Zn 2+ , Mn 2+ and Cr 6+ on sulfate-reducing bacteria (SRB) and heavy metal removal were investigated using the SRB system and SRB+Fe 0 system. The heavy metal toxicity coefficient (β) and the heavy metal concentration resulting in 50% inhibition of sulfate reduction (I) from a modeling process were proposed to evaluate the heavy metal toxicity and nonlinear regression was applied to search for evaluation indices β and I. The heavy metal toxicity order was Cr 6+  > Mn 2+  > Zn 2+ . Compared with the SRB system, the SRB+Fe 0 system exhibited a better capability for sulfate reduction and heavy metal removal. The heavy metal removal was above 99% in the SRB+Fe 0 system, except for Mn 2+ . The energy-dispersive spectroscopy (EDS) analysis showed that the precipitates were removed primarily as sulfide for Zn 2+ and hydroxide for Mn 2+ and Cr 6+ .The method of evaluating the heavy metal toxicity on SRB was of great significance to understand the fundamentals of the heavy metal toxicity and inhibition effects on the microorganism and regulate the process of microbial sulfate reduction. Copyright © 2017 Elsevier Ltd. All rights reserved.

Melimine-Coated Antimicrobial Contact Lenses Reduce Microbial Keratitis in an Animal Model.

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Dutta, Debarun; Vijay, Ajay K; Kumar, Naresh; Willcox, Mark D P

2016-10-01

To determine the ability of antimicrobial peptide melimine-coated contact lenses to reduce the incidence of microbial keratitis (MK) in a rabbit model of contact lens wear. In vitro antimicrobial activity of melimine-coated contact lenses was determined against Pseudomonas aeruginosa by viable count and a radiolabeled assay. The amount of lipopolysaccharide (LPS) associated with bacteria bound to melimine-coated and control lenses was determined. Ocular swabs from rabbit eyes were collected for assessment of ocular microflora. A rabbit model for MK was developed that used overnight wear of contact lenses colonized by P. aeruginosa in the absence of a corneal scratch. During lens wear, detailed ocular examinations were performed, and the incidence of MK was investigated. Bacteria associated with worn lenses and infected corneas were determined by viable plate count. Inhibition in viable and total P. aeruginosa adhesion by melimine-coated contact lenses was 3.1 log10 and 0.4 log10, respectively. After colonization, the amount of LPS on lenses was approximately the same with or without melimine. Gram-positive bacteria were found in all the ocular swabs followed by fungus (42%). Melimine-coated lens wear was protective and significantly (odds ratio 10.12; P = 0.012) reduced the incidence of P. aeruginosa-driven MK in the rabbit model. The antimicrobial lenses were associated with significantly (P lenses can produce MK without corneal epithelial defect in an animal model. Melimine-coated contact lenses reduced the incidence of MK associated with P. aeruginosa in vivo. Development of MK requires viable bacteria adherent to contact lenses, and bacterial debris adherent at the lens surface did not cause keratitis.

Toxicity effects on metal sequestration by microbially-induced carbonate precipitation

Energy Technology Data Exchange (ETDEWEB)

Mugwar, Ahmed J. [Cardiff School of Engineering, Cardiff University, Queen’s Buildings, The Parade, Cardiff CF24 3AA (United Kingdom); College of Engineering, Al-Muthanna University, Samawah (Iraq); Harbottle, Michael J., E-mail: harbottlem@cardiff.ac.uk [Cardiff School of Engineering, Cardiff University, Queen’s Buildings, The Parade, Cardiff CF24 3AA (United Kingdom)

2016-08-15

Highlights: • Minimum inhibitory concentrations (MIC) are determined for S. pasteurii with a range of metals. • Zinc & cadmium bioprecipitation is strongly linked to microbial carbonate generation. • Lead & copper carbonate bioprecipitation is limited & abiotic processes may be significant. • Bioprecipitation allows survival at & remediation of higher metal concentrations than expected. - Abstract: Biological precipitation of metallic contaminants has been explored as a remedial technology for contaminated groundwater systems. However, metal toxicity and availability limit the activity and remedial potential of bacteria. We report the ability of a bacterium, Sporosarcina pasteurii, to remove metals in aerobic aqueous systems through carbonate formation. Its ability to survive and grow in increasingly concentrated aqueous solutions of zinc, cadmium, lead and copper is explored, with and without a metal precipitation mechanism. In the presence of metal ions alone, bacterial growth was inhibited at a range of concentrations depending on the metal. Microbial activity in a urea-amended medium caused carbonate ion generation and pH elevation, providing conditions suitable for calcium carbonate bioprecipitation, and consequent removal of metal ions. Elevation of pH and calcium precipitation are shown to be strongly linked to removal of zinc and cadmium, but only partially linked to removal of lead and copper. The dependence of these effects on interactions between the respective metal and precipitated calcium carbonate are discussed. Finally, it is shown that the bacterium operates at higher metal concentrations in the presence of the urea-amended medium, suggesting that the metal removal mechanism offers a defence against metal toxicity.

Metal Transport, Heavy Metal Speciation and Microbial Fixation Through Fluvial Subenvironments, Lower Coeur D'Alene River Valley, Idaho

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Hooper, R. L.; Mahoney, J. B.

2001-12-01

The lower Coeur d'Alene River Valley of northern Idaho is the site of extensive lead and zinc contamination resulting from both direct riverine tailings disposal and flood remobilization of contaminated sediments derived from the Coeur d'Alene mining district upstream. Variations in the hydrologic regime, redox conditions, porosity/permeability, organic content and microbial activity results in complicated metal transport pathways. Documentation of these pathways is a prerequisite to effective remediation, and requires accurate analysis of lateral and vertical variations. An analytical approach combining sequential extraction, electron microscopy, and microanalysis provides a comprehensive assessment of particulate speciation in this complex hydrologic system. Rigorously controlled sample preparation and a new sequential extraction protocol provide unprecedented insight into the role of metal sequestration in fluvial subenvironments. Four subenvironments were investigated: bedload, overbank (levee), marsh, and lacustrine. Periodic floods remobilize primary ore minerals and secondary minerals from upstream tailings (primarily oxyhydroxides, sulfides and carbonates). The bedload in the lower valley is a reducing environment and acts as a sink for detrital carbonates and sulfides moving downstream. In addition, authigenic/biogenic Fe, Pb and Zn sulfides and phosphates are common in bedload sediments near the sediment/water interface. Flood redistribution of oxide, sulfide and carbonate phases results in periodic contaminant recharge generating a complex system of metal dissolution, mobilization, migration and precipitation. In levee environments, authigenic sulfides from flood scouring are quickly oxidized resulting in development of oxide coated grain surfaces. Stability of detrital minerals on the levee is variable depending on sediment permeability, grain size and mineralogy resulting in a complex stratigraphy of oxide zones mottled with zones dominated by detrital

Microbially catalyzed nitrate-dependent metal/radionuclide oxidation in shallow subsurface sediments

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Weber, K.; Healy, O.; Spanbauer, T. L.; Snow, D. D.

2011-12-01

Anaerobic, microbially catalyzed nitrate-dependent metal/radionuclide oxidation has been demonstrated in a variety of sediments, soils, and groundwater. To date, studies evaluating U bio-oxidation and mobilization have primarily focused on anthropogenically U contaminated sites. In the Platte River Basin U originating from weathering of uranium-rich igneous rocks in the Rocky Mountains was deposited in shallow alluvial sediments as insoluble reduced uranium minerals. These reduced U minerals are subject to reoxidation by available oxidants, such nitrate, in situ. Soluble uranium (U) from natural sources is a recognized contaminant in public water supplies throughout the state of Nebraska and Colorado. Here we evaluate the potential of anaerobic, nitrate-dependent microbially catalyzed metal/radionuclide oxidation in subsurface sediments near Alda, NE. Subsurface sediments and groundwater (20-64ft.) were collected from a shallow aquifer containing nitrate (from fertilizer) and natural iron and uranium. The reduction potential revealed a reduced environment and was confirmed by the presence of Fe(II) and U(IV) in sediments. Although sediments were reduced, nitrate persisted in the groundwater. Nitrate concentrations decreased, 38 mg/L to 30 mg/L, with increasing concentrations of Fe(II) and U(IV). Dissolved U, primarily as U(VI), increased with depth, 30.3 μg/L to 302 μg/L. Analysis of sequentially extracted U(VI) and U(IV) revealed that virtually all U in sediments existed as U(IV). The presence of U(IV) is consistent with reduced Fe (Fe(II)) and low reduction potential. The increase in aqueous U concentrations with depth suggests active U cycling may occur at this site. Tetravalent U (U(IV)) phases are stable in reduced environments, however the input of an oxidant such as oxygen or nitrate into these systems would result in oxidation. Thus co-occurrence of nitrate suggests that nitrate could be used by bacteria as a U(IV) oxidant. Most probable number

Microbially-reduced graphene scaffolds to facilitate extracellular electron transfer in microbial fuel cells.

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Yuan, Yong; Zhou, Shungui; Zhao, Bo; Zhuang, Li; Wang, Yueqiang

2012-07-01

A one-pot method is exploited by adding graphene oxide (GO) and acetate into an microbial fuel cell (MFC) in which GO is microbially reduced, leading to in situ construction of a bacteria/graphene network in the anode. The obtained microbially reduced graphene (MRG) exhibits comparable conductivity and physical characteristics to the chemically reduced graphene. Electrochemical measurements reveal that the number of exoelectrogens involved in extracellular electron transfer (EET) to the solid electrode, increases due to the presence of graphene scaffolds, and the EET is facilitated in terms of electron transfer kinetics. As a result, the maximum power density of the MFC is enhanced by 32% (from 1440 to 1905 mW m(-2)) and the coulombic efficiency is improved by 80% (from 30 to 54%). The results demonstrate that the construction of the bacteria/graphene network is an effective alternative to improve the MFC performance. Copyright © 2012 Elsevier Ltd. All rights reserved.

Effects of heavy metal Cd pollution on microbial activities in soil.

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Shi, Weilin; Ma, Xiying

2017-12-23

Heavy metal contamination of soil occurs when heavy metals are introduced to soil through human activities, leading to the gradual deterioration of the ecology and environment. Microorganism activity reflects the intensity of various biochemical reactions in soil, and changes in it reflect the level of heavy metal pollution affecting the soil. The effects were studied of heavy metal Cd on the microbial activity of soil at different concentrations by investigating the respiratory intensity, urease activity, and catalase activity in forest soil and garden soil. The results showed that the respiratory intensity, urease and catalase activities in the garden soil were all higher than in the forest soil. Cd has obvious inhibitory effects on microbial activities. The three parameters exhibited a downward trend with increasing concentrations of Cd. Catalase activity increased when the mass concentration of Cd reached 1.0 mg/kg, indicating that low concentrations of Cd can promote the activity of some microorganisms. Respiratory intensity and urease activity also increased when the concentration reached 10.0 mg/kg, showing that respiratory intensity and urease activity have strong response mechanisms to adverse conditions. The effective state of Cd in soil, as well as inhibition of microbial activity, decreased with incubation time.

Effects of heavy metal Cd pollution on microbial activities in soil

Directory of Open Access Journals (Sweden)

Weilin Shi

2017-12-01

Full Text Available Heavy metal contamination of soil occurs when heavy metals are introduced to soil through human activities, leading to the gradual deterioration of the ecology and environment. Microorganism activity reflects the intensity of various biochemical reactions in soil, and changes in it reflect the level of heavy metal pollution affecting the soil. The effects were studied of heavy metal Cd on the microbial activity of soil at different concentrations by investigating the respiratory intensity, urease activity, and catalase activity in forest soil and garden soil. The results showed that the respiratory intensity, urease and catalase activities in the garden soil were all higher than in the forest soil. Cd has obvious inhibitory effects on microbial activities. The three parameters exhibited a downward trend with increasing concentrations of Cd. Catalase activity increased when the mass concentration of Cd reached 1.0 mg/kg, indicating that low concentrations of Cd can promote the activity of some microorganisms. Respiratory intensity and urease activity also increased when the concentration reached 10.0 mg/kg, showing that respiratory intensity and urease activity have strong response mechanisms to adverse conditions. The effective state of Cd in soil, as well as inhibition of microbial activity, decreased with incubation time.

A New Strategy for Heavy Metal Polluted Environments: A Review of Microbial Biosorbents

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Ayangbenro, Ayansina Segun; Babalola, Olubukola Oluranti

2017-01-01

Persistent heavy metal pollution poses a major threat to all life forms in the environment due to its toxic effects. These metals are very reactive at low concentrations and can accumulate in the food web, causing severe public health concerns. Remediation using conventional physical and chemical methods is uneconomical and generates large volumes of chemical waste. Bioremediation of hazardous metals has received considerable and growing interest over the years. The use of microbial biosorbents is eco-friendly and cost effective; hence, it is an efficient alternative for the remediation of heavy metal contaminated environments. Microbes have various mechanisms of metal sequestration that hold greater metal biosorption capacities. The goal of microbial biosorption is to remove and/or recover metals and metalloids from solutions, using living or dead biomass and their components. This review discusses the sources of toxic heavy metals and describes the groups of microorganisms with biosorbent potential for heavy metal removal. PMID:28106848

A New Strategy for Heavy Metal Polluted Environments: A Review of Microbial Biosorbents

Directory of Open Access Journals (Sweden)

Ayansina Segun Ayangbenro

2017-01-01

Full Text Available Persistent heavy metal pollution poses a major threat to all life forms in the environment due to its toxic effects. These metals are very reactive at low concentrations and can accumulate in the food web, causing severe public health concerns. Remediation using conventional physical and chemical methods is uneconomical and generates large volumes of chemical waste. Bioremediation of hazardous metals has received considerable and growing interest over the years. The use of microbial biosorbents is eco-friendly and cost effective; hence, it is an efficient alternative for the remediation of heavy metal contaminated environments. Microbes have various mechanisms of metal sequestration that hold greater metal biosorption capacities. The goal of microbial biosorption is to remove and/or recover metals and metalloids from solutions, using living or dead biomass and their components. This review discusses the sources of toxic heavy metals and describes the groups of microorganisms with biosorbent potential for heavy metal removal.

Understanding the performance of sulfate reducing bacteria based packed bed reactor by growth kinetics study and microbial profiling.

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Dev, Subhabrata; Roy, Shantonu; Bhattacharya, Jayanta

2016-07-15

A novel marine waste extract (MWE) as alternative nitrogen source was explored for the growth of sulfate reducing bacteria (SRB). Variation of sulfate and nitrogen (MWE) showed that SRB growth follows an uncompetitive inhibition model. The maximum specific growth rates (μmax) of 0.085 and 0.124 h(-1) and inhibition constants (Ki) of 56 and 4.6 g/L were observed under optimized sulfate and MWE concentrations, respectively. The kinetic data shows that MWE improves the microbial growth by 27%. The packed bed bioreactor (PBR) under optimized sulfate and MWE regime showed sulfate removal efficiency of 62-66% and metals removal efficiency of 66-75% on using mine wastewater. The microbial community analysis using DGGE showed dominance of SRB (87-89%). The study indicated the optimum dosing of sulfate and cheap organic nitrogen to promote the growth of SRB over other bacteria. Copyright © 2016 Elsevier Ltd. All rights reserved.

Heavy metal immobilization via microbially induced carbonate precipitation and co-precipitation

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Lauchnor, E. G.; Stoick, E.

2017-12-01

Microbially induced CaCO3 precipitation (MICP) has been successfully used in applications such as porous media consolidation and sealing of leakage pathways in the subsurface, and it has the potential to be used for remediation of metal and radionuclide contaminants in surface and groundwater. In this work, MICP is investigated for removal of dissolved heavy metals from contaminated mine discharge water via co-precipitation in CaCO3 or formation of other metal carbonates. The bacterially catalyzed hydrolysis of urea produces inorganic carbon and ammonium and increases pH and the saturation index of carbonate minerals to promote precipitation of CaCO3. Other heavy metal cations can be co-precipitated in CaCO3 as impurities or by replacing Ca2+ in the crystal lattice. We performed laboratory batch experiments of MICP in alkaline mine drainage sampled from an abandoned mine site in Montana and containing a mixture of heavy metals at near neutral pH. Both a model bacterium, Sporosarcina pasteurii, and a ureolytic bacterium isolated from sediments on the mine site were used to promote MICP. Removal of dissolved metals from the aqueous phase was determined via inductively coupled plasma mass spectrometry and resulting precipitates were analyzed via electron microscopy and energy dispersive x-ray spectroscopy (EDX). Both S. pasteurii and the native ureolytic isolate demonstrated ureolysis, increased the pH and promoted precipitation of CaCO3 in batch tests. MICP by the native bacterium reduced concentrations of the heavy metals zinc, copper, cadmium, nickel and manganese in the water. S. pasteurii was also able to promote MICP, but with less removal of dissolved metals. Analysis of precipitates revealed calcium carbonate and phosphate minerals were likely present. The native isolate is undergoing identification via 16S DNA sequencing. Ongoing work will evaluate biofilm formation and MICP by the isolate in continuous flow, gravel-filled laboratory columns. This research

Effect of co-existing plant specie on soil microbial activity under heavy metal stress

International Nuclear Information System (INIS)

Nwuche, C. O.; Ugoji, E. O.

2010-01-01

The influence of plant primary compounds on the activity of soil microbial communities under heavy metal stress was studied in a pot-culture field experiment conducted in a green house. Amaranthus spinosus was cultivated in an agricultural soil previously amended in the laboratory with solutions of different trace elements in two separate treatment modes: singly and in combination. Culture-independent metabolism based indices such as the rate of carbon and nitrogen mineralization, microbial biomass carbon and soil basal respiration were monitored fortnightly over a period of six weeks. Result shows that plant detritus have significant modifying effect on soil microbe-metal interactions. Data on microbial and biochemical processes in the respective mesocosms did not vary from control; not even in mesocosms containing very high concentrations of copper, zinc and nickel. The soil microbial biomass carbon and the rate of carbon and nitrogen cycling were not impeded by the respective metal treatment while the respiration responses increased as a result of increase in metabolic activity of the soil microbes. The plant based substrates enabled the soil microflora to resist high metal contamination because of its tendency to absorb large amounts of inorganic cations.

Value added phytoremediation of metal stressed soils using phosphate solubilizing microbial consortium.

Science.gov (United States)

Gupta, Pratishtha; Kumar, Vipin

2017-01-01

The presence of heavy metals in the soil is a matter of growing concern due to their toxic and non-biodegradable nature. Lack of effectiveness of various conventional methods due to economic and technical constraints resulted in the search for an eco-friendly and cost-effective biological techniques for heavy metal removal from the environment. Until now, phytoremediation has emerged as an innovative technique to address the problem. However, the efficiency of phytoremediation process is hindered under the high metal concentration conditions. Hence, phosphate solubilizing microbes (PSM) assisted phytoremediation technique is gaining more insight as it can reduce the contamination load even under elevated metal stressed conditions. These microbes convert heavy metals into soluble and bioavailable forms, which consequently facilitate phytoremediation. Several studies have reported that the use of microbial consortium for remediation is considered more effective as compared to single strain pure culture. Therefore, this review paper focuses on the current trends in research related to PSM mediated uptake of heavy metal by plants. The efficiency of PSM consortia in enhancing the phytoremediation process has also been reviewed. Moreover, the role of phosphatase enzymes in the mineralization of organic forms of phosphate in soil is further discussed. Biosurfactant mediated bioremediation of metal polluted soils is a matter of extensive research nowadays. Hence, the recent advancement of using biosurfactants in enhanced phytoremediation of metal stressed soils is also described.

Final Report: Stability of U (VII) and Tc (VII) Reducing Microbial Communities To Environmental Perturbation

Energy Technology Data Exchange (ETDEWEB)

Istok, Jonathan D

2008-07-07

'Bioimmobilization' of redox-sensitive metals and radionuclides is being investigated as a way to remediate contaminated groundwater and sediments. In this approach, growth-limiting substrates are added to stimulate the activity of targeted groups of indigenous microorganisms and create conditions favorable for the microbially-mediated precipitation ('bioimmobilization') of targeted contaminants. This project investigated a fundamentally new approach for modeling this process that couples thermodynamic descriptions for microbial growth with associated geochemical reactions. In this approach, a synthetic microbial community is defined as a collection of defined microbial groups; each with a growth equation derived from bioenergetic principles. The growth equations and standard-state free energy yields are appended to a thermodynamic database for geochemical reactions and the combined equations are solved simultaneously to predict the effect of added substrates on microbial biomass, community composition, and system geochemistry. This approach, with a single set of thermodynamic parameters (one for each growth equation), was used to predict the results of laboratory and field bioimmobilization experiments at two geochemically diverse research sites. Predicted effects of ethanol or acetate addition on uranium and technetium solubility, major ion geochemistry, mineralogy, microbial biomass and community composition were in general agreement with experimental observations although the available experimental data precluded rigorous model testing. Model simulations provide insight into the long-standing difficulty in transferring experimental results from the laboratory to the field and from one field site to the next, especially if the form, concentration, or delivery of growth substrate is varied from one experiment to the next. Although originally developed for use in better understanding bioimmobilization of uranium and technetium via reductive

Impact of heavy metal on activity of some microbial enzymes in the riverbed sediments: Ecotoxicological implications in the Ganga River (India).

Science.gov (United States)

Jaiswal, Deepa; Pandey, Jitendra

2018-04-15

We studied the extracellular enzyme activity (EEA) in the riverbed sediment along a 518km gradient of the Ganga River receiving carbon and nutrient load from varied human sources. Also, we tested, together with substrate-driven stimulation, if the heavy metal accumulated in the sediment inhibits enzyme activities. Because pristine values are not available, we considered Dev Prayag, a least polluted site located 624km upstream to main study stretch, as a reference site. There were distinct increases in enzyme activities in the sediment along the study gradient from Dev Prayag, however, between-site differences were in concordance with sediment carbon(C), nitrogen (N) and phosphorus (P). Fluorescein diacetate hydrolysis (FDAase), β-glucosidase (Glu) and protease activities showed positive correlation with C, N and P while alkaline phosphatase was found negatively correlated with P. Enzyme activities were found negatively correlated with heavy metal, although ecological risk index (E R i ) varied with site and metal species. Dynamic fit curves showed significant positive correlation between heavy metal and microbial metabolic quotient (qCO 2 ) indicating a decrease in microbial activity in response to increasing heavy metal concentrations. This study forms the first report linking microbial enzyme activities to regional scale sediment heavy metal accumulation in the Ganga River, suggests that the microbial enzyme activities in the riverbed sediment were well associated with the proportion of C, N and P and appeared to be a sensitive indicator of C, N and P accumulation in the river. Heavy metal accumulated in the sediment inhibits enzyme activities, although C rich sediment showed relatively low toxicity due probably to reduced bioavailability of the metal. The study has relevance from ecotoxicological as well as from biomonitoring perspectives. Copyright © 2017 Elsevier Inc. All rights reserved.

Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

International Nuclear Information System (INIS)

Wang, Yifeng; Papenguth, Hans W.

2000-01-01

Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation

Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

Energy Technology Data Exchange (ETDEWEB)

WANG,YIFENG; PAPENGUTH,HANS W.

2000-05-04

Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation.

Response of rhizosphere microbial community structure and diversity to heavy metal co-pollution in arable soil.

Science.gov (United States)

Deng, Linjing; Zeng, Guangming; Fan, Changzheng; Lu, Lunhui; Chen, Xunfeng; Chen, Ming; Wu, Haipeng; He, Xiaoxiao; He, Yan

2015-10-01

Due to the emerging environmental issues related to heavy metals, concern about the soil quality of farming lands near manufacturing district is increasing. Investigating the function of soil microorganisms exposed to long-term heavy metal contamination is meaningful and important for agricultural soil utilization. This article studied the potential influence of several heavy metals on microbial biomass, activity, abundance, and community composition in arable soil near industrial estate in Zhuzhou, Hunan province, China. The results showed that soil organic contents (SOC) were significantly positive correlated with heavy metals, whereas dehydrogenase activity (DHA) was greatly depressed by the heavy metal stress. Negative correlation was found between heavy metals and basal soil respiration (BSR), and no correlation was found between heavy metals and microbial biomass content (MBC). The quantitative PCR (QPCR) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis could suggest that heavy metal pollution has significantly decreased abundance of bacteria and fungi and also changed their community structure. The results could contribute to evaluate heavy metal pollution level in soil. By combining different environmental parameters, it would promote the better understanding of heavy metal effect on the size, structure, and activity of microbial community in arable soil.

Biostimulation of Iron Reduction and Uranium Immobilization: Microbial and Mineralogical Controls

International Nuclear Information System (INIS)

Joel E. Kostka; Lainie Petrie; Nadia North; David L. Balkwill; Joseph W. Stucki; Lee Kerkhof

2004-01-01

The overall objective of our project is to understand the microbial and geochemical mechanisms controlling the reduction and immobilization of U(VI) during biostimulation in subsurface sediments of the Field Research Center (FRC) which are cocontaminated with uranium and nitrate. The focus will be on activity of microbial populations (metal- and nitrate-reducing bacteria) and iron minerals which are likely to make strong contributions to the fate of uranium during in situ bioremediation. The project will: (1) quantify the relationships between active members of the microbial communities, iron mineralogy, and nitrogen transformations in the field and in laboratory incubations under a variety of biostimulation conditions, (2) purify and physiologically characterize new model metal-reducing bacteria isolated from moderately acidophilic FRC subsurface sediments, and (3) elucidate the biotic and abiotic mechanisms by which FRC aluminosilicate clay minerals are reduced and dissolved under environmental conditions resembling those during biostimulation. Active microbial communities will be assessed using quantitative molecular techniques along with geochemical measurements to determine the different terminal-electron-accepting pathways. Iron minerals will be characterized using a suite of physical, spectroscopic, and wet chemical methods. Monitoring the activity and composition of the denitrifier community in parallel with denitrification intermediates during nitrate removal will provide a better understanding of the indirect effects of nitrate reduction on uranium speciation. Through quantification of the activity of specific microbial populations and an in-depth characterization of Fe minerals likely to catalyze U sorption/precipitation, we will provide important inputs for reaction-based biogeochemical models which will provide the basis for development of in situ U bioremediation strategies. In collaboration with Jack Istok and Lee Krumholz, we have begun to study the

Bioleaching of heavy metal polluted sediment: kinetics of leaching and microbial sulfur oxidation

Energy Technology Data Exchange (ETDEWEB)

Loeser, C. [Technische Universitaet Dresden, Institut fuer Lebenmitteltechnik und Bioverfahrenstechnik, D-01062 Dresden (Germany); Zehnsdorf, A. [UFZ-Umweltforschungszentrum Leipzig-Halle GmbH, Umwelt- und Biotechnologisches Zentrum (UBZ), Permoserstrasse 15, D-04318 Leipzig (Germany); Goersch, K.; Seidel, H. [UFZ-Umweltforschungszentrum Leipzig-Halle GmbH, Department Bioremediation, Permoserstrasse 15, D-04318 Leipzig (Germany)

2005-12-01

Remediation of heavy metal polluted sediment through bioleaching using elemental sulfur (S{sup 0}) as the leaching agent can be regarded as a two-step process: firstly, the microbial oxidation of the added S{sup 0} to sulfuric acid and, secondly, the reaction of the produced acid with the sediment. Here, both subprocesses were studied in detail independently: oxidized river sediment was either suspended in sulfuric acid of various strengths, or mixed with various amounts of finely ground S{sup 0} powder (diameter of the S{sup 0} particles between 1 and 175 {mu}m with a Rosin-Rammler-Sperling-Bennet (RRSB) distribution and an average diameter of 35 {mu}m) and suspended in water. The leaching process was observed by repeated analysis of the suspension concerning pH, soluble sulfate and metals, and remaining S{sup 0}. In the case of abiotic leaching with H{sub 2}SO{sub 4}, the reaction between the acid and the sediment resulted in a gradual increase in pH and a solubilization of sediment-borne heavy metals which required some time; 80 % of the finally solubilized heavy metals was dissolved after 1 h, 90 % after 10 h, and 100 % after 100 h. In the case of bioleaching, the rate of S{sup 0} oxidation was maximal at the beginning, gradually diminished with time, and was proportional to the initial amount of S{sup 0}. Due to its very low solubility in water, S{sup 0} is oxidized in a surface reaction catalyzed by attached bacteria. The oxidation let the particles shrink, their surface became smaller and, thus, the S{sup 0} oxidation rate gradually decreased. The shrinking rate was time-invariant and, at 30 C, amounted to 0.5 {mu}m/day (or 100 {mu}g/cm{sup 2}/day). Within 21 days, 90 % of the applied S{sup 0} was oxidized. Three models with a different degree of complexity have been developed that describe this S{sup 0} oxidation, assuming S{sup 0} particles of uniform size (I), using a measured particle size distribution (II), or applying an adapted RRSB distribution (III

Modeling adaptation of carbon use efficiency in microbial communities

Directory of Open Access Journals (Sweden)

Steven D Allison

2014-10-01

Full Text Available In new microbial-biogeochemical models, microbial carbon use efficiency (CUE is often assumed to decline with increasing temperature. Under this assumption, soil carbon losses under warming are small because microbial biomass declines. Yet there is also empirical evidence that CUE may adapt (i.e. become less sensitive to warming, thereby mitigating negative effects on microbial biomass. To analyze potential mechanisms of CUE adaptation, I used two theoretical models to implement a tradeoff between microbial uptake rate and CUE. This rate-yield tradeoff is based on thermodynamic principles and suggests that microbes with greater investment in resource acquisition should have lower CUE. Microbial communities or individuals could adapt to warming by reducing investment in enzymes and uptake machinery. Consistent with this idea, a simple analytical model predicted that adaptation can offset 50% of the warming-induced decline in CUE. To assess the ecosystem implications of the rate-yield tradeoff, I quantified CUE adaptation in a spatially-structured simulation model with 100 microbial taxa and 12 soil carbon substrates. This model predicted much lower CUE adaptation, likely due to additional physiological and ecological constraints on microbes. In particular, specific resource acquisition traits are needed to maintain stoichiometric balance, and taxa with high CUE and low enzyme investment rely on low-yield, high-enzyme neighbors to catalyze substrate degradation. In contrast to published microbial models, simulations with greater CUE adaptation also showed greater carbon storage under warming. This pattern occurred because microbial communities with stronger CUE adaptation produced fewer degradative enzymes, despite increases in biomass. Thus the rate-yield tradeoff prevents CUE adaptation from driving ecosystem carbon loss under climate warming.

Two-phase alkali-metal experiments in reduced gravity

International Nuclear Information System (INIS)

Antoniak, Z.I.

1986-06-01

Future space missions envision the use of large nuclear reactors utilizing either a single or a two-phase alkali-metal working fluid. The design and analysis of such reactors require state-of-the-art computer codes that can properly treat alkali-metal flow and heat transfer in a reduced-gravity environment. A literature search of relevant experiments in reduced gravity is reported on here, and reveals a paucity of data for such correlations. The few ongoing experiments in reduced gravity are noted. General plans are put forth for the reduced-gravity experiments which will have to be performed, at NASA facilities, with benign fluids. A similar situation exists regarding two-phase alkali-metal flow and heat transfer, even in normal gravity. Existing data are conflicting and indequate for the task of modeling a space reactor using a two-phase alkali-metal coolant. The major features of past experiments are described here. Data from the reduced-gravity experiments with innocuous fluids are to be combined with normal gravity data from the two-phase alkali-metal experiments. Analyses undertaken here give every expectation that the correlations developed from this data base will provide a valid representation of alkali-metal heat transfer and pressure drop in reduced gravity

Studies of heavy metal contents and microbial composition of ...

African Journals Online (AJOL)

This study investigated the heavy metal content and microbial composition of rhizosphere of Panicum maximum obtained from some auto mechanic workshops in Benin City, Nigeria. The grass was uprooted and soil sample was taken from its rhizosphere. The sample were labeled appropriately and immediately transported ...

Binding of heavy metal ions in aggregates of microbial cells, EPS and biogenic iron minerals measured in-situ using metal- and glycoconjugates-specific fluorophores

Science.gov (United States)

Hao, Likai; Guo, Yuan; Byrne, James M.; Zeitvogel, Fabian; Schmid, Gregor; Ingino, Pablo; Li, Jianli; Neu, Thomas R.; Swanner, Elizabeth D.; Kappler, Andreas; Obst, Martin

2016-05-01

compounds. In summary, the information obtained by the present approach using a microbial model system provides important information to better understand the interactions between heavy metals and biofilms, and microbially formed Fe(III) minerals and heavy metals in complex natural environments.

Metal impacts on microbial biomass in the anoxic sediments of a contaminated lake

Energy Technology Data Exchange (ETDEWEB)

Gough, Heidi L.; Dahl, Amy L.; Nolan, Melissa A.; Gaillard, Jean-Francois; Stahl, David A.

2008-04-26

Little is known about the long-term impacts of metal contamination on the microbiota of anoxic lake sediments. In this study, we examined microbial biomass and metals (arsenic, cadmium, chromium, copper, iron, lead, manganese, and zinc) in the sediments of Lake DePue, a backwater lake located near a former zinc smelter. Sediment core samples were examined using two independent measures for microbial biomass (total microscopic counts and total phospholipid-phosphate concentrations), and for various fractions of each metal (pore water extracts, sequential extractions, and total extracts of all studied metals and zinc speciation by X-ray absorption fine structure (XAFS). Zinc concentrations were up to 1000 times higher than reported for sediments in the adjacent Illinois River, and ranged from 21,400 mg/kg near the source to 1,680 mg/kg near the river. However, solid metal fractions were not well correlated with pore water concentrations, and were not good predictors of biomass concentrations. Instead, biomass, which varied among sites by as much as two-times, was inversely correlated with concentrations of pore water zinc and arsenic as established by multiple linear regression. Monitoring of other parameters known to naturally influence biomass in sediments (e.g., organic carbon concentrations, nitrogen concentrations, pH, sediment texture, and macrophytes) revealed no differences that could explain observed biomass trends. This study provides strong support for control of microbial abundance by pore water metal concentrations in contaminated freshwater sediments.

Microbial and Plant-Assisted Bioremediation of Heavy Metal Polluted Environments: A Review

Directory of Open Access Journals (Sweden)

Omena Bernard Ojuederie

2017-12-01

Full Text Available Environmental pollution from hazardous waste materials, organic pollutants and heavy metals, has adversely affected the natural ecosystem to the detriment of man. These pollutants arise from anthropogenic sources as well as natural disasters such as hurricanes and volcanic eruptions. Toxic metals could accumulate in agricultural soils and get into the food chain, thereby becoming a major threat to food security. Conventional and physical methods are expensive and not effective in areas with low metal toxicity. Bioremediation is therefore an eco-friendly and efficient method of reclaiming environments contaminated with heavy metals by making use of the inherent biological mechanisms of microorganisms and plants to eradicate hazardous contaminants. This review discusses the toxic effects of heavy metal pollution and the mechanisms used by microbes and plants for environmental remediation. It also emphasized the importance of modern biotechnological techniques and approaches in improving the ability of microbial enzymes to effectively degrade heavy metals at a faster rate, highlighting recent advances in microbial bioremediation and phytoremediation for the removal of heavy metals from the environment as well as future prospects and limitations. However, strict adherence to biosafety regulations must be followed in the use of biotechnological methods to ensure safety of the environment.

Microbial and Plant-Assisted Bioremediation of Heavy Metal Polluted Environments: A Review

Science.gov (United States)

Ojuederie, Omena Bernard

2017-01-01

Environmental pollution from hazardous waste materials, organic pollutants and heavy metals, has adversely affected the natural ecosystem to the detriment of man. These pollutants arise from anthropogenic sources as well as natural disasters such as hurricanes and volcanic eruptions. Toxic metals could accumulate in agricultural soils and get into the food chain, thereby becoming a major threat to food security. Conventional and physical methods are expensive and not effective in areas with low metal toxicity. Bioremediation is therefore an eco-friendly and efficient method of reclaiming environments contaminated with heavy metals by making use of the inherent biological mechanisms of microorganisms and plants to eradicate hazardous contaminants. This review discusses the toxic effects of heavy metal pollution and the mechanisms used by microbes and plants for environmental remediation. It also emphasized the importance of modern biotechnological techniques and approaches in improving the ability of microbial enzymes to effectively degrade heavy metals at a faster rate, highlighting recent advances in microbial bioremediation and phytoremediation for the removal of heavy metals from the environment as well as future prospects and limitations. However, strict adherence to biosafety regulations must be followed in the use of biotechnological methods to ensure safety of the environment. PMID:29207531

Metagenomic insights into evolution of heavy metal-contaminated groundwater microbial community

Energy Technology Data Exchange (ETDEWEB)

Hemme, C.L.; Deng, Y.; Gentry, T.J.; Fields, M.W.; Wu, L.; Barua, S.; Barry, K.; Green-Tringe, S.; Watson, D.B.; He, Z.; Hazen, T.C.; Tiedje, J.M.; Rubin, E.M.; Zhou, J.

2010-07-01

Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents ({approx}50 years) has resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying {gamma}- and {beta}-proteobacterial populations. The resulting community is overabundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could have a key function in rapid response and adaptation to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.

Synthesis, characterization, anti-microbial, DNA binding and cleavage studies of Schiff base metal complexes

Directory of Open Access Journals (Sweden)

Poomalai Jayaseelan

2016-09-01

Full Text Available A novel Schiff base ligand has been prepared by the condensation between butanedione monoxime with 3,3′-diaminobenzidine. The ligand and metal complexes have been characterized by elemental analysis, UV, IR, 1H NMR, conductivity measurements, EPR and magnetic studies. The molar conductance studies of Cu(II, Ni(II, Co(II and Mn(II complexes showed non-electrolyte in nature. The ligand acts as dibasic with two N4-tetradentate sites and can coordinate with two metal ions to form binuclear complexes. The spectroscopic data of metal complexes indicated that the metal ions are complexed with azomethine nitrogen and oxyimino nitrogen atoms. The binuclear metal complexes exhibit octahedral arrangements. DNA binding properties of copper(II metal complex have been investigated by electronic absorption spectroscopy. Results suggest that the copper(II complex bind to DNA via an intercalation binding mode. The nucleolytic cleavage activities of the ligand and their complexes were assayed on CT-DNA using gel electrophoresis in the presence and absence of H2O2. The ligand showed increased nuclease activity when administered as copper complex and copper(II complex behave as efficient chemical nucleases with hydrogen peroxide activation. The anti-microbial activities and thermal studies have also been studied. In anti-microbial activity all complexes showed good anti-microbial activity higher than ligand against gram positive, gram negative bacteria and fungi.

The influence of soil organic carbon on interactions between microbial parameters and metal concentrations at a long-term contaminated site

Energy Technology Data Exchange (ETDEWEB)

Muhlbachova, G. [Crop Research Institute, Drnovska 507, 161 06 Prague 6, Ruzyne (Czech Republic); Sagova-Mareckova, M., E-mail: sagova@vurv.cz [Crop Research Institute, Drnovska 507, 161 06 Prague 6, Ruzyne (Czech Republic); Omelka, M. [Charles University, Faculty of Mathematics and Physics, Dept. of Probability and Mathematical Statistics, Prague 8, Karlin (Czech Republic); Szakova, J.; Tlustos, P. [Czech University of Life Sciences, Department of Agroenvironmental Chemistry and Plant Nutrition, Prague 6, Suchdol (Czech Republic)

2015-01-01

The effects of lead, zinc, cadmium, arsenic and copper deposits on soil microbial parameters were investigated at a site exposed to contamination for over 200 years. Soil samples were collected in triplicates at 121 sites differing in contamination and soil organic carbon (SOC). Microbial biomass, respiration, dehydrogenase activity and metabolic quotient were determined and correlated with total and extractable metal concentrations in soil. The goal was to analyze complex interactions between toxic metals and microbial parameters by assessing the effect of soil organic carbon in the relationships. The effect of SOC was significant in all interactions and changed the correlations between microbial parameters and metal fractions from negative to positive. In some cases, the effect of SOC was combined with that of clay and soil pH. In the final analysis, dehydrogenase activity was negatively correlated to total metal concentrations and acetic acid extractable metals, respiration and metabolic quotient were to ammonium nitrate extractable metals. Dehydrogenase activity was the most sensitive microbial parameter correlating most frequently with contamination. Total and extractable zinc was most often correlated with microbial parameters. The large data set enabled robust explanation of discrepancies in organic matter functioning occurring frequently in analyzing of contaminated soil processes. - Highlights: • Soil organic carbon affected all interactions between metals and microorganisms. • Soil organic carbon adjustment changed correlations from positive to negative. • Ammonium nitrate extractable metals were the most influencing fraction. • Dehydrogenase activity was the most affected soil parameter. • Zinc was the most toxic metal among studied metals.

The influence of soil organic carbon on interactions between microbial parameters and metal concentrations at a long-term contaminated site

International Nuclear Information System (INIS)

Muhlbachova, G.; Sagova-Mareckova, M.; Omelka, M.; Szakova, J.; Tlustos, P.

2015-01-01

The effects of lead, zinc, cadmium, arsenic and copper deposits on soil microbial parameters were investigated at a site exposed to contamination for over 200 years. Soil samples were collected in triplicates at 121 sites differing in contamination and soil organic carbon (SOC). Microbial biomass, respiration, dehydrogenase activity and metabolic quotient were determined and correlated with total and extractable metal concentrations in soil. The goal was to analyze complex interactions between toxic metals and microbial parameters by assessing the effect of soil organic carbon in the relationships. The effect of SOC was significant in all interactions and changed the correlations between microbial parameters and metal fractions from negative to positive. In some cases, the effect of SOC was combined with that of clay and soil pH. In the final analysis, dehydrogenase activity was negatively correlated to total metal concentrations and acetic acid extractable metals, respiration and metabolic quotient were to ammonium nitrate extractable metals. Dehydrogenase activity was the most sensitive microbial parameter correlating most frequently with contamination. Total and extractable zinc was most often correlated with microbial parameters. The large data set enabled robust explanation of discrepancies in organic matter functioning occurring frequently in analyzing of contaminated soil processes. - Highlights: • Soil organic carbon affected all interactions between metals and microorganisms. • Soil organic carbon adjustment changed correlations from positive to negative. • Ammonium nitrate extractable metals were the most influencing fraction. • Dehydrogenase activity was the most affected soil parameter. • Zinc was the most toxic metal among studied metals

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

Science.gov (United States)

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

Microbial community analysis of perchlorate-reducing cultures growing on zero-valent iron

International Nuclear Information System (INIS)

Son, Ahjeong; Schmidt, Carl J.; Shin, Hyejin; Cha, Daniel K.

2011-01-01

Anaerobic microbial mixed cultures demonstrated its ability to completely remove perchlorate in the presence of zero-valent iron. In order to understand the major microbial reaction in the iron-supported culture, community analysis comprising of microbial fatty acids and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) techniques was performed for perchlorate reducing cultures. Analysis of fatty acid methyl esters (FAMEs) and subsequent principal component analysis (PCA) showed clear distinctions not only between iron-supported perchlorate reducing culture and seed bacteria, but also among perchlorate-reducing cultures receiving different electron donors. The DGGE pattern targeting the chlorite dismutase (cld) gene showed that iron-supported perchlorate reducing culture is similar to hydrogen-fed cultures as compared to acetate-fed culture. The phylogenetic tree suggested that the dominant microbial reaction may be a combination of the autotrophic and heterotrophic reduction of perchlorate. Both molecular and chemotaxonomic experimental results support further understanding in the function of zero-valent iron as an adequate electron source for enhancing the microbial perchlorate reduction in natural and engineered systems.

Microbial community analysis of perchlorate-reducing cultures growing on zero-valent iron

Energy Technology Data Exchange (ETDEWEB)

Son, Ahjeong, E-mail: ason@auburn.edu [Department of Civil Engineering, Auburn University, Auburn, AL 36849 (United States); Schmidt, Carl J. [Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716 (United States); Shin, Hyejin [Department of Mathematics and Statistics, Auburn University, Auburn, AL 36849 (United States); Cha, Daniel K. [Department of Civil and Environmental Engineering, University of Delaware, Newark, DE 19716 (United States)

2011-01-30

Anaerobic microbial mixed cultures demonstrated its ability to completely remove perchlorate in the presence of zero-valent iron. In order to understand the major microbial reaction in the iron-supported culture, community analysis comprising of microbial fatty acids and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) techniques was performed for perchlorate reducing cultures. Analysis of fatty acid methyl esters (FAMEs) and subsequent principal component analysis (PCA) showed clear distinctions not only between iron-supported perchlorate reducing culture and seed bacteria, but also among perchlorate-reducing cultures receiving different electron donors. The DGGE pattern targeting the chlorite dismutase (cld) gene showed that iron-supported perchlorate reducing culture is similar to hydrogen-fed cultures as compared to acetate-fed culture. The phylogenetic tree suggested that the dominant microbial reaction may be a combination of the autotrophic and heterotrophic reduction of perchlorate. Both molecular and chemotaxonomic experimental results support further understanding in the function of zero-valent iron as an adequate electron source for enhancing the microbial perchlorate reduction in natural and engineered systems.

Changes in soil microbial community functionality and structure in a metal-polluted site: The effect of digestate and fly ash applications.

Science.gov (United States)

Garcia-Sánchez, M; Garcia-Romera, I; Cajthaml, T; Tlustoš, P; Száková, J

2015-10-01

Soil from Trhové Dušníky (Příbram, Czech Republic) is characterized by its high polymetallic accumulations in Pb-Ag-Zn due to mining and smelting activities. In previous studies performed in our research group, we have evaluated the potential use of amendments that would reduce the mobility and availability of metals such as Hg. We have observed that the application of digestate and fly ash in metal-polluted soil has an impact in immobilizing these metals. However, until now we have lacked information about the effect of these amendments on soil microbial functionality and communities. The multi-contaminated soil was used to grow wheat in a pot experiment to evaluate the impact of digestate and fly ash application in soil microbial communities. Soil samples were collected after 30 and 60 days of treatment. The digestate application improved chemical attributes such as the content in total organic carbon (TOC), water soluble carbon (WSOC), total soluble carbon (C), total soluble nitrogen (N), and inorganic N forms (NO3(-)) as consequence of high content in C and N which is contained in digestate. Likewise, microbial activity was greatly enhanced by digestate application, as was physiological diversity. Bacterial and fungal communities were increased, and the microbial biomass was highly enhanced. These effects were evident after 30 and 60 days of treatment. In contrast, fly ash did not have a remarkable effect when compared to digestate, but soil microbial biomass was positively affected as a consequence of macro- and micro-nutrient sources applied by the addition of fly ash. This study indicates that digestate can be used successfully in the remediation of metal-contaminated soil. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microbially influenced corrosion: studies on enterobacteria isolated from seawater environment and influence of toxic metals on bacterial biofilm and bio-corrosion

Energy Technology Data Exchange (ETDEWEB)

Bermond-Tilly, D.; Pineau, S.; Dupont-Morral, I. [Corrodys, 50 - Equeurdreville (France); Janvier, M.; Grimont, P.A.D. [Institut Pasteur, Unite BBPE, 75 - Paris (France)

2004-07-01

Full text of publication follows: The most widely involved bacteria in Microbially Induced Corrosion (MIC usually called bio-corrosion) are sulfate/thiosulfate-reducing bacteria. The sulfate-reducing bacteria (SRB) are major contributors to the anaerobic bio-corrosion of steel. However, corrosion process of pipelines (or off shores platforms) was found to be associated with many other bacteria. These bacteria are able to produce sulfides from the reduction of thiosulfate in anaerobic conditions. By this way, a thiosulfate-reducing non sulfate-reducing bacteria, Dethiosulfovibrio peptidovorans, showed a significant corrosive activity similar to or higher than that recorded for SRB involved in bio-corrosion, (Magot et al., 1997). Furthermore, a bacteria, Citrobacter amalonaticus, which belongs to the family of the Enterobacteriaceae, is involved in severe pitting corrosion process (Angeles Chavez et al., 2002). Recently, some bacteria (Citrobacter freundii, Proteus mirabilis and Klebsiella planticola characterized as belonging to the family of Enterobacteriaceae) were isolated from biofilm developed on carbon steel coupons immersed in natural seawater. The latter bacteria were also associated in severe pitting corrosion process on carbon steel coupons (Bermond-Tilly et al., 2003). Biofilm forms a protective layer, reducing the exposure of the metal surface to the external environment. However, bacteria included in the biofilm could also cause localized corrosion by consuming cathodic hydrogen from the steel or by producing corrosive metabolic end products and by the Extracellular Polymeric Substances (EPS) production. Thus, EPS can also play an important role in the corrosion of the metals (e.g. can complex metal ions). However, sulfate/thiosulfate-reducing bacteria and some Enterobacteria are highly efficient to bioremediation by precipitation of toxic metals from wastewater as metal sulfides. Recently it was shown that toxic metal may be involved in the formation

Reduced material model for closed cell metal foam infiltrated with phase change material based on high resolution numerical studies

International Nuclear Information System (INIS)

Ohsenbrügge, Christoph; Marth, Wieland; Navarro y de Sosa, Iñaki; Drossel, Welf-Guntram; Voigt, Axel

2016-01-01

Highlights: • Closed cell metal foam sandwich structures were investigated. • High resolution numerical studies were conducted using CT scan data. • A reduced model for use in commercial FE software reduces needed degrees of freedom. • Thermal inertia is increased about 4 to 5 times in PCM filled structures. • The reduced material model was verified using experimental data. - Abstract: The thermal behaviour of closed cell metal foam infiltrated with paraffin wax as latent heat storage for application in high precision tool machines was examined. Aluminium foam sandwiches with metallically bound cover layers were prepared in a powder metallurgical process and cross-sectional images of the structures were generated with X-ray computed tomography. Based on the image data a three dimensional highly detailed model was derived and prepared for simulation with the adaptive FE-library AMDiS. The pores were assumed to be filled with paraffin wax. The thermal conductivity and the transient thermal behaviour in the phase-change region were investigated. Based on the results from the highly detailed simulations a reduced model for use in commercial FE-software (ANSYS) was derived. It incorporates the properties of the matrix and the phase change material into a homogenized material. A sandwich-structure with and without paraffin was investigated experimentally under constant thermal load. The results were used to verify the reduced material model in ANSYS.

Initial steps in the microbially influenced corrosion (MIC) of metallic surfaces in a natural marine environment

International Nuclear Information System (INIS)

Esteso, M.A.; Estrella, C.N.; Dolores de la Rosa, M.; Martinez-Trujillo, R.; Rosales, B.M.; Podesta, J.J.

1992-01-01

Immersion of various metal samples in polluted seawater from Tenerife Harbor was followed by microbial attachment as an intermediate step in fouling development. The purpose of this research was to determine the initial steps in MIC by identifying the different microbial species attached to the respective metal or alloy. Image analysis was used to determine the morphologic changes in the metal surfaces. The corrosion products were determined by X-ray diffraction. The open circuit potentials were measured periodically and their variation with time used to assess the electrochemical behavior in the aforementioned marine environment

Removal of dissolved heavy metals and radionuclides by microbial spores

International Nuclear Information System (INIS)

Revis, N.W.; Hadden, C.T.; Edenborn, H.

1997-01-01

Microbial systems have been shown to remove specific heavy metals from contaminated aqueous waste to levels acceptable to EPA for environmental release. However, systems capable of removing a variety of heavy metals from aqueous waste to environmentally acceptable levels remain to be reported. The present studies were performed to determine the specificity of spores of the bacterium Bacillus megaterium for the adsorption of dissolved metals and radionuclides from aqueous waste. The spores effectively adsorbed eight heavy metals from a prepared metal mix and from a plating rinse waste to EPA acceptable levels for waste water. These results suggest that spores have multiple binding sites for the adsorption of heavy metals. Spores were also effective in adsorbing the radionuclides 85 strontium and 197 cesium. The presence of multiple sites in spores for the adsorption of heavy metals and radionuclides makes this biosorbent a good candidate for the treatment of aqueous wastes associated with the plating and nuclear industries. 17 refs., 4 tabs

Developing Model Benchtop Systems for Microbial Experimental Evolution

Science.gov (United States)

Gentry, D.; Wang, J.; Arismendi, D.; Alvarez, J.; Ouandji, C.; Blaich, J.

2017-12-01

Understanding how microbes impact an ecosystem has improved through advances of molecular and genetic tools, but creating complex systems that emulate natural biology goes beyond current technology. In fact, many chemical, biological, and metabolic pathways of even model organisms are still poorly characterized. Even then, standard laboratory techniques for testing microbial impact on environmental change can have many drawbacks; they are time-consuming, labor intensive, and are at risk of contamination. By having an automated process, many of these problems can be reduced or even eliminated. We are developing a benchtop system that can run for long periods of time without the need for human intervention, involve multiple environmental stressors at once, perform real-time adjustments of stressor exposure based on current state of the population, and minimize contamination risks. Our prototype device allows operators to generate an analogue of real world micro-scale ecosystems that can be used to model the effects of disruptive environmental change on microbial ecosystems. It comprises of electronics, mechatronics, and fluidics based systems to control, measure, and evaluate the before and after state of microbial cultures from exposure to environmental stressors. Currently, it uses four parallel growth chambers to perform tests on liquid cultures. To measure the population state, optical sensors (LED/photodiode) are used. Its primary selection pressure is UV-C radiation, a well-studied stressor known for its cell- and DNA- damaging effects and as a mutagen. Future work will involve improving the current growth chambers, as well as implementing additional sensors and environmental stressors into the system. Full integration of multiple culture testing will allow inter-culture comparisons. Besides the temperature and OD sensors, other types of sensors can be integrated such as conductivity, biomass, pH, and dissolved gasses such as CO2 and O2. Additional

The influence of bioavailable heavy metals and microbial parameters of soil on the metal accumulation in rice grain.

Science.gov (United States)

Xiao, Ling; Guan, Dongsheng; Peart, M R; Chen, Yujuan; Li, Qiqi; Dai, Jun

2017-10-01

A field-based study was undertaken to analyze the effects of soil bioavailable heavy metals determined by a sequential extraction procedure, and soil microbial parameters on the heavy metal accumulation in rice grain. The results showed that Cd, Cr, Cu, Ni, Pb and Zn concentrations in rice grain decreases by 65.9%, 78.9%, 32.6%, 80.5%, 61.0% and 15.7%, respectively in the sites 3 (far-away), compared with those in sites 1 (close-to). Redundancy analysis (RDA) indicated that soil catalase activity, the MBC/MBN ratio, along with bioavailable Cd, Cr and Ni could explain 68.9% of the total eigenvalue, indicating that these parameters have a great impact on the heavy metal accumulation in rice grain. The soil bioavailable heavy metals have a dominant impact on their accumulation in rice grain, with a variance contribution of 60.1%, while the MBC/MBN has a regulatory effect, with a variance contribution of 4.1%. Stepwise regression analysis showed that the MBC/MBN, urease and catalase activities are the key microbial parameters that affect the heavy metal accumulation in rice by influencing the soil bioavailable heavy metals or the translocation of heavy metals in rice. RDA showed an interactive effect between Cu, Pb and Zn in rice grain and the soil bioavailable Cd, Cr and Ni. The heavy metals in rice grain, with the exception of Pb, could be predicted by their respective soil bioavailable heavy metals. The results suggested that Pb accumulation in rice grain was mainly influenced by the multi-metal interactive effects, and less affected by soil bioavailable Pb. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

Science.gov (United States)

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.

Metagenomic Insights into Evolution of a Heavy Metal-Contaminated Groundwater Microbial Community

Energy Technology Data Exchange (ETDEWEB)

Hemme, Christopher L.; Deng, Ye; Gentry, Terry J.; Fields, Matthew W.; Wu, Liyou; Barua, Soumitra; Barry, Kerrie; Tringe, Susannah G.; Watson, David B.; He, Zhili; Hazen, Terry C.; Tiedje, James M.; Rubin, Edward M.; Zhou, Jizhong

2010-02-15

Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents (~;;50 years) have resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying ?- and ?-proteobacterial populations. The resulting community is over-abundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could be a key mechanism in rapidly responding and adapting to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.

Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine.

Science.gov (United States)

Epelde, Lur; Lanzén, Anders; Blanco, Fernando; Urich, Tim; Garbisu, Carlos

2015-01-01

Toxicity of metals released from mine tailings may cause severe damage to ecosystems. A diversity of microorganisms, however, have successfully adapted to such sites. In this study, our objective was to advance the understanding of the indigenous microbial communities of mining-impacted soils. To this end, a metatranscriptomic approach was used to study a heavily metal-contaminated site along a metal concentration gradient (up to 3220 000 and 97 000 mg kg(-1) of Cd, Pb and Zn, respectively) resulting from previous mining. Metal concentration, soil pH and amount of clay were the most important factors determining the structure of soil microbial communities. Interestingly, evenness of the microbial communities, but not its richness, increased with contamination level. Taxa with high metabolic plasticity like Ktedonobacteria and Chloroflexi were found with higher relative abundance in more contaminated samples. However, several taxa belonging to the phyla Actinobacteria and Acidobacteria followed opposite trends in relation to metal pollution. Besides, functional transcripts related to transposition or transfer of genetic material and membrane transport, potentially involved in metal resistance mechanisms, had a higher expression in more contaminated samples. Our results provide an insight into microbial communities in long-term metal-contaminated environments and how they contrast to nearby sites with lower contamination. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

Science.gov (United States)

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. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

MICROBIAL SURFACTANTS IN ENVIRONMENTAL TECHNOLOGIES

Directory of Open Access Journals (Sweden)

T. P. Pirog

2015-08-01

Full Text Available It was shown literature and own experimental data concerning the use of microbial surface active glycolipids (rhamno-, sophoro- and trehalose lipids and lipopeptides for water and soil purification from oil and other hydrocarbons, removing toxic heavy metals (Cu2+, Cd2+, Ni2+, Pb2+, degradation of complex pollution (oil and other hydrocarbons with heavy metals, and the role of microbial surfactants in phytoremediation processes. The factors that limit the use of microbial surfactants in environmental technologies are discussed. Thus, at certain concentrations biosurfactant can exhibit antimicrobial properties and inhibit microorganisms destructing xenobiotics. Microbial biodegradability of surfactants may also reduce the effectiveness of bioremediation. Development of effective technologies using microbial surfactants should include the following steps: monitoring of contaminated sites to determine the nature of pollution and analysis of the autochthonous microbiota; determining the mode of surfactant introduction (exogenous addition of stimulation of surfactant synthesis by autochthonous microbiota; establishing an optimal concentration of surfactant to prevent exhibition of antimicrobial properties and rapid biodegradation; research both in laboratory and field conditions.

Microbial biofilms control economic metal mobility in an acid-sulfate hydrothermal system

Science.gov (United States)

Phillips-Lander, C. M.; Roberts, J. A.; Hernandez, W.; Mora, M.; Fowle, D. A.

2012-12-01

Trace metal cycling in hydrothermal systems has been the subject of a variety of geochemical and economical geology studies. Typically in these settings these elements are sequestered in sulfide and oxide mineral fractions, however in near-surface low-temperature environments organic matter and microorganisms (typically in mats) have been implicated in their mobility through sorption. Here we specifically examine the role of microbial biofilms on metal partitioning in an acid-sulfate hydrothermal system. We studied the influence of microorganisms and microbial biofilms on trace metal adsorption in Pailas de Aguas I, an acid-sulfate hot spring on the southwest flank of Rincon de la Vieja, a composite stratovolcano in the Guanacaste Province, Costa Rica. Spring waters contain high suspended loads, and are characterized by high T (79.6-89.3oC), low pH (2.6-4), and high ionic strengths (I= 0.5-0.8). Waters contain high concentrations of the biogeochemically active elements Fe (4-6 mmol/l) and SO42- (38 mmol/l), but PO43- are below detection limits (bdl). Silver, Ni, and Mo concentrations are bdl; however other trace metals are present in solution in concentrations of 0.1-0.2 mg/l Cd, 0.2-0.4 mg/l Cr and V, 0.04-1 mg/l Cu,. Preliminary 16S rRNA analyses of microorganisms in sediments reveal several species of algae, including Galderia sp., Cyanidium sp, γ-proteobacteria, Acidithiobacillus caldus, Euryarcheota, and methanogens. To evaluate microbial biofilms' impact on trace metal mobility we analyzed a combination of suspended, bulk and biofilm associated sediment samples via X-ray diffraction (XRD) and trace element sequential extractions (SE). XRD analysis indicated all samples were primarily composed of Fe/Al clay minerals (nontronite, kaolinite), 2- and 6-line ferrihydrite, goethite, and hematite, quartz, and opal-α. SE showed the highest concentrations of Cu, Mo, and V were found in the suspended load. Molybdenum was found primarily in the residual and organic

A bioenergetics-kinetics coupled modeling study on subsurface microbial metabolism in a field biostimulation experiment

Science.gov (United States)

Jin, Q.; Zheng, Z.; Zhu, C.

2006-12-01

Microorganisms in nature conserve energy by catalyzing various geochemical reactions. To build a quantitative relationship between geochemical conditions and metabolic rates, we propose a bioenergetics-kinetics coupled modeling approach. This approach describes microbial community as a metabolic network, i.e., fermenting microbes degrade organic substrates while aerobic respirer, nitrate reducer, metal reducer, sulfate reducer, and methanogen consume the fermentation products. It quantifies the control of substrate availability and biological energy conservation on the metabolic rates using thermodynamically consistent rate laws. We applied this simulation approach to study the progress of microbial metabolism during a field biostimulation experiment conducted in Oak Ridge, Tennessee. In the experiment, ethanol was injected into a monitoring well and groundwater was sampled to monitor changes in the chemistry. With time, concentrations of ethanol and SO42- decreased while those of NH4+, Fe2+, and Mn2+ increased. The simulation results fitted well to the observation, indicating simultaneous ethanol degradation and terminal electron accepting processes. The rates of aerobic respiration and denitrification were mainly controlled by substrate concentrations while those of ethanol degradation, sulfate reduction, and methanogenesis were controlled dominantly by the energy availability. The simulation results suggested two different microbial growth statuses in the subsurface. For the functional groups with significant growth, variations with time in substrate concentrations demonstrated a typical S curve. For the groups without significant growth, initial decreases in substrate concentrations were linear with time. Injecting substrates followed by monitoring environmental chemistry therefore provides a convenient approach to characterize microbial growth in the subsurface where methods for direct observation are currently unavailable. This research was funded by the

Metal availability and the expanding network of microbial metabolisms in the Archaean eon

Science.gov (United States)

Moore, Eli K.; Jelen, Benjamin I.; Giovannelli, Donato; Raanan, Hagai; Falkowski, Paul G.

2017-09-01

Life is based on energy gained by electron-transfer processes; these processes rely on oxidoreductase enzymes, which often contain transition metals in their structures. The availability of different metals and substrates has changed over the course of Earth's history as a result of secular changes in redox conditions, particularly global oxygenation. New metabolic pathways using different transition metals co-evolved alongside changing redox conditions. Sulfur reduction, sulfate reduction, methanogenesis and anoxygenic photosynthesis appeared between about 3.8 and 3.4 billion years ago. The oxidoreductases responsible for these metabolisms incorporated metals that were readily available in Archaean oceans, chiefly iron and iron-sulfur clusters. Oxygenic photosynthesis appeared between 3.2 and 2.5 billion years ago, as did methane oxidation, nitrogen fixation, nitrification and denitrification. These metabolisms rely on an expanded range of transition metals presumably made available by the build-up of molecular oxygen in soil crusts and marine microbial mats. The appropriation of copper in enzymes before the Great Oxidation Event is particularly important, as copper is key to nitrogen and methane cycling and was later incorporated into numerous aerobic metabolisms. We find that the diversity of metals used in oxidoreductases has increased through time, suggesting that surface redox potential and metal incorporation influenced the evolution of metabolism, biological electron transfer and microbial ecology.

Stability of U(VI) and Tc(VII) Reducing Microbial Communities to Environmental Perturbation: Development and Testing of a Thermodynamic Network Model

International Nuclear Information System (INIS)

McKinley, James P.; Istok, Jonathan

2005-01-01

Previously published research from in situ field experiments at the NABIR Field Research Center have shown that cooperative metabolism of denitrifiers and Fe(III)/sulfate reducers is essential for creating subsurface conditions favorable for U(VI) and Tc(VII) bioreduction (Istok et al., 2004). The overall goal of this project is to develop and test a thermodynamic network model for predicting the effects of substrate additions and environmental perturbations on the composition and functional stability of subsurface microbial communities. The overall scientific hypothesis is that a thermodynamic analysis of the energy-yielding reactions performed by broadly defined groups of microorganisms can be used to make quantitative and testable predictions of the change in microbial community composition that will occur when a substrate is added to the subsurface or when environmental conditions change. An interactive computer program was developed to calculate the overall growth equation and free energy yield for microorganisms that grow by coupling selected combinations of electron acceptor and electron donor half-reactions. Each group performs a specific function (e.g. oxidation of acetate coupled to reduction of nitrate); collectively the groups provide a theoretical description of the entire natural microbial community. The microbial growth data are combined with an existing thermodynamic data base for associated geochemical reactions and used to simulate the coupled microbial-geochemical response of a complex natural system to substrate addition or any other environmental perturbations

Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing “Stress-on-Stress” Responses

Directory of Open Access Journals (Sweden)

Hamed Azarbad

2016-06-01

Full Text Available Many microbial ecology studies have demonstrated profound changes in community composition caused by environmental pollution, as well as adaptation processes allowing survival of microbes in polluted ecosystems. Soil microbial communities in polluted areas with a long-term history of contamination have been shown to maintain their function by developing metal-tolerance mechanisms. In the present work, we review recent experiments, with specific emphasis on studies that have been conducted in polluted areas with a long-term history of contamination that also applied DNA-based approaches. We evaluate how the “costs” of adaptation to metals affect the responses of metal-tolerant communities to other stress factors (“stress-on-stress”. We discuss recent studies on the stability of microbial communities, in terms of resistance and resilience to additional stressors, focusing on metal pollution as the initial stress, and discuss possible factors influencing the functional and structural stability of microbial communities towards secondary stressors. There is increasing evidence that the history of environmental conditions and disturbance regimes play central roles in responses of microbial communities towards secondary stressors.

Microbial community composition and functions are resilient to metal pollution along two forest soil gradients.

Science.gov (United States)

Azarbad, Hamed; Niklińska, Maria; Laskowski, Ryszard; van Straalen, Nico M; van Gestel, Cornelis A M; Zhou, Jizhong; He, Zhili; Wen, Chongqing; Röling, Wilfred F M

2015-01-01

Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long-term metal pollution. Studying 12 sites located along two distinct gradients of metal pollution in Southern Poland revealed that functional potential and diversity (assessed using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level did, however, significantly impact bacterial community structure (as shown by MiSeq Illumina sequencing of 16S rRNA genes), but not bacterial taxon richness and community composition. Metal pollution caused changes in the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal-resistance genes showed significant correlations with metal concentrations in soil. Our study showed that microbial communities are resilient to metal pollution; despite differences in community structure, no clear impact of metal pollution levels on overall functional diversity was observed. While screens of phylogenetic marker genes, such as 16S rRNA genes, provide only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appears to be a more promising strategy. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Trace Metal Requirements for Microbial Enzymes Involved in the Production and Consumption of Methane and Nitrous Oxide

Science.gov (United States)

Glass, Jennifer B.; Orphan, Victoria J.

2011-01-01

Fluxes of greenhouse gases to the atmosphere are heavily influenced by microbiological activity. Microbial enzymes involved in the production and consumption of greenhouse gases often contain metal cofactors. While extensive research has examined the influence of Fe bioavailability on microbial CO2 cycling, fewer studies have explored metal requirements for microbial production and consumption of the second- and third-most abundant greenhouse gases, methane (CH4), and nitrous oxide (N2O). Here we review the current state of biochemical, physiological, and environmental research on transition metal requirements for microbial CH4 and N2O cycling. Methanogenic archaea require large amounts of Fe, Ni, and Co (and some Mo/W and Zn). Low bioavailability of Fe, Ni, and Co limits methanogenesis in pure and mixed cultures and environmental studies. Anaerobic methane oxidation by anaerobic methanotrophic archaea (ANME) likely occurs via reverse methanogenesis since ANME possess most of the enzymes in the methanogenic pathway. Aerobic CH4 oxidation uses Cu or Fe for the first step depending on Cu availability, and additional Fe, Cu, and Mo for later steps. N2O production via classical anaerobic denitrification is primarily Fe-based, whereas aerobic pathways (nitrifier denitrification and archaeal ammonia oxidation) require Cu in addition to, or possibly in place of, Fe. Genes encoding the Cu-containing N2O reductase, the only known enzyme capable of microbial N2O conversion to N2, have only been found in classical denitrifiers. Accumulation of N2O due to low Cu has been observed in pure cultures and a lake ecosystem, but not in marine systems. Future research is needed on metalloenzymes involved in the production of N2O by enrichment cultures of ammonia oxidizing archaea, biological mechanisms for scavenging scarce metals, and possible links between metal bioavailability and greenhouse gas fluxes in anaerobic environments where metals may be limiting due to sulfide-metal

Long-term performance of anaerobic digestion for crop residues containing heavy metals and response of microbial communities.

Science.gov (United States)

Lee, Jongkeun; Kim, Joonrae Roger; Jeong, Seulki; Cho, Jinwoo; Kim, Jae Young

2017-01-01

In order to investigate the long-term stability on the performance of the anaerobic digestion process, a laboratory-scale continuous stirred-tank reactor (CSTR) was operated for 1100 days with sunflower harvested in a heavy metal contaminated site. Changes of microbial communities during digestion were identified using pyrosequencing. According to the results, soluble heavy metal concentrations were lower than the reported inhibitory level and the reactor performance remained stable up to OLR of 2.0g-VS/L/day at HRT of 20days. Microbial communities commonly found in anaerobic digestion for cellulosic biomass were observed and stably established with respect to the substrate. Thus, the balance of microbial metabolism was maintained appropriately and anaerobic digestion seems to be feasible for disposal of heavy metal-containing crop residues from phytoremediation sites. Copyright © 2016 Elsevier Ltd. All rights reserved.

Soil microbial communities as suitable bioindicators of trace metal pollution in agricultural volcanic soils

Science.gov (United States)

Parelho, Carolina; dos Santos Rodrigues, Armindo; do Carmo Barreto, Maria; Gonçalo Ferreira, Nuno; Garcia, Patrícia

2015-04-01

Summary: The biological, chemical and physical properties of soil confer unique characteristics that enhance or influence its overall biodiversity. The adaptive character of soil microbial communities (SMCs) to metal pollution allows discriminating soil health, since changes in microbial populations and activities may function as excellent indicators of soil pollutants. 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 (TM). In our previous works, we identified priority TM affecting agricultural Andosols under different agricultural land uses. Within this particular context, the objectives of this study were to (i) assess the effect of soil TM pollution in different agricultural systems (conventional, traditional and organic) on the following soil properties: microbial biomass carbon, basal soil respiration, metabolic quotient, enzymatic activities (β-glucosidase, acid phosphatase and dehydrogenase) and RNA to DNA ratio; and (ii) evaluate the impact of TM in the soil ecosystem using the integrated biomarker response (IBR) based on a set of biochemical responses of SMCs. This multi-biomarker approach will support the development of the "Trace Metal Footprint" for different agricultural land uses in volcanic soils. Methods: The study was conducted in S. Miguel Island (Azores, Portugal). Microbial biomass carbon was measured by chloroform-fumigation-incubation-assay (Vance et al., 1987). Basal respiration was determined by the Jenkinson & Powlson (1976) technique. Metabolic quotient was calculated as the ratio of basal respiration to microbial biomass C (Sparkling & West, 1988). The enzymatic activities of β-glucosidase and acid phosphatase were determined by the Dick et al. (1996) method and dehydrogenase activity by the Rossel et al. (1997) method. The RNA and DNA were co-extracted from the same

Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model

International Nuclear Information System (INIS)

Fang, Yilin; Scheibe, Timothy D.; Mahadevan, Radhakrishnan; Garg, Srinath; Long, Philip E.; Lovley, Derek R.

2011-01-01

The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species, multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The

Impact of metal pollution and Thlaspi caerulescens growth on soil microbial communities.

NARCIS (Netherlands)

Epelde, L.; Becerril, J.M.; Kowalchuk, G.A.; Deng, Y.; Zhou, J.; Garbisu, C.

2010-01-01

been proposed as indicators of soil functioning, making them potentially useful in evaluating the recovery of polluted soils via phytoremediation strategies. To evaluate microbial responses to metal phytoextraction using hyperaccumulators, a microcosm experiment was carried out to study the impacts

Microbial Communities Model Parameter Calculation for TSPA/SR

International Nuclear Information System (INIS)

D. Jolley

2001-01-01

This calculation has several purposes. First the calculation reduces the information contained in ''Committed Materials in Repository Drifts'' (BSC 2001a) to useable parameters required as input to MING V1.O (CRWMS M and O 1998, CSCI 30018 V1.O) for calculation of the effects of potential in-drift microbial communities as part of the microbial communities model. The calculation is intended to replace the parameters found in Attachment II of the current In-Drift Microbial Communities Model revision (CRWMS M and O 2000c) with the exception of Section 11-5.3. Second, this calculation provides the information necessary to supercede the following DTN: M09909SPAMING1.003 and replace it with a new qualified dataset (see Table 6.2-1). The purpose of this calculation is to create the revised qualified parameter input for MING that will allow ΔG (Gibbs Free Energy) to be corrected for long-term changes to the temperature of the near-field environment. Calculated herein are the quadratic or second order regression relationships that are used in the energy limiting calculations to potential growth of microbial communities in the in-drift geochemical environment. Third, the calculation performs an impact review of a new DTN: M00012MAJIONIS.000 that is intended to replace the currently cited DTN: GS9809083 12322.008 for water chemistry data used in the current ''In-Drift Microbial Communities Model'' revision (CRWMS M and O 2000c). Finally, the calculation updates the material lifetimes reported on Table 32 in section 6.5.2.3 of the ''In-Drift Microbial Communities'' AMR (CRWMS M and O 2000c) based on the inputs reported in BSC (2001a). Changes include adding new specified materials and updating old materials information that has changed

Microbial community composition and functions are resilient to metal pollution along two forest soil gradients.

NARCIS (Netherlands)

Azarbad, H.; Niklinska, M.; Laskowski, R.; van Straalen, N.M.; van Gestel, C.A.M.; Zhou, J.; He, Z.; Wen, C.; Roling, W.F.M.

2015-01-01

Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long-term metal pollution. Studying 12 sites located along two distinct gradients of metal pollution in Southern Poland revealed that functional

Soil biochar amendment shapes the composition of N_2O-reducing microbial communities

International Nuclear Information System (INIS)

Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H.; Kappler, Andreas; Behrens, Sebastian

2016-01-01

Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N_2O) emissions. N_2O is a potent greenhouse gas. The main sources of N_2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N_2O emission mitigation and the abundance and activity of N_2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described ‘atypical’ nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N_2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N_2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N_2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. - Highlights: • Biochar promoted anaerobic, alkalinity-adapted, and polymer-degrading microbial taxa. • Biochar fostered the development of distinct N_2O-reducing microbial taxa. • Taxonomic shifts among N_2O-reducing microbes might explain lower N_2O emissions.

Microbial and trace metal content of well water in three rural ...

African Journals Online (AJOL)

Microbial and trace metal content of well water in three rural communities in Bauchi State, Nigeria*. E Ikeh, PN Durfee, RH Glew, R Amato, FJ Frost, DJ Vanderjagt. Abstract. No Abstract. Nigerian Journal of Health and Biomedical Sciences Vol. 5 (2) 2006: 66-70. Full Text: EMAIL FULL TEXT EMAIL FULL TEXT

Energy-positive wastewater treatment and desalination in an integrated microbial desalination cell (MDC)-microbial electrolysis cell (MEC)

Science.gov (United States)

Li, Yan; Styczynski, Jordyn; Huang, Yuankai; Xu, Zhiheng; McCutcheon, Jeffrey; Li, Baikun

2017-07-01

Simultaneous removal of nitrogen in municipal wastewater, metal in industrial wastewater and saline in seawater was achieved in an integrated microbial desalination cell-microbial electrolysis cell (MDC-MEC) system. Batch tests showed that more than 95.1% of nitrogen was oxidized by nitrification in the cathode of MDC and reduced by heterotrophic denitrification in the anode of MDC within 48 h, leading to the total nitrogen removal rate of 4.07 mg L-1 h-1. Combining of nitrogen removal and desalination in MDC effectively solved the problem of pH fluctuation in anode and cathode, and led to 63.7% of desalination. Power generation of MDC (293.7 mW m-2) was 2.9 times higher than the one without salt solution. The electric power of MDC was harvested by a capacitor circuit to supply metal reduction in a MEC, and 99.5% of lead (II) was removed within 48 h. A kinetic MDC model was developed to elucidate the correlation of voltage output and desalination efficiency. Ratio of wastewater and sea water was calculated for MDC optimal operation. Energy balance of nutrient removal, metal removal and desalination in the MDC-MEC system was positive (0.0267 kW h m-3), demonstrating the promise of utilizing low power output of MDCs.

Microbial profile on metallic and ceramic bracket materials.

Science.gov (United States)

Anhoury, Patrick; Nathanson, Dan; Hughes, Christopher V; Socransky, Sigmund; Feres, Magda; Chou, Laisheng Lee

2002-08-01

The placement of orthodontic appliances creates a favorable environment for the accumulation of a microbiota and food residues, which, in time, may cause caries or exacerbate any pre-existing periodontal disease. The purpose of the present study was to compare the total bacterial counts present on metallic and ceramic orthodontic brackets in order to clarify which bracket type has a higher plaque retaining capacity and to determine the levels of Streptococcus mutans and Lactobacillus spp on both types of brackets. Thirty-two metallic brackets and 24 ceramic brackets were collected from orthodontic patients at the day of debonding. Two brackets were collected from each patient; one from a maxillary central incisor and another from a maxillary second premolar. Sixteen patients who used metallic brackets and 12 patients who used ceramic brackets were sampled. Bacterial populations were studied using "checkerboard" DNA-DNA hybridization, which uses DNA probes to identify species in complex microbial samples. The significance of differences between groups was determined using the Mann-Whitney U-test. Results showed no significant differences between metallic and ceramic brackets with respect to the caries-inducing S mutans and L acidophilus spp counts. Mean counts of 8 of 35 additional species differed significantly between metallic and ceramic brackets with no obvious pattern favoring one bracket type over the other. This study showed higher mean counts of Treponema denticola, Actinobacillus actinomycetemcomitans, Fusobacterium nucleatum ss vincentii, Streptococcus anginosus, and Eubacterium nodatum on metallic brackets while higher counts of Eikenella corrodens, Campylobacter showae, and Selenomonas noxia were found on ceramic brackets.

A theoretical reassessment of microbial maintenance and implications for microbial ecology modeling.

Science.gov (United States)

Wang, Gangsheng; Post, Wilfred M

2012-09-01

We attempted to reconcile three microbial maintenance models (Herbert, Pirt, and Compromise) through a theoretical reassessment. We provided a rigorous proof that the true growth yield coefficient (Y(G)) is the ratio of the specific maintenance rate (a in Herbert) to the maintenance coefficient (m in Pirt). Other findings from this study include: (1) the Compromise model is identical to the Herbert for computing microbial growth and substrate consumption, but it expresses the dependence of maintenance on both microbial biomass and substrate; (2) the maximum specific growth rate in the Herbert (μ(max,H)) is higher than those in the other two models (μ(max,P) and μ(max,C)), and the difference is the physiological maintenance factor (m(q) = a); and (3) the overall maintenance coefficient (m(T)) is more sensitive to m(q) than to the specific growth rate (μ(G)) and Y(G). Our critical reassessment of microbial maintenance provides a new approach for quantifying some important components in soil microbial ecology models. © This article is a US government work and is in the public domain in the USA.

Synthetic biology for microbial heavy metal biosensors.

Science.gov (United States)

Kim, Hyun Ju; Jeong, Haeyoung; Lee, Sang Jun

2018-02-01

Using recombinant DNA technology, various whole-cell biosensors have been developed for detection of environmental pollutants, including heavy metal ions. Whole-cell biosensors have several advantages: easy and inexpensive cultivation, multiple assays, and no requirement of any special techniques for analysis. In the era of synthetic biology, cutting-edge DNA sequencing and gene synthesis technologies have accelerated the development of cell-based biosensors. Here, we summarize current technological advances in whole-cell heavy metal biosensors, including the synthetic biological components (bioparts), sensing and reporter modules, genetic circuits, and chassis cells. We discuss several opportunities for improvement of synthetic cell-based biosensors. First, new functional modules must be discovered in genome databases, and this knowledge must be used to upgrade specific bioparts through molecular engineering. Second, modules must be assembled into functional biosystems in chassis cells. Third, heterogeneity of individual cells in the microbial population must be eliminated. In the perspectives, the development of whole-cell biosensors is also discussed in the aspects of cultivation methods and synthetic cells.

The Importance of Transition Metals in the Expanding Network of Microbial Metabolism in the Archean Eon

Science.gov (United States)

Moore, E. K.; Jelen, B. I.; Giovannelli, D.; Prabhu, A.; Raanan, H.; Falkowski, P. G.

2017-12-01

Deep time changes in Earth surface redox conditions, particularly due to global oxygenation, has impacted the availability of different metals and substrates that are central in biology. Oxidoreductase proteins are molecular nanomachines responsible for all biological electron transfer processes across the tree of life. These enzymes largely contain transition metals in their active sites. Microbial metabolic pathways form a global network of electron transfer, which expanded throughout the Archean eon. Older metabolisms (sulfur reduction, methanogenesis, anoxygenic photosynthesis) accessed negative redox potentials, while later evolving metabolisms (oxygenic photosynthesis, nitrification/denitrification, aerobic respiration) accessed positive redox potentials. The incorporation of different transition metals facilitated biological innovation and the expansion of the network of microbial metabolism. Network analysis was used to examine the connections between microbial taxa, metabolic pathways, crucial metallocofactors, and substrates in deep time by incorporating biosignatures preserved in the geologic record. Nitrogen fixation and aerobic respiration have the highest level of betweenness among metabolisms in the network, indicating that the oldest metabolisms are not the most central. Fe has by far the highest betweenness among metals. Clustering analysis largely separates High Metal Bacteria (HMB), Low Metal Bacteria (LMB), and Archaea showing that simple un-weighted links between taxa, metabolism, and metals have phylogenetic relevance. On average HMB have the highest betweenness among taxa, followed by Archaea and LMB. There is a correlation between the number of metallocofactors and metabolic pathways in representative bacterial taxa, but Archaea do not follow this trend. In many cases older and more recently evolved metabolisms were clustered together supporting previous findings that proliferation of metabolic pathways is not necessarily chronological.

Effects of deposition of heavy-metal-polluted harbor mud on microbial diversity and metal resistance in sandy marine sediments

DEFF Research Database (Denmark)

Toes, Ann-Charlotte M; Finke, Niko; Kuenen, J Gijs

2008-01-01

Deposition of dredged harbor sediments in relatively undisturbed ecosystems is often considered a viable option for confinement of pollutants and possible natural attenuation. This study investigated the effects of deposition of heavy-metal-polluted sludge on the microbial diversity of sandy...... the finding that some groups of clones were shared between the metal-impacted sandy sediment and the harbor control, comparative analyses showed that the two sediments were significantly different in community composition. Consequences of redeposition of metal-polluted sediment were primarily underlined...... with cultivation-dependent techniques. Toxicity tests showed that the percentage of Cd- and Cu-tolerant aerobic heterotrophs was highest among isolates from the sandy sediment with metal-polluted mud on top....

Microbial Metabolite Production for Accelerated Metal and Radionuclide Bioremediation (Microbial Metabolite Production Report)

International Nuclear Information System (INIS)

TURICK, CHARLES

2004-01-01

Biogeochemical activity is an ongoing and dynamic process due to bacterial activity in the subsurface. Bacteria contribute significantly to biotransformation of metals and radionuclides. As basic science reveals more information about specific mechanisms of bacterial-metal reduction, an even greater contribution of bacteria to biogeochemical activities is realized. An understanding and application of the mechanisms of metal and radionuclide reduction offers tremendous potential for development into bioremedial processes and technologies. Most bacteria are capable of biogeochemical transformation as a result of meeting nutrient requirements. These assimilatory mechanisms for metals transformation include production of small molecules that serve as electron shuttles for metal reduction. This contribution to biogeochemistry is small however due to only trace requirements for minerals by bacteria. Dissimilatory metal reducing bacteria (DMRB) reduce oxidized metals and insoluble mineral oxides as a means for biological energy production during growth. These types of bacteria offer considerable potential for bioremediation of environments contaminated with toxic metals and radionuclides because of the relatively large amount of metal biotransformation they require for growth. One of the mechanisms employed by some DMRB for electron transfer to insoluble metal oxides is melanin production. The electrochemical properties of melanin provide this polymeric, humic-type compound with electron shuttling properties. Melanin, specifically, pyomelanin, increases the rate and degree of metal reduction in DMRB as a function of pyomelanin concentration. Due to its electron shuttling behavior, only low femtogram quantities per cell are required to significantly increase metal reduction capacity of DMRB. Melanin production is not limited to DMRB. In fact melanin is one of the most common pigments produced by biological systems. Numerous soil microorganisms produce melanin, contributing

Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model.

Science.gov (United States)

Fang, Yilin; Scheibe, Timothy D; Mahadevan, Radhakrishnan; Garg, Srinath; Long, Philip E; Lovley, Derek R

2011-03-25

The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint-based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species and multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The

Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model

Science.gov (United States)

Fang, Yilin; Scheibe, Timothy D.; Mahadevan, Radhakrishnan; Garg, Srinath; Long, Philip E.; Lovley, Derek R.

2011-03-01

The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint-based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species and multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The

Modeling of Heavy Metal Transformation in Soil Ecosystem

Science.gov (United States)

Kalinichenko, Kira; Nikovskaya, Galina N.

2017-04-01

The intensification of industrial activity leads to an increase in heavy metals pollution of soils. In our opinion, sludge from biological treatment of municipal waste water, stabilized under aerobic-anaerobic conditions (commonly known as biosolid), may be considered as concentrate of natural soil. In their chemical, physical and chemical and biological properties these systems are similar gel-like nanocomposites. These contain microorganisms, humic substances, clay, clusters of nanoparticles of heavy metal compounds, and so on involved into heteropolysaccharides matrix. It is known that microorganisms play an important role in the transformation of different nature substances in soil and its health maintenance. The regularities of transformation of heavy metal compounds in soil ecosystem were studied at the model of biosolid. At biosolid swelling its structure changing (gel-sol transition, weakening of coagulation contacts between metal containing nanoparticles, microbial cells and metabolites, loosening and even destroying of the nanocomposite structure) can occur [1, 2]. The promotion of the sludge heterotrophic microbial activities leads to solubilization of heavy metal compounds in the system. The microbiological process can be realized in alcaligeneous or acidogeneous regimes in dependence on the type of carbon source and followed by the synthesis of metabolites with the properties of flocculants and heavy metals extragents [3]. In this case the heavy metals solubilization (bioleaching) in the form of nanoparticles of hydroxycarbonate complexes or water soluble complexes with oxycarbonic acids is observed. Under the action of biosolid microorganisms the heavy metals-oxycarbonic acids complexes can be transformed (catabolised) into nano-sizing heavy metals- hydroxycarbonates complexes. These ecologically friendly complexes and microbial heteropolysaccharides are able to interact with soil colloids, stay in the top soil profile, and improve soil structure due

Density-dependent microbial turnover improves soil carbon model predictions of long-term litter manipulations

Science.gov (United States)

Georgiou, Katerina; Abramoff, Rose; Harte, John; Riley, William; Torn, Margaret

2017-04-01

Climatic, atmospheric, and land-use changes all have the potential to alter soil microbial activity via abiotic effects on soil or mediated by changes in plant inputs. Recently, many promising microbial models of soil organic carbon (SOC) decomposition have been proposed to advance understanding and prediction of climate and carbon (C) feedbacks. Most of these models, however, exhibit unrealistic oscillatory behavior and SOC insensitivity to long-term changes in C inputs. Here we diagnose the sources of instability in four models that span the range of complexity of these recent microbial models, by sequentially adding complexity to a simple model to include microbial physiology, a mineral sorption isotherm, and enzyme dynamics. We propose a formulation that introduces density-dependence of microbial turnover, which acts to limit population sizes and reduce oscillations. We compare these models to results from 24 long-term C-input field manipulations, including the Detritus Input and Removal Treatment (DIRT) experiments, to show that there are clear metrics that can be used to distinguish and validate the inherent dynamics of each model structure. We find that widely used first-order models and microbial models without density-dependence cannot readily capture the range of long-term responses observed across the DIRT experiments as a direct consequence of their model structures. The proposed formulation improves predictions of long-term C-input changes, and implies greater SOC storage associated with CO2-fertilization-driven increases in C inputs over the coming century compared to common microbial models. Finally, we discuss our findings in the context of improving microbial model behavior for inclusion in Earth System Models.

Incorporating Geochemical And Microbial Kinetics In Reactive Transport Models For Generation Of Acid Rock Drainage

Science.gov (United States)

Andre, B. J.; Rajaram, H.; Silverstein, J.

2010-12-01

Acid mine drainage, AMD, results from the oxidation of metal sulfide minerals (e.g. pyrite), producing ferrous iron and sulfuric acid. Acidophilic autotrophic bacteria such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans obtain energy by oxidizing ferrous iron back to ferric iron, using oxygen as the electron acceptor. Most existing models of AMD do not account for microbial kinetics or iron geochemistry rigorously. Instead they assume that oxygen limitation controls pyrite oxidation and thus focus on oxygen transport. These models have been successfully used for simulating conditions where oxygen availability is a limiting factor (e.g. source prevention by capping), but have not been shown to effectively model acid generation and effluent chemistry under a wider range of conditions. The key reactions, oxidation of pyrite and oxidation of ferrous iron, are both slow kinetic processes. Despite being extensively studied for the last thirty years, there is still not a consensus in the literature about the basic mechanisms, limiting factors or rate expressions for microbially enhanced oxidation of metal sulfides. An indirect leaching mechanism (chemical oxidation of pyrite by ferric iron to produce ferrous iron, with regeneration of ferric iron by microbial oxidation of ferrous iron) is used as the foundation of a conceptual model for microbially enhanced oxidation of pyrite. Using literature data, a rate expression for microbial consumption of ferrous iron is developed that accounts for oxygen, ferrous iron and pH limitation. Reaction rate expressions for oxidation of pyrite and chemical oxidation of ferrous iron are selected from the literature. A completely mixed stirred tank reactor (CSTR) model is implemented coupling the kinetic rate expressions, speciation calculations and flow. The model simulates generation of AMD and effluent chemistry that qualitatively agrees with column reactor and single rock experiments. A one dimensional reaction

Meta-Transcriptomic Analysis of a Chromate-Reducing Aquifer Microbial Community

Science.gov (United States)

Beller, H. R.; Brodie, E. L.; Han, R.; Karaoz, U.

2010-12-01

A major challenge for microbial ecology that has become more tractable in the advent of new molecular techniques is characterizing gene expression in complex microbial communities. We are using meta-transcriptomic analysis to characterize functional changes in an aquifer-derived, chromate-reducing microbial community as it transitions through various electron-accepting conditions. We inoculated anaerobic microcosms with groundwater from the Cr-contaminated Hanford 100H site and supplemented them with lactate and electron acceptors present at the site, namely, nitrate, sulfate, and Fe(III). The microcosms progressed successively through various electron-accepting conditions (e.g., denitrifying, sulfate-reducing, and ferric iron-reducing conditions, as well as nitrate-dependent, chemolithotrophic Fe(II)-oxidizing conditions). Cr(VI) was rapidly reduced initially and again upon further Cr(VI) amendments. Extensive geochemical sampling and analysis (e.g., lactate, acetate, chloride, nitrate, nitrite, sulfate, dissolved Cr(VI), total Fe(II)), RNA/DNA harvesting, and PhyloChip analyses were conducted. Methods were developed for removal of rRNA from total RNA in preparation for meta-transcriptome sequencing. To date, samples representing denitrifying and fermentative/sulfate-reducing conditions have been sequenced using 454 Titanium technology. Of the non-rRNA related reads for the denitrifying sample (which was also actively reducing chromate), ca. 8% were associated with denitrification and ca. 0.9% were associated with chromate resistance/transport, in contrast to the fermentative/sulfate-reducing sample (in which chromate had already been reduced), which had zero reads associated with either of these categories but many predicted proteins associated with sulfate-reducing bacteria. We observed sequences for key functional transcripts that were unique at the nucleotide level compared to the GenBank non-redundant database [such as L-lactate dehydrogenase (iron

Soil biochar amendment shapes the composition of N{sub 2}O-reducing microbial communities

Energy Technology Data Exchange (ETDEWEB)

Harter, Johannes; Weigold, Pascal [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); El-Hadidi, Mohamed; Huson, Daniel H. [Algorithms in Bioinformatics, Center for Bioinformatics, University of Tuebingen, Sand 14, 72076 Tuebingen (Germany); Kappler, Andreas [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); Behrens, Sebastian, E-mail: sbehrens@umn.edu [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Drive S.E., Minneapolis, MN 55455-0116 (United States); BioTechnology Institute, 140 Gortner Labs, 1479 Gortner Avenue, St. Paul, MN 55108-6106 (United States)

2016-08-15

Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N{sub 2}O) emissions. N{sub 2}O is a potent greenhouse gas. The main sources of N{sub 2}O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N{sub 2}O emission mitigation and the abundance and activity of N{sub 2}O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described ‘atypical’ nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N{sub 2}O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N{sub 2}O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N{sub 2}O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. - Highlights: • Biochar promoted anaerobic, alkalinity-adapted, and polymer-degrading microbial taxa. • Biochar fostered the development of distinct N{sub 2}O-reducing microbial taxa. • Taxonomic shifts among N{sub 2}O-reducing microbes

Virtual Institute of Microbial Stress and Survival: Deduction of Stress Response Pathways in Metal and Radionuclide Reducing Microorganisms

Energy Technology Data Exchange (ETDEWEB)

None

2004-04-17

The projects application goals are to: (1) To understand bacterial stress-response to the unique stressors in metal/radionuclide contamination sites; (2) To turn this understanding into a quantitative, data-driven model for exploring policies for natural and biostimulatory bioremediation; (3) To implement proposed policies in the field and compare results to model predictions; and (4) Close the experimental/computation cycle by using discrepancies between models and predictions to drive new measurements and construction of new models. The projects science goals are to: (1) Compare physiological and molecular response of three target microorganisms to environmental perturbation; (2) Deduce the underlying regulatory pathways that control these responses through analysis of phenotype, functional genomic, and molecular interaction data; (3) Use differences in the cellular responses among the target organisms to understand niche specific adaptations of the stress and metal reduction pathways; (4) From this analysis derive an understanding of the mechanisms of pathway evolution in the environment; and (5) Ultimately, derive dynamical models for the control of these pathways to predict how natural stimulation can optimize growth and metal reduction efficiency at field sites.

Microbial mineral illization of montmorillonite in low-permeability oil reservoirs for microbial enhanced oil recovery.

Science.gov (United States)

Cui, Kai; Sun, Shanshan; Xiao, Meng; Liu, Tongjing; Xu, Quanshu; Dong, Honghong; Wang, Di; Gong, Yejing; Sha, Te; Hou, Jirui; Zhang, Zhongzhi; Fu, Pengcheng

2018-05-11

Microbial mineral illization has been investigated for its role in the extraction and recovery of metals from ores. Here we report our application of mineral bioillization for the microbial enhanced oil recovery in low-permeability oil reservoirs. It aimed to reveal the etching mechanism of the four Fe (III)-reducing microbial strains under anaerobic growth conditions on the Ca-montmorillonite. The mineralogical characterization of the Ca-montmorillonite was performed by Fourier transform infrared spectroscopy, X-ray powder diffraction, scanning electron microscopy and energy dispersive spectrometer. Results showed that the microbial strains could efficiently reduce Fe (III) at an optimal rate of 71 %, and alter the crystal lattice structure of the lamella to promote the interlayer cation exchange, and to efficiently inhibit the Ca-montmorillonite swelling at an inhibitory rate of 48.9 %. Importance Microbial mineral illization is ubiquitous in the natural environment. Microbes in low-permeability reservoirs are able to enable the alteration of the structure and phase of the Fe-poor minerals by reducing Fe (III) and inhibiting clay swelling which is still poorly studied. This study aimed to reveal the interaction mechanism between Fe (III)-reducing bacterial strains and Ca-montmorillonite under anaerobic atmosphere, and to investigate the extent and rates of Fe (III) reduction and phase changes with their activities. Application of Fe (III)-reducing bacteria will provide a new way to inhibit clay swelling, to elevate reservoir permeability, and to reduce pore throat resistance after water flooding for enhanced oil recovery in low-permeability reservoirs. Copyright © 2018 American Society for Microbiology.

Microbial Diversity in KURT Groundwater and Biomineralization Characteristics

International Nuclear Information System (INIS)

Roh, Yul; Rhee, Sung Keun; Oh, Jong Min; Park, Byung Jun

2009-03-01

The Underground Research Tunnel (URT) located in Korea Atomic Energy Research Institute (KAERI), Daejeon, South Korea was recently constructed as an experimental site to study radionuclide transport, biogeochemistry, radionuclide-mineral interactions for the geological disposal of high level nuclear waste. Groundwater sampled from URT was used to examine microbial diversity and to enrich metal reducing bacteria for studying microbe-metal interactions. Genomic analysis indicated that the groundwater contained diverse microorganisms such as metal reducers, metal oxidizers, anaerobic denitrifying bacteria, and bacteria for reductive dechlorination. Metal-reducing bacteria enriched from the groundwater was used to study metal reduction and biomineralization. The metal-reducing bacteria enriched with acetate or lactate as the electron donors showed the bacteria reduced Fe(III)-citrate, Fe(III) oxyhydroxides, Mn(IV) oxide, and Cr(VI) as the electron acceptors. Preliminary study indicated that the enriched bacteria were able to use glucose, lactate, acetate, and hydrogen as electron donors while reducing Fe(III)-citrate or Fe(III) oxyhydroxide as the electron acceptor. The bacteria exhibited diverse mineral precipitation capabilities including the formation of magnetite, siderite, and rhodochrosite. The results indicated that Fe(III)- and metal-reducing communities are present in URT at the KAERI

The Abundance and Activity of Nitrate-Reducing Microbial Populations in Estuarine Sediments

Science.gov (United States)

Cardarelli, E.; Francis, C. A.

2014-12-01

Estuaries are productive ecosystems that ameliorate nutrient and metal contaminants from surficial water supplies. At the intersection of terrestrial and aquatic environments, estuarine sediments host major microbially-mediated geochemical transformations. These include denitrification (the conversion of nitrate to nitrous oxide and/or dinitrogen) and dissimilatory nitrate reduction to ammonium (DNRA). Denitrification has historically been seen as the predominant nitrate attenuation process and functions as an effective sink for nitrate. DNRA has previously been believed to be a minor nitrate reduction process and transforms nitrate within the ecosystem to ammonium, a more biologically available N species. Recent studies have compared the two processes in coastal environments and determined fluctuating environmental conditions may suppress denitrification, supporting an increased role for DNRA in the N cycle. Nitrate availability and salinity are factors thought to influence the membership of the microbial communities present, and the nitrate reduction process that predominates. The aim of this study is to investigate how nitrate concentration and salinity alter the transcript abundances of N cycling functional gene markers for denitrification (nirK, nirS) and DNRA (nrfA) in estuarine sediments at the mouth of the hypernutrified Old Salinas River, CA. Short-term whole core incubations amended with artificial freshwater/artificial seawater (2 psu, 35 psu) and with varying NO3- concentrations (200mM, 2000mM) were conducted to assess the activity as well as the abundance of the nitrate-reducing microbial populations present. Gene expression of nirK, nirS, and nrfA at the conclusion of the incubations was quantified using reverse transcription quantitative polymerase chain reaction (RT-qPCR). High abundances of nirK, nirS, and nrfA under particular conditions coupled with the resulting geochemical data ultimately provides insight onto how the aforementioned factors

Microbial links between sulfate reduction and metal retention in uranium- and heavy metal-contaminated soil

DEFF Research Database (Denmark)

Sitte, Jana; Akob, Denise M.; Kaufmann, Christian

2010-01-01

Sulfate-reducing bacteria (SRB) can affect metal mobility either directly by reductive transformation of metal ions, e.g., uranium, into their insoluble forms or indirectly by formation of metal sulfides. This study evaluated in situ and biostimulated activity of SRB in groundwater-influenced soils...... from a creek bank contaminated with heavy metals and radionuclides within the former uranium mining district of Ronneburg, Germany. In situ activity of SRB, measured by the 35SO42– radiotracer method, was restricted to reduced soil horizons with rates of 142 ± 20 nmol cm–3 day–1. Concentrations...... of heavy metals were enriched in the solid phase of the reduced horizons, whereas pore water concentrations were low. X-ray absorption near-edge structure (XANES) measurements demonstrated that 80% of uranium was present as reduced uranium but appeared to occur as a sorbed complex. Soil-based dsrAB clone...

Biotechnological Aspects of Microbial Extracellular Electron Transfer

Science.gov (United States)

Kato, Souichiro

2015-01-01

Extracellular electron transfer (EET) is a type of microbial respiration that enables electron transfer between microbial cells and extracellular solid materials, including naturally-occurring metal compounds and artificial electrodes. Microorganisms harboring EET abilities have received considerable attention for their various biotechnological applications, in addition to their contribution to global energy and material cycles. In this review, current knowledge on microbial EET and its application to diverse biotechnologies, including the bioremediation of toxic metals, recovery of useful metals, biocorrosion, and microbial electrochemical systems (microbial fuel cells and microbial electrosynthesis), were introduced. Two potential biotechnologies based on microbial EET, namely the electrochemical control of microbial metabolism and electrochemical stimulation of microbial symbiotic reactions (electric syntrophy), were also discussed. PMID:26004795

Advanced Experimental Analysis of Controls on Microbial Fe(III) Oxide Reduction - Final Report - 09/16/1996 - 03/16/2001; FINAL

International Nuclear Information System (INIS)

Roden, Eric E.

2001-01-01

Considering the broad influence that microbial Fe(III) oxide reduction can have on subsurface metal/organic contaminant biogeochemistry, understanding the mechanisms that control this process is critical for predicting the behavior and fate of these contaminants in anaerobic subsurface environments. Knowledge of the factors that influence the rates of growth and activity of Fe(III) oxide-reducing bacteria is critical for predicting (i.e., modeling) the long-term influence of these organisms on the fate of contaminants in the subsurface, and for effectively utilizing Fe(III) oxide reduction and associated geochemical affects for the purpose of subsurface metal/organic contamination bioremediation. This research project will refine existing models for microbiological and geochemical controls on Fe(III) oxide reduction, using laboratory reactor systems that mimic, to varying degrees, the physical and chemical conditions of the subsurface. Novel experimental methods for studying the kinetics of microbial Fe(III) oxide reduction and measuring growth rates of Fe(III) oxide-reducing bacteria will be developed. These new methodologies will be directly applicable to studies on subsurface contaminant transformations directly coupled to or influenced by microbial Fe(III) oxide reduction

Elevated temperature alters carbon cycling in a model microbial community

Science.gov (United States)

Mosier, A.; Li, Z.; Thomas, B. C.; Hettich, R. L.; Pan, C.; Banfield, J. F.

2013-12-01

Earth's climate is regulated by biogeochemical carbon exchanges between the land, oceans and atmosphere that are chiefly driven by microorganisms. Microbial communities are therefore indispensible to the study of carbon cycling and its impacts on the global climate system. In spite of the critical role of microbial communities in carbon cycling processes, microbial activity is currently minimally represented or altogether absent from most Earth System Models. Method development and hypothesis-driven experimentation on tractable model ecosystems of reduced complexity, as presented here, are essential for building molecularly resolved, benchmarked carbon-climate models. Here, we use chemoautotropic acid mine drainage biofilms as a model community to determine how elevated temperature, a key parameter of global climate change, regulates the flow of carbon through microbial-based ecosystems. This study represents the first community proteomics analysis using tandem mass tags (TMT), which enable accurate, precise, and reproducible quantification of proteins. We compare protein expression levels of biofilms growing over a narrow temperature range expected to occur with predicted climate changes. We show that elevated temperature leads to up-regulation of proteins involved in amino acid metabolism and protein modification, and down-regulation of proteins involved in growth and reproduction. Closely related bacterial genotypes differ in their response to temperature: Elevated temperature represses carbon fixation by two Leptospirillum genotypes, whereas carbon fixation is significantly up-regulated at higher temperature by a third closely related genotypic group. Leptospirillum group III bacteria are more susceptible to viral stress at elevated temperature, which may lead to greater carbon turnover in the microbial food web through the release of viral lysate. Overall, this proteogenomics approach revealed the effects of climate change on carbon cycling pathways and other

Field Deployment for In-situ Metal and Radionuclide Stabilization by Microbial Metabolites

Energy Technology Data Exchange (ETDEWEB)

Turick, C. E.; Knox, A. S.; Dixon, K. L.; Roseberry, R. J.; Kritzas, Y. G

2005-09-26

A novel biotechnology is reported here that was demonstrated at SRS that facilitates metal and actinide immobilization by incorporating the physiology and ecology of indigenous bacteria. This technology is based on our previous work with pyomelanin-producing bacteria isolated from SRS soils. Through tyrosine supplementation, overproduction of pyomelanin was achieved, which lead ultimately to metal and actinide immobilization, both in-vitro and in-situ. Pyomelanin is a recalcitrant microbial pigment and a humic type compound in the class of melanin pigments. Pyomelanin has electron shuttling and metal chelation capabilities and thus accelerates the bacterial reduction and/or immobilization of metals. Pyomelanin is produced outside the cell and either diffuses away or attaches to the cell surface. In either case, the reduced pyomelanin is capable of transferring electrons to metals as well as chelating metals. Because of its recalcitrance and redox cycling properties, pyomelanin molecules can be used over and over again for metal transformation. When produced in excess, pyomelanin produced by one bacterial species can be used by other species for metal reduction, thereby extending the utility of pyomelanin and further accelerating metal immobilization rates. Soils contaminated with Ni and U were the focus of this study in order to develop in-situ, metal bioimmobilization technologies. We have demonstrated pyomelanin production in soil from the Tims Branch area of SRS as a result of tyrosine amendments. These results were documented in laboratory soil column studies and field deployment studies. The amended soils demonstrated increased redox behavior and sequestration capacity of U and transition metals following pyomelanin production. Treatments incorporating tyrosine and lactate demonstrated the highest levels of pyomelanin production. In order to determine the potential use of this technology at other areas of SRS, pyomelanin producing bacteria were also quantified

Porosity and Organic Carbon Controls on Naturally Reduced Zone (NRZ) Formation Creating Microbial ';Hotspots' for Fe, S, and U Cycling in Subsurface Sediments

Science.gov (United States)

Jones, M. E.; Janot, N.; Bargar, J.; Fendorf, S. E.

2013-12-01

Previous studies have illustrated the importance of Naturally Reduced Zones (NRZs) within saturated sediments for the cycling of metals and redox sensitive contaminants. NRZs can provide a source of reducing equivalents such as reduced organic compounds or hydrogen to stimulate subsurface microbial communities. These NRZ's are typically characterized by low permeability and elevated concentrations of organic carbon and trace metals. However, both the formation of NRZs and their importance to the overall aquifer carbon remineralization is not fully understood. Within NRZs the hydrolysis of particulate organic carbon (POC) and subsequent fermentation of dissolved organic carbon (DOC) to form low molecular weight dissolved organic carbon (LMW-DOC) provides electron donors necessary for the respiration of Fe, S, and in the case of the Rifle aquifer, U. Rates of POC hydrolysis and subsequent fermentation have been poorly constrained and rates in excess and deficit to the rates of subsurface anaerobic respiratory processes have been suggested. In this study, we simulate the development of NRZ sediments in diffusion-limited aggregates to investigate the physical and chemical conditions required for NRZ formation. Effects of sediment porosity and POC loading on Fe, S, and U cycling on molecular and nanoscale are investigated with synchrotron-based Near Edge X-ray Absorption Fine Structure Spectroscopy (NEXAFS). Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) and Fourier Transform Infrared spectroscopy (FTIR) are used to characterize the transformations in POC and DOC. Sediment aggregates are inoculated with the natural microbial biota from the Rifle aquifer and population dynamics are monitored by 16S RNA analysis. Overall, establishment of low permeability NRZs within the aquifer stimulate microbial respiration beyond the diffusion-limited zones and can limit the transport of U through a contaminated aquifer. However, the long-term stability of

Exogenous Nitrogen Addition Reduced the Temperature Sensitivity of Microbial Respiration without Altering the Microbial Community Composition

Directory of Open Access Journals (Sweden)

Hui Wei

2017-12-01

Full Text Available Atmospheric nitrogen (N deposition is changing in both load quantity and chemical composition. The load effects have been studied extensively, whereas the composition effects remain poorly understood. We conducted a microcosm experiment to study how N chemistry affected the soil microbial community composition characterized by phospholipid fatty acids (PLFAs and activity indicated by microbial CO2 release. Surface and subsurface soils collected from an old-growth subtropical forest were supplemented with three N-containing materials (ammonium, nitrate, and urea at the current regional deposition load (50 kg ha-1 yr-1 and incubated at three temperatures (10, 20, and 30°C to detect the interactive effects of N deposition and temperature. The results showed that the additions of N, regardless of form, did not alter the microbial PLFAs at any of the three temperatures. However, the addition of urea significantly stimulated soil CO2 release in the early incubation stage. Compared with the control, N addition consistently reduced the temperature dependency of microbial respiration, implying that N deposition could potentially weaken the positive feedback of the warming-stimulated soil CO2 release to the atmosphere. The consistent N effects for the surface and subsurface soils suggest that the effects of N on soil microbial communities may be independent of soil chemical contents and stoichiometry.

Microbial physiology-based model of ethanol metabolism in subsurface sediments

Science.gov (United States)

Jin, Qusheng; Roden, Eric E.

2011-07-01

A biogeochemical reaction model was developed based on microbial physiology to simulate ethanol metabolism and its influence on the chemistry of anoxic subsurface environments. The model accounts for potential microbial metabolisms that degrade ethanol, including those that oxidize ethanol directly or syntrophically by reducing different electron acceptors. Out of the potential metabolisms, those that are active in the environment can be inferred by fitting the model to experimental observations. This approach was applied to a batch sediment slurry experiment that examined ethanol metabolism in uranium-contaminated aquifer sediments from Area 2 at the U.S. Department of Energy Field Research Center in Oak Ridge, TN. According to the simulation results, complete ethanol oxidation by denitrification, incomplete ethanol oxidation by ferric iron reduction, ethanol fermentation to acetate and H 2, hydrogenotrophic sulfate reduction, and acetoclastic methanogenesis: all contributed significantly to the degradation of ethanol in the aquifer sediments. The assemblage of the active metabolisms provides a frame work to explore how ethanol amendment impacts the chemistry of the environment, including the occurrence and levels of uranium. The results can also be applied to explore how diverse microbial metabolisms impact the progress and efficacy of bioremediation strategies.

Adaptive long-term monitoring of soil health in metal phytostabilization: ecological attributes and ecosystem services based on soil microbial parameters.

Science.gov (United States)

Epelde, Lur; Becerril, José M; Alkorta, Itziar; Garbisu, Carlos

2014-01-01

Phytostabilization is a promising option for the remediation of metal contaminated soils which requires the implementation of long-term monitoring programs. We here propose to incorporate the paradigm of "adaptive monitoring", which enables monitoring programs to evolve iteratively as new information emerges and research questions change, to metal phytostabilization. Posing good questions that cover the chemical, toxicological and ecological concerns associated to metal contaminated soils is critical for an efficient long-term phytostabilization monitoring program. Regarding the ecological concerns, soil microbial parameters are most valuable indicators of the effectiveness of metal phytostabilization processes in terms of recovery of soil health. We suggest to group soil microbial parameters in higher-level categories such as "ecological attributes" (vigor, organization, stability) or "ecosystem services" in order to facilitate interpretation and, most importantly, to provide long-term phytostabilization monitoring programs with the required stability through time against changes in techniques, methods, interests, etc. that will inevitably occur during the monitoring program. Finally, a Phytostabilization Monitoring Card, based on both ecological attributes and ecosystem services, for soil microbial properties is provided.

Microbes in Heavy Metal Remediation: A Review on Current Trends and Patents.

Science.gov (United States)

Mishra, Geetesh Kumar

2017-01-01

Heavy metal pollution in the environmental samples like soil, water and runoff water is a worldwide problem. Such contamination of environmental matrices by the heavy metals accumulates due to various activities involving human driven sources and industries, although agriculture and sewage disposal are the largest source for the heavy metal contamination. Disposal of heavy metals or waste products containing heavy metals in the environment postures a trivial threat to public safety and health. Heavy metals are persistence and they can also cause biomagnifications and accumulate in food chain. Microbial bioremediation of heavy metal is emerging as an effective technique. Microbial bioremediation is a highly efficient environmental friendly procedure which also reduces the cost of cleanup process associated with heavy metal contamination. New methods for removal of heavy metals from the environmental samples are under development and most recent advancements have been made in exploring the knowledge of metal-microbes interactions and its use for heavy metal remediation. This review paper will focus on the microbial bioremediation process and highlight some of the newly developed patented methods for microbial bioremediation of the heavy metals from the environmental samples using microbial populations. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Reducing Uncertainty in the Daycent Model of Heterotrophic Respiration with a More Mechanistic Representation of Microbial Processes.

Science.gov (United States)

Berardi, D.; Gomez-Casanovas, N.; Hudiburg, T. W.

2017-12-01

Improving the certainty of ecosystem models is essential to ensuring their legitimacy, value, and ability to inform management and policy decisions. With more than a century of research exploring the variables controlling soil respiration, a high level of uncertainty remains in the ability of ecosystem models to accurately estimate respiration with changing climatic conditions. Refining model estimates of soil carbon fluxes is a high priority for climate change scientists to determine whether soils will be carbon sources or sinks in the future. We found that DayCent underestimates heterotrophic respiration by several magnitudes for our temperate mixed conifer forest site. While traditional ecosystem models simulate decomposition through first order kinetics, recent research has found that including microbial mechanisms explains 20 percent more spatial heterogeneity. We manipulated the DayCent heterotrophic respiration model to include a more mechanistic representation of microbial dynamic and compared the new model with continuous and survey observations from our experimental forest site in the Northern Rockies ecoregion. We also calibrated the model's sensitivity to soil moisture and temperature to our experimental data. We expect to improve the accuracy of the model by 20-30 percent. By using a more representative and calibrated model of soil carbon dynamics, we can better predict feedbacks between climate and soil carbon pools.

Efficacy of Moss as a Bioindicator of Heavy Metals When Controlling for Microbial Variables

Science.gov (United States)

Hall, K. M.; Atkinson, D. B.

2017-12-01

Interest in pollution has lead to the use of plants as indicators of particulate levels, acting as a cheaper, more widely dispersed resource than human manufactured alternatives. These biomonitors could provide accurate, current data across cities and in localized regions once the mechanism of accumulation is fully understood. One possible variable that could affect the efficacy of mosses as bioindicators of heavy metal absorption is the microbial colonies that thrive on the surface of these non vascular plants. Each micro organism has shown variance in absorption of heavy metals, leading to the question how much do the colonies contribute to measured variation? For this experiment samples of living mosses were collected from different trees in a region, each showing a different set of organisms growing on them. Measurements of cadmium were taken from a portion of the first samples, and second samples will be taken after dosing the rest of the living samples in a lab environment over time. Two of the mosses are being treated to limit microbial growth to compare to samples from the same tree. We hypothesize that there will be a significant difference either from one tree's absorption to the next, or between mosses from the same tree with limited growth due to the variation of microbial influence.

The efficacy of different anti-microbial metals at preventing the formation of, and eradicating bacterial biofilms of pathogenic indicator strains.

Science.gov (United States)

Gugala, Natalie; Lemire, Joe A; Turner, Raymond J

2017-06-01

The emergence of multidrug-resistant pathogens and the prevalence of biofilm-related infections have generated a demand for alternative anti-microbial therapies. Metals have not been explored in adequate detail for their capacity to combat infectious disease. Metal compounds can now be found in textiles, medical devices and disinfectants-yet, we know little about their efficacy against specific pathogens. To help fill this knowledge gap, we report on the anti-microbial and antibiofilm activity of seven metals: silver, copper, titanium, gallium, nickel, aluminum and zinc against three bacterial strains, Pseudomonas aeruginosa, Staphylococcus aureus and Escherichia coli. To evaluate the capacity of metal ions to prevent the growth of, and eradicate biofilms and planktonic cells, bacterial cultures were inoculated in the Calgary Biofilm Device (minimal biofilm eradication concentration) in the presence of the metal salts. Copper, gallium and titanium were capable of preventing planktonic and biofilm growth, and eradicating established biofilms of all tested strains. Further, we observed that the efficacies of the other tested metal salts displayed variable efficacy against the tested strains. Further, contrary to the enhanced resistance anticipated from bacterial biofilms, particular metal salts were observed to be more effective against biofilm communities versus planktonic cells. In this study, we have demonstrated that the identity of the bacterial strain must be considered before treatment with a particular metal ion. Consequent to the use of metal ions as anti-microbial agents to fight multidrug-resistant and biofilm-related infections increases, we must aim for more selective deployment in a given infectious setting.

Mathematical modeling of microbial growth in milk

Directory of Open Access Journals (Sweden)

Jhony Tiago Teleken

2011-12-01

Full Text Available A mathematical model to predict microbial growth in milk was developed and analyzed. The model consists of a system of two differential equations of first order. The equations are based on physical hypotheses of population growth. The model was applied to five different sets of data of microbial growth in dairy products selected from Combase, which is the most important database in the area with thousands of datasets from around the world, and the results showed a good fit. In addition, the model provides equations for the evaluation of the maximum specific growth rate and the duration of the lag phase which may provide useful information about microbial growth.

ECONOMIC RETURNS FROM REDUCING POULTRY LITTER PHOSPHORUS WITH MICROBIAL PHYTASE

OpenAIRE

Bosch, Darrell J.; Zhu, Minkang; Kornegay, Ervin T.

1997-01-01

Requiring that crop applications of manure be based on phosphorus content (P-standard) could increase poultry litter disposal costs. Microbial phytase reduces litter P content and could reduce litter disposal costs under a P-standard. For a representative Virginia turkey farm, phytase costs $2,500 and could increase value of litter used for fertilizer on the turkey farm by $390 and reduce supplemental P feed costs by $1,431. Based on assumed litter demand and supply, estimated litter export p...

Soil biochar amendment shapes the composition of N2O-reducing microbial communities.

Science.gov (United States)

Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H; Kappler, Andreas; Behrens, Sebastian

2016-08-15

Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N2O) emissions. N2O is a potent greenhouse gas. The main sources of N2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N2O emission mitigation and the abundance and activity of N2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described 'atypical' nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

Are underground clay disposal conditions favorable for microbial activity and bio-corrosion?

Energy Technology Data Exchange (ETDEWEB)

Libert, M.; Kerber-Schuetz, M.; Bildstein, O. [CEA, DEN/DTN/SMTM/LMTE, bat. 307, 13108 Saint Paul Lez Durance Cedex (France); Esnault, L. [ECOGEOSAFE, Technopole de l' Environnement Arbois- Mediterranee, BP 90027 Aix en Provence (France)

2013-07-01

The French concept for geological disposal of high-level radioactive waste is based on a multi-barrier system including metallic containers confined in a clay-stone layer. The main alteration vector is water coming from the host rock and triggering corrosion of metallic components. Despite extreme conditions, microorganisms can adapt and survive in these environments. Anoxic corrosion of metallic containers and water radiolysis produce H{sub 2}, which potentially represents an abundant energetic source for microbial development, especially in this type of environment containing low amounts of biodegradable organic matter. Moreover, formation of Fe(III)-bearing corrosion products such as magnetite (Fe{sub 3}O{sub 4}) can provide electron acceptors for microbial development. Therefore, bio-corrosion studies are needed in order to investigate the activity of hydrogenotrophic bacteria able to reduce sulphates or Fe(III) from iron oxides (passive layer). These studies help in evaluating such microbial impacts on the long-term stability of metallic components involved in radioactive waste disposal. (authors)

Microbial Diversity and Characteristics in Anaerobic Environments in KURT Groundwater

International Nuclear Information System (INIS)

Roh, Yul; Oh, Jong Min; Rhee, Sung Keun; Yong, Jong Joong

2008-03-01

The Underground Research Tunnel (URT) located in Korea Atomic Energy Research Institute (KAERI), Daejeon, South Korea was recently constructed as an experimental site to study radionuclide transport, biogeochemistry, radionuclide-mineral interactions for the geological disposal of high level nuclear waste. Groundwater sampled from URT was used to examine microbial diversity and to enrich metal reducing bacteria for studying microbe-metal interactions. Genomic analysis indicated that the groundwater contained diverse microorganisms such as metal reducers, metal oxidizers, anaerobic denitrifying bacteria, and bacteria for reductive dechlorination. Metal-reducing bacteria enriched from the groundwater was used to study metal reduction and biomineralization. The metal-reducing bacteria enriched with acetate or lactate as the electron donors showed the bacteria reduced Fe(III)-citrate, Fe(III) oxyhydroxide, Mn(IV) oxide, and Cr(VI) as the electron acceptors. Preliminary study indicated that the enriched bacteria were able to use glucose, lactate, acetate, and hydrogen as electron donors while reducing Fe(III)-citrate or Fe(III) oxyhydroxide as the electron acceptor. The bacteria exhibited diverse mineral precipitation capabilities including the formation of magnetite, siderite, and rhodochrosite. The results indicated that Fe(III)- and metal-reducing communities are present in URT at the KAERI

Functioning of metal contaminated garden soil after remediation

International Nuclear Information System (INIS)

Jelusic, Masa; Grcman, Helena; Vodnik, Dominik; Suhadolc, Metka; Lestan, Domen

2013-01-01

The effect of remediation using three EDTA doses (10, 30, 60 mmol kg −1 ) on soil functioning was assessed using column experiment and Brassica rapa. Soil washing removed up to 77, 29 and 72% of metals from soil contaminated with 1378, 578 and 8.5 mg kg −1 of Pb, Zn and Cd, respectively. Sequential extraction indicated removal from the carbonate soil fraction. Metal oral-accessibility from the stomach phase was reduced by up to 75 and from the small intestine by up to 79% (Pb). Part of metals (up to 0.8% Cd) was lost due to leaching from columns. Remediation reduced toxic metal soil-root transfer by up to 61% but did not prevent metal accumulation in leaves. The fitness of plants grown on EDTA washed soils (gas exchange, fluorescence) was not compromised. Remediation initially reduced the soil DNA content (up to 29%, 30 mmol kg −1 EDTA) and changed the structure of microbial population. -- Highlights: ► Toxic metals contaminated garden soil was remediated in a pilot-scale. ► EDTA washing reduced soil Pb, Zn and Cd content and bioavailability. ► Remediated soil preserved the function of plant and microbial substrate. ► Remediation didn't prevent the accumulation of toxic metals in the test plant. -- EDTA soil washing effectively removed toxic metals and reduced their transfer from the soil to plant roots but did not prevent their accumulation in leaves

Evaluating the microbial community and gene regulation involved in crystallization kinetics of ZnS formation in reduced environments

Science.gov (United States)

Falk, Nicholas; Chaganti, Subba Rao; Weisener, Christopher G.

2018-01-01

In anoxic environments, sulfate-reducing bacteria (SRB) may precipitate sparingly-soluble, fine-grained sulfides as by-products of dissimilatory sulfate reduction. This bio-mechanism lends importance to acid rock drainage (ARD) remediation efforts for its ability to immobilize harmful metals from contaminant pathways, including Zn. However, SRB often coexist alongside multiple bacterial guilds in these environments, and may be sustained or hindered by the activities and metabolic by-products of their cohorts, driven by the commonly available substrates. Thus, the effectiveness of onset sulfate reduction and resultant metal-sulfide generation in ARD treatment can be enhanced by unravelling the complexities associated with these interactions. This research used material sourced from a passive bioreactor system located at the Stockton Coal Mine, New Zealand to investigate SRB activity and associated community function. RNA sequencing showed spore-forming Desulfitobacterium and Desulfotomaculum as the dominant SRB enriched from the reduced zone of the bioreactor. Metatranscriptomic analysis revealed acetogenic bacteria as syntrophic partners in substrate availability and Pseudomonas as metal-resistant community members. ZnS precipitates were observed by scanning electron microscopy (SEM) in short-term batch enrichments as well as long-term raw bioreactor material, with observed differences in mineral arrangement indicative of different nucleation scenarios. Syntrophy, metal response mechanisms, and the capacity for sporulation were observed as key microbial functions in mine waste reclamation settings. Here, Zn and S mass balance calculations coupled with RNA sequence data and microscopy illuminated favourable physicochemical and biological conditions for early metal sulfide precipitation in passive treatment systems for ARD and highlight the advantages of linking both lab and field-scale studies.

Microbial Ecology and Evolution in the Acid Mine Drainage Model System.

Science.gov (United States)

Huang, Li-Nan; Kuang, Jia-Liang; Shu, Wen-Sheng

2016-07-01

Acid mine drainage (AMD) is a unique ecological niche for acid- and toxic-metals-adapted microorganisms. These low-complexity systems offer a special opportunity for the ecological and evolutionary analyses of natural microbial assemblages. The last decade has witnessed an unprecedented interest in the study of AMD communities using 16S rRNA high-throughput sequencing and community genomic and postgenomic methodologies, significantly advancing our understanding of microbial diversity, community function, and evolution in acidic environments. This review describes new data on AMD microbial ecology and evolution, especially dynamics of microbial diversity, community functions, and population genomes, and further identifies gaps in our current knowledge that future research, with integrated applications of meta-omics technologies, will fill. Copyright © 2016 Elsevier Ltd. All rights reserved.

Measures of Microbial Biomass for Soil Carbon Decomposition Models

Science.gov (United States)

Mayes, M. A.; Dabbs, J.; Steinweg, J. M.; Schadt, C. W.; Kluber, L. A.; Wang, G.; Jagadamma, S.

2014-12-01

Explicit parameterization of the decomposition of plant inputs and soil organic matter by microbes is becoming more widely accepted in models of various complexity, ranging from detailed process models to global-scale earth system models. While there are multiple ways to measure microbial biomass, chloroform fumigation-extraction (CFE) is commonly used to parameterize models.. However CFE is labor- and time-intensive, requires toxic chemicals, and it provides no specific information about the composition or function of the microbial community. We investigated correlations between measures of: CFE; DNA extraction yield; QPCR base-gene copy numbers for Bacteria, Fungi and Archaea; phospholipid fatty acid analysis; and direct cell counts to determine the potential for use as proxies for microbial biomass. As our ultimate goal is to develop a reliable, more informative, and faster methods to predict microbial biomass for use in models, we also examined basic soil physiochemical characteristics including texture, organic matter content, pH, etc. to identify multi-factor predictive correlations with one or more measures of the microbial community. Our work will have application to both microbial ecology studies and the next generation of process and earth system models.

Soil microbial effects of smelter induced heavy metal contamination

Energy Technology Data Exchange (ETDEWEB)

Nordgren, A

1986-01-01

The soil concentrations of Cu and Zn at the secondary smelter were 20 00 mu g/g dry soil. Close to the primary smelter the soil was contaminated with more than ten elements including Pb, Zn, Cu and As at levels ranging between 6000 and 1000 mu g/g dry soil. The correlations between the concentrations of the metals were high at both smelters. Soil respiration rate decreased by about 75% close to both smelters. Total and fluorescein diacetate stained mycelial lengths decrease with increasing heavy metal pollution at the secondary but not at the primary smelter. The fungal community structure was strongly affected by the contamination. General common in coniferous forest soils such as Penicillium and Oidiodendron virtually vanished, while less frequent species like Paecilomyces farinosus and Geomyces pannorum dominated the site close to the smelter. Colony forming units of a number of functional groups of bacteria were found to be very sensitive to metal contamination. The urease activity of the soil was inhibited. Multivariate statistical analyses showed that the metal contamination was the major environmental influence on the microbiotain the soils studied. A study of about 200 decomposition curves resulting from glutamic acid additions to the different soils produced four microbially related parameters: basal respiration rate, initial respiration rate after the addition of the glutamic acid, specific respiration rate during the exponential increase of the respiration rate and the lag time before the exponential phase. With 53 refs.

Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

Directory of Open Access Journals (Sweden)

B. Orcutt

2008-11-01

Full Text Available Anaerobic oxidation of methane (AOM is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H₂, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal were examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species can cause the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007, none of the potential intermediates considered here is able to support metabolic activity matching the measured rates.

Deriving site-specific soil clean-up values for metals and metalloids: rationale for including protection of soil microbial processes.

Science.gov (United States)

Kuperman, Roman G; Siciliano, Steven D; Römbke, Jörg; Oorts, Koen

2014-07-01

Although it is widely recognized that microorganisms are essential for sustaining soil fertility, structure, nutrient cycling, groundwater purification, and other soil functions, soil microbial toxicity data were excluded from the derivation of Ecological Soil Screening Levels (Eco-SSL) in the United States. Among the reasons for such exclusion were claims that microbial toxicity tests were too difficult to interpret because of the high variability of microbial responses, uncertainty regarding the relevance of the various endpoints, and functional redundancy. Since the release of the first draft of the Eco-SSL Guidance document by the US Environmental Protection Agency in 2003, soil microbial toxicity testing and its use in ecological risk assessments have substantially improved. A wide range of standardized and nonstandardized methods became available for testing chemical toxicity to microbial functions in soil. Regulatory frameworks in the European Union and Australia have successfully incorporated microbial toxicity data into the derivation of soil threshold concentrations for ecological risk assessments. This article provides the 3-part rationale for including soil microbial processes in the development of soil clean-up values (SCVs): 1) presenting a brief overview of relevant test methods for assessing microbial functions in soil, 2) examining data sets for Cu, Ni, Zn, and Mo that incorporated soil microbial toxicity data into regulatory frameworks, and 3) offering recommendations on how to integrate the best available science into the method development for deriving site-specific SCVs that account for bioavailability of metals and metalloids in soil. Although the primary focus of this article is on the development of the approach for deriving SCVs for metals and metalloids in the United States, the recommendations provided in this article may also be applicable in other jurisdictions that aim at developing ecological soil threshold values for protection of

Heavy metal removal and recovery using microorganisms

Energy Technology Data Exchange (ETDEWEB)

Wilde, E.W. (Westinghouse Savannah River Co., Aiken, SC (United States)); Benemann, J.R. (Benemann (J.R.), Pinole, CA (United States))

1991-02-01

Microorganisms -- bacteria, fungi, and microalgae -- can accumulate relatively large amounts of toxic heavy metals and radionuclides from the environment. These organisms often exhibit specificity for particular metals. The metal content of microbial biomass can be a substantial fraction of total dry weight with concentration factors (metal in dry biomass to metal in solution) exceeding one million in some cases. Both living and inert (dead) microbial biomass can be used to reduce heavy metal concentrations in contaminated waters to very low levels -- parts per billion and even lower. In many respects (e.g. specificity, residual metal concentrations, accumulation factors, and economics) microbial bioremoval processes can be superior to conventional processes, such as ion exchange and caustic (lime or hydroxide) precipitation for heavy metals removal from waste and contaminated waters. Thus, bioremoval could be developed to contribute to the clean-up of wastes at the Savannah River Site (SRS) and other DOE facilities. However, the potential advantages of bioremoval processes must still be developed into practical operating systems. A detailed review of the literature suggests that appropriate bioremoval processes could be developed for the SRS. There is great variability from one biomass source to another in bioremoval capabilities. Bioremoval is affected by pH, other ions, temperature, and many other factors. The biological (living vs. dead) and physical (immobilized vs. dispersed) characteristics of the biomass also greatly affect metal binding. Even subtle differences in the microbial biomass, such as the conditions under which it was cultivated, can have major effects on heavy metal binding.

Heavy metal removal and recovery using microorganisms

International Nuclear Information System (INIS)

Wilde, E.W.; Benemann, J.R.

1991-02-01

Microorganisms -- bacteria, fungi, and microalgae -- can accumulate relatively large amounts of toxic heavy metals and radionuclides from the environment. These organisms often exhibit specificity for particular metals. The metal content of microbial biomass can be a substantial fraction of total dry weight with concentration factors (metal in dry biomass to metal in solution) exceeding one million in some cases. Both living and inert (dead) microbial biomass can be used to reduce heavy metal concentrations in contaminated waters to very low levels -- parts per billion and even lower. In many respects (e.g. specificity, residual metal concentrations, accumulation factors, and economics) microbial bioremoval processes can be superior to conventional processes, such as ion exchange and caustic (lime or hydroxide) precipitation for heavy metals removal from waste and contaminated waters. Thus, bioremoval could be developed to contribute to the clean-up of wastes at the Savannah River Site (SRS) and other DOE facilities. However, the potential advantages of bioremoval processes must still be developed into practical operating systems. A detailed review of the literature suggests that appropriate bioremoval processes could be developed for the SRS. There is great variability from one biomass source to another in bioremoval capabilities. Bioremoval is affected by pH, other ions, temperature, and many other factors. The biological (living vs. dead) and physical (immobilized vs. dispersed) characteristics of the biomass also greatly affect metal binding. Even subtle differences in the microbial biomass, such as the conditions under which it was cultivated, can have major effects on heavy metal binding

Microbial links between sulfate reduction and metal retention in uranium- and heavy metal-contaminated soil.

Science.gov (United States)

Sitte, Jana; Akob, Denise M; Kaufmann, Christian; Finster, Kai; Banerjee, Dipanjan; Burkhardt, Eva-Maria; Kostka, Joel E; Scheinost, Andreas C; Büchel, Georg; Küsel, Kirsten

2010-05-01

Sulfate-reducing bacteria (SRB) can affect metal mobility either directly by reductive transformation of metal ions, e.g., uranium, into their insoluble forms or indirectly by formation of metal sulfides. This study evaluated in situ and biostimulated activity of SRB in groundwater-influenced soils from a creek bank contaminated with heavy metals and radionuclides within the former uranium mining district of Ronneburg, Germany. In situ activity of SRB, measured by the (35)SO(4)(2-) radiotracer method, was restricted to reduced soil horizons with rates of metals were enriched in the solid phase of the reduced horizons, whereas pore water concentrations were low. X-ray absorption near-edge structure (XANES) measurements demonstrated that approximately 80% of uranium was present as reduced uranium but appeared to occur as a sorbed complex. Soil-based dsrAB clone libraries were dominated by sequences affiliated with members of the Desulfobacterales but also the Desulfovibrionales, Syntrophobacteraceae, and Clostridiales. [(13)C]acetate- and [(13)C]lactate-biostimulated soil microcosms were dominated by sulfate and Fe(III) reduction. These processes were associated with enrichment of SRB and Geobacteraceae; enriched SRB were closely related to organisms detected in soils by using the dsrAB marker. Concentrations of soluble nickel, cobalt, and occasionally zinc declined uranium increased in carbon-amended treatments, reaching metal attenuation and (ii) the fate of uranium mobility is not predictable and may lead to downstream contamination of adjacent ecosystems.

Modelling heavy metal and phosphorus balances for farming systems

NARCIS (Netherlands)

Keller, A.N.; Schulin, R.

2003-01-01

Accounting for agricultural activities such as P fertilization in regional models of heavy metal accumulation provides suitable sustainable management strategies to reduce nutrient surpluses and metal inputs in agricultural soils. Using the balance model PROTERRA-S, we assessed the phosphorus ( P),

Strategies for Reducing the Start-up Operation of Microbial Electrochemical Treatments of Urban Wastewater

Directory of Open Access Journals (Sweden)

Zulema Borjas

2015-12-01

Full Text Available Microbial electrochemical technologies (METs constitute the core of a number of emerging technologies with a high potential for treating urban wastewater due to a fascinating reaction mechanism—the electron transfer between bacteria and electrodes to transform metabolism into electrical current. In the current work, we focus on the model electroactive microorganism Geobacter sulfurreducens to explore both the design of new start-up procedures and electrochemical operations. Our chemostat-grown plug and play cells, were able to reduce the start-up period by 20-fold while enhancing chemical oxygen demand (COD removal by more than 6-fold during this period. Moreover, a filter-press based bioreactor was successfully tested for both acetate-supplemented synthetic wastewater and real urban wastewater. This proof-of-concept pre-pilot treatment included a microbial electrolysis cell (MEC followed in time by a microbial fuel cell (MFC to finally generate electrical current of ca. 20 A·m−2 with a power of 10 W·m−2 while removing 42 g COD day−1·m−2. The effective removal of acetate suggests a potential use of this modular technology for treating acetogenic wastewater where Geobacter sulfurreducens outcompetes other organisms.

Research on treatment of wastewater containing heavy metal by microbial fuel cell

Science.gov (United States)

Chen, Zixuan; Lu, Xun; Yin, Ruixia; Luo, Yunyi; Mai, Hanjian; Zhang, Nan; Xiong, Jingfang; Zhang, Hongguo; Tang, Jinfeng; Luo, Dinggui

2018-02-01

With rapid development of social economy, serious problem has been caused by wastewater containing heavy metals, which was difficult to be treated by many kinds of traditional treatment methods, such as complex processes, high cost or easy to cause secondary pollution. As a novel biological treatment technology, microbial fuel cells (MFC) can generate electric energy while dealing with wastewater, which was proposed and extensively studied. This paper introduced the working principle of MFC, the classification of cathode, and the research progress on the treatment of wastewater containing Cr(VI), Cu(II), Ag(I), Mn(II) and Cd(II) by MFC. The study found that different cathode, different heavy metals anddifferent hybrid systems would affect the performance of the system and removal effect for heavy metal in MFC. MFC was a highly potential pollution control technology. Until now, the research was still in the laboratory stage. Its industrial application for recovery of heavy metal ion, improving the energy recovery rate and improvement or innovation of system were worthy of further research.

Modeling of phytoextraction efficiency of microbially stimulated Salix dasyclados L. in the soils with different speciation of heavy metals.

Science.gov (United States)

Złoch, Michał; Kowalkowski, Tomasz; Tyburski, Jarosław; Hrynkiewicz, Katarzyna

2017-12-02

Bioaugmentation of soils with selected microorganisms during phytoextraction can be the key solution for successful bioremediation and should be accurately calculated for different physicochemical soil properties and heavy metal availability to guarantee the universality of this method. Equally important is the development of an accurate prediction tool to manage phytoremediation process. The main objective of this study was to evaluate the role of three metallotolerant siderophore-producing Streptomyces sp. B1-B3 strains in the phytoremediation of heavy metals with the use of S. dasyclados L. growing in four metalliferrous soils as well as modeling the efficiency of this process based on physicochemical and microbiological properties of the soils using artificial neural network (ANN) analysis. The bacterial inoculation of plants significantly stimulated plant biomass and reduced oxidative stress. Moreover, the bacteria affected the speciation of heavy metals and finally their mobility, thereby enhancing the uptake and bioaccumulation of Zn, Cd, and Pb in the biomass. The best capacity for phytoextraction was noted for strain B1, which had the highest siderophore secretion ability. Finally, ANN model permitted to predict efficiency of phytoextraction based on both the physicochemical properties of the soils and the activity of the soil microbiota with high precision.

An in Situ method for establishing the presence and predicting the activity of heavy metal-reducing microbes in the subsurface. Final Report

International Nuclear Information System (INIS)

Hatfield, K.

2003-01-01

Tracer method to establish presence and distribution of chromium reducing microbes. The primary objective of this research was to establish an in situ tracer method for detecting the presence. distribution. and activity of subsurface heavy metal-reducing microorganisms. Research focused on microbial systems responsible for the reduction of chromium and a suite of biotracers coupled to the reduction process. The tracer method developed may be used to characterize sites contaminated with chromium or expedite bioremediation: and although research focused on chromium. the method can be easily extended to other metals, organics, and radionuclides. This brief final report contains three major sections. The first identifies specific products of the research effort such as students supported and publications. The second section briefly presents major research findings, while the last section summarizes the overall research effort

In Situ Tracer method for establishing the presence and predicting the activity of heavy metal-reducing microbes in the subsurface. Final Report

Energy Technology Data Exchange (ETDEWEB)

Hatfield, K.

2003-07-01

Tracer method to establish presence and distribution of chromium reducing microbes. The primary objective of this research was to establish an in situ tracer method for detecting the presence. distribution. and activity of subsurface heavy metal-reducing microorganisms. Research focused on microbial systems responsible for the reduction of chromium and a suite of biotracers coupled to the reduction process. The tracer method developed may be used to characterize sites contaminated with chromium or expedite bioremediation: and although research focused on chromium. the method can be easily extended to other metals, organics, and radionuclides. This brief final report contains three major sections. The first identifies specific products of the research effort such as students supported and publications. The second section briefly presents major research findings, while the last section summarizes the overall research effort.

Microbial fuel cell driving electrokinetic remediation of toxic metal contaminated soils.

Science.gov (United States)

Habibul, Nuzahat; Hu, Yi; Sheng, Guo-Ping

2016-11-15

An investigation of the feasibility of in-situ electrokinetic remediation for toxic metal contaminated soil driven by microbial fuel cell (MFC) is presented. Results revealed that the weak electricity generated from MFC could power the electrokinetic remediation effectively. The metal removal efficiency and its influence on soil physiological properties were also investigated. With the electricity generated through the oxidation of organics in soils by microorganisms, the metals in the soils would mitigate from the anode to the cathode. The concentrations of Cd and Pb in the soils increased gradually through the anode to the cathode regions after remediation. After about 143days and 108 days' operation, the removal efficiencies of 31.0% and 44.1% for Cd and Pb at the anode region could be achieved, respectively. Soil properties such as pH and soil conductivity were also significantly redistributed from the anode to the cathode regions. The study shows that the MFC driving electrokinetic remediation technology is cost-effective and environmental friendly, with a promising application in soil remediation. Copyright © 2016 Elsevier B.V. All rights reserved.

Bioelectrochemical metal recovery with microbial fuel cells

NARCIS (Netherlands)

Rodenas Motos, Pau

2017-01-01

This thesis aims to explain the metal recovery through the study of their components using Copper as a model compound of the heavy metals. Different electrochemical cells distribution and sizes were used to improve efficiency and current density. Two different electron donors were tested, acetate

Deduction and Analysis of the Interacting Stress Response Pathways of Metal/Radionuclide-reducing Bacteria

Energy Technology Data Exchange (ETDEWEB)

Zhou, Jizhong [University of Oklahoma; He, Zhili [University of Oklahoma

2010-02-28

Project Title: Deduction and Analysis of the Interacting Stress Response Pathways of Metal/Radionuclide-reducing Bacteria DOE Grant Number: DE-FG02-06ER64205 Principal Investigator: Jizhong (Joe) Zhou (University of Oklahoma) Key members: Zhili He, Aifen Zhou, Christopher Hemme, Joy Van Nostrand, Ye Deng, and Qichao Tu Collaborators: Terry Hazen, Judy Wall, Adam Arkin, Matthew Fields, Aindrila Mukhopadhyay, and David Stahl Summary Three major objectives have been conducted in the Zhou group at the University of Oklahoma (OU): (i) understanding of gene function, regulation, network and evolution of Desulfovibrio vugaris Hildenborough in response to environmental stresses, (ii) development of metagenomics technologies for microbial community analysis, and (iii) functional characterization of microbial communities with metagenomic approaches. In the past a few years, we characterized four CRP/FNR regulators, sequenced ancestor and evolved D. vulgaris strains, and functionally analyzed those mutated genes identified in salt-adapted strains. Also, a new version of GeoChip 4.0 has been developed, which also includes stress response genes (StressChip), and a random matrix theory-based conceptual framework for identifying functional molecular ecological networks has been developed with the high throughput functional gene array hybridization data as well as pyrosequencing data from 16S rRNA genes. In addition, GeoChip and sequencing technologies as well as network analysis approaches have been used to analyze microbial communities from different habitats. Those studies provide a comprehensive understanding of gene function, regulation, network, and evolution in D. vulgaris, and microbial community diversity, composition and structure as well as their linkages with environmental factors and ecosystem functioning, which has resulted in more than 60 publications.

Middle East Desert Dust Exposure: Health Risks from Metals and Microbial Pathogens

Science.gov (United States)

Lyles, M. B.

2014-12-01

In the Middle East, dust and sand storms are a persistent problem and can deliver significant amounts of micro-particulates via inhalation into the mouth, nasal pharynx, & lungs due to the fine size and abundance of these micro-particulates. The chronic and acute health risks of this dust inhalation have not been well studied nor has the dust been effectively characterized as to its chemical composition, mineral content, or microbial flora. Scientific experiments were designed to study the Kuwaiti and Iraqi dust as to its physical, chemical, and biological characteristics and for its potential to cause adverse health effects. First, dust samples from different locations were collected and processed and exposure data collected. Initial chemical and physical characterization of each sample including particle size distribution and inorganic analysis was conducted, followed by characterization of biologic flora of the dust, including bacteria, fungi and viruses. Data indicates that the mineralized dust is composed of calcium carbonate over a matrix of metallic silicate nanocrystals containing a variety of trace and heavy metals constituting ~3 % of the PM10 particles by weight, of which ~1% is bioaccessible aluminum and reactive iron, each. The particles also consist of ~1% bioavailable aluminum and reactive iron each. Microbial analysis reveals a significant biodiversity of bacterial, fungi, and viruses of which ~30% are known pathogens. Of the microbes identified, several have hemolytic properties and most have significant antibiotic resistance. Viral analysis indicates a tremendous amount of virons with a large percent of RNA viruses. The level of total suspended particle mass at PM 10 along with environmental & physiological conditions present constitute an excessive exposure to micro-particulates including PM 2.5 and the potential for adverse health effects. Reported data on cell culture and animal studies have indicated a high level of toxicity to these dust

Integrating microbial diversity in soil carbon dynamic models parameters

Science.gov (United States)

Louis, Benjamin; Menasseri-Aubry, Safya; Leterme, Philippe; Maron, Pierre-Alain; Viaud, Valérie

2015-04-01

Faced with the numerous concerns about soil carbon dynamic, a large quantity of carbon dynamic models has been developed during the last century. These models are mainly in the form of deterministic compartment models with carbon fluxes between compartments represented by ordinary differential equations. Nowadays, lots of them consider the microbial biomass as a compartment of the soil organic matter (carbon quantity). But the amount of microbial carbon is rarely used in the differential equations of the models as a limiting factor. Additionally, microbial diversity and community composition are mostly missing, although last advances in soil microbial analytical methods during the two past decades have shown that these characteristics play also a significant role in soil carbon dynamic. As soil microorganisms are essential drivers of soil carbon dynamic, the question about explicitly integrating their role have become a key issue in soil carbon dynamic models development. Some interesting attempts can be found and are dominated by the incorporation of several compartments of different groups of microbial biomass in terms of functional traits and/or biogeochemical compositions to integrate microbial diversity. However, these models are basically heuristic models in the sense that they are used to test hypotheses through simulations. They have rarely been confronted to real data and thus cannot be used to predict realistic situations. The objective of this work was to empirically integrate microbial diversity in a simple model of carbon dynamic through statistical modelling of the model parameters. This work is based on available experimental results coming from a French National Research Agency program called DIMIMOS. Briefly, 13C-labelled wheat residue has been incorporated into soils with different pedological characteristics and land use history. Then, the soils have been incubated during 104 days and labelled and non-labelled CO2 fluxes have been measured at ten

Microbial fuel cell based on electroactive sulfate-reducing biofilm

International Nuclear Information System (INIS)

Angelov, Anatoliy; Bratkova, Svetlana; Loukanov, Alexandre

2013-01-01

Highlights: ► Regulation and management of electricity generation by variation of residence time. ► Design of microbial fuel cell based on electroactive biofilm on zeolite. ► Engineering solution for removing of the obtained elemental sulfur. - abstract: A two chambered laboratory scale microbial fuel cell (MFC) has been developed, based on natural sulfate-reducing bacterium consortium in electroactive biofilm on zeolite. The MFC utilizes potassium ferricyanide in the cathode chamber as an electron acceptor that derives electrons from the obtained in anode chamber H 2 S. The molecular oxygen is finally used as a terminal electron acceptor at cathode compartment. The generated power density was 0.68 W m −2 with current density of 3.2 A m −2 at 150 Ω electrode resistivity. The hydrogen sulfide itself is produced by microbial dissimilative sulfate reduction process by utilizing various organic substrates. Finally, elemental sulfur was identified as the predominant final oxidation product in the anode chamber. It was removed from MFC through medium circulation and gathering in an external tank. This report reveals dependence relationship between the progress of general electrochemical parameters and bacterial sulfate-reduction rate. The presented MFC design can be used for simultaneous sulfate purification of mining drainage wastewater and generation of renewable electricity

Application of Nonlinear Analysis Methods for Identifying Relationships Between Microbial Community Structure and Groundwater Geochemistry

International Nuclear Information System (INIS)

Schryver, Jack C.; Brandt, Craig C.; Pfiffner, Susan M.; Palumbo, A V.; Peacock, Aaron D.; White, David C.; McKinley, James P.; Long, Philip E.

2006-01-01

The relationship between groundwater geochemistry and microbial community structure can be complex and difficult to assess. We applied nonlinear and generalized linear data analysis methods to relate microbial biomarkers (phospholipids fatty acids, PLFA) to groundwater geochemical characteristics at the Shiprock uranium mill tailings disposal site that is primarily contaminated by uranium, sulfate, and nitrate. First, predictive models were constructed using feedforward artificial neural networks (NN) to predict PLFA classes from geochemistry. To reduce the danger of overfitting, parsimonious NN architectures were selected based on pruning of hidden nodes and elimination of redundant predictor (geochemical) variables. The resulting NN models greatly outperformed the generalized linear models. Sensitivity analysis indicated that tritium, which was indicative of riverine influences, and uranium were important in predicting the distributions of the PLFA classes. In contrast, nitrate concentration and inorganic carbon were least important, and total ionic strength was of intermediate importance. Second, nonlinear principal components (NPC) were extracted from the PLFA data using a variant of the feedforward NN. The NPC grouped the samples according to similar geochemistry. PLFA indicators of Gram-negative bacteria and eukaryotes were associated with the groups of wells with lower levels of contamination. The more contaminated samples contained microbial communities that were predominated by terminally branched saturates and branched monounsaturates that are indicative of metal reducers, actinomycetes, and Gram-positive bacteria. These results indicate that the microbial community at the site is coupled to the geochemistry and knowledge of the geochemistry allows prediction of the community composition

Influence of heavy metals and PCBs pollution on the enzyme activity and microbial community of paddy soils around an e-waste recycling workshop.

Science.gov (United States)

Tang, Xianjin; Hashmi, Muhammad Z; Long, Dongyan; Chen, Litao; Khan, Muhammad I; Shen, Chaofeng

2014-03-14

Due to the emerging environmental issues related to e-waste there is concern about the quality of paddy soils near e-waste workshops. The levels of heavy metals and PCBs and their influence on the enzyme activity and microbial community of paddy soils obtained from the immediate vicinity of an e-waste workshop were investigated in the present study. The results indicated that the heavy metal and PCB pollution did not differ significantly with an increase of the sampling point distances (5 to 30 m). The concentration of Cd (2.16 mg·kg-1) and Cu (69.2 mg·kg-1) were higher, and the PCB pollution was also serious, ranging from 4.9 to 21.6 μg·kg-1. The highest enzyme activity was found for urease compared to phosphatase and catalase, and a fluctuating trend in soil enzyme activity was observed in soils from different sampling sites. The microbial analysis revealed that there was no apparent correlation between the microbial community and the pollutants. However, a slight influence for soil microbial communities could be found based on DGGE, the Shannon index and PCA analysis. The present study suggests that the contamination stress of heavy metals and PCBs might have a slight influence on microbial activity in paddy soils. This study provides the baseline data for enzyme activities and microbial communities in paddy soil under the influence of mixed contamination.

Influence of Heavy Metals and PCBs Pollution on the Enzyme Activity and Microbial Community of Paddy Soils around an E-Waste Recycling Workshop

Directory of Open Access Journals (Sweden)

Xianjin Tang

2014-03-01

Full Text Available Due to the emerging environmental issues related to e-waste there is concern about the quality of paddy soils near e-waste workshops. The levels of heavy metals and PCBs and their influence on the enzyme activity and microbial community of paddy soils obtained from the immediate vicinity of an e-waste workshop were investigated in the present study. The results indicated that the heavy metal and PCB pollution did not differ significantly with an increase of the sampling point distances (5 to 30 m. The concentration of Cd (2.16 mg·kg−1 and Cu (69.2 mg·kg−1 were higher, and the PCB pollution was also serious, ranging from 4.9 to 21.6 μg·kg−1. The highest enzyme activity was found for urease compared to phosphatase and catalase, and a fluctuating trend in soil enzyme activity was observed in soils from different sampling sites. The microbial analysis revealed that there was no apparent correlation between the microbial community and the pollutants. However, a slight influence for soil microbial communities could be found based on DGGE, the Shannon index and PCA analysis. The present study suggests that the contamination stress of heavy metals and PCBs might have a slight influence on microbial activity in paddy soils. This study provides the baseline data for enzyme activities and microbial communities in paddy soil under the influence of mixed contamination.

Influence of Heavy Metals and PCBs Pollution on the Enzyme Activity and Microbial Community of Paddy Soils around an E-Waste Recycling Workshop

Science.gov (United States)

Tang, Xianjin; Hashmi, Muhammad Z.; Long, Dongyan; Chen, Litao; Khan, Muhammad I.; Shen, Chaofeng

2014-01-01

Due to the emerging environmental issues related to e-waste there is concern about the quality of paddy soils near e-waste workshops. The levels of heavy metals and PCBs and their influence on the enzyme activity and microbial community of paddy soils obtained from the immediate vicinity of an e-waste workshop were investigated in the present study. The results indicated that the heavy metal and PCB pollution did not differ significantly with an increase of the sampling point distances (5 to 30 m). The concentration of Cd (2.16 mg·kg−1) and Cu (69.2 mg·kg−1) were higher, and the PCB pollution was also serious, ranging from 4.9 to 21.6 μg·kg−1. The highest enzyme activity was found for urease compared to phosphatase and catalase, and a fluctuating trend in soil enzyme activity was observed in soils from different sampling sites. The microbial analysis revealed that there was no apparent correlation between the microbial community and the pollutants. However, a slight influence for soil microbial communities could be found based on DGGE, the Shannon index and PCA analysis. The present study suggests that the contamination stress of heavy metals and PCBs might have a slight influence on microbial activity in paddy soils. This study provides the baseline data for enzyme activities and microbial communities in paddy soil under the influence of mixed contamination. PMID:24637907

Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels

Energy Technology Data Exchange (ETDEWEB)

Waldron, P.J.; Wu, L.; Van Nostrand, J.D.; Schadt, C.W.; Watson, D.B.; Jardine, P.M.; Palumbo, A.V.; Hazen, T.C.; Zhou, J.

2009-06-15

To understand how contaminants affect microbial community diversity, heterogeneity, and functional structure, six groundwater monitoring wells from the Field Research Center of the U.S. Department of Energy Environmental Remediation Science Program (ERSP; Oak Ridge, TN), with a wide range of pH, nitrate, and heavy metal contamination were investigated. DNA from the groundwater community was analyzed with a functional gene array containing 2006 probes to detect genes involved in metal resistance, sulfate reduction, organic contaminant degradation, and carbon and nitrogen cycling. Microbial diversity decreased in relation to the contamination levels of the wells. Highly contaminated wells had lower gene diversity but greater signal intensity than the pristine well. The microbial composition was heterogeneous, with 17-70% overlap between different wells. Metal-resistant and metal-reducing microorganisms were detected in both contaminated and pristine wells, suggesting the potential for successful bioremediation of metal-contaminated groundwaters. In addition, results of Mantel tests and canonical correspondence analysis indicate that nitrate, sulfate, pH, uranium, and technetium have a significant (p < 0.05) effect on microbial community structure. This study provides an overall picture of microbial community structure in contaminated environments with functional gene arrays by showing that diversity and heterogeneity can vary greatly in relation to contamination.

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation.

Science.gov (United States)

Steinbach, Annelie; Schulz, Stefanie; Giebler, Julia; Schulz, Stephan; Pronk, Geertje J; Kögel-Knabner, Ingrid; Harms, Hauke; Wick, Lukas Y; Schloter, Michael

2015-07-01

Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant 'seed bank'.

Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution.

Science.gov (United States)

Coelho, Francisco J R C; Cleary, Daniel F R; Costa, Rodrigo; Ferreira, Marina; Polónia, Ana R M; Silva, Artur M S; Simões, Mário M Q; Oliveira, Vanessa; Gomes, Newton C M

2016-09-01

There is growing concern that predicted changes to global ocean chemistry will interact with anthropogenic pollution to significantly alter marine microbial composition and function. However, knowledge of the compounding effects of climate change stressors and anthropogenic pollution is limited. Here, we used 16S and 18S rRNA (cDNA)-based activity profiling to investigate the differential responses of selected microbial taxa to ocean acidification and oil hydrocarbon contamination under controlled laboratory conditions. Our results revealed that a lower relative abundance of sulphate-reducing bacteria (Desulfosarcina/Desulfococcus clade) due to an adverse effect of seawater acidification and oil hydrocarbon contamination (reduced pH-oil treatment) may be coupled to changes in sediment archaeal communities. In particular, we observed a pronounced compositional shift and marked reduction in the prevalence of otherwise abundant operational taxonomic units (OTUs) belonging to the archaeal Marine Benthic Group B and Marine Hydrothermal Vent Group (MHVG) in the reduced pH-oil treatment. Conversely, the abundance of several putative hydrocarbonoclastic fungal OTUs was higher in the reduced pH-oil treatment. Sediment hydrocarbon profiling, furthermore, revealed higher concentrations of several alkanes in the reduced pH-oil treatment, corroborating the functional implications of the structural changes to microbial community composition. Collectively, our results advance the understanding of the response of a complex microbial community to the interaction between reduced pH and anthropogenic pollution. In future acidified marine environments, oil hydrocarbon contamination may alter the typical mixotrophic and k-/r-strategist composition of surface sediment microbiomes towards a more heterotrophic state with lower doubling rates, thereby impairing the ability of the ecosystem to recover from acute oil contamination events. © 2016 John Wiley & Sons Ltd.

Metal contamination disturbs biochemical and microbial properties of calcareous agricultural soils of the Mediterranean area.

Science.gov (United States)

de Santiago-Martín, Ana; Cheviron, Natalie; Quintana, Jose R; González, Concepción; Lafuente, Antonio L; Mougin, Christian

2013-04-01

Mediterranean climate characteristics and carbonate are key factors governing soil heavy-metal accumulation, and low organic matter (OM) content could limit the ability of microbial populations to cope with resulting stress. We studied the effects of metal contamination on a combination of biological parameters in soils having these characteristics. With this aim, soils were spiked with a mixture of cadmium, copper, lead, and zinc, at the two limit values proposed by current European legislation, and incubated for ≤12 months. Then we measured biochemical (phosphatase, urease, β-galactosidase, arylsulfatase, and dehydrogenase activities) and microbial (fungal and bacterial DNA concentration by quantitative polymerase chain reaction) parameters. All of the enzyme activities were strongly affected by metal contamination and showed the following inhibition sequence: phosphatase (30-64 %) soils was attributed to the different proportion of fine mineral fraction, OM, crystalline iron oxides, and divalent cations in soil solution. The decrease of fungal DNA concentration in metal-spiked soils was negligible, whereas the decrease of bacterial DNA was ~1-54 % at the lowest level and 2-69 % at the highest level of contamination. The lowest bacterial DNA decrease occurred in soils with the highest OM, clay, and carbonate contents. Finally, regarding the strong inhibition of the biological parameters measured and the alteration of the fungal/bacterial DNA ratio, we provide strong evidence that disturbance on the system, even within the limiting values of contamination proposed by the current European Directive, could alter key soil processes. These limiting values should be established according to soil characteristics and/or revised when contamination is produced by a mixture of heavy metals.

Modelling coupled microbial processes in the subsurface: Model development, verification, evaluation and application

Science.gov (United States)

Masum, Shakil A.; Thomas, Hywel R.

2018-06-01

To study subsurface microbial processes, a coupled model which has been developed within a Thermal-Hydraulic-Chemical-Mechanical (THCM) framework is presented. The work presented here, focuses on microbial transport, growth and decay mechanisms under the influence of multiphase flow and bio-geochemical reactions. In this paper, theoretical formulations and numerical implementations of the microbial model are presented. The model has been verified and also evaluated against relevant experimental results. Simulated results show that the microbial processes have been accurately implemented and their impacts on porous media properties can be predicted either qualitatively or quantitatively or both. The model has been applied to investigate biofilm growth in a sandstone core that is subjected to a two-phase flow and variable pH conditions. The results indicate that biofilm growth (if not limited by substrates) in a multiphase system largely depends on the hydraulic properties of the medium. When the change in porewater pH which occurred due to dissolution of carbon dioxide gas is considered, growth processes are affected. For the given parameter regime, it has been shown that the net biofilm growth is favoured by higher pH; whilst the processes are considerably retarded at lower pH values. The capabilities of the model to predict microbial respiration in a fully coupled multiphase flow condition and microbial fermentation leading to production of a gas phase are also demonstrated.

Combustion of Metals in Reduced-Gravity and Extra Terrestrial Environments

Science.gov (United States)

Branch, M.C.; Abbud-Madrid, A.; Daily, J. W.

1999-01-01

The combustion of metals is a field with important practical applications in rocket propellants, high-temperature flames, and material synthesis. Also, the safe operation of metal containers in high-pressure oxygen systems and with cryogenic fuels and oxidizers remains an important concern in industry. The increasing use of metallic components in spacecraft and space structures has also raised concerns about their flammability properties and fire suppression mechanisms. In addition, recent efforts to embark on unmanned and manned planetary exploration, such as on Mars, have also renewed the interest in metal/carbon-dioxide combustion as an effective in situ resource utilization technology. In spite of these practical applications, the understanding of the combustion properties of metals remains far behind that of the most commonly used fuels such as hydrocarbons. The lack of understanding is due to the many problems unique to metal- oxidizer reactions such as: low-temperature surface oxidation prior to ignition, heterogeneous reactions, very high combustion temperatures, product condensation, high emissivity of products, and multi-phase interactions. Very few analytical models (all neglecting the influence of gravity) have been developed to predict the burning characteristics and the flame structure details. Several experimental studies attempting to validate these models have used small metal particles to recreate gravity-free conditions. The high emissivity of the flames, rapid reaction, and intermittent explosions experienced by these particles have made the gathering of any useful information on burning rates and flame structure very difficult. The use of a reduced gravity environment is needed to clarify some of the complex interactions among the phenomena described above. First, the elimination of the intrusive buoyant flows that plague all combustion phenomena is of paramount importance in metal reactions due to the much higher temperatures reached during

Simulated Carbon Cycling in a Model Microbial Mat.

Science.gov (United States)

Decker, K. L.; Potter, C. S.

2006-12-01

We present here the novel addition of detailed organic carbon cycling to our model of a hypersaline microbial mat ecosystem. This ecosystem model, MBGC (Microbial BioGeoChemistry), simulates carbon fixation through oxygenic and anoxygenic photosynthesis, and the release of C and electrons for microbial heterotrophs via cyanobacterial exudates and also via a pool of dead cells. Previously in MBGC, the organic portion of the carbon cycle was simplified into a black-box rate of accumulation of simple and complex organic compounds based on photosynthesis and mortality rates. We will discuss the novel inclusion of fermentation as a source of carbon and electrons for use in methanogenesis and sulfate reduction, and the influence of photorespiration on labile carbon exudation rates in cyanobacteria. We will also discuss the modeling of decomposition of dead cells and the ultimate release of inorganic carbon. The detailed modeling of organic carbon cycling is important to the accurate representation of inorganic carbon flux through the mat, as well as to accurate representation of growth models of the heterotrophs under different environmental conditions. Because the model ecosystem is an analog of ancient microbial mats that had huge impacts on the atmosphere of early earth, this MBGC can be useful as a biological component to either early earth models or models of other planets that potentially harbor life.

Approaches to reducing photon dose calculation errors near metal implants

Energy Technology Data Exchange (ETDEWEB)

Huang, Jessie Y.; Followill, David S.; Howell, Rebecca M.; Mirkovic, Dragan; Kry, Stephen F., E-mail: sfkry@mdanderson.org [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030 and Graduate School of Biomedical Sciences, The University of Texas Health Science Center Houston, Houston, Texas 77030 (United States); Liu, Xinming [Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030 and Graduate School of Biomedical Sciences, The University of Texas Health Science Center Houston, Houston, Texas 77030 (United States); Stingo, Francesco C. [Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030 and Graduate School of Biomedical Sciences, The University of Texas Health Science Center Houston, Houston, Texas 77030 (United States)

2016-09-15

Purpose: Dose calculation errors near metal implants are caused by limitations of the dose calculation algorithm in modeling tissue/metal interface effects as well as density assignment errors caused by imaging artifacts. The purpose of this study was to investigate two strategies for reducing dose calculation errors near metal implants: implementation of metal-based energy deposition kernels in the convolution/superposition (C/S) dose calculation method and use of metal artifact reduction methods for computed tomography (CT) imaging. Methods: Both error reduction strategies were investigated using a simple geometric slab phantom with a rectangular metal insert (composed of titanium or Cerrobend), as well as two anthropomorphic phantoms (one with spinal hardware and one with dental fillings), designed to mimic relevant clinical scenarios. To assess the dosimetric impact of metal kernels, the authors implemented titanium and silver kernels in a commercial collapsed cone C/S algorithm. To assess the impact of CT metal artifact reduction methods, the authors performed dose calculations using baseline imaging techniques (uncorrected 120 kVp imaging) and three commercial metal artifact reduction methods: Philips Healthcare’s O-MAR, GE Healthcare’s monochromatic gemstone spectral imaging (GSI) using dual-energy CT, and GSI with metal artifact reduction software (MARS) applied. For the simple geometric phantom, radiochromic film was used to measure dose upstream and downstream of metal inserts. For the anthropomorphic phantoms, ion chambers and radiochromic film were used to quantify the benefit of the error reduction strategies. Results: Metal kernels did not universally improve accuracy but rather resulted in better accuracy upstream of metal implants and decreased accuracy directly downstream. For the clinical cases (spinal hardware and dental fillings), metal kernels had very little impact on the dose calculation accuracy (<1.0%). Of the commercial CT artifact

Approaches to reducing photon dose calculation errors near metal implants

International Nuclear Information System (INIS)

Huang, Jessie Y.; Followill, David S.; Howell, Rebecca M.; Mirkovic, Dragan; Kry, Stephen F.; Liu, Xinming; Stingo, Francesco C.

2016-01-01

Purpose: Dose calculation errors near metal implants are caused by limitations of the dose calculation algorithm in modeling tissue/metal interface effects as well as density assignment errors caused by imaging artifacts. The purpose of this study was to investigate two strategies for reducing dose calculation errors near metal implants: implementation of metal-based energy deposition kernels in the convolution/superposition (C/S) dose calculation method and use of metal artifact reduction methods for computed tomography (CT) imaging. Methods: Both error reduction strategies were investigated using a simple geometric slab phantom with a rectangular metal insert (composed of titanium or Cerrobend), as well as two anthropomorphic phantoms (one with spinal hardware and one with dental fillings), designed to mimic relevant clinical scenarios. To assess the dosimetric impact of metal kernels, the authors implemented titanium and silver kernels in a commercial collapsed cone C/S algorithm. To assess the impact of CT metal artifact reduction methods, the authors performed dose calculations using baseline imaging techniques (uncorrected 120 kVp imaging) and three commercial metal artifact reduction methods: Philips Healthcare’s O-MAR, GE Healthcare’s monochromatic gemstone spectral imaging (GSI) using dual-energy CT, and GSI with metal artifact reduction software (MARS) applied. For the simple geometric phantom, radiochromic film was used to measure dose upstream and downstream of metal inserts. For the anthropomorphic phantoms, ion chambers and radiochromic film were used to quantify the benefit of the error reduction strategies. Results: Metal kernels did not universally improve accuracy but rather resulted in better accuracy upstream of metal implants and decreased accuracy directly downstream. For the clinical cases (spinal hardware and dental fillings), metal kernels had very little impact on the dose calculation accuracy (<1.0%). Of the commercial CT artifact

Computer Modeling of Direct Metal Laser Sintering

Science.gov (United States)

Cross, Matthew

2014-01-01

A computational approach to modeling direct metal laser sintering (DMLS) additive manufacturing process is presented. The primary application of the model is for determining the temperature history of parts fabricated using DMLS to evaluate residual stresses found in finished pieces and to assess manufacturing process strategies to reduce part slumping. The model utilizes MSC SINDA as a heat transfer solver with imbedded FORTRAN computer code to direct laser motion, apply laser heating as a boundary condition, and simulate the addition of metal powder layers during part fabrication. Model results are compared to available data collected during in situ DMLS part manufacture.

Sequester of metals and mineralization of organic contaminants with microbial mats

International Nuclear Information System (INIS)

Bender, J.; Phillips, P.; Gould, J.P.

1995-01-01

Several recalcitrant organic contaminants are completely mineralized to simple products by microbial mats. Contaminants include chlordane, PCB, TNT, petroleum distillates, BM compounds and TCE in a mixed contaminant solution containing Zn. Degradation rates are relatively rapid under both dark and light conditions. In addition to complete degradation of organic materials, mats have been used to reduce selenate to elemental selenium, remove Pb, Cd, Cu, Zn, Co, Cr, Fe and Mn from water and sequester uranium (U 238 ) at a rate of 3.19 mg/m 2 /h. Results of three pilot projects, including field pond treatment of mine drainage and bioreactor treatment of BTEX compounds will be reported. Microbial mats are natural heterotrophic and autotrophic communities dominated by cyanobacteria (blue-green algae). They are self-organized laminated structures annealed fightly together by slimy secretions from various microbial components. The surface slime of the mats effectively immobilizes the ecosystem to a variety of substrates, thereby stabilizing the most efficient internal microbial structure. Cyanobacteria mats are generated for bioremediation applications by enriching a water surface with ensiled grass clippings together with mat inocula developed in the laboratory

Coupled modeling of groundwater flow solute transport, chemical reactions and microbial processes in the 'SP' island

Energy Technology Data Exchange (ETDEWEB)

Samper, Javier; Molinero, Jorg; Changbing, Yang; Zhang, Guoxiang

2003-12-01

The Redox Zone Experiment was carried out at the Aespoe HRL in order to study the redox behavior and the hydrochemistry of an isolated vertical fracture zone disturbed by the excavation of an access tunnel. Overall results and interpretation of the Redox Zone Project were reported by /Banwart et al, 1995/. Later, /Banwart et al, 1999/ presented a summary of the hydrochemistry of the Redox Zone Experiment. Coupled groundwater flow and reactive transport models of this experiment were carried out by /Molinero, 2000/ who proposed a revised conceptual model for the hydrogeology of the Redox Zone Experiment which could explain simultaneously measured drawdown and salinity data. The numerical model was found useful to understand the natural system. Several conclusions were drawn about the redox conditions of recharge waters, cation exchange capacity of the fracture zone and the role of mineral phases such as pyrite, calcite, hematite and goethite. This model could reproduce the measured trends of dissolved species, except for bicarbonate and sulfate which are affected by microbially-mediated processes. In order to explore the role of microbial processes, a coupled numerical model has been constructed which accounts for water flow, reactive transport and microbial processes. The results of this model is presented in this report. This model accounts for groundwater flow and reactive transport in a manner similar to that of /Molinero, 2000/ and extends the preliminary microbial model of /Zhang, 2001/ by accounting for microbially-driven organic matter fermentation and organic matter oxidation. This updated microbial model considers simultaneously the fermentation of particulate organic matter by yeast and the oxidation of dissolved organic matter, a product of fermentation. Dissolved organic matter is produced by yeast and serves also as a substrate for iron-reducing bacteria. Model results reproduce the observed increase in bicarbonate and sulfate concentration, thus

Direct and indirect effects of metal contamination on soil biota in a Zn-Pb post-mining and smelting area (S Poland)

International Nuclear Information System (INIS)

Kapusta, Pawel; Szarek-Lukaszewska, Grazyna; Stefanowicz, Anna M.

2011-01-01

Effects of metal contamination on soil biota activity were investigated at 43 sites in 5 different habitats (defined by substratum and vegetation type) in a post-mining area. Sites were characterised in terms of soil pH and texture, nutrient status, total and exchangeable metal concentrations, as well as plant species richness and cover, abundances of enchytraeids, nematodes and tardigrades, and microbial respiration and biomass. The concentrations of total trace metals were highest in soils developed on mining waste (metal-rich dolomite), but these habitats were more attractive than sandy sites for plants and soil biota because of their higher content of organic matter, clay and nutrients. Soil mesofauna and microbes were strongly dependent on natural habitat properties. Pollution (exchangeable Zn and Cd) negatively affected only enchytraeid density; due to a positive relationship between enchytraeids and microbes it indirectly reduced microbial activity. - Highlights: → Bioavailable zinc and cadmium reduce enchytraeid density. → Enchytraeids positively influence microbial respiration and biomass. → Total contents of heavy metals in soil are poor predictors of the distribution of plants and soil biota. - Elevated concentrations of exchangeable Zn and Cd reduce enchytraeid density and indirectly affect microbial activity adversely.

Direct and indirect effects of metal contamination on soil biota in a Zn-Pb post-mining and smelting area (S Poland)

Energy Technology Data Exchange (ETDEWEB)

Kapusta, Pawel, E-mail: p.kapusta@botany.pl [Department of Ecology, W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Krakow (Poland); Szarek-Lukaszewska, Grazyna; Stefanowicz, Anna M. [Department of Ecology, W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Krakow (Poland)

2011-06-15

Effects of metal contamination on soil biota activity were investigated at 43 sites in 5 different habitats (defined by substratum and vegetation type) in a post-mining area. Sites were characterised in terms of soil pH and texture, nutrient status, total and exchangeable metal concentrations, as well as plant species richness and cover, abundances of enchytraeids, nematodes and tardigrades, and microbial respiration and biomass. The concentrations of total trace metals were highest in soils developed on mining waste (metal-rich dolomite), but these habitats were more attractive than sandy sites for plants and soil biota because of their higher content of organic matter, clay and nutrients. Soil mesofauna and microbes were strongly dependent on natural habitat properties. Pollution (exchangeable Zn and Cd) negatively affected only enchytraeid density; due to a positive relationship between enchytraeids and microbes it indirectly reduced microbial activity. - Highlights: > Bioavailable zinc and cadmium reduce enchytraeid density. > Enchytraeids positively influence microbial respiration and biomass. > Total contents of heavy metals in soil are poor predictors of the distribution of plants and soil biota. - Elevated concentrations of exchangeable Zn and Cd reduce enchytraeid density and indirectly affect microbial activity adversely.

Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions.

Science.gov (United States)

He, Shaomei; Malfatti, Stephanie A; McFarland, Jack W; Anderson, Frank E; Pati, Amrita; Huntemann, Marcel; Tremblay, Julien; Glavina del Rio, Tijana; Waldrop, Mark P; Windham-Myers, Lisamarie; Tringe, Susannah G

2015-05-19

Wetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial community composition and functions are associated with wetland hydrology, biogeochemistry, and methane emission, which is critical to modeling the microbial component in wetland methane fluxes and to managing restoration projects for maximal carbon sequestration. Here, we couple sequence-based methods with biogeochemical and greenhouse gas measurements to interrogate microbial communities from a pilot-scale restored wetland in the Sacramento-San Joaquin Delta of California, revealing considerable spatial heterogeneity even within this relatively small site. A number of microbial populations and functions showed strong correlations with electron acceptor availability and methane production; some also showed a preference for association with plant roots. Marker gene phylogenies revealed a diversity of major methane-producing and -consuming populations and suggested novel diversity within methanotrophs. Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches. Notably, methanogens were negatively correlated with nitrate-, sulfate-, and metal-reducing bacteria and were most abundant at sampling sites with high peat accretion and low electron acceptor availability, where methane production was highest. Wetlands are the largest nonanthropogenic source of atmospheric methane but also a key global carbon reservoir. Characterizing belowground microbial communities

Physicochemical and sensory analyses on egg powder irradiated to inactivate Salmonella and reduce microbial load

International Nuclear Information System (INIS)

Narvaiz, P.; Lescano, G.; Kairiyama, E.

1992-01-01

Egg powder was treated with 0, 2, 5 and 10 kGy of gamma radiation at 20 C to inactivate Salmonella and to stabilize its microbial load. Microbial, physicochemical and sensory determinations were performed during 4 months of storage to select the optimal radiation dose to attain the objective without significantly reducing egg quality. Microbial results show that 2.0 kGy inactivated Salmonella and reduced microbial load to levels below those stipulated by the Argentine regulations. Physicochemical determinations of egg powder extracts for peroxide number, spectrophotometric measurements in the visible and ultraviolet regions, functional properties on sponge cakes made with egg powder (height, compression-relaxation cycle parameters), foam stability and viscosity showed that gamma radiation at the dose of 2 kGy, did not cause significant changes in these parameters. Higher radiation doses (5 and 10 kGy) did increase rancidity, pigment loss and protein chain scission. Sensory determinations performed on egg powder, and on cakes manufactured with it, agreed with the physicochemical results. After 110 storage days, 2 kGy was the most suitable of the tested doses

Preparation of metal-resistant immobilized sulfate reducing bacteria beads for acid mine drainage treatment.

Science.gov (United States)

Zhang, Mingliang; Wang, Haixia; Han, Xuemei

2016-07-01

Novel immobilized sulfate-reducing bacteria (SRB) beads were prepared for the treatment of synthetic acid mine drainage (AMD) containing high concentrations of Fe, Cu, Cd and Zn using up-flow anaerobic packed-bed bioreactor. The tolerance of immobilized SRB beads to heavy metals was significantly enhanced compared with that of suspended SRB. High removal efficiencies of sulfate (61-88%) and heavy metals (>99.9%) as well as slightly alkaline effluent pH (7.3-7.8) were achieved when the bioreactor was fed with acidic influent (pH 2.7) containing high concentrations of multiple metals (Fe 469 mg/L, Cu 88 mg/L, Cd 92 mg/L and Zn 128 mg/L), which showed that the bioreactor filled with immobilized SRB beads had tolerance to AMD containing high concentrations of heavy metals. Partially decomposed maize straw was a carbon source and stabilizing agent in the initial phase of bioreactor operation but later had to be supplemented by a soluble carbon source such as sodium lactate. The microbial community in the bioreactor was characterized by denaturing gradient gel electrophoresis (DGGE) and sequencing of partial 16S rDNA genes. Synergistic interaction between SRB (Desulfovibrio desulfuricans) and co-existing fermentative bacteria could be the key factor for the utilization of complex organic substrate (maize straw) as carbon and nutrients source for sulfate reduction. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biochar-enhanced composts reduce the potential leaching of nutrients and heavy metals and suppress plant-parasitic nematodes in excessively fertilized cucumber soils.

Science.gov (United States)

Cao, Yune; Gao, Yanming; Qi, Yanbin; Li, Jianshe

2018-03-01

Excessive fertilization is a common agricultural practice that has largely reduced soil nutrient retention capacity and led to nutrient leaching in China. To reduce nutrient leaching, in this study, we evaluated the application of biochar, compost, and biochar-compost on soil properties, leaching water quality, and cucumber plant growth in soils with different nutrient levels. In general, the concentrations of nutrients and heavy metals in leaching water were higher under high-nutrient conditions than under low-nutrient conditions. Both biochar and compost efficiently enhanced soil cation exchange capacity (CEC), water holding capacity (WHC), and microbial biomass carbon (MBC), nitrogen (MBN), and phosphorus (MBP), reduced the potential leaching of nutrients and heavy metals, and improved plant growth. The efficiency of biochar and compost in soil CEC, WHC, MBC, MBN, and MBP and plant growth was enhanced when applied jointly. In addition, biochar and biochar-enhanced compost efficiently suppressed plant-parasitic nematode infestation in a soil with high levels of both N and P. Our results suggest that biochar-enhanced compost can reduce the potential environmental risks in excessively fertilized vegetable soils.

A fermented meat model system for studies of microbial aroma formation

DEFF Research Database (Denmark)

Tjener, Karsten; Stahnke, Louise Heller; Andersen, L.

2003-01-01

A fermented meat model system was developed, by which microbial formation of volatiles could be examined The model was evaluated against dry, fermented sausages with respect to microbial growth, pH and volatile profiles. Fast and slowly acidified sausages and models were produced using the starte......H, microbial growth and volatile profiles was similar to sausage production. Based on these findings, the model system was considered valid for studies of aroma formation of meat cultures for fermented sausage.......A fermented meat model system was developed, by which microbial formation of volatiles could be examined The model was evaluated against dry, fermented sausages with respect to microbial growth, pH and volatile profiles. Fast and slowly acidified sausages and models were produced using the starter...... cultures Pediococcus pentosaceus and Staphylococcus xylosus. Volatiles were collected and analysed by dynamic headspace sampling and GC MS. The analysis was primarily focused on volatiles arising from amino acid degradation and a total of 24 compounds, of which 19 were quantified, were used...

Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia...

Energy Technology Data Exchange (ETDEWEB)

Terence L. Marsh

2004-05-26

The goals of this study were: (1) survey the microbial community in soil samples from a site contaminated with heavy metals using new rapid molecular techniques that are culture-independent; (2) identify phylogenetic signatures of microbial populations that correlate with metal ion contamination; and (3) cultivate these diagnostic strains using traditional as well as novel cultivation techniques in order to identify organisms that may be of value in site evaluation/management or bioremediation.

A Workflow to Model Microbial Loadings in Watersheds

Science.gov (United States)

Many watershed models simulate overland and instream microbial fate and transport, but few actually provide loading rates on land surfaces and point sources to the water body network. This paper describes the underlying general equations for microbial loading rates associated wit...

Models of microbiome evolution incorporating host and microbial selection.

Science.gov (United States)

Zeng, Qinglong; Wu, Steven; Sukumaran, Jeet; Rodrigo, Allen

2017-09-25

Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbes randomly from parents and/or from the environment. Additionally, the environmental pool of available microbes was constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation. In this paper, we extend our neutral models to allow selection to operate on both hosts and microbes. We do this by constructing a phenome for each microbial OTU consisting of a sample of traits that influence host and microbial fitnesses independently. Microbial traits can influence the fitness of hosts ("host selection") and the fitness of microbes ("trait-mediated microbial selection"). Additionally, the fitness effects of traits on microbes can be modified by their hosts ("host-mediated microbial selection"). We simulate the effects of these three types of selection, individually or in combination, on microbiome diversities and the fitnesses of hosts and microbes over several thousand generations of hosts. We show that microbiome diversity is strongly influenced by selection acting on microbes. Selection acting on hosts only influences microbiome diversity when there is near-complete direct or indirect parental contribution to the microbiomes of offspring. Unsurprisingly, microbial fitness increases under microbial selection. Interestingly, when host selection operates, host fitness only increases under two conditions: (1) when there is a strong parental contribution to microbial communities or (2) in the absence of a strong

Microorganisms in heavy metal bioremediation: strategies for applying microbial-community engineering to remediate soils

Directory of Open Access Journals (Sweden)

Jennifer L. Wood

2016-06-01

Full Text Available The remediation of heavy-metal-contaminated soils is essential as heavy metals persist and do not degrade in the environment. Remediating heavy-metal-contaminated soils requires metals to be mobilized for extraction whilst, at the same time, employing strategies to avoid mobilized metals leaching into ground-water or aquatic systems. Phytoextraction is a bioremediation strategy that extracts heavy metals from soils by sequestration in plant tissues and is currently the predominant bioremediation strategy investigated for remediating heavy-metal-contaminated soils. Although the efficiency of phytoextraction remains a limiting feature of the technology, there are numerous reports that soil microorganisms can improve rates of heavy metal extraction.This review highlights the unique challenges faced when remediating heavy-metal-contaminated soils as compared to static aquatic systems and suggests new strategies for using microorganisms to improve phytoextraction. We compare how microorganisms are used in soil bioremediation (i.e. phytoextraction and water bioremediation processes, discussing how the engineering of microbial communities, used in water remediation, could be applied to phytoextraction. We briefly outline possible approaches for the engineering of soil communities to improve phytoextraction either by mobilizing metals in the rhizosphere of the plant or by promoting plant growth to increase the root-surface area available for uptake of heavy metals. We highlight the technological advances that make this research direction possible and how these technologies could be employed in future research.

Application of manures to mitigate the harmful effects of electrokinetic remediation of heavy metals on soil microbial properties in polluted soils.

Science.gov (United States)

Tahmasbian, Iman; Safari Sinegani, Ali Akbar; Nguyen, Thi Thu Nhan; Che, Rongxiao; Phan, Thuc D; Hosseini Bai, Shahla

2017-12-01

Ethylenediaminetetraacetic acid (EDTA) used with electrokinetic (EK) to remediate heavy metal-polluted soils is a toxic chelate for soil microorganisms. Therefore, this study aimed to evaluate the effects of alternative organic chelates to EDTA on improving the microbial properties of a heavy metal-polluted soil subjected to EK. Cow manure extract (CME), poultry manure extract (PME) and EDTA were applied to a lead (Pb) and zinc (Zn)-polluted calcareous soil which were subjected to two electric intensities (1.1 and 3.3 v/cm). Soil carbon pools, microbial activity, microbial abundance (e.g., fungal, actinomycetes and bacterial abundances) and diethylenetriaminepentaacetic acid (DTPA)-extractable Pb and Zn (available forms) were assessed in both cathodic and anodic soils. Applying the EK to soil decreased all the microbial variables in the cathodic and anodic soils in the absence or presence of chelates. Both CME and PME applied with two electric intensities decreased the negative effect of EK on soil microbial variables. The lowest values of soil microbial variables were observed when EK was combined with EDTA. The following order was observed in values of soil microbial variables after treating with EK and chelates: EK + CME or EK + PME > EK > EK + EDTA. The CME and PME could increase the concentrations of available Pb and Zn, although the increase was less than that of EDTA. Overall, despite increasing soil available Pb and Zn, the combination of EK with manures (CME or PME) mitigated the negative effects of using EK on soil microbial properties. This study suggested that the synthetic chelates such as EDTA could be replaced with manures to alleviate the environmental risks of EK application.

Physiological and metagenomic analyses of microbial mats involved in self-purification of mine waters contaminated with heavy metals

Directory of Open Access Journals (Sweden)

Lukasz Drewniak

2016-08-01

Full Text Available Two microbial mats found inside two old (gold and uranium mines in Zloty Stok and Kowary located in SW Poland seem to form a natural barrier that traps heavy metals leaking from dewatering systems. We performed complex physiological and metagenomic analyses to determine which microorganisms are the main driving agents responsible for self-purification of the mine waters and identify metabolic processes responsible for the observed features. SEM and energy dispersive X-ray microanalysis showed accumulation of heavy metals on the mat surface, whereas, sorption experiments showed that neither microbial mats were completely saturated with heavy metals present in the mine waters, indicating that they have a large potential to absorb significant quantities of metal. The metagenomic analysis revealed that Methylococcaceae and Methylophilaceae families were the most abundant in both communities, moreover, it strongly suggest that backbones of both mats were formed by filamentous bacteria, such as Leptothrix, Thiothrix, and Beggiatoa. The Kowary bacterial community was enriched with the Helicobacteraceae family, whereas the Zloty Stok community consist mainly of Sphingomonadaceae, Rhodobacteraceae, and Caulobacteraceae families. Functional (culture-based and metagenome (sequence-based analyses showed that bacteria involved in immobilization of heavy metals, rather than those engaged in mobilization, were the main driving force within the analyzed communities. In turn, a comparison of functional genes revealed that the biofilm formation and heavy metal resistance functions are more desirable in microorganisms engaged in water purification than the ability to utilize heavy metals in the respiratory process (oxidation-reduction. These findings provide insight on the activity of bacteria leading, from biofilm formation to self-purification, of mine waters contaminated with heavy metals

Modeling of microbial quality of food

NARCIS (Netherlands)

Zwietering, M.

1993-01-01

In this thesis it is shown that predictive modeling is a promising tool in food research, to be used to optimize food chains. Various models are developed and validated to be used to describe microbial growth in foods.

A tool is developed to discriminate between different models and

Microbial Biosynthesis of Silver Nanoparticles in Different Culture Media.

Science.gov (United States)

Luo, Ke; Jung, Samuel; Park, Kyu-Hwan; Kim, Young-Rok

2018-01-31

Microbial biosynthesis of metal nanoparticles has been extensively studied for the applications in biomedical sciences and engineering. However, the mechanism for their synthesis through microorganism is not completely understood. In this study, several culture media were investigated for their roles in the microbial biosynthesis of silver nanoparticles (AgNPs). The size and morphology of the synthesized AgNPs were analyzed by UV-vis spectroscopy, Fourier-transform-infrared (FT-IR), transmission electron microscopy (TEM), and dynamic light scattering (DLS). The results demonstrated that nutrient broth (NB) and Mueller-Hinton broth (MHB) among tested media effectively reduced silver ions to form AgNPs with different particle size and shape. Although the involved microorganism enhanced the reduction of silver ions, the size and shape of the particles were shown to mainly depend on the culture media. Our findings suggest that the growth media of bacterial culture play an important role in the synthesis of metallic nanoparticles with regard to their size and shape. We believe our findings would provide useful information for further exploration of microbial biosynthesis of AgNPs and their biomedical applications.

Reply to 'Comment on kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' by J. Griffioen

Science.gov (United States)

Hunter, K. S.; Van Cappellen, P.

2000-01-01

Our paper, 'Kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' (Hunter et al., 1998), presents a theoretical exploration of biogeochemical reaction networks and their importance to the biogeochemistry of groundwater systems. As with any other model, the kinetic reaction-transport model developed in our paper includes only a subset of all physically, biologically and chemically relevant processes in subsurface environments. It considers aquifer systems where the primary energy source driving microbial activity is the degradation of organic matter. In addition to the primary biodegradation pathways of organic matter (i.e. respiration and fermentation), the redox chemistry of groundwaters is also affected by reactions not directly involving organic matter oxidation. We refer to the latter as secondary reactions. By including secondary redox reactions which consume reduced reaction products (e.g., Mn2+, FeS, H2S), and in the process compete with microbial heterotrophic populations for available oxidants (i.e. O2, NO3-, Mn(IV), Fe(III), SO42-), we predict spatio-temporal distributions of microbial activity which differ significantly from those of models which consider only the biodegradation reactions. That is, the secondary reactions have a significant impact on the distributions of the rates of heterotrophic and chemolithotrophic metabolic pathways. We further show that secondary redox reactions, as well as non-redox reactions, significantly influence the acid-base chemistry of groundwaters. The distributions of dissolved inorganic redox species along flowpaths, however, are similar in simulations with and without secondary reactions (see Figs. 3(b) and 7(b) in Hunter et al., 1998), indicating that very different biogeochemical reaction dynamics may lead to essentially the same chemical redox zonation of a groundwater system.

Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

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Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

2016-06-01

Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural

The worm has turned--microbial virulence modeled in Caenorhabditis elegans.

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Sifri, Costi D; Begun, Jakob; Ausubel, Frederick M

2005-03-01

The nematode Caenorhabditis elegans is emerging as a facile and economical model host for the study of evolutionarily conserved mechanisms of microbial pathogenesis and innate immunity. A rapidly growing number of human and animal microbial pathogens have been shown to injure and kill nematodes. In many cases, microbial genes known to be important for full virulence in mammalian models have been shown to be similarly required for maximum pathogenicity in nematodes. C. elegans has been used in mutation-based screening systems to identify novel virulence-related microbial genes and immune-related host genes, many of which have been validated in mammalian models of disease. C. elegans-based pathogenesis systems hold the potential to simultaneously explore the molecular genetic determinants of both pathogen virulence and host defense.

Increasing atmospheric deposition nitrogen and ammonium reduced microbial activity and changed the bacterial community composition of red paddy soil.

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Zhou, Fengwu; Cui, Jian; Zhou, Jing; Yang, John; Li, Yong; Leng, Qiangmei; Wang, Yangqing; He, Dongyi; Song, Liyan; Gao, Min; Zeng, Jun; Chan, Andy

2018-03-27

Atmospheric deposition nitrogen (ADN) increases the N content in soil and subsequently impacts microbial activity of soil. However, the effects of ADN on paddy soil microbial activity have not been well characterized. In this study, we studied how red paddy soil microbial activity responses to different contents of ADN through a 10-months ADN simulation on well managed pot experiments. Results showed that all tested contents of ADN fluxes (27, 55, and 82kgNha -1 when its ratio of NH 4 + /NO 3 - -N (R N ) was 2:1) enhanced the soil enzyme activity and microbial biomass carbon and nitrogen and 27kgNha -1 ADN had maximum effects while comparing with the fertilizer treatment. Generally, increasing of both ADN flux and R N (1:2, 1:1 and 2:1 with the ADN flux of 55kgNha -1 ) had similar reduced effects on microbial activity. Furthermore, both ADN flux and R N significantly reduced soil bacterial alpha diversity (pADN flux and R N were the main drivers in shaping paddy soil bacteria community. Overall, the results have indicated that increasing ADN flux and ammonium reduced soil microbial activity and changed the soil bacterial community. The finding highlights how paddy soil microbial community response to ADN and provides information for N management in paddy soil. Copyright © 2018 Elsevier B.V. All rights reserved.

Evaluating the Metal Tolerance Capacity of Microbial Communities Isolated from Alberta Oil Sands Process Water.

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Mathew L Frankel

Full Text Available Anthropogenic activities have resulted in the intensified use of water resources. For example, open pit bitumen extraction by Canada's oil sands operations uses an estimated volume of three barrels of water for every barrel of oil produced. The waste tailings-oil sands process water (OSPW-are stored in holding ponds, and present an environmental concern as they are comprised of residual hydrocarbons and metals. Following the hypothesis that endogenous OSPW microbial communities have an enhanced tolerance to heavy metals, we tested the capacity of planktonic and biofilm populations from OSPW to withstand metal ion challenges, using Cupriavidus metallidurans, a known metal-resistant organism, for comparison. The toxicity of the metals toward biofilm and planktonic bacterial populations was determined by measuring the minimum biofilm inhibitory concentrations (MBICs and planktonic minimum inhibitory concentrations (MICs using the MBEC ™ assay. We observed that the OSPW community and C. metallidurans had similar tolerances to 22 different metals. While thiophillic elements (Te, Ag, Cd, Ni were found to be most toxic, the OSPW consortia demonstrated higher tolerance to metals reported in tailings ponds (Al, Fe, Mo, Pb. Metal toxicity correlated with a number of physicochemical characteristics of the metals. Parameters reflecting metal-ligand affinities showed fewer and weaker correlations for the community compared to C. metallidurans, suggesting that the OSPW consortia may have developed tolerance mechanisms toward metals present in their environment.

Heavy metal-immobilizing organoclay facilitates polycyclic aromatic hydrocarbon biodegradation in mixed-contaminated soil

International Nuclear Information System (INIS)

Biswas, Bhabananda; Sarkar, Binoy; Mandal, Asit; Naidu, Ravi

2015-01-01

Highlights: • A novel metal-immobilizing organoclay (MIOC) synthesized and characterized. • MIOC immobilizes toxic metals and reduces metal bioavailability. • It enhances PAH-bioavailability to soil bacteria. • It improves microbial growth and activities in mixed-contaminated soils. • MIOC facilitates PAH-biodegradation in metal co-contaminated soils. - Abstract: Soils contaminated with a mixture of heavy metals and polycyclic aromatic hydrocarbons (PAHs) pose toxic metal stress to native PAH-degrading microorganisms. Adsorbents such as clay and modified clay minerals can bind the metal and reduce its toxicity to microorganisms. However, in a mixed-contaminated soil, an adsorption process more specific to the metals without affecting the bioavailability of PAHs is desired for effective degradation. Furthermore, the adsorbent should enhance the viability of PAH-degrading microorganisms. A metal-immobilizing organoclay (Arquad ® 2HT-75-bentonite treated with palmitic acid) (MIOC) able to reduce metal (cadmium (Cd)) toxicity and enhance PAH (phenanthrene) biodegradation was developed and characterized in this study. The MIOC differed considerably from the parent clay in terms of its ability to reduce metal toxicity (MIOC > unmodified bentonite > Arquad–bentonite). The MIOC variably increased the microbial count (10–43%) as well as activities (respiration 3–44%; enzymatic activities up to 68%), and simultaneously maintained phenanthrene in bioavailable form in a Cd-phenanthrene mixed-contaminated soil over a 21-day incubation period. This study may lead to a new MIOC-assisted bioremediation technique for PAHs in mixed-contaminated soils

Heavy metal-immobilizing organoclay facilitates polycyclic aromatic hydrocarbon biodegradation in mixed-contaminated soil

Energy Technology Data Exchange (ETDEWEB)

Biswas, Bhabananda; Sarkar, Binoy [Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes Campus, SA 5095 (Australia); Cooperative Research Centre for Contamination Assessment and Remediation of the Environment, P.O. Box 486, Salisbury, SA 5106 (Australia); Mandal, Asit [Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes Campus, SA 5095 (Australia); Division of Soil Biology, Indian Institute of Soil Science, Bhopal, Madhya Pradesh (India); Naidu, Ravi [Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes Campus, SA 5095 (Australia); Cooperative Research Centre for Contamination Assessment and Remediation of the Environment, P.O. Box 486, Salisbury, SA 5106 (Australia)

2015-11-15

Highlights: • A novel metal-immobilizing organoclay (MIOC) synthesized and characterized. • MIOC immobilizes toxic metals and reduces metal bioavailability. • It enhances PAH-bioavailability to soil bacteria. • It improves microbial growth and activities in mixed-contaminated soils. • MIOC facilitates PAH-biodegradation in metal co-contaminated soils. - Abstract: Soils contaminated with a mixture of heavy metals and polycyclic aromatic hydrocarbons (PAHs) pose toxic metal stress to native PAH-degrading microorganisms. Adsorbents such as clay and modified clay minerals can bind the metal and reduce its toxicity to microorganisms. However, in a mixed-contaminated soil, an adsorption process more specific to the metals without affecting the bioavailability of PAHs is desired for effective degradation. Furthermore, the adsorbent should enhance the viability of PAH-degrading microorganisms. A metal-immobilizing organoclay (Arquad{sup ®} 2HT-75-bentonite treated with palmitic acid) (MIOC) able to reduce metal (cadmium (Cd)) toxicity and enhance PAH (phenanthrene) biodegradation was developed and characterized in this study. The MIOC differed considerably from the parent clay in terms of its ability to reduce metal toxicity (MIOC > unmodified bentonite > Arquad–bentonite). The MIOC variably increased the microbial count (10–43%) as well as activities (respiration 3–44%; enzymatic activities up to 68%), and simultaneously maintained phenanthrene in bioavailable form in a Cd-phenanthrene mixed-contaminated soil over a 21-day incubation period. This study may lead to a new MIOC-assisted bioremediation technique for PAHs in mixed-contaminated soils.

Modeling microbial diversity in anaerobic digestion through an extended ADM1 model.

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Ramirez, Ivan; Volcke, Eveline I P; Rajinikanth, Rajagopal; Steyer, Jean-Philippe

2009-06-01

The anaerobic digestion process comprises a whole network of sequential and parallel reactions, of both biochemical and physicochemical nature. Mathematical models, aiming at understanding and optimization of the anaerobic digestion process, describe these reactions in a structured way, the IWA Anaerobic Digestion Model No. 1 (ADM1) being the most well established example. While these models distinguish between different microorganisms involved in different reactions, to our knowledge they all neglect species diversity between organisms with the same function, i.e. performing the same reaction. Nevertheless, available experimental evidence suggests that the structure and properties of a microbial community may be influenced by process operation and on their turn also determine the reactor functioning. In order to adequately describe these phenomena, mathematical models need to consider the underlying microbial diversity. This is demonstrated in this contribution by extending the ADM1 to describe microbial diversity between organisms of the same functional group. The resulting model has been compared with the traditional ADM1 in describing experimental data of a pilot-scale hybrid Upflow Anaerobic Sludge Filter Bed (UASFB) reactor, as well as in a more detailed simulation study. The presented model is further shown useful in assessing the relationship between reactor performance and microbial community structure in mesophilic CSTRs seeded with slaughterhouse wastewater when facing increasing levels of ammonia.

The benzoquinone-mediated electrochemical microbial biosensor for water biotoxicity assay

International Nuclear Information System (INIS)

Li, Jiuming; Yu, Yuan; Wang, Yuning; Qian, Jun; Zhi, Jinfang

2013-01-01

Graphical abstract: The mediator can participate in microorganism respiration, accept the electrons from respiratory chains, and therefore be reduced by microorganism. The re-oxidization currents of mediators on electrode can reflect the microbial activity, and when respiration is suppressed by toxicants, it can be detected by the resulting change of currents. Unlike other biotoxicity tests, which record the toxic effect after a fixed time for incubation of biocomponents and toxicants, this mediated whole cell biosensor can provide a real-time monitor of the microbial activity during the measurement. -- Abstract: A simple mediated microbial biosensor providing real-time monitoring of water quality and evaluation of biotoxicity was fabricated by entrapping Escherichia coli (E. coli) cells in gelatin on glassy carbon electrode with benzoquinone as the redox mediator. The biotoxicity assay was based on the respiratory activity of E. coli cells estimated by the oxidation current of microbially reduced benzoquinone. The neutrality and lipophilicity rendered benzoquinone better efficiency than ferricyanide in mediated microbial reactions. After the optimization of preparation conditions, the prepared microbial biosensors have measured several common toxicants with different concentrations. In addition, the biotoxicity of binary mixtures of heavy metals and wastewater were investigated. The fabricated biosensor exhibited good repeatability and stability in the biotoxicity measurements

Impaired microbial activity caused by metal pollution: A field study in a deactivated uranium mining area

International Nuclear Information System (INIS)

Antunes, Sara Cristina; Pereira, Ruth; Marques, Sérgio Miguel; Castro, Bruno Branco; Gonçalves, Fernando

2011-01-01

European frameworks for the ecological risk assessment (ERA) of contaminated sites integrate information from three lines of evidence: chemical, ecotoxicological, and ecological. Regarding the last one, field observations at the contaminated sites are compared to reference site(s) and the differences recorded are analysed at the light of a cause-effect relationship, taking into account the site-specific contamination. Thus, included in the tier 2 of a site-specific risk assessment that is being carried out in an deactivated uranium mining area, a battery of soil enzyme activities (dehydrogenases, urease, arysulphatase, cellulase, acid phosphate) and potential nitrification were assessed in seven sampling sites (A–D–E–F–G–H–I) at different distances from the mine pit. These parameters have been considered good indicators of impacts on soil microbial communities and, subsequently, on soil functions. Soil enzyme activities were impaired in the most contaminated site (A, near the mine pit), for which a higher degree of risk was determined in the tier 1 of ERA. Three other sites within the mining area (F, G, and D) were discriminated on the basis of their low microbial activity, using uni- and multivariate approaches, and validating what had been previously found with chemical and ecotoxicological lines of evidence. We observed considerable among-site heterogeneity in terms of soil physical and chemical properties, combined with seasonal differences in enzyme activities. Still, the correlation between microbial parameters and soil general physical and chemical parameters was weak. In opposition, significant and negative correlations were found between soil enzyme activities and several metallic elements (Al, Be, Cu, U). These findings suggest a clear correlation between compromised soil function (nutrient recycling) and metal contamination. Such information reinforces the evidence of risks for some sites within the mining area and is an important

A Modeling Comparison of Methanogenesis from Noncompetitive vs Competitive Substrates in a Simulated Hypersaline Microbial Mat

Science.gov (United States)

Decker, K. L.; Potter, C.; Hoehler, T.

2005-12-01

The well-documented assumption about methanogens that co-occur in hypersaline mat communities with sulfate-reducing bacteria (SRB) is that they rely entirely on non-competitive substrates for methanogenesis. The reason for this is that during sulfate reduction, sulfur-reducing bacteria efficiently utilize H2, leaving a concentration too low for methanogenesis. Early results from recent work on a hypersaline microbial mat from salt evaporation ponds of Guerrero Negro, Baja, Mexico cast doubt that methanogenesis only occurs via non-competitive substrates, because it shows an excess of H2 in the mat rather than a paucity. We explore the use of our simulation model of the microbial biogeochemistry of a hypersaline mat (named MBGC) to compare methane production rates in a 1 cm thick mat when the methanogens use competitive substrates versus noncompetitive substrates. In the `non-competitive substrate' version of the model, methanogens rely exclusively on methylated amines that are accumulated as compatible solutes in cyanobacteria and released after lysis. In contrast, the `competitive substrate' models examine methanogen use of substrates (such as H2 + acetate) with different SRB population sizes (from absent to low). The comparison of these models of methane and sulfide biogeochemistry of a hypersaline mat has both ecological and geobiological significance, as one hypothesis of Archean microbial mats is that they existed in a low sulfate environment.

Metabolic network modeling of microbial interactions in natural and engineered environmental systems

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Octavio ePerez-Garcia

2016-05-01

Full Text Available We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA, experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e. i lumped networks, ii compartment per guild networks, iii bi-level optimization simulations and iv dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial

Calibration and analysis of genome-based models for microbial ecology.

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Louca, Stilianos; Doebeli, Michael

2015-10-16

Microbial ecosystem modeling is complicated by the large number of unknown parameters and the lack of appropriate calibration tools. Here we present a novel computational framework for modeling microbial ecosystems, which combines genome-based model construction with statistical analysis and calibration to experimental data. Using this framework, we examined the dynamics of a community of Escherichia coli strains that emerged in laboratory evolution experiments, during which an ancestral strain diversified into two coexisting ecotypes. We constructed a microbial community model comprising the ancestral and the evolved strains, which we calibrated using separate monoculture experiments. Simulations reproduced the successional dynamics in the evolution experiments, and pathway activation patterns observed in microarray transcript profiles. Our approach yielded detailed insights into the metabolic processes that drove bacterial diversification, involving acetate cross-feeding and competition for organic carbon and oxygen. Our framework provides a missing link towards a data-driven mechanistic microbial ecology.

Accounting for microbial habitats in modeling soil organic matter dynamics

Science.gov (United States)

Chenu, Claire; Garnier, Patricia; Nunan, Naoise; Pot, Valérie; Raynaud, Xavier; Vieublé, Laure; Otten, Wilfred; Falconer, Ruth; Monga, Olivier

2017-04-01

The extreme heterogeneity of soils constituents, architecture and inhabitants at the microscopic scale is increasingly recognized. Microbial communities exist and are active in a complex 3-D physical framework of mineral and organic particles defining pores of various sizes, more or less inter-connected. This results in a frequent spatial disconnection between soil carbon, energy sources and the decomposer organisms and a variety of microhabitats that are more or less suitable for microbial growth and activity. However, current biogeochemical models account for C dynamics at the macroscale (cm, m) and consider time- and spatially averaged relationships between microbial activity and soil characteristics. Different modelling approaches have intended to account for this microscale heterogeneity, based either on considering aggregates as surrogates for microbial habitats, or pores. Innovative modelling approaches are based on an explicit representation of soil structure at the fine scale, i.e. at µm to mm scales: pore architecture and their saturation with water, localization of organic resources and of microorganisms. Three recent models are presented here, that describe the heterotrophic activity of either bacteria or fungi and are based upon different strategies to represent the complex soil pore system (Mosaic, LBios and µFun). These models allow to hierarchize factors of microbial activity in soil's heterogeneous architecture. Present limits of these approaches and challenges are presented, regarding the extensive information required on soils at the microscale and to up-scale microbial functioning from the pore to the core scale.

Contaminant immobilization via microbial activity

International Nuclear Information System (INIS)

1991-11-01

The aim of this study was to search the literature to identify biological techniques that could be applied to the restoration of contaminated groundwaters near uranium milling sites. Through bioremediation it was hypothesized that the hazardous heavy metals could be immobilized in a stable, low-solubility form, thereby halting their progress in the migrating groundwater. Three basic mechanisms were examined: reduction of heavy metals by microbially produced hydrogen sulfide; direct microbial mediated reduction; and biosorption

Heavy Metal Phytoremediation: Microbial Indicators of Soil Health for the Assessment of Remediation Efficiency

Science.gov (United States)

Epelde, Lur; Ma Becerril, José; Alkorta, Itziar; Garbisu, Carlos

Phytoremediation is an effective, non-intrusive, inexpensive, aesthetically pleasing, socially accepted, promising phytotechnology for the remediation of polluted soils. The objective of any soil remediation process must be not only to remove the contaminant(s) from the soil but, most importantly, to restore the continued capacity of the soil to perform or function according to its potential (i.e., to recover soil health). Hence, indicators of soil health are needed to properly assess the efficiency of a phytoremediation process. Biological indicators of soil health, especially those related to the size, activity and diversity of the soil microbial communities, are becoming increasingly used, due to their sensitivity and capacity to provide information that integrates many environmental factors. In particular, microbial indicators of soil health are valid tools to evaluate the success of metal phytoremediation procedures such as phytoextraction and phytostabilization processes.

Orenia metallireducens sp. nov. Strain Z6, a Novel Metal-Reducing Member of the Phylum Firmicutes from the Deep Subsurface

Science.gov (United States)

Sanford, Robert A.; Boyanov, Maxim I.; Kemner, Kenneth M.; O'Loughlin, Edward J.; Chang, Yun-juan; Locke, Randall A.; Weber, Joseph R.; Egan, Sheila M.; Mackie, Roderick I.; Cann, Isaac; Fouke, Bruce W.

2016-01-01

ABSTRACT A novel halophilic and metal-reducing bacterium, Orenia metallireducens strain Z6, was isolated from briny groundwater extracted from a 2.02 km-deep borehole in the Illinois Basin, IL. This organism shared 96% 16S rRNA gene similarity with Orenia marismortui but demonstrated physiological properties previously unknown for this genus. In addition to exhibiting a fermentative metabolism typical of the genus Orenia, strain Z6 reduces various metal oxides [Fe(III), Mn(IV), Co(III), and Cr(VI)], using H2 as the electron donor. Strain Z6 actively reduced ferrihydrite over broad ranges of pH (6 to 9.6), salinity (0.4 to 3.5 M NaCl), and temperature (20 to 60°C). At pH 6.5, strain Z6 also reduced more crystalline iron oxides, such as lepidocrocite (γ-FeOOH), goethite (α-FeOOH), and hematite (α-Fe2O3). Analysis of X-ray absorption fine structure (XAFS) following Fe(III) reduction by strain Z6 revealed spectra from ferrous secondary mineral phases consistent with the precipitation of vivianite [Fe3(PO4)2] and siderite (FeCO3). The draft genome assembled for strain Z6 is 3.47 Mb in size and contains 3,269 protein-coding genes. Unlike the well-understood iron-reducing Shewanella and Geobacter species, this organism lacks the c-type cytochromes for typical Fe(III) reduction. Strain Z6 represents the first bacterial species in the genus Orenia (order Halanaerobiales) reported to reduce ferric iron minerals and other metal oxides. This microbe expands both the phylogenetic and physiological scopes of iron-reducing microorganisms known to inhabit the deep subsurface and suggests new mechanisms for microbial iron reduction. These distinctions from other Orenia spp. support the designation of strain Z6 as a new species, Orenia metallireducens sp. nov. IMPORTANCE A novel iron-reducing species, Orenia metallireducens sp. nov., strain Z6, was isolated from groundwater collected from a geological formation located 2.02 km below land surface in the Illinois Basin, USA

Effects of Microbial and Heavy Metal Contaminants on Environmental/Ecological Health and Revitalization of Coastal Ecosystems in Delaware Bay

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Gulnihal Ozbay

2017-06-01

Full Text Available The presence of heavy metals, excess nutrients, and microbial contaminants in aquatic systems of coastal Delaware has become a public concern as human population increases and land development continues. Delaware's coastal lagoons have been subjected to problems commonly shared by other coastal Mid-Atlantic states: turbidity, sedimentation, eutrophication, periodic hypoxic/anoxic conditions, toxic substances, and high bacterial levels. The cumulative impact of pollutants from run-off and point sources has degraded water quality, reduced the diversity and abundance of various fish species, invertebrates, and submerged aquatic vegetation. The effects are especially pronounced within the manmade dead end canal systems. In this article, we present selected case studies conducted in the Delaware Inland Bays. Due to the ecological services provided by bivalves, our studies in Delaware Inland Bays are geared toward oysters with special focus on the microbial loads followed by the water quality assessments of the bay. The relationships between oysters (Crassostrea virginica, microbial loads and nutrient levels in the water were investigated. The heavy metal levels monitored further away from the waste water treatment plant in the inland bays are marginally higher than the recommended EPA limits. Also, our studies confirmed that aerobic bacteria and Vibrionaceae levels are salinity dependent. Total bacteria in oysters increased when nitrate and total suspended solids increased in the waters. Studies such as these are important because every year millions of Americans consume raw oysters. Data collected over the last 10 years from our studies may be used to build a predictive index of conditions that are favorable for the proliferation of human pathogenic bacteria. Results from this study will benefit the local community by helping them understand the importance of oyster aquaculture and safe consumption of oysters while making them appreciate their

Microbial reduction of uranium using cellulosic substrates

International Nuclear Information System (INIS)

Thombre, M.S.; Thomson, B.M.; Barton, L.L.

1996-01-01

Previous work at the University of New Mexico and elsewhere has shown that sulfate-reducing bacteria are capable of reducing uranium from the soluble +6 oxidation state to the insoluble +4 oxidation state. This chemistry forms the basis of a proposed ground water remediation strategy in which microbial reduction would be used to immobilize soluble uranium. One such system would consist of a subsurface permeable barrier which would stimulate microbial growth resulting in the reduction of sulfate and nitrate and immobilization of metals while permitting the unhindered flow of ground water through it. This research investigated some of the engineering considerations associated with a microbial reducing barrier such as identifying an appropriate biological substrate, estimating the rate of substrate utilization, and identifying the final fate of the contaminants concentrated in the barrier matrix. The performance of batch reactors and column systems that treated simulated plume water was evaluated using cellulose, wheat straw, alfalfa hay, sawdust, and soluble starch as substrates. The concentrations of sulfate, nitrate, and U(VI) were monitored over time. Precipitates from each system were collected, and the precipitated U(IV) was determined to be crystalline UO 2(s) by x-ray diffraction. The results of this study support the proposed use of cellulosic substrates as candidate barrier materials

Microbial control of pollution

Energy Technology Data Exchange (ETDEWEB)

Fry, J C; Gadd, G M; Herbert, R A; Jones, C W; Watson-Craik, I A [eds.

1992-01-01

12 papers are presented on the microbial control of pollution. Topics covered include: bioremediation of oil spills; microbial control of heavy metal pollution; pollution control using microorganisms and magnetic separation; degradation of cyanide and nitriles; nitrogen removal from water and waste; and land reclamation and restoration.

Effect of heavy metals ondecolorization of reactive brilliant red by newly isolated microorganisms

International Nuclear Information System (INIS)

Nosheen, S.; Arshad, M.

2011-01-01

This study involves aerobic decolorisation of reactive azo dye reactive brilliant red 2KBP by newly isolated microbial strains (two bacterial and one fungal strain) in presence of heavy metals including cobalt chloride, ferric chloride, zinc sulphate, copper sulphate and nickel chloride. Many heavy metals are necessary for microbial growth and are required in very small amounts however at higher levels they become toxic. So was the objective of present work to check the effect of concentration of heavy metals on the potential of microbial strains to decolorize azo dyes. All the heavy metals under consideration were added in range of 0.5 gl-1-2.5gl/sup -1/. All heavy metals showed inhibitory effect on decolorization capacity of bacterial as well as fungal strain .At optimum conditions bacterial strains named as B1 and B2 removed 84% and 78% while fungal strain decolorized 90.4% of dye. Cobalt and nickel showed greater inhibitors on% decolorization of dyes than Zinc and iron. Fungal strain showed greater negative effect. Heavy metals might affect enzyme activities and thus reducing removal of dye. (author)

Nitrogen Deposition Reduces Decomposition Rates Through Shifts in Microbial Community Composition and Function

Science.gov (United States)

Waldrop, M.; Zak, D.; Sinsabaugh, R.

2002-12-01

Atmospheric nitrogen (N) deposition may alter soil biological activity in northern hardwood forests by repressing phenol oxidase enzyme activity and altering microbial community composition, thereby slowing decomposition and increasing the export of phenolic compounds. We tested this hypothesis by adding 13C-labelled cellobiose, vanillin, and catechol to control and N fertilized soils (30 and 80 kg ha-1) collected from three forests; two dominated by Acer Saccharum and one dominated by Quercus Alba and Quercus Velutina. While N deposition increased total microbial respiration, it decreased soil oxidative enzyme activities, resulting in slower degradation rates of all compounds, and larger DOC pools. This effect was larger in the oak forest, where fungi dominate C-cycling processes. DNA and 13C-phospolipid analyses showed that N addition altered the fungal community and reduced the activity of fungal and bacterial populations in soil, potentially explaining reduced soil enzyme activities and incomplete decomposition.

A Workflow to Model Microbial Loadings in Watersheds (proceedings)

Science.gov (United States)

Many watershed models simulate overland and instream microbial fate and transport, but few actually provide loading rates on land surfaces and point sources to the water body network. This paper describes the underlying general equations for microbial loading rates associated wit...

Removal heavy metals and sulphate from waste waters by sulphate-reducing bacteria

Directory of Open Access Journals (Sweden)

Kušnierová Mária

2000-09-01

Full Text Available This article is devoted to the process of bacterial sulphate reduction, which is used to removal of heavy metals and sulphate ions from waste waters.The life of animals and plants depends on the existence of microscopic organisms – microorganisms (MO, which play an important role in cycle changes of biogenic elements on the earth. The sulphur cycle in the nature is considered as one of the oldest and most significant biological systems (Fig. 1. The sulphate-reducing bacteria (SRB miss the assimilatory part of the cycle and produce sulphides. The microbial population of this dissimilatory part is called “sulfuretum”. The SRB can be found in anaerobic mud and sediments of freshwater, thermal or non-thermal sulphur springs, mining waters from sulphide deposits, oil deposits, sea and ocean beds, and in the gastrointestinal tract of man and animals. The SRB represent a group of chemoorganotrophic, strictly anaerobic and gramnegative bacteria, which exhibit a great morphological and physiological diversity. Despite of their considerable morphological variety, they have one property in common, which is the ability to utilise preferentially sulphates (occasionally sulphites, thiosulphates, tetrathionates as electron acceptors, which are reduced to sulphides, during anaerobic respiration. The electron donors in these processes are simple organic compounds as lactate, malate, etc.,(heterotrophically reduction or gaseous hydrogen (autotrophically reduction. SRB can produce a considerable amount of hydrogen sulphide, which reacts easily in aqueous solution with the cations of heavy metals, forming metal sulphides that have low solubility. The bacterial sulphate reduction can be used for the treatment of acid mine drainage waters, which is considered to be the major problem associated with mining activities.In order to remove heavy metals from waste waters, e.g., from galvanizing plants, mine waters (Smolnik, Šobov locality and metallurgic plants (works

Functional and compositional responses in soil microbial communities along two metal pollution gradients: does the level of historical pollution affect resistance against secondary stress?

NARCIS (Netherlands)

Azarbad, H.; Niklinska, M.; Nikiel, K.; van Straalen, N.M.; Röling, W.F.M.

2015-01-01

We examined how the exposure to secondary stressors affected the functional and compositional responses of microbial communities along two metal pollution gradients in Polish forests and whether responses were influenced by the level of metal pollution. Basal respiration rate and community

Full-scale agricultural biogas plant metal content and process parameters in relation to bacterial and archaeal microbial communities over 2.5 year span.

Science.gov (United States)

Repinc, Sabina Kolbl; Šket, Robert; Zavec, Domen; Mikuš, Katarina Vogel; Fermoso, Fernando G; Stres, Blaž

2018-05-01

A start-up of 4 MW agricultural biogas plant in Vučja vas, Slovenia, was monitored from 2011 to 2014. The start-up was carried out in 3 weeks with the intake of biomass from three operating full-scale 1-2 MW donor agricultural biogas plants. The samples were taken from donor digesters and from two serial digesters during the start-up over the course of 2.5 years. Bacterial and Archaeal microbial communities progressively diverged from the composition of donor digesters during the start-up phase. The rate of change of Bacterial community decreased exponentially over the first 2.5 years as dynamics within the first 70 days was comparable to that of the next 1.5 years, whereas approximately constant rate was observed for Archaea. Despite rearrangements, the microbial communities remained functionally stable and produced biogas throughout the whole 2.5 years of observation. All systems parameters measured were ordered according to their Kernel density (Gaussian function) ranging from the most dispersed (substrate categories used as cosubstrates, quantities of each cosubstrate, substate dry and volatile matter, process parameters) towards progressively least dispersed (trace metal and ion profiles, aromatic-polyphenolic compounds, biogas plant functional output (energy)). No deficiency was detected in trace metal content as the distribution of metals and elements fluctuated within the suggested limits for biogas over 2.5 year observation. In contrast to the recorded process variables, Bacterial and Archaeal microbial communities exhibited directed changes oriented in time. Variation partitioning showed that a large fraction of variability in the Bacterial and Archaeal microbial communities (55% and 61%, respectively) remained unexplained despite numerous measured variables (n = 44) and stable biogas production. Our results show that the observed reorganization of microbial communities was not directly associated with impact on the full-scale biogas reactor

Dehydrochlorination of 1,1,1-trichloroethane and pentachloroethane by microbially reduced ferruginous smectite.

Science.gov (United States)

Cervini-Silva, Javiera; Kostka, Joel E; Larson, Richard A; Stucki, Joseph W; Wu, Jun

2003-05-01

Reduction of structural Fe(III) in smectite clay minerals has been identified as a means to promote dechlorination of polychlorinated ethanes, but its environmental significance has yet to be fully assessed because Fe reduction has normally been achieved by agents uncommon in the environment (e.g., dithionite). This study reports the dehydrochlorination of pentachloroethane and 1,1,1-trichloroethane in the presence of ferruginous smectite reduced by two cultures of microorganisms, Shewanella oneidensis strain MR-1 (MR-R) and an enrichment culture from rice paddy soils (PS-R), in aqueous suspension under anoxic conditions. Microbially reduced ferruginous smectite facilitated dehydrochlorination of 1,1,1-trichloroethane to 1,1-dichloroethene with up to 60% conversion within 3 h of incubation time. In contrast, no formation of 1,1-dichloroethene was observed after incubation of 1,1,1-trichloroethane with chemically reduced ferruginous smectite for 24 h. Microbially reduced ferruginous smectite by MR-R and PS-R promoted the dehydrochlorination of pentachloroethane to tetrachloroethene by 80 and 15%, respectively, after 3 h of incubation time. The conversion of pentachloroethane to tetrachloroethene in the presence of chemically reduced ferruginous smectite after 24 h was 65%. These results indicate that structural Fe(II) in clay minerals has the potential to be an important reductant controlling the fate of organic chemicals in contaminated sediments.

Heavy metal and microbial loads in sewage irrigated vegetables of Kabul, Afghanistan

Directory of Open Access Journals (Sweden)

Andreas Buerkert

2011-06-01

Full Text Available Little is known about the heavy metal and microbial contamination of vegetables produced in Central Asian cities. We therefore measured the concentration of cadmium (Cd, copper (Cu, lead (Pb, and zinc (Zn and of faecal pathogens (Coliform bacteria, Salmonella sp., Shigella sp., Ascaris lubricoides, Entamoeba sp. and pinworms [Oxyuris vermicularis syn. Enterobius vermicularis] in soil, irrigation water, and marketed vegetables of Kabul City, Afghanistan. Leaf Pb and Zn concentrations of leafy vegetables were with 1–5 and 33–160 mg kg^{-1} dry weight (DW several-fold above respective international thresholds of 0.3 mg Pb kg^{-1} and 50 mg Zn kg^{-1}. The tissue concentration of Cu was below threshold limits in all samples except for spinach in one farm. Above-threshold loads of microbes and parasites on vegetables were found in five out of six gardens with coliforms ranging from 0.5–2 × 10^7 cells 100g^{-1} fresh weight (FW, but no Salmonella and Shigella were found. Contamination with 0.2 × 10^7 eggs 100g^{-1} FW of Ascaris was detected on produce of three farms and critical concentrations of Entamoeba in a single case, while Oxyuris vermicularis, and Enterobius vermicularis were found on produce of three and four farms, respectively. Irrigation water had Ascaris, Coliforms, Salmonella, Shigella, Entamoeba, and Oxyuris vermicularis syn. Enterobius vermicularis ranging from 0.35 × 10^7 to 2 × 10^7 cells l^{-1}. The heavy metal and microbial loads on fresh UPA vegetables are likely the result of contamination from rising traffic, residues of the past decades of war and lacking treatment of sewage which needs urgent attention.

Kinetic comparison of microbial assemblages for the anaerobic treatment of wastewater with high sulfate and heavy metal contents.

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Sinbuathong, Nusara; Sirirote, Pramote; Liengcharernsit, Winai; Khaodhiar, Sutha; Watts, Daniel J

2009-01-01

Mixed-microbial assemblages enriched from a septic tank, coastal sediment samples, the digester sludge of a brewery wastewater treatment plant and acidic sulfate soil samples were compared on the basis of growth rate, waste and sulfate reduction rate under sulfate reducing conditions at 30 degrees C. The specific growth rate of various cultures was in the range 0.0013-0.0022 hr(-1). Estimates of waste and sulfate reduction rate were obtained by fitting substrate depletion and sulfate reduction data with the Michaelis-Menten equation. The waste reduction rates were in the range 4x10(-8)-1x10(-7) I mg(-1) hr(-1) and generally increased in the presence of copper, likely by copper sulfide precipitation that reduced sulfide and copper toxicity and thus protected the anaerobic microbes. Anaerobic microorganisms from a brewery digester sludge were found to be the most appropriate culture for the treatment of wastewater with high sulfate and heavy metal content due to their growth rate, and waste and sulfate reduction rate.

Genome-based Modeling and Design of Metabolic Interactions in Microbial Communities.

Science.gov (United States)

Mahadevan, Radhakrishnan; Henson, Michael A

2012-01-01

Biotechnology research is traditionally focused on individual microbial strains that are perceived to have the necessary metabolic functions, or the capability to have these functions introduced, to achieve a particular task. For many important applications, the development of such omnipotent microbes is an extremely challenging if not impossible task. By contrast, nature employs a radically different strategy based on synergistic combinations of different microbial species that collectively achieve the desired task. These natural communities have evolved to exploit the native metabolic capabilities of each species and are highly adaptive to changes in their environments. However, microbial communities have proven difficult to study due to a lack of suitable experimental and computational tools. With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research.

A fermented meat model system for studies of microbial aroma formation

DEFF Research Database (Denmark)

Tjener, Karsten; Stahnke, Louise Heller; Andersen, L.

2003-01-01

A fermented meat model system was developed, by which microbial formation of volatiles could be examined The model was evaluated against dry, fermented sausages with respect to microbial growth, pH and volatile profiles. Fast and slowly acidified sausages and models were produced using the starter......H, microbial growth and volatile profiles was similar to sausage production. Based on these findings, the model system was considered valid for studies of aroma formation of meat cultures for fermented sausage....... for multivariate data analysis. Growth of lactic acid bacteria was comparable for model and sausages, whereas survival of S. xylosus was better in the model. Multivariate analysis of volatiles showed that differences between fast and slowly acidified samples were identical for model and sausage. For both sausage...

Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments.

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Mayor, Daniel J; Gray, Nia B; Elver-Evans, Joanna; Midwood, Andrew J; Thornton, Barry

2013-01-01

Copper is essential for healthy cellular functioning, but this heavy metal quickly becomes toxic when supply exceeds demand. Marine sediments receive widespread and increasing levels of copper contamination from antifouling paints owing to the 2008 global ban of organotin-based products. The toxicity of copper will increase in the coming years as seawater pH decreases and temperature increases. We used a factorial mesocosm experiment to investigate how increasing sediment copper concentrations and the presence of a cosmopolitan bioturbating amphipod, Corophium volutator, affected a range of ecosystem functions in a soft sediment microbial community. The effects of copper on benthic nutrient release, bacterial biomass, microbial community structure and the isotopic composition of individual microbial membrane [phospholipid] fatty acids (PLFAs) all differed in the presence of C. volutator. Our data consistently demonstrate that copper contamination of global waterways will have pervasive effects on the metabolic functioning of benthic communities that cannot be predicted from copper concentrations alone; impacts will depend upon the resident macrofauna and their capacity for bioturbation. This finding poses a major challenge for those attempting to manage the impacts of copper contamination on ecosystem services, e.g. carbon and nutrient cycling, across different habitats. Our work also highlights the paucity of information on the processes that result in isotopic fractionation in natural marine microbial communities. We conclude that the assimilative capacity of benthic microbes will become progressively impaired as copper concentrations increase. These effects will, to an extent, be mitigated by the presence of bioturbating animals and possibly other processes that increase the influx of oxygenated seawater into the sediments. Our findings support the move towards an ecosystem approach for environmental management.

Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments.

Directory of Open Access Journals (Sweden)

Daniel J Mayor

Full Text Available Copper is essential for healthy cellular functioning, but this heavy metal quickly becomes toxic when supply exceeds demand. Marine sediments receive widespread and increasing levels of copper contamination from antifouling paints owing to the 2008 global ban of organotin-based products. The toxicity of copper will increase in the coming years as seawater pH decreases and temperature increases. We used a factorial mesocosm experiment to investigate how increasing sediment copper concentrations and the presence of a cosmopolitan bioturbating amphipod, Corophium volutator, affected a range of ecosystem functions in a soft sediment microbial community. The effects of copper on benthic nutrient release, bacterial biomass, microbial community structure and the isotopic composition of individual microbial membrane [phospholipid] fatty acids (PLFAs all differed in the presence of C. volutator. Our data consistently demonstrate that copper contamination of global waterways will have pervasive effects on the metabolic functioning of benthic communities that cannot be predicted from copper concentrations alone; impacts will depend upon the resident macrofauna and their capacity for bioturbation. This finding poses a major challenge for those attempting to manage the impacts of copper contamination on ecosystem services, e.g. carbon and nutrient cycling, across different habitats. Our work also highlights the paucity of information on the processes that result in isotopic fractionation in natural marine microbial communities. We conclude that the assimilative capacity of benthic microbes will become progressively impaired as copper concentrations increase. These effects will, to an extent, be mitigated by the presence of bioturbating animals and possibly other processes that increase the influx of oxygenated seawater into the sediments. Our findings support the move towards an ecosystem approach for environmental management.

In situ Microbial Community Control of the Stability of Bio-Reduced Uranium

International Nuclear Information System (INIS)

Long, Phillip E.; McKinley, James P.; White, David C.

2006-01-01

In aerobic aquifers typical of many Department of Energy (DOE) legacy waste sites, uranium is present in the oxidized U(VI) form which is soluble and thus mobile compared to U(IV). Previous work at the Old Rifle Uranium Mill Tailings Remedial Action (UMTRA) site demonstrated that biostimulation by acetate injection promoted growth of Geobacteraceae and stimulated the microbial reduction of U(VI) to less soluble U(IV) (1, 4). Despite the potential for oxidative dissolution of bio-reduced U(IV), field experiments at the Old Rifle site show that although the rate of U(VI) reduction decreases following the on-set of sulfate reduction, U(VI) reduction continues even following the cessation of acetate injection (1, 4). However, U(VI) reduction is reversible and the basis for the observed maintenance of U(VI) reduction post-stimulation is a critical but as yet unresolved issue for the application of biostimulation as a treatment technology. The continued U(VI) reduction and the maintenance of reduced U(IV) may result from many factors including U(VI) reduction by sulfate reducing bacteria (SRB), generation of H2S or FeS0.9 which serves as an oxygen sink, or the preferential sorption of U(VI) by microbial cells or biopolymers. The overall goal of the project is to develop an understanding of the mechanisms for the maintenance of bio-reduced uranium in an aerobic aquifer under field conditions following the cessation of electron donor addition

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

Science.gov (United States)

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

2016-01-01

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

Comparison of model microbial allocation parameters in soils of varying texture

Science.gov (United States)

Hagerty, S. B.; Slessarev, E.; Schimel, J.

2017-12-01

The soil microbial community decomposes the majority of carbon (C) inputs to the soil. However, not all of this C is respired—rather, a substantial portion of the carbon processed by microbes may remain stored in the soil. The balance between C storage and respiration is controlled by microbial turnover rates and C allocation strategies. These microbial community properties may depend on soil texture, which has the potential to influence both the nature and the fate of microbial necromass and extracellular products. To evaluate the role of texture on microbial turnover and C allocation, we sampled four soils from the University of California's Hastings Reserve that varied in texture (one silt loam, two sandy loam, and on clay soil), but support similar grassland plant communities. We added 14C- glucose to the soil and measured the concentration of the label in the carbon dioxide (CO2), microbial biomass, and extractable C pools over 7 weeks. The labeled biomass turned over the slowest in the clay soil; the concentration of labeled biomass was more than 1.5 times the concentration of the other soils after 8 weeks. The clay soil also had the lowest mineralization rate of the label, and mineralization slowed after two weeks. In contrast, in the sandier soils mineralization rates were higher and did not plateau until 5 weeks into the incubation period. We fit the 14C data to a microbial allocation model and estimated microbial parameters; assimilation efficiency, exudation, and biomass specific respiration and turnover for each soil. We compare these parameters across the soil texture gradient to assess the extent to which models may need to account for variability in microbial C allocation across soils of different texture. Our results suggest that microbial C turns over more slowly in high-clay soils than in sandy soils, and that C lost from microbial biomass is retained at higher rates in high-clay soils. Accounting for these differences in microbial allocation

Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.

Science.gov (United States)

Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K; Jardine, Philip M; Zhou, Jizhong; Criddle, Craig S; Marsh, Terence L; Tiedje, James M

2010-10-01

Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.

The Study of Microbial Environmental Processes Related to the Natural Attenuation of Uranium at the Rifle Site using Systems-level Biology

Energy Technology Data Exchange (ETDEWEB)

Methe, Barbara [J. Craig Venter Inst. (JCVI), Rockville, MD (United States); Lipton, Mary [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Mahadevan, Krishna [Univ. of Toronto, ON (Canada)

2016-08-31

Microbes exist in communities in the environment where they are fundamental drivers of global carbon, nutrient and metal cycles. In subsurface environments, they possess significant metabolic potential to affect these global cycles including the transformation of radionuclides. This study examined the influence of microbial communities in sediment zones undergoing biogeochemical cycling of carbon, nutrients and metals including natural attenuation of uranium. This study examined the relationship of both the microbiota (taxonomy) and their metabolic capacity (function) in driving carbon, nutrient and metal cycles including uranium reduction at the Department of Energy (DOE) Rifle Integrated Field Research Challenge (RIFRC). Objectives of this project were: 1) to apply systems-level biology through application of ‘metaomics’ approaches (collective analyses of whole microbial community DNA, RNA and protein) to the study of microbial environmental processes and their relationship to C, N and metals including the influence of microbial communities on uranium contaminant mobility in subsurface settings undergoing natural attenuation, 2) improve methodologies for data generation using metaomics (collectively metagenomics, metatranscriptomics and proteomics) technologies and analysis and interpretation of that data and 3) use the data generated from these studies towards microbial community-scale metabolic modeling. The strategy for examining these subsurface microbial communities was to generate sequence reads from microbial community DNA (metagenomics or whole genome shotgun sequencing (WGS)) and RNA (metatranscriptomcs or RNAseq) and protein information using proteomics. Results were analyzed independently and through computational modeling. Overall, the community model generated information on the microbial community structure that was observed using metaomic approaches at RIFRC sites and thus provides an important framework for continued community modeling

Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities

Energy Technology Data Exchange (ETDEWEB)

Duncan, Kathleen E.; Gieg, Lisa M.; Parisi, Victoria A.; Tanner, Ralph S.; Green Tringe, Susannah; Bristow, Jim; Suflita, Joseph M.

2009-09-16

Corrosion of metallic oilfield pipelines by microorganisms is a costly but poorly understood phenomenon, with standard treatment methods targeting mesophilic sulfatereducing bacteria. In assessing biocorrosion potential at an Alaskan North Slope oil field, we identified thermophilic hydrogen-using methanogens, syntrophic bacteria, peptideand amino acid-fermenting bacteria, iron reducers, sulfur/thiosulfate-reducing bacteria and sulfate-reducing archaea. These microbes can stimulate metal corrosion through production of organic acids, CO2, sulfur species, and via hydrogen oxidation and iron reduction, implicating many more types of organisms than are currently targeted. Micromolar quantities of putative anaerobic metabolites of C1-C4 n-alkanes in pipeline fluids were detected, implying that these low molecular weight hydrocarbons, routinely injected into reservoirs for oil recovery purposes, are biodegraded and provide biocorrosive microbial communities with an important source of nutrients.

Redox zone II. Coupled modeling of groundwater flow, solute transport, chemical reactions and microbial processes in the Aespoe island

International Nuclear Information System (INIS)

Samper, Javier; Molinero, Jorge; Changbing Yang; Guoxiang Zhang

2003-12-01

The Redox Zone Experiment was carried out at the Aespoe HRL in order to study the redox behaviour and the hydrochemistry of an isolated vertical fracture zone disturbed by the excavation of an access tunnel. Overall results and interpretation of the Redox Zone Project were reported by Banwart et al. Later, Banwart presented a summary of the hydrochemistry of the Redox Zone Experiment. Coupled groundwater flow and reactive transport models of this experiment were carried out by Molinero who proposed a revised conceptual model for the hydrogeology of the Redox Zone Experiment which could explain simultaneously measured drawdown and salinity data. The numerical model was found useful to understand the natural system. Several conclusions were drawn about the redox conditions of recharge waters, cation exchange capacity of the fracture zone and the role of mineral phases such as pyrite, calcite, hematite and goethite. This model could reproduce the measured trends of dissolved species, except for bicarbonate and sulphate which are affected by microbially-mediated processes. In order to explore the role of microbial processes, a coupled numerical model has been constructed which accounts for water flow, reactive transport and microbial processes. The results of this model is presented in this report. This model accounts for groundwater flow and reactive transport in a manner similar to that of Molinero and extends the preliminary microbial model of Zhang by accounting for microbially-driven organic matter fermentation and organic matter oxidation. This updated microbial model considers simultaneously the fermentation of particulate organic matter by yeast and the oxidation of dissolved organic matter, a product of fermentation. Dissolved organic matter is produced by yeast and serves also as a substrate for iron-reducing bacteria. Model results reproduce the observed increase in bicarbonate and sulfaphe concentration, thus adding additional evidence for the possibility

Redox zone II. Coupled modeling of groundwater flow, solute transport, chemical reactions and microbial processes in the Aespoe island

Energy Technology Data Exchange (ETDEWEB)

Samper, Javier; Molinero, Jorge; Changbing Yang; Guoxiang Zhang [Univ. Da Coruna (Spain)

2003-12-01

The Redox Zone Experiment was carried out at the Aespoe HRL in order to study the redox behaviour and the hydrochemistry of an isolated vertical fracture zone disturbed by the excavation of an access tunnel. Overall results and interpretation of the Redox Zone Project were reported by Banwart et al. Later, Banwart presented a summary of the hydrochemistry of the Redox Zone Experiment. Coupled groundwater flow and reactive transport models of this experiment were carried out by Molinero who proposed a revised conceptual model for the hydrogeology of the Redox Zone Experiment which could explain simultaneously measured drawdown and salinity data. The numerical model was found useful to understand the natural system. Several conclusions were drawn about the redox conditions of recharge waters, cation exchange capacity of the fracture zone and the role of mineral phases such as pyrite, calcite, hematite and goethite. This model could reproduce the measured trends of dissolved species, except for bicarbonate and sulphate which are affected by microbially-mediated processes. In order to explore the role of microbial processes, a coupled numerical model has been constructed which accounts for water flow, reactive transport and microbial processes. The results of this model is presented in this report. This model accounts for groundwater flow and reactive transport in a manner similar to that of Molinero and extends the preliminary microbial model of Zhang by accounting for microbially-driven organic matter fermentation and organic matter oxidation. This updated microbial model considers simultaneously the fermentation of particulate organic matter by yeast and the oxidation of dissolved organic matter, a product of fermentation. Dissolved organic matter is produced by yeast and serves also as a substrate for iron-reducing bacteria. Model results reproduce the observed increase in bicarbonate and sulfaphe concentration, thus adding additional evidence for the possibility

Enhanced rice production but greatly reduced carbon emission following biochar amendment in a metal-polluted rice paddy.

Science.gov (United States)

Zhang, Afeng; Bian, Rongjun; Li, Lianqing; Wang, Xudong; Zhao, Ying; Hussain, Qaiser; Pan, Genxing

2015-12-01

Soil amendment of biochar (BSA) had been shown effective for mitigating greenhouse gas (GHG) emission and alleviating metal stress to plants and microbes in soil. It has not yet been addressed if biochar exerts synergy effects on crop production, GHG emission, and microbial activity in metal-polluted soils. In a field experiment, biochar was amended at sequential rates at 0, 10, 20, and 40 t ha(-1), respectively, in a cadmium- and lead-contaminated rice paddy from the Tai lake Plain, China, before rice cropping in 2010. Fluxes of soil carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) were monitored using a static chamber method during the whole rice growing season (WRGS) of 2011. BSA significantly reduced soil CaCl2 extractable pool of Cd, and DTPA extractable pool of Cd and Pb. As compared to control, soil CO2 emission under BSA was observed to have no change at 10 t ha(-1) but decreased by 16-24% at 20 and 40 t ha(-1). In a similar trend, BSA at 20 and 40 t ha(-1) increased rice yield by 25-26% and thus enhanced ecosystem CO2 sequestration by 47-55% over the control. Seasonal total N2O emission was reduced by 7.1, 30.7, and 48.6% under BSA at 10, 20, and 40 t ha(-1), respectively. Overall, a net reduction in greenhouse gas balance (NGHGB) by 53.9-62.8% and in greenhouse gas intensity (GHGI) by 14.3-28.6% was observed following BSA at 20 and 40 t ha(-1). The present study suggested a great potential of biochar to enhancing grain yield while reducing carbon emission in metal-polluted rice paddies.

Ecological effects of soil properties and metal concentrations on the composition and diversity of microbial communities associated with land use patterns in an electronic waste recycling region.

Science.gov (United States)

Wu, Wencheng; Dong, Changxun; Wu, Jiahui; Liu, Xiaowen; Wu, Yingxin; Chen, Xianbin; Yu, Shixiao

2017-12-01

Soil microbes play vital roles in ecosystem functions, and soil microbial communities may be strongly structured by land use patterns associated with electronic waste (e-waste) recycling activities, which can increase the heavy metal concentration in soils. In this study, a suite of soils from five land use types (paddy field, vegetable field, dry field, forest field, and e-waste recycling site) were collected in Longtang Town, Guangdong Province, South China. Soil physicochemical properties and heavy metal concentrations were measured, and the indigenous microbial assemblages were profiled using 16S rRNA high-throughput sequencing and clone library analyses. The results showed that mercury concentration was positively correlated with both Faith's PD and Chao1 estimates, suggesting that the soil microbial alpha diversity was predominantly regulated by mercury. In addition, redundancy analysis indicated that available phosphorus, soil moisture, and mercury were the three major drivers affecting the microbial assemblages. Overall, the microbial composition was determined primarily by land use patterns, and this study provides a novel insight on the composition and diversity of microbial communities in soils associated with e-waste recycling activities. Copyright © 2017 Elsevier B.V. All rights reserved.

Combustion of Metals in Reduced-Gravity and Extraterrestrial Environment

Science.gov (United States)

Abbud-Madrid, A.; Omaly, P.; Branch, M. C.; Daily, J. W.

1999-01-01

-floating spherical metal samples and their corresponding long burning times available in reduced gravity. The first set of experiments has been conducted with magnesium (Mg) samples burning in the low-gravity environment generated by an aircraft flying parabolic trajectories. Owing to its high adiabatic flame temperature, oxidizer/fuel ratio, and heat per unit mass of fuel, as well as its low toxicity and low ignition temperature, Mg has been identified as a promising metal fuel with CO2 as oxidizer. The experimental effort is complemented by the development of a numerical model combining gas-phase chemical kinetics and transport mechanisms.

Microbial activities and communities in oil sands tailings ponds

Energy Technology Data Exchange (ETDEWEB)

Gieg, Lisa; Ramos, Esther; Clothier, Lindsay; Bordenave, Sylvain; Lin, Shiping; Voordouw, Gerrit; Dong, Xiaoli; Sensen, Christoph [University of Calgary (Canada)

2011-07-01

This paper discusses how the microbial communities and their activity play a vital role in tailings ponds. The ponds contain microorganisms along with metals, hydrocarbon diluent, naphthenic acid and others. The ponds play an important role in mining operations because they store bitumen extraction waste and also allow water to be re-used in the bitumen extraction process. Pond management presents a few challenges that include, among others, gas emissions and the presence of toxic and corrosive acids. Microbial activities and communities help in managing these ponds. Microbial activity measurement in active and inactive ponds is described and analyzed and the results are presented. The conditions for reducing sulfate, nitrate and iron are also presented. From the results it can be concluded that naphthenic acids can potentially serve as substrates for anaerobic populations in tailings ponds.

DEVELOPMENT OF AN ENVIRONMENTALLY BENIGN MICROBIAL INHIBITOR TO CONTROL INTERNAL PIPELINE CORROSION

Energy Technology Data Exchange (ETDEWEB)

Kristine L. Lowe; Bill W. Bogan; Wendy R. Sullivan; Kristine Mila H. Cruz; Brigid M. Lamb; John J. Kilbane II

2004-07-30

The overall program objective is to develop and evaluate environmentally benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is to develop one or more environmentally benign (a.k.a. ''green'') products that can be applied to maintain the structure and dependability of the natural gas infrastructure. Previous testing indicated that the growth, and the metal corrosion caused by pure cultures of sulfate reducing bacteria were inhibited by hexane extracts of some pepper plants. This quarter tests were performed with mixed bacterial cultures obtained from natural gas pipelines. Treatment with the pepper extracts affected the growth and metabolic activity of the microbial consortia. Specifically, the growth and metabolism of sulfate reducing bacteria was inhibited. The demonstration that pepper extracts can inhibit the growth and metabolism of sulfate reducing bacteria in mixed cultures is a significant observation validating a key hypothesis of the project. Future tests to determine the effects of pepper extracts on mature/established biofilms will be performed next.

Microbial weathering processes after release of heavy metals and arsenic from fluvial tailing deposits; Mikrobielle Verwitterungsprozesse bei der Freisetzung von Schwermetallen und Arsen aus fluvialen Tailingablagerungen

Energy Technology Data Exchange (ETDEWEB)

Willscher, S. [Technische Univ. Dresden (Germany). Fak. fuer Forst, Geo und Hydrowissenschaften, Inst. fuer Abfallwirtschaft und Altlasten

2006-07-01

Microbial processes play an important role in global metal cycles. The microbial weathering of mineral surfaces, including deposited anthropogenic mineral remainders, is a natural occurring process, taking place on uncovered dump surfaces as well as in deeper zones of dumps. Such weathering processes also occur in metal contaminated soils and sediments. In this work, a sulfidic fluvial tailing sediment was investigated for its acidity and salinity generating potential and the subsequent mobilisation of heavy metals, generated by biogeochemical processes. The long-term risks of such a deposit were evaluated. Unstabilised deposits of such materials can generate a considerable contamination of the surrounding ground and surface water. It could be shown in the experiments that in acid generating dumps and tailing materials besides the well known acidophilic autotrophs also acidotolerant heterotrophic microorganisms play a role in the mobilisation of metals. (orig.)

GENOME-BASED MODELING AND DESIGN OF METABOLIC INTERACTIONS IN MICROBIAL COMMUNITIES

Directory of Open Access Journals (Sweden)

Radhakrishnan Mahadevan

2012-10-01

With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research.

Microbial communities in riparian soils of a settling pond for mine drainage treatment.

Science.gov (United States)

Fan, Miaochun; Lin, Yanbing; Huo, Haibo; Liu, Yang; Zhao, Liang; Wang, Entao; Chen, Weimin; Wei, Gehong

2016-06-01

Mine drainage leads to serious contamination of soil. To assess the effects of mine drainage on microbial communities in riparian soils, we used an Illumina MiSeq platform to explore the soil microbial composition and diversity along a settling pond used for mine drainage treatment. Non-metric multidimensional scaling analysis showed that the microbial communities differed significantly among the four sampling zones (influent, upstream, downstream and effluent), but not seasonally. Constrained analysis of principal coordinates indicated heavy metals (zinc, lead and copper), total sulphur, pH and available potassium significantly influenced the microbial community compositions. Heavy metals were the key determinants separating the influent zone from the other three zones. Lower diversity indices were observed in the influent zone. However, more potential indicator species, related to sulphur and organic matter metabolism were found there, such as the sulphur-oxidizing genera Acidiferrobacter, Thermithiobacillus, Limnobacter, Thioprofundum and Thiovirga, and the sulphur-reducing genera Desulfotomaculum and Desulfobulbus; the organic matter degrading genera, Porphyrobacter and Paucimonas, were also identified. The results indicated that more microorganisms related to sulphur- and carbon-cycles may exist in soils heavily contaminated by mine drainage. Copyright © 2016 Elsevier Ltd. All rights reserved.

Reductive dehalogenation in microbial and electrolytic model systems

International Nuclear Information System (INIS)

Criddle, C.S.

1990-01-01

This research addresses the principles or reductive dehalogenation, with a focus on microbial processes. Carbon tetrachloride (CT) was selected as a model compound for intensive investigation. Three different experimental systems were studied: pure cultures of Escherichia coli k-12, pure cultures of a denitrifying Pseudomonad isolated from aquifer solids (Pseudomonas sp. strain KC), and an electrolysis cell. The product distributions were consistent with the hypothesis that CT undergoes a rate-limiting reduction to radical species which rapidly react with constituents of the surrounding milieu. In cultures of E. coli k-12, use of oxygen and nitrate as terminal electron acceptors generally prevented CT transformation. At low oxygen levels (∼ 1%), however, transformation of 14 C-CT to 14 C-CO 2 and attachment to cell material did occur in accord with reports of CT fate in mammalian cell cultures. Under fumarate-respiring conditions, 14 C-CT was recovered as 14 C-C 2 , chloroform (CF), and in a non-volatile fraction. In contrast, fermenting conditions resulted in more CF, more cell-bound 14 C, and almost no 14 C-CO 2 . Rates were faster under fermenting conditions than under fumarate-respiring conditions. Rates also decreased over time suggesting the gradual exhaustion of transformation activity. This loss was modeled with a simple exponential decay term. Pseudomonas sp. strain KC converted 14 C-CT to 14 C-CO 2 under denitrifying conditions, without CF production. Strain KC was the only organism of several denitrifiers that transformed CT. Induction of CT transformation by strain KC depended upon the presence of trace metals. Addition of ferrous iron and cobalt inhibited CT transformation. For strain KC, CT transformation is apparently linked to its mechanism for trace metal acquisition

IN-DRIFT MICROBIAL COMMUNITIES MODEL VALIDATION CALCULATIONS

Energy Technology Data Exchange (ETDEWEB)

D.M. Jolley

2001-12-18

The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M&O 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M&O 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN M09909SPAMINGl.003 using its replacement DTN M00106SPAIDMO 1.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M&O (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 200 1) which includes controls for the management of electronic data.

In-Drift Microbial Communities Model Validation Calculations

Energy Technology Data Exchange (ETDEWEB)

D. M. Jolley

2001-09-24

The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M&O 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M&O 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN MO9909SPAMING1.003 using its replacement DTN MO0106SPAIDM01.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M&O (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 2001) which includes controls for the management of electronic data.

In-Drift Microbial Communities Model Validation Calculation

Energy Technology Data Exchange (ETDEWEB)

D. M. Jolley

2001-10-31

The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M&O 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M&O 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN MO9909SPAMING1.003 using its replacement DTN MO0106SPAIDM01.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M&O (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 2001) which includes controls for the management of electronic data.

In-Drift Microbial Communities Model Validation Calculations

International Nuclear Information System (INIS)

Jolley, D.M.

2001-01-01

The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS MandO 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS MandO 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN MO9909SPAMING1.003 using its replacement DTN MO0106SPAIDM01.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS MandO 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS MandO (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 2001) which includes controls for the management of electronic data

IN-DRIFT MICROBIAL COMMUNITIES MODEL VALIDATION CALCULATIONS

International Nuclear Information System (INIS)

D.M. Jolley

2001-01-01

The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M andO 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M andO 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN M09909SPAMINGl.003 using its replacement DTN M00106SPAIDMO 1.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M andO 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M andO (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 200 1) which includes controls for the management of electronic data

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

Directory of Open Access Journals (Sweden)

Pablo Araujo Granda

2016-01-01

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

Mechanistic model for microbial growth on hydrocarbons

Energy Technology Data Exchange (ETDEWEB)

Mallee, F M; Blanch, H W

1977-12-01

Based on available information describing the transport and consumption of insoluble alkanes, a mechanistic model is proposed for microbial growth on hydrocarbons. The model describes the atypical growth kinetics observed, and has implications in the design of large scale equipment for single cell protein (SCP) manufacture from hydrocarbons. The model presents a framework for comparison of the previously published experimental kinetic data.

Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach▿ †

Science.gov (United States)

Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K.; Jardine, Philip M.; Zhou, Jizhong; Criddle, Craig S.; Marsh, Terence L.; Tiedje, James M.

2010-01-01

Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared. PMID:20729318

A new rapid chemical route to prepare reduced graphene oxide using copper metal nanoparticles

International Nuclear Information System (INIS)

Wu Tao; Gao Jianping; Xu Xiaoyang; Qiu Haixia; Wang Wei; Gao Chunjuan

2013-01-01

Copper metal nanoparticles were used as a reducing agent to reduce graphene oxide (GO). The reaction was complete in about 10 min and did not involve the use of any toxic reagents or acids that are typically used in the reduction of GO by Zn and Fe powders. The high reduction activity of the Cu nanoparticles, compared to Cu powder, may be the result of the formation of Cu 2 O nanoparticles. The effect of the mass ratio of the metal to GO for this reduction was also investigated. The reduction of the GO was verified by ultraviolet–visible absorption spectroscopy, x-ray diffraction, thermogravimetric analysis, Raman spectroscopy, x-ray photoelectron spectroscopy and transmission electron microscopy. After reduction, Cu 2 O supported on reduced GO was formed and showed superior catalytic ability for the degradation of a model dye pollutant, methylene blue. (paper)

Chemically reducing decontamination method for radioactive metal

International Nuclear Information System (INIS)

Tanaka, Akio; Onuma, Tsutomu; Sato, Hitoshi.

1994-01-01

The present invention concerns a decontamination method of electrolytically reducing radioactive metal wastes, then chemically dissolving the surface thereof with a strong acid decontaminating solution. This method utilizes dissolving characteristics of stainless steels in the strong acid solution. That is, in the electrolytic reduction operation, a portion of the metal wastes is brought into contact with a strong acid decontaminating solution, and voltage and current are applied to the portion and keep it for a long period of time so as to make the potential of the immersed portion of the metal wastes to an active soluble region. Then, the electrolytic reduction operation is stopped, and the metal wastes are entirely immersed in the decontaminating solution to decontaminate by chemical dissolution. As the decontaminating solution, strong acid such as sulfuric acid, nitric acid is used. Since DC current power source capacity required for causing reaction in the active soluble region can be decreased, the decontamination facility can be minimized and simplified, and necessary electric power can be saved even upon decontamination of radioactive metal wastes made of stainless steels and having a great area. Further, chemical dissolution can be conducted without adding an expensive oxidizing agent. (N.H.)

A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.

Science.gov (United States)

Budinich, Marko; Bourdon, Jérémie; Larhlimi, Abdelhalim; Eveillard, Damien

2017-01-01

Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs) for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients. This study presents two multi-objective extensions of CBMs for modeling communities: multi-objective flux balance analysis (MO-FBA) and multi-objective flux variability analysis (MO-FVA). Both methods were applied to a hot spring mat model ecosystem. As a result, multiple trade-offs between nutrients and growth rates, as well as thermodynamically favorable relative abundances at community level, were emphasized. We expect this approach to be used for integrating genomic information in microbial ecosystems. Following models will provide insights about behaviors (including diversity) that take place at the ecosystem scale.

Characterization of Co(III) EDTA-Reducing Bacteria in Metal- and Radionuclide-Contaminated Groundwater

Energy Technology Data Exchange (ETDEWEB)

Gao, Weimin [Arizona State University; Gentry, Terry J [ORNL; Mehlhorn, Tonia L [ORNL; Carroll, Sue L [ORNL; Jardine, Philip M [ORNL; Zhou, Jizhong [University of Oklahoma, Norman

2010-01-01

The Waste Area Grouping 5 (WAG5) site at Oak Ridge National Laboratory has a potential to be a field site for evaluating the effectiveness of various bioremediation approaches and strategies. The site has been well studied in terms of its geological and geochemical properties over the past decade. However, despite the importance of microorganisms in bioremediation processes, the microbiological populations at the WAG5 site and their potential in bioremediation have not been similarly evaluated. In this study, we initiated research to characterize the microbial populations in WAG5 groundwater. Approximately 100 isolates from WAG5 groundwater were isolated and selected based on colony morphology. Fifty-five unique isolates were identified by BOX-PCR and subjected to further characterization. 16S rRNA sequences indicated that these isolates belong to seventeen bacterial genera including Alcaligenes (1 isolate), Aquamonas (1), Aquaspirillum (1), Bacillus (10), Brevundimonas (5), Caulobacter (7), Dechloromonas (2), Janibacter (1), Janthinobacterium (2), Lactobacillus (1), Paenibacillus (4), Pseudomonas (9), Rhodoferax (1), Sphingomonas (1), Stenotrophomonas (6), Variovorax (2), and Zoogloea (1). Metal respiration assays identified several isolates, which phylogenically belong or are close to Caulobacter, Stenotrophomonas, Bacillus, Paenibacillus and Pseudomonas, capable of reducing Co(III)EDTA- to Co(II)EDTA{sup 2-} using the defined M1 medium under anaerobic conditions. In addition, using WAG5 groundwater directly as the inoculants, we found that organisms associated with WAG5 groundwater can reduce both Fe(III) and Co(III) under anaerobic conditions. Further assays were then performed to determine the optimal conditions for Co(III) reduction. These assays indicated that addition of various electron donors including ethanol, lactate, methanol, pyruvate, and acetate resulted in metal reduction. These experiments will provide useful background information for future

Impact of repeated single-metal and multi-metal pollution events on soil quality.

Science.gov (United States)

Burges, Aritz; Epelde, Lur; Garbisu, Carlos

2015-02-01

Most frequently, soil metal pollution results from the occurrence of repeated single-metal and, above all, multi-metal pollution events, with concomitant adverse consequences for soil quality. Therefore, in this study, we evaluated the impact of repeated single-metal and multi-metal (Cd, Pb, Cu, Zn) pollution events on soil quality, as reflected by the values of a variety of soil microbial parameters with potential as bioindicators of soil functioning. Specifically, parameters of microbial activity (potentially mineralizable nitrogen, β-glucosidase and acid phosphatase activity) and biomass (fungal and bacterial gene abundance by RT-qPCR) were determined, in the artificially metal-polluted soil samples, at regular intervals over a period of 26 weeks. Similarly, we studied the evolution over time of CaCl2-extractable metal fractions, in order to estimate metal bioavailability in soil. Different metals showed different values of bioavailability and relative bioavailability ([metal]bio/[metal]tot) in soil throughout the experiment, under both repeated single-metal and multi-metal pollution events. Both repeated Zn-pollution and multi-metal pollution events led to a significant reduction in the values of acid phosphatase activity, and bacterial and fungal gene abundance, reflecting the negative impact of these repeated events on soil microbial activity and biomass, and, hence, soil quality. Copyright © 2014 Elsevier Ltd. All rights reserved.

A unique model system of microbial carbonate precipitation: Stromatolites of Lagoa Vermelha, Brazil

Science.gov (United States)

Warthmann, R. J.; Vasoncelos, C.; van Lith, Y.; Visscher, P. T.; McKenzie, J. A.

2003-04-01

Modern stromatolites are recognized as analogues to fossil laminated structures, which are remains of microbial activity that are widely found in sedimentary rocks beginning in the Neo-Archean, but are quite rare today. The key difference of modern microbial mats and stromatolites compared to ancient examples is the type of lithification. A few marine and hypersaline microbial mats have been observed to precipitate carbonates, and only in Shark Bay (Western, Australia) and Highborne Cay (Bahamas) has the formation of continuous laminae of carbonates been observed. Lagoa Vermelha, a moderate hypersaline lagoon in Rio de Janeiro, Brazil, offers the ideal conditions to promote lithification. Calcified, sometimes dolomitic stromatolites grow on the sediment surface, whereas within the sediments dolomite precipitates. The factors controlling carbonate precipitation in Lagoa Vermelha are the changing water chemistry and the special hydrology, combined with a high primary production by cyanobacteria, a high rate of respiration and the absence of higher organisms. Here, we present a study of the physico-chemical parameters, microbial processes and bio-minerals associated with these stromatolites and microbial mats. This approach provides boundary conditions to better understand dolomite formation. Several discrete lithified calcium carbonate layers are present. The first lithified layer is found beneath a 2-mm-thick biofilm, which contains Gloeocapsa. Below the underlying dense Microcoleus layer, the second micrite deposit is observed at 4-5 mm depth. Successive micritic laminae are preserved in the layer of decaying cyanobacteria that harbors large numbers of purple sulfur bacteria, heterotrophic microbes and sulfate-reducing bacteria. C-isotope studies of the carbonate layers indicate a contribution of organic derived carbon associated with microbial processes, such as sulfate reduction. The O-isotopic values indicate an evaporitic enrichment of the water. Understanding

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

Science.gov (United States)

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; van Nostrand, J. D.; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-10-01

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

Microbially influenced corrosion communities associated with fuel-grade ethanol environments.

Science.gov (United States)

Williamson, Charles H D; Jain, Luke A; Mishra, Brajendra; Olson, David L; Spear, John R

2015-08-01

Microbially influenced corrosion (MIC) is a costly problem that impacts hydrocarbon production and processing equipment, water distribution systems, ships, railcars, and other types of metallic infrastructure. In particular, MIC is known to cause considerable damage to hydrocarbon fuel infrastructure including production, transportation, and storage systems, often times with catastrophic environmental contamination results. As the production and use of alternative fuels such as fuel-grade ethanol (FGE) increase, it is important to consider MIC of engineered materials exposed to these "newer fuels" as they enter existing infrastructure. Reports of suspected MIC in systems handling FGE and water prompted an investigation of the microbial diversity associated with these environments. Small subunit ribosomal RNA gene pyrosequencing surveys indicate that acetic-acid-producing bacteria (Acetobacter spp. and Gluconacetobacter spp.) are prevalent in environments exposed to FGE and water. Other microbes previously implicated in corrosion, such as sulfate-reducing bacteria and methanogens, were also identified. In addition, acetic-acid-producing microbes and sulfate-reducing microbes were cultivated from sampled environments containing FGE and water. Results indicate that complex microbial communities form in these FGE environments and could cause significant MIC-related damage that may be difficult to control. How to better manage these microbial communities will be a defining aspect of improving mitigation of global infrastructure corrosion.

Influence of Calcium on Microbial Reduction of Solid Phase Uranium (VI)

International Nuclear Information System (INIS)

Liu, Chongxuan; Jeon, Byong-Hun; Zachara, John M.; Wang, Zheming

2007-01-01

The effect of calcium on microbial reduction of a solid phase U(VI), sodium boltwoodite (NaUO2SiO3OH · 1.5H2O), was evaluated in a culture of a dissimilatory metal-reducing bacterium (DMRB), Shewanella oneidensis strain MR-1. Batch experiments were performed in a non-growth bicarbonate medium with lactate as electron donor at pH 7 buffered with PIPES. Calcium increased both the rate and extent of Na-boltwoodite dissolution by increasing its solubility through the formation of a ternary aqueous calcium-uranyl-carbonate species. The ternary species, however, decreased the rates of microbial reduction of aqueous U(VI). Laser-induced fluorescence spectroscopy (LIFS) and transmission electron microscopy (TEM) revealed that microbial reduction of solid phase U(VI) is a sequentially coupled process of Na-boltwoodite dissolution, U(VI) aqueous speciation, and microbial reduction of dissolved U(VI) to U(IV) that accumulated on bacterial surfaces/periplasm. The overall rates of microbial reduction of solid phase U(VI) can be described by the coupled rates of dissolution and microbial reduction that were both influenced by calcium. The results demonstrated that dissolved U(VI) concentration during microbial reduction was a complex function of solid phase U(VI) dissolution kinetics, aqueous U(VI) speciation, and microbial activity

Cd Mobility in Anoxic Fe-Mineral-Rich Environments - Potential Use of Fe(III)-Reducing Bacteria in Soil Remediation

Science.gov (United States)

Muehe, E. M.; Adaktylou, I. J.; Obst, M.; Schröder, C.; Behrens, S.; Hitchcock, A. P.; Tylsizczak, T.; Michel, F. M.; Krämer, U.; Kappler, A.

2014-12-01

Agricultural soils are increasingly burdened with heavy metals such as Cd from industrial sources and impure fertilizers. Metal contaminants enter the food chain via plant uptake from soil and negatively affect human and environmental health. New remediation approaches are needed to lower soil metal contents. To apply these remediation techniques successfully, it is necessary to understand how soil microbes and minerals interact with toxic metals. Here we show that microbial Fe(III) reduction initially mobilizes Cd before its immobilization under anoxic conditions. To study how microbial Fe(III) reduction influences Cd mobility, we isolated a new Cd-tolerant, Fe(III)-reducing Geobacter sp. from a heavily Cd-contaminated soil. In lab experiments, this Geobacter strain first mobilized Cd from Cd-loaded Fe(III) hydroxides followed by precipitation of Cd-bearing mineral phases. Using Mössbauer spectroscopy and scanning electron microscopy, the original and newly formed Cd-containing Fe(II) and Fe(III) mineral phases, including Cd-Fe-carbonates, Fe-phosphates and Fe-(oxyhydr)oxides, were identified and characterized. Using energy-dispersive X-ray spectroscopy and synchrotron-based scanning transmission X-ray microscopy, Cd was mapped in the Fe(II) mineral aggregates formed during microbial Fe(III) reduction. Microbial Fe(III) reduction mobilizes Cd prior to its precipitation in Cd-bearing mineral phases. The mobilized Cd could be taken up by phytoremediating plants, resulting in a net removal of Cd from contaminated sites. Alternatively, Cd precipitation could reduce Cd bioavailability in the environment, causing less toxic effects to crops and soil microbiota. However, the stability and thus bioavailability of these newly formed Fe-Cd mineral phases needs to be assessed thoroughly. Whether phytoremediation or immobilization of Cd in a mineral with reduced Cd bioavailability are feasible mechanisms to reduce toxic effects of Cd in the environment remains to be

A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.

Directory of Open Access Journals (Sweden)

Marko Budinich

Full Text Available Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients. This study presents two multi-objective extensions of CBMs for modeling communities: multi-objective flux balance analysis (MO-FBA and multi-objective flux variability analysis (MO-FVA. Both methods were applied to a hot spring mat model ecosystem. As a result, multiple trade-offs between nutrients and growth rates, as well as thermodynamically favorable relative abundances at community level, were emphasized. We expect this approach to be used for integrating genomic information in microbial ecosystems. Following models will provide insights about behaviors (including diversity that take place at the ecosystem scale.

Microbial transformations of natural organic compounds and radionuclides in subsurface environments

International Nuclear Information System (INIS)

Francis, A.J.

1985-10-01

A major national concern in the subsurface disposal of energy wastes is the contamination of ground and surface waters by waste leachates containing radionuclides, toxic metals, and organic compounds. Microorganisms play an important role in the transformation of organic compounds, radionuclides, and toxic metals present in the waste and affect their mobility in subsurface environments. Microbial processes involved in dissolution, mobilization, and immobilization of toxic metals under aerobic and anaerobic conditions are briefly reviewed. Metal complexing agents and several organic acids produced by microbial action affect mobilization of radionuclides and toxic metals in subsurface environments. Information on the persistence of and biodegradation rates of synthetic as well as microbiologically produced complexing agents is scarce but important in determining the mobility of metal organic complexes in subsoils. Several gaps in knowledge in the area of microbial transformation of naturally occurring organics, radionuclides, and toxic metals have been identified, and further basic research has been suggested. 31 refs., 1 fig., 3 tabs

Performance and microbial community dynamics of a sulfate-reducing bioreactor treating coal generated acid mine drainage.

Science.gov (United States)

Burns, Andrew S; Pugh, Charles W; Segid, Yosief T; Behum, Paul T; Lefticariu, Liliana; Bender, Kelly S

2012-06-01

The effectiveness of a passive flow sulfate-reducing bioreactor processing acid mine drainage (AMD) generated from an abandoned coal mine in Southern Illinois was evaluated using geochemical and microbial community analysis 10 months post bioreactor construction. The results indicated that the treatment system was successful in both raising the pH of the AMD from 3.09 to 6.56 and in lowering the total iron level by 95.9%. While sulfate levels did decrease by 67.4%, the level post treatment (1153 mg/l) remained above recommended drinking water levels. Stimulation of biological sulfate reduction was indicated by a +2.60‰ increase in δ(34)S content of the remaining sulfate in the water post-treatment. Bacterial community analysis targeting 16S rRNA and dsrAB genes indicated that the pre-treated samples were dominated by bacteria related to iron-oxidizing Betaproteobacteria, while the post-treated water directly from the reactor outflow was dominated by sequences related to sulfur-oxidizing Epsilonproteobacteria and complex carbon degrading Bacteroidetes and Firmicutes phylums. Analysis of the post-treated water, prior to environmental release, revealed that the community shifted back to predominantly iron-oxidizing Betaproteobacteria. DsrA analysis implied limited diversity in the sulfate-reducing population present in both the bioreactor outflow and oxidation pond samples. These results support the use of passive flow bioreactors to lower the acidity, metal, and sulfate levels present in the AMD at the Tab-Simco mine, but suggest modifications of the system are necessary to both stimulate sulfate-reducing bacteria and inhibit sulfur-oxidizing bacteria.

Biotic interactions reduce microbial carbon use efficiency

Science.gov (United States)

Bradford, M.; Maynard, D. S.

2017-12-01

The efficiency by which microbes decompose organic matter governs the amount of carbon that is retained in microbial biomass versus lost to the atmosphere as respiration. This carbon use efficiency (CUE) is affected by various abiotic conditions, such as temperature and nutrient availability. In biogeochemical model simulations, CUE is a key variable regulating how much soil carbon is stored or lost from ecosystems under simulated global changes, such as climate warming. Theoretically, the physiological costs of biotic interactions such as competition should likewise alter CUE, yet the direction and magnitude of these costs are untested. Here we conduct a microcosm experiment to quantify how competitive interactions among saprotrophic fungi alter growth, respiration, and CUE. Free-living decomposer fungi representing a broad range of traits and phylogenies were grown alone, in pairwise competition, and in multi-species (up to 15) communities. By combing culturing and stable carbon isotope approaches, we could resolve the amount of carbon substrate allocated to fungal biomass versus respiration, and so estimate CUE. By then comparing individual performance to community-level outcomes, we show that species interactions induce consistent declines in CUE, regardless of abiotic conditions. Pairwise competition lowers CUE by as much as 25%, with the magnitude of these costs equal to or greater than the observed variation across abiotic conditions. However, depending on the competitive network structure, increasing species richness led to consistent gains or declines in CUE. Our results suggest that the extent to which microbial-mediated carbon fluxes respond to environmental change may be influenced strongly by competitive interactions. As such, knowledge of abiotic conditions and community composition is necessary to confidently project CUE and hence ecosystem carbon dynamics.

The nanostructure of microbially-reduced graphene oxide fosters thick and highly-performing electrochemically-active biofilms

Science.gov (United States)

Virdis, Bernardino; Dennis, Paul G.

2017-07-01

Biofilms of electrochemically-active organisms are used in microbial electrochemical technologies (METs) to catalyze bioreactions otherwise not possible at bare electrodes. At present, however, achievable current outputs are still below levels considered sufficient for economic viability of large-scale METs implementations. Here, we report three-dimensional, self-aggregating biofilm composites comprising of microbial cells embedded with microbially-reduced graphene oxide (rGO) nanoparticles to form a thick macro-porous network with superior electrochemical properties. In the presence of metabolic substrate, these hybrid biofilms are capable of producing up to five times more catalytic current than the control biofilms. Cyclic voltammetry, linear sweep voltammetry, and electrochemical impedance spectroscopy, show that in spite of the increased thickness, the biofilms amended with GO display lower polarization/charge transfer resistance compared to the controls, which we ascribe to the incorporation of rGO into the biofilms, which (1) promotes fast electron transfer, yet conserving a macroporous structure that allows free diffusion of reactants and products, and (2) enhances the interfacial dynamics by allowing a higher load of microbial cells per electrode surface area. These results suggest an easy-to-apply and cost-effective method to produce high-performing electrochemically-active biofilms in situ.

Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate‐reducing benthic microbial populations

Science.gov (United States)

Saad, Sainab; Bhatnagar, Srijak; Tegetmeyer, Halina E.; Geelhoed, Jeanine S.; Strous, Marc

2017-01-01

Summary For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate‐reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investigated the community response. Chemical measurements, provisional genomes and transcriptomic profiles revealed trophic networks of microbial populations. Sulfate reducers coexisted with facultative nitrate reducers or aerobes enabling the community to adjust to nitrate or oxygen pulses. Exposure to oxygen and nitrate impacted the community structure, but did not suppress fermentation or sulfate reduction as community functions, highlighting their stability under dynamic conditions. The most abundant sulfate reducer in all cultures, related to Desulfotignum balticum, appeared to have coupled both acetate‐ and hydrogen oxidation to sulfate reduction. We describe a novel representative of the widespread uncultured candidate phylum Fermentibacteria (formerly candidate division Hyd24‐12). For this strictly anaerobic, obligate fermentative bacterium, we propose the name ‘USabulitectum silens’ and identify it as a partner of sulfate reducers in marine sediments. Overall, we provide insights into the function of fermentative, as well as sulfate‐reducing microbial communities and their adaptation to a dynamic environment. PMID:28836729

Ambient ultraviolet radiation in the Arctic reduces root biomass and alters microbial community composition but has no effects on microbial biomass

DEFF Research Database (Denmark)

Rinnan, R.; Keinänen, M.M.; Kasurinen, A.

2005-01-01

We assessed the effects of ambient solar ultraviolet (UV) radiation on below-ground parameters in an arctic heath in north-eastern Greenland. We hypothesized that the current UV fluxes would reduce root biomass and mycorrhizal colonization and that these changes would lead to lower soil microbial...... biomass and altered microbial community composition. These hypotheses were tested on cored soil samples from a UV reduction experiment with three filter treatments (Mylar, 60% UV-B reduction; Lexan, up to 90% UV-B reduction+UV-A reduction; UV transparent Teflon, filter control) and an open control...... treatment in two study sites after 3 years' manipulation. Reduction of both UV-A and UV-B radiation caused over 30% increase in the root biomass of Vaccinium uliginosum, which was the dominant plant species. UV reduction had contrasting effects on ericoid mycorrhizal colonization of V. uliginosum roots...

D:L-Amino Acid Modeling Reveals Fast Microbial Turnover of Days to Months in the Subsurface Hydrothermal Sediment of Guaymas Basin.

Science.gov (United States)

Møller, Mikkel H; Glombitza, Clemens; Lever, Mark A; Deng, Longhui; Morono, Yuki; Inagaki, Fumio; Doll, Mechthild; Su, Chin-Chia; Lomstein, Bente A

2018-01-01

We investigated the impact of temperature on the microbial turnover of organic matter (OM) in a hydrothermal vent system in Guaymas Basin, by calculating microbial bio- and necromass turnover times based on the culture-independent D:L-amino acid model. Sediments were recovered from two stations near hydrothermal mounds (community of microorganisms in the hydrothermal sediment demonstrated short turnover times. The modeled turnover times of microbial bio- and necromass in the hydrothermal sediments were notably faster (biomass: days to months; necromass: up to a few hundred years) than in the cold sediments (biomass: tens of years; necromass: thousands of years), suggesting that temperature has a significant influence on the microbial turnover rates. We suggest that short biomass turnover times are necessary for maintance of essential cell funtions and to overcome potential damage caused by the increased temperature.The reduced OM quality at the hyrothemal sites might thus only allow for a small population size of microorganisms.

Metal artifact reduction algorithm based on model images and spatial information

Energy Technology Data Exchange (ETDEWEB)

Wu, Jay [Institute of Radiological Science, Central Taiwan University of Science and Technology, Taichung, Taiwan (China); Shih, Cheng-Ting [Department of Biomedical Engineering and Environmental Sciences, National Tsing-Hua University, Hsinchu, Taiwan (China); Chang, Shu-Jun [Health Physics Division, Institute of Nuclear Energy Research, Taoyuan, Taiwan (China); Huang, Tzung-Chi [Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung, Taiwan (China); Sun, Jing-Yi [Institute of Radiological Science, Central Taiwan University of Science and Technology, Taichung, Taiwan (China); Wu, Tung-Hsin, E-mail: tung@ym.edu.tw [Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, No.155, Sec. 2, Linong Street, Taipei 112, Taiwan (China)

2011-10-01

Computed tomography (CT) has become one of the most favorable choices for diagnosis of trauma. However, high-density metal implants can induce metal artifacts in CT images, compromising image quality. In this study, we proposed a model-based metal artifact reduction (MAR) algorithm. First, we built a model image using the k-means clustering technique with spatial information and calculated the difference between the original image and the model image. Then, the projection data of these two images were combined using an exponential weighting function. At last, the corrected image was reconstructed using the filter back-projection algorithm. Two metal-artifact contaminated images were studied. For the cylindrical water phantom image, the metal artifact was effectively removed. The mean CT number of water was improved from -28.95{+-}97.97 to -4.76{+-}4.28. For the clinical pelvic CT image, the dark band and the metal line were removed, and the continuity and uniformity of the soft tissue were recovered as well. These results indicate that the proposed MAR algorithm is useful for reducing metal artifact and could improve the diagnostic value of metal-artifact contaminated CT images.

Abundance, composition and activity of denitrifier communities in metal polluted paddy soils

Science.gov (United States)

Liu, Yuan; Liu, Yongzhuo; Zhou, Huimin; Li, Lianqing; Zheng, Jinwei; Zhang, Xuhui; Zheng, Jufeng; Pan, Genxing

2016-01-01

Denitrification is one of the most important soil microbial processes leading to the production of nitrous oxide (N2O). The potential changes with metal pollution in soil microbial community for N2O production and reduction are not well addressed. In this study, topsoil samples were collected both from polluted and non-polluted rice paddy fields and denitrifier communities were characterized with molecular fingerprinting procedures. All the retrieved nirK sequences could be grouped into neither α- nor β- proteobacteria, while most of the nosZ sequences were affiliated with α-proteobacteria. The abundances of the nirK and nosZ genes were reduced significantly in the two polluted soils. Thus, metal pollution markedly affected composition of both nirK and nosZ denitrifiers. While the total denitrifying activity and N2O production rate were both reduced under heavy metal pollution of the two sites, the N2O reduction rate showed no significant change. These findings suggest that N2O production activity could be sensitive to heavy metal pollution, which could potentially lead to a decrease in N2O emission in polluted paddies. Therefore, metal pollution could have potential impacts on soil N transformation and thus on N2O emission from paddy soils. PMID:26739424

Metal artifact reduction in CT using tissue-class modeling and adaptive prefiltering

International Nuclear Information System (INIS)

Bal, Matthieu; Spies, Lothar

2006-01-01

High-density objects such as metal prostheses, surgical clips, or dental fillings generate streak-like artifacts in computed tomography images. We present a novel method for metal artifact reduction by in-painting missing information into the corrupted sinogram. The information is provided by a tissue-class model extracted from the distorted image. To this end the image is first adaptively filtered to reduce the noise content and to smooth out streak artifacts. Consecutively, the image is segmented into different material classes using a clustering algorithm. The corrupted and missing information in the original sinogram is completed using the forward projected information from the tissue-class model. The performance of the correction method is assessed on phantom images. Clinical images featuring a broad spectrum of metal artifacts are studied. Phantom and clinical studies show that metal artifacts, such as streaks, are significantly reduced and shadows in the image are eliminated. Furthermore, the novel approach improves detectability of organ contours. This can be of great relevance, for instance, in radiation therapy planning, where images affected by metal artifacts may lead to suboptimal treatment plans

Silver nanoparticles uptake by salt marsh plants - Implications for phytoremediation processes and effects in microbial community dynamics.

Science.gov (United States)

Fernandes, Joana P; Mucha, Ana P; Francisco, Telmo; Gomes, Carlos Rocha; Almeida, C Marisa R

2017-06-15

This study investigated the uptake of silver nanoparticles (AgNPs) by a salt marsh plant, Phragmites australis, as well as AgNPs effects on rhizospheric microbial community, evaluating the implications for phytoremediation processes. Experiments were carried out with elutriate solution doped with Ag, either in ionic form or in NP form. Metal uptake was evaluated in plant tissues, elutriate solutions and sediments (by AAS) and microbial community was characterized in terms of bacterial community structure (evaluated by ARISA). Results showed Ag accumulation but only in plant belowground tissues and only in the absence of rhizosediment, the presence of sediment reducing Ag availability. But in plant roots Ag accumulation was higher when Ag was in NP form. Multivariate analysis of ARISA profiles showed significant effect of the absence/presence of Ag either in ionic or NP form on microbial community structure, although without significant differences among bacterial richness and diversity. Overall, P. australis can be useful for phytoremediation of medium contaminated with Ag, including with AgNPs. However, the presence of Ag in either forms affected the microbial community structure, which may cause disturbances in ecosystems function and compromise phytoremediation processes. Such considerations need to be address regarding environmental management strategies applied to the very important estuarine areas. The form in which the metal was added affected metal uptake by Phragmites australis and rhizosediment microbial community structure, which can affect phytoremediation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Experimental Study and Dynamic Modeling of Metal Rubber Isolating Bearing

International Nuclear Information System (INIS)

Zhang, Ke; Zhou, Yanguo; Jiang, Jian

2015-01-01

In this paper, dynamic shear mechanical properties of a new metal rubber isolating bearing is tested and studied. The mixed damping model is provided for theoretical modeling of MR isolating bearing, the shear stiffness and damping characteristics of the MR bearing can be analyzed separately and easily discussed, and the mixed damping model is proved to be an rather effective approach. The test results indicate that loading frequency bears little impact over shear property of metal rubber isolating bearing, the total energy consumption of metal rubber isolating bearing increases with the increase in loading amplitude. With the increase in loading amplitude, the stiffness of the isolating bearing will reduce showing its “soft property”; and the type of damping force gradually changes to be close to dry friction. The features of “soft property” and dry friction energy consumption of metal rubber isolating bearing are very useful in practical engineering application. (paper)

Modelling microbial interactions and food structure in predictive microbiology

NARCIS (Netherlands)

Malakar, P.K.

2002-01-01

Keywords: modelling, dynamic models, microbial interactions, diffusion, microgradients, colony growth, predictive microbiology.

Growth response of microorganisms in foods is a complex process. Innovations in food production and preservation techniques have resulted in adoption of

Coupled Transport/Reaction Modelling of Copper Canister Corrosion Aided by Microbial Processes

Energy Technology Data Exchange (ETDEWEB)

Liu, Jinsong [Royal Institute of Technology, Stockholm (Sweden). Dept. of Chemical Engineering and Technology

2006-04-15

Copper canister corrosion is an important issue in the concept of a nuclear fuel repository. Previous studies indicate that the oxygen-free copper canister could hold its integrity for more than 100,000 years in the repository environment. Microbial processes may reduce sulphate to sulphide and considerably increase the amount of sulphides available for corrosion. In this paper, a coupled transport/reaction model is developed to account for the transport of chemical species produced by microbial processes. The corroding agents like sulphide would come not only from the groundwater flowing in a fracture that intersects the canister, but also from the reduction of sulphate near the canister. The reaction of sulphate-reducing bacteria and the transport of sulphide in the bentonite buffer are included in the model. The depth of copper canister corrosion is calculated by the model. With representative 'central values' of the concentrations of sulphate and methane at repository depth at different sites in Fennoscandian Shield the corrosion depth predicted by the model is a few millimetres during 10{sup 5} years. As the concentrations of sulphate and methane are extremely site-specific and future climate changes may significantly influence the groundwater compositions at potential repository sites, sensitivity analyses have been conducted. With a broad perspective of the measured concentrations at different sites in Sweden and in Finland, and some possible mechanisms (like the glacial meltwater intrusion and interglacial seawater intrusion) that may introduce more sulphate into the groundwater at intermediate depths during future climate changes, higher concentrations of either/both sulphate and methane than what is used as the representative 'central' values would be possible. In worst cases. locally, half of the canister thickness could possibly be corroded within 10{sup 5} years.

Coupled Transport/Reaction Modelling of Copper Canister Corrosion Aided by Microbial Processes

International Nuclear Information System (INIS)

Jinsong Liu

2006-04-01

Copper canister corrosion is an important issue in the concept of a nuclear fuel repository. Previous studies indicate that the oxygen-free copper canister could hold its integrity for more than 100,000 years in the repository environment. Microbial processes may reduce sulphate to sulphide and considerably increase the amount of sulphides available for corrosion. In this paper, a coupled transport/reaction model is developed to account for the transport of chemical species produced by microbial processes. The corroding agents like sulphide would come not only from the groundwater flowing in a fracture that intersects the canister, but also from the reduction of sulphate near the canister. The reaction of sulphate-reducing bacteria and the transport of sulphide in the bentonite buffer are included in the model. The depth of copper canister corrosion is calculated by the model. With representative 'central values' of the concentrations of sulphate and methane at repository depth at different sites in Fennoscandian Shield the corrosion depth predicted by the model is a few millimetres during 10 5 years. As the concentrations of sulphate and methane are extremely site-specific and future climate changes may significantly influence the groundwater compositions at potential repository sites, sensitivity analyses have been conducted. With a broad perspective of the measured concentrations at different sites in Sweden and in Finland, and some possible mechanisms (like the glacial meltwater intrusion and interglacial seawater intrusion) that may introduce more sulphate into the groundwater at intermediate depths during future climate changes, higher concentrations of either/both sulphate and methane than what is used as the representative 'central' values would be possible. In worst cases. locally, half of the canister thickness could possibly be corroded within 10 5 years

Coupled Transport/Reaction Modelling of Copper Canister Corrosion Aided by Microbial Processes

Energy Technology Data Exchange (ETDEWEB)

Jinsong Liu [Royal Institute of Technology, Stockholm (Sweden). Dept. of Chemical Engineering and Technology

2006-04-15

Copper canister corrosion is an important issue in the concept of a nuclear fuel repository. Previous studies indicate that the oxygen-free copper canister could hold its integrity for more than 100,000 years in the repository environment. Microbial processes may reduce sulphate to sulphide and considerably increase the amount of sulphides available for corrosion. In this paper, a coupled transport/reaction model is developed to account for the transport of chemical species produced by microbial processes. The corroding agents like sulphide would come not only from the groundwater flowing in a fracture that intersects the canister, but also from the reduction of sulphate near the canister. The reaction of sulphate-reducing bacteria and the transport of sulphide in the bentonite buffer are included in the model. The depth of copper canister corrosion is calculated by the model. With representative 'central values' of the concentrations of sulphate and methane at repository depth at different sites in Fennoscandian Shield the corrosion depth predicted by the model is a few millimetres during 10{sup 5} years. As the concentrations of sulphate and methane are extremely site-specific and future climate changes may significantly influence the groundwater compositions at potential repository sites, sensitivity analyses have been conducted. With a broad perspective of the measured concentrations at different sites in Sweden and in Finland, and some possible mechanisms (like the glacial meltwater intrusion and interglacial seawater intrusion) that may introduce more sulphate into the groundwater at intermediate depths during future climate changes, higher concentrations of either/both sulphate and methane than what is used as the representative 'central' values would be possible. In worst cases. locally, half of the canister thickness could possibly be corroded within 10{sup 5} years.

Design, Modeling, and Development of Microbial Cell Factories

KAUST Repository

Kodzius, Rimantas

2014-03-26

Using Metagenomic analysis, computational modeling, single cell and genome editing technologies, we will express desired microbial genes and their networks in suitable hosts for mass production of energy, food, and fine chemicals.

Design, Modeling, and Development of Microbial Cell Factories

KAUST Repository

Kodzius, Rimantas; Behzad, H.; Archer, John A.C.; Bajic, Vladimir B.; Gojobori, Takashi

2014-01-01

Using Metagenomic analysis, computational modeling, single cell and genome editing technologies, we will express desired microbial genes and their networks in suitable hosts for mass production of energy, food, and fine chemicals.

Anomalous electrical signals associated with microbial activity: Results from Iron and Nitrate-Reducing Columns

Science.gov (United States)

Aaron, R. B.; Zheng, Q.; Flynn, P.; Singha, K.; Brantley, S.

2008-12-01

Three flow-through columns outfitted with Ag/AgCl electrodes were constructed to test the effects of different microbial processes on the geophysical measurements of self potential (SP), bulk electrical conductivity (σ b), and induced polarization (IP). The columns were filled with sieved, Fe-bearing subsurface sediment from the Delmarva Peninsula near Oyster, VA, inoculated (9:1 ratio) with a freshly-collected, shallow subsurface sediment from a wetland floodplain (Dorn Creek) near Madison, WI. Each of the columns was fed anoxic and sterile PIPES buffered artificial groundwater (PBAGW) containing different concentrations of acetate and nitrate. The medium fed to Column 1 (nitrate-reducing) was amended with 100 μM acetate and 2 mM nitrate. Column 2 (iron-reducing) was run with PBAGW containing 1.0 mM acetate and 0 mM nitrate. Column 3 (alternating redox state) was operated under conditions designed to alternately stimulate nitrate-reducing and iron-reducing populations to provide conditions, i.e., the presence of both nitrate and microbially-produced Fe(II), that would allow growth of nitrate-dependent Fe(II)-oxidizing populations. We operated Column 3 with a cycling strategy of 14-18 days of high C medium (1 mM acetate and 100 μ M nitrate) followed by 14-18 days of low C medium (100 μ M acetate and 2 mM nitrate). Effluent chemistry (NO3-, NO2-, NH4+, acetate, and Fe2+) was sampled daily for four months so as to be concurrent with the electrical measurements. We observed chemical evidence of iron reduction (dissolved [Fe(II)] = 0.2mM) in the effluent from the iron reduction and alternating redox columns. Chemical depletion of NO3- ([NO3-] ranged from 1 to 0.02mM), the production of NO2-, and possible production of NH4+ (0.2 mM) was observed in the nitrate reducing column as well as the alternating redox column. All three columns displayed loss of acetate as microbial activity progressed. σ b remained constant in the alternating redox column (~0.15 S

Effects of chlortetracycline and copper on tetracyclines and copper resistance genes and microbial community during swine manure anaerobic digestion.

Science.gov (United States)

Wang, Rui; Chen, Meixue; Feng, Feng; Zhang, Junya; Sui, Qianwen; Tong, Juan; Wei, Yuansong; Wei, Dongbin

2017-08-01

As antibiotic and heavy metals are over used in the livestock industry, animal manure is a reservoir of antibiotic resistance genes (ARGs). Anaerobic digestion has been reported to have the potential to reduce ARGs. However, few studies investigated whether reduction of ARGs would be affected by different external pressures including antibiotics and heavy metals during anaerobic digestion. The purpose of this study was thus to investigate effects of both chlortetracycline (CTC) and Cu on reduction of ARGs, heavy metal resistance genes (HMRGs) and mobile genetic elements (MGEs) during the swine manure anaerobic digestion. The results showed that the predominant ARGs (tetO, tetW, tetX, tetL) could be effectively reduced (approximately 1.00 log copies/g TS) through mesophilic anaerobic digestion. Microbial community evolution was the main driver. It was interesting that Treponema might indicate the termination of anaerobic digestion and compete with ARGs host bacteria. Addition of CTC, Cu and CTC+Cu affected microbial community change and hindered removal of ARGs, especially, CTC+Cu seriously affected Treponema and ARGs during anaerobic digestion. Copyright © 2017 Elsevier Ltd. All rights reserved.

Remediation of contaminated subsurface materials by a metal-reducing bacterium

International Nuclear Information System (INIS)

Gorby, Y.A.; Amonette, J.E.; Fruchter, J.S.

1994-11-01

A biotic approach for remediating subsurface sediments and groundwater contaminated with carbon tetrachloride (CT) and chromium was evaluated. Cells of the Fe(iii)-reducing bacterium strain BrY were added to sealed, anoxic flasks containing Hanford groundwater, natural subsurface sediments, and either carbon tetrachloride, CT, or oxidized chromium, Cr(VI). With lactate as the electron donor, BrY transformed CT to chloroform (CF), which accumulated to about 1 0 % of the initial concentration of CT. The remainder of the CT was transformed to unidentified, nonvolatile compounds. Transformation of CT by BrY was an indirect process Cells reduced solid phase Fe(ill) to chemically reactive FE(II) that chemically transformed the chlorinated contaminant. Cr(VI), in contrast, was reduced by a direct enzymatic reaction in the presence or absence of Fe(III)-bearing sediments. These results demonstrate that Fe(ill)-reducing bacteria provide potential for transforming CT and for reducing CR(VI) to less toxic Cr(III). Technologies for stimulating indigenous populations of metal-reducing bacteria or for introducing specific metal-reducing bacteria to the subsurface are being investigated

Reduced Nutrient Excretion and Environmental Microbial Load with the Addition of a Combination of Enzymes and Direct-Fed Microbials to the Diet of Broiler Chickens

Directory of Open Access Journals (Sweden)

MFFM Praes

2016-03-01

Full Text Available Abstract This study evaluated the effects of the dietary inclusion of an enzyme blend and a direct-fed microbials in broiler diets on litter production and quality. In total, 900 Cobb 500(r broiler chicks were distributed according to a completely randomized design into 4 treatments and 9 replicates of 25 birds each. Broilers were reared from 1 to 42 days of age. The treatments consisted of the following diets: NC: negative control; DFM: NC + 500 ppm of direct-fed microbials product (DFM, containing Bacillus subtilis and Bacillus licheniformis; ENZ: diet formulated with an enzyme blend (20 ppm phytase, 200 ppm protease and 200 ppm of xylanase; DFM+E: ENZ + DFM. Birds and litter were weighed at the start and end of the rearing period, for litter production and waste ratio (Rw determination. Litter samples were analyzed for dry matter (DM content, total and thermotolerant coliform counts, nutrient composition (nitrogen (N, phosphorous (P and potassium (K, and fiber fraction (neutral detergent fiber (NDF, acid detergent fiber (ADF and lignin. The dietary inclusion of the evaluated additivesdid not influence litter production or Rw; however, ADF (%, NDF (kg and kg/kg DM litter, and total and thermotolerant coliform counts were reduced, and N content increased in the litter. The diets containing enzymes (ENZ and DFM+E reduced litter P content. The addition of exogenous enzymes and their combination with a DFM based on Bacillus spp .Did not affect waste production, and reduced litter microbial load, and the contents of P and insoluble fiber in the litter.

Development of dielectric barrier discharge for reducing microbial contamination in pepper (Piper nigrum) and sesame (Sesamum indicum Linn.) powder

Science.gov (United States)

Promping, J.; Prakongsil, P.; Picha, R.; Traikool, T.

2017-09-01

This research is designed to determine the efficacy of DBD plasma to reduce the microbial contamination of pepper and sesame powder. The AC high voltage power supply was used with voltages of up to 20 kV and the frequency of 5.5 kHz was applied to the DBD. The gap of DBD electrodes was set at 5 mm. In raw initial samples, the total aerobic count of pepper (Piper nigrum) was found at quite a high level at 5.40 × 105 CFU/g. Coliform bacteria was also found in both the sesame (Sesamum indicum Linn.) powder and pepper (Piper nigrum) powder. Both kinds of samples were treated with plasma for 2, 4, 6 and 10 minutes. Results indicated that plasma treatment at 2-10 minutes reduced the total aerobic count of pepper allowed to achieve the acceptable microbial level for spices. The plasma treatment times in this experiment were also effective in reducing faecal coliform bacteria in both pepper and sesame powders (MPN/g <3) as indicated in the standard. Plasma from dielectric barrier charge can reduce Staphylococcus epidermidis in sesame powder which was artificially contaminated with 3.50 × 102 CFU/g resulting in 0.15-0.5 log cycle reductions of microbial load.

Process control for sheet-metal stamping process modeling, controller design and shop-floor implementation

CERN Document Server

Lim, Yongseob; Ulsoy, A Galip

2014-01-01

Process Control for Sheet-Metal Stamping presents a comprehensive and structured approach to the design and implementation of controllers for the sheet metal stamping process. The use of process control for sheet-metal stamping greatly reduces defects in deep-drawn parts and can also yield large material savings from reduced scrap. Sheet-metal forming is a complex process and most often characterized by partial differential equations that are numerically solved using finite-element techniques. In this book, twenty years of academic research are reviewed and the resulting technology transitioned to the industrial environment. The sheet-metal stamping process is modeled in a manner suitable for multiple-input multiple-output control system design, with commercially available sensors and actuators. These models are then used to design adaptive controllers and real-time controller implementation is discussed. Finally, experimental results from actual shopfloor deployment are presented along with ideas for further...

Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations.

Science.gov (United States)

Saad, Sainab; Bhatnagar, Srijak; Tegetmeyer, Halina E; Geelhoed, Jeanine S; Strous, Marc; Ruff, S Emil

2017-12-01

For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate-reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investigated the community response. Chemical measurements, provisional genomes and transcriptomic profiles revealed trophic networks of microbial populations. Sulfate reducers coexisted with facultative nitrate reducers or aerobes enabling the community to adjust to nitrate or oxygen pulses. Exposure to oxygen and nitrate impacted the community structure, but did not suppress fermentation or sulfate reduction as community functions, highlighting their stability under dynamic conditions. The most abundant sulfate reducer in all cultures, related to Desulfotignum balticum, appeared to have coupled both acetate- and hydrogen oxidation to sulfate reduction. We describe a novel representative of the widespread uncultured candidate phylum Fermentibacteria (formerly candidate division Hyd24-12). For this strictly anaerobic, obligate fermentative bacterium, we propose the name ' U Sabulitectum silens' and identify it as a partner of sulfate reducers in marine sediments. Overall, we provide insights into the function of fermentative, as well as sulfate-reducing microbial communities and their adaptation to a dynamic environment. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. I. Model and validation

Energy Technology Data Exchange (ETDEWEB)

Hegde, Ganesh, E-mail: ghegde@purdue.edu; Povolotskyi, Michael; Kubis, Tillmann; Klimeck, Gerhard, E-mail: gekco@purdue.edu [Network for Computational Nanotechnology (NCN), Department of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907 (United States); Boykin, Timothy [Department of Electrical and Computer Engineering, University of Alabama, Huntsville, Alabama (United States)

2014-03-28

Semi-empirical Tight Binding (TB) is known to be a scalable and accurate atomistic representation for electron transport for realistically extended nano-scaled semiconductor devices that might contain millions of atoms. In this paper, an environment-aware and transferable TB model suitable for electronic structure and transport simulations in technologically relevant metals, metallic alloys, metal nanostructures, and metallic interface systems are described. Part I of this paper describes the development and validation of the new TB model. The new model incorporates intra-atomic diagonal and off-diagonal elements for implicit self-consistency and greater transferability across bonding environments. The dependence of the on-site energies on strain has been obtained by appealing to the Moments Theorem that links closed electron paths in the system to energy moments of angular momentum resolved local density of states obtained ab initio. The model matches self-consistent density functional theory electronic structure results for bulk face centered cubic metals with and without strain, metallic alloys, metallic interfaces, and metallic nanostructures with high accuracy and can be used in predictive electronic structure and transport problems in metallic systems at realistically extended length scales.

An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. I. Model and validation

International Nuclear Information System (INIS)

Hegde, Ganesh; Povolotskyi, Michael; Kubis, Tillmann; Klimeck, Gerhard; Boykin, Timothy

2014-01-01

Semi-empirical Tight Binding (TB) is known to be a scalable and accurate atomistic representation for electron transport for realistically extended nano-scaled semiconductor devices that might contain millions of atoms. In this paper, an environment-aware and transferable TB model suitable for electronic structure and transport simulations in technologically relevant metals, metallic alloys, metal nanostructures, and metallic interface systems are described. Part I of this paper describes the development and validation of the new TB model. The new model incorporates intra-atomic diagonal and off-diagonal elements for implicit self-consistency and greater transferability across bonding environments. The dependence of the on-site energies on strain has been obtained by appealing to the Moments Theorem that links closed electron paths in the system to energy moments of angular momentum resolved local density of states obtained ab initio. The model matches self-consistent density functional theory electronic structure results for bulk face centered cubic metals with and without strain, metallic alloys, metallic interfaces, and metallic nanostructures with high accuracy and can be used in predictive electronic structure and transport problems in metallic systems at realistically extended length scales

An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. I. Model and validation

Science.gov (United States)

Hegde, Ganesh; Povolotskyi, Michael; Kubis, Tillmann; Boykin, Timothy; Klimeck, Gerhard

2014-03-01

Semi-empirical Tight Binding (TB) is known to be a scalable and accurate atomistic representation for electron transport for realistically extended nano-scaled semiconductor devices that might contain millions of atoms. In this paper, an environment-aware and transferable TB model suitable for electronic structure and transport simulations in technologically relevant metals, metallic alloys, metal nanostructures, and metallic interface systems are described. Part I of this paper describes the development and validation of the new TB model. The new model incorporates intra-atomic diagonal and off-diagonal elements for implicit self-consistency and greater transferability across bonding environments. The dependence of the on-site energies on strain has been obtained by appealing to the Moments Theorem that links closed electron paths in the system to energy moments of angular momentum resolved local density of states obtained ab initio. The model matches self-consistent density functional theory electronic structure results for bulk face centered cubic metals with and without strain, metallic alloys, metallic interfaces, and metallic nanostructures with high accuracy and can be used in predictive electronic structure and transport problems in metallic systems at realistically extended length scales.

Gut Microbial Diversity in Rat Model Induced by Rhubarb

Science.gov (United States)

Peng, Ying; Wu, Chunfu; Yang, Jingyu; Li, Xiaobo

2014-01-01

Rhubarb is often used to establish chronic diarrhea and spleen (Pi)-deficiency syndrome animal models in China. In this study, we utilized the enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) method to detect changes in bacterial diversity in feces and the bowel mucosa associated with this model. Total microbial genomic DNA from the small bowel (duodenum, jejunum, and ileum), large bowel (proximal colon, distal colon, and rectum), cecum, and feces of normal and rhubarb-exposed rats were used as templates for the ERIC-PCR analysis. We found that the fecal microbial composition did not correspond to the bowel bacteria mix. More bacterial diversity was observed in the ileum of rhubarb-exposed rats (Panalysis with the SPSS software, the Canonical Discriminant Function Formulae for model rats was established. PMID:25048267

Synthesis and characterization of some reduced ternary and quaternary molybdenum oxide phases with strong metal-metal bonds

International Nuclear Information System (INIS)

Lii, K.H.

1985-10-01

In the course of our research on reduced ternary and quaternary molybdenum oxides, very interesting compounds with strong metal-metal bonds were discovered. Among these solid-state materials are found discrete cluster arrays and structures with extended metal-metal bonding. Further study in this system has revealed that many new structures exist in this new realm. The synthesis, structures, bonding, and properties of these new oxides, which are briefly summarized in tabular form, are presented in this thesis. 144 refs., 63 figs., 79 tabs

Relationships between waste physicochemical properties, microbial activity and vegetation at coal ash and sludge disposal sites.

Science.gov (United States)

Woch, Marcin W; Radwańska, Magdalena; Stanek, Małgorzata; Łopata, Barbara; Stefanowicz, Anna M

2018-06-11

The aim of the study was to assess the relationships between vegetation, physicochemical and microbial properties of substrate at coal ash and sludge disposal sites. The study was performed on 32 plots classified into 7 categories: dried ash sedimentation ponds, dominated by a grass Calamagrostis epigejos (AH-Ce), with the admixture of Pinus sylvestris (AH-CePs) or Robinia pseudoacacia (AH-CeRp), dry ash landfill dominated by Betula pendula and Pinus sylvestris (AD-BpPs) or Salix viminalis (AD-Sv) and coal sludge pond with drier parts dominated by Tussilago farfara (CS-Tf) and the wetter ones by Cyperus flavescens (CS-Cf). Ash sites were covered with soil layer imported as a part of technical reclamation. Ash had relatively high concentrations of some alkali and alkaline earth metals, Mn and pH, while coal sludge had high water and C, S, P and K contents. Concentrations of heavy metals were lower than allowable limits in all substrate types. Microbial biomass and, particularly, enzymatic activity in ash and sludge were generally low. The only exception were CS-Tf plots characterized by the highest microbial biomass, presumably due to large deposits of organic matter that became available for aerobic microbial biomass when water level fell. The properties of ash and sludge adversely affected microbial biomass and enzymatic activity as indicated by significant negative correlations between the content of alkali/alkaline earth metals, heavy metals, and macronutrients with enzymatic activity and/or microbial biomass, as well as positive correlations of these parameters with metabolic quotient (qCO 2 ). Plant species richness and cover were relatively high, which may be partly associated with alleviating influence of soil covering the ash. The effect of the admixture of R. pseudoacacia or P. sylvestris to stands dominated by C. epigejos was smaller than expected. The former species increased NNH 4 , NNO 3 and arylsulfatase activity, while the latter reduced activity of

[Effects of heavy metals pollution on soil microbial communities metabolism and soil enzyme activities in coal mining area of Tongchuan, Shaanxi Province of Northwest China].

Science.gov (United States)

Guo, Xing-Liang; Gu, Jie; Chen, Zhi-Xue; Gao, Hua; Qin, Qing-Jun; Sun, Wei; Zhang, Wei-Juan

2012-03-01

This paper studied the metabolism of soil microbes, functions of soil microbial communities, and activities of soil enzymes in a coal mining area of Tongchuan. In the coal mining area, the concentrations of soil Cu, Zn, Cd, and Pb were significantly higher than those in the non-mining area, of which, Cd contributed most to the heavy metals pollution. By adopting Biolog method combining with principal component analysis (PCA) and cluster analysis, it was found that the metabolic characteristics of different soil microbial communities varied significantly with increasing soil heavy metals pollution, and the variation was mainly manifested in the metabolic patterns of carbon sources such as saccharides and amino acids. In slightly and moderately polluted soils, the utilization of carbon sources by soil microbial communities was activated; while in heavily polluted soils, the carbon sources utilization was inhibited. The activities of soil urease, protease, alkaline phosphatase, and catalase all tended to decline with intensifying soil heavy metals pollution. The soil urease, protease, alkaline phosphatase, and catalase activities in the coal mining area were 50.5%-65.1%, 19.1%-57.1%, 87.2%-97.5%, and 77.3%-86.0% higher than those in the non-mining area, respectively. The activities of soil sucrase and cellulase were activated in slightly and moderately polluted soils, but inhibited in heavily polluted soils.

Flow-through Column Experiments and Modeling of Microbially Mediated Cr(VI) Reduction at Hanford 100H

Science.gov (United States)

Yang, L.; Molins, S.; Beller, H. R.; Brodie, E. L.; Steefel, C.; Nico, P. S.; Han, R.

2010-12-01

Microbially mediated Cr(VI) reduction at the Hanford 100H area was investigated by flow-through column experiments. Three separate experiments were conducted to promote microbial activities associated with denitrification, iron and sulfate reduction, respectively. Replicate columns packed with natural sediments from the site under anaerobic environment were injected with 5mM Lactate as the electron donor and 5 μM Cr(VI) in all experiments. Sulfate and nitrate solutions were added to act as the main electron acceptors in the respective experiments, while iron columns relied on the indigenous sediment iron (and manganese) oxides as electron acceptors. Column effluent solutions were analyzed by IC and ICP-MS to monitor the microbial consumption/conversion of lactate and the associated Cr(VI) reduction. Biogeochemical reactive transport modeling was performed to gain further insights into the reaction mechanisms and Cr(VI) bioreduction rates. All experimental columns showed a reduction of the injected Cr(VI). Columns under denitrifying conditions showed the least Cr(VI) reduction at early stages (simulations indicated that biomass growth completely depleted influent ammonium, and called for an additional source of N to account for the measured reduction rates. Iron columns were the least active with undetectable consumption of the injected lactate, slowest cell growth, and the smallest change in Cr(VI) concentrations during the course of the experiment. In contrast, columns under sulfate-reducing/fermentative conditions exhibited the greatest Cr(VI) reduction capacity. Two sulfate columns evolved to complete lactate fermentation with acetate and propionate produced in the column effluent after 40 days of experiments. These fermenting columns showed a complete removal of injected Cr(VI), visible precipitation of sulfide minerals, and a significant increase in effluent Fe and Mn concentrations. Reactive transport simulations suggested that direct reduction of Cr(VI) by

Heavy metal removal and recovery using microorganisms. Volume 1, State-of-the-art and potential applications at the SRS

Energy Technology Data Exchange (ETDEWEB)

Wilde, E.W. [Westinghouse Savannah River Co., Aiken, SC (United States); Benemann, J.R. [Benemann (J.R.), Pinole, CA (United States)

1991-02-01

Microorganisms -- bacteria, fungi, and microalgae -- can accumulate relatively large amounts of toxic heavy metals and radionuclides from the environment. These organisms often exhibit specificity for particular metals. The metal content of microbial biomass can be a substantial fraction of total dry weight with concentration factors (metal in dry biomass to metal in solution) exceeding one million in some cases. Both living and inert (dead) microbial biomass can be used to reduce heavy metal concentrations in contaminated waters to very low levels -- parts per billion and even lower. In many respects (e.g. specificity, residual metal concentrations, accumulation factors, and economics) microbial bioremoval processes can be superior to conventional processes, such as ion exchange and caustic (lime or hydroxide) precipitation for heavy metals removal from waste and contaminated waters. Thus, bioremoval could be developed to contribute to the clean-up of wastes at the Savannah River Site (SRS) and other DOE facilities. However, the potential advantages of bioremoval processes must still be developed into practical operating systems. A detailed review of the literature suggests that appropriate bioremoval processes could be developed for the SRS. There is great variability from one biomass source to another in bioremoval capabilities. Bioremoval is affected by pH, other ions, temperature, and many other factors. The biological (living vs. dead) and physical (immobilized vs. dispersed) characteristics of the biomass also greatly affect metal binding. Even subtle differences in the microbial biomass, such as the conditions under which it was cultivated, can have major effects on heavy metal binding.

Siderophores mediate reduced and increased uptake of cadmium by Streptomyces tendae F4 and sunflower (Helianthus annuus), respectively.

Science.gov (United States)

Dimkpa, C O; Merten, D; Svatos, A; Büchel, G; Kothe, E

2009-11-01

As a toxic metal, cadmium (Cd) affects microbial and plant metabolic processes, thereby potentially reducing the efficiency of microbe or plant-mediated remediation of Cd-polluted soil. The role of siderophores produced by Streptomyces tendae F4 in the uptake of Cd by bacteria and plant was investigated to gain insight into the influence of siderophores on Cd availability to micro-organisms and plants. The bacterium was cultured under siderophore-inducing conditions in the presence of Cd. The kinetics of siderophore production and identification of the siderophores and their metal-bound forms were performed using electrospray ionization mass spectrometry. Inductively coupled plasma spectroscopy was used to measure iron (Fe) and Cd contents in the bacterium and in sunflower plant grown in Cd-amended soil. Siderophores significantly reduced the Cd uptake by the bacterium, while supplying it with iron. Bacterial culture filtrates containing three hydroxamate siderophores secreted by S. tendae F4 significantly promoted plant growth and enhanced uptake of Cd and Fe by the plant, relative to the control. Furthermore, application of siderophores caused slightly more Cd, but similar Fe uptake, compared with EDTA. Bioinoculation with Streptomyces caused a dramatic increase in plant Fe content, but resulted only in slight increase in plant Cd content. It is concluded that siderophores can help reduce toxic metal uptake in bacteria, while simultaneously facilitating the uptake of such metals by plants. Also, EDTA is not superior to hydroxamate siderophores in terms of metal solubilization for plant uptake. The study showed that microbial processes could indirectly influence the availability and amount of toxic metals taken up from the rhizosphere of plants. Furthermore, although EDTA is used for chelator-enhanced phytoremediation, microbial siderophores would be ideal for this purpose.

Impaired microbial activity caused by metal pollution: A field study in a deactivated uranium mining area.

Science.gov (United States)

Antunes, Sara Cristina; Pereira, Ruth; Marques, Sérgio Miguel; Castro, Bruno Branco; Gonçalves, Fernando

2011-12-01

European frameworks for the ecological risk assessment (ERA) of contaminated sites integrate information from three lines of evidence: chemical, ecotoxicological, and ecological. Regarding the last one, field observations at the contaminated sites are compared to reference site(s) and the differences recorded are analysed at the light of a cause-effect relationship, taking into account the site-specific contamination. Thus, included in the tier 2 of a site-specific risk assessment that is being carried out in an deactivated uranium mining area, a battery of soil enzyme activities (dehydrogenases, urease, arysulphatase, cellulase, acid phosphate) and potential nitrification were assessed in seven sampling sites (A-D-E-F-G-H-I) at different distances from the mine pit. These parameters have been considered good indicators of impacts on soil microbial communities and, subsequently, on soil functions. Soil enzyme activities were impaired in the most contaminated site (A, near the mine pit), for which a higher degree of risk was determined in the tier 1 of ERA. Three other sites within the mining area (F, G, and D) were discriminated on the basis of their low microbial activity, using uni- and multivariate approaches, and validating what had been previously found with chemical and ecotoxicological lines of evidence. We observed considerable among-site heterogeneity in terms of soil physical and chemical properties, combined with seasonal differences in enzyme activities. Still, the correlation between microbial parameters and soil general physical and chemical parameters was weak. In opposition, significant and negative correlations were found between soil enzyme activities and several metallic elements (Al, Be, Cu, U). These findings suggest a clear correlation between compromised soil function (nutrient recycling) and metal contamination. Such information reinforces the evidence of risks for some sites within the mining area and is an important contribution for the

Ecological and soil hydraulic implications of microbial responses to stress - A modeling analysis

Science.gov (United States)

Brangarí, Albert C.; Fernàndez-Garcia, Daniel; Sanchez-Vila, Xavier; Manzoni, Stefano

2018-06-01

A better understanding of microbial dynamics in porous media may lead to improvements in the design and management of a number of technological applications, ranging from the degradation of contaminants to the optimization of agricultural systems. To this aim, there is a recognized need for predicting the proliferation of soil microbial biomass (often organized in biofilms) under different environments and stresses. We present a general multi-compartment model to account for physiological responses that have been extensively reported in the literature. The model is used as an explorative tool to elucidate the ecological and soil hydraulic consequences of microbial responses, including the production of extracellular polymeric substances (EPS), the induction of cells into dormancy, and the allocation and reuse of resources between biofilm compartments. The mechanistic model is equipped with indicators allowing the microorganisms to monitor environmental and biological factors and react according to the current stress pressures. The feedbacks of biofilm accumulation on the soil water retention are also described. Model runs simulating different degrees of substrate and water shortage show that adaptive responses to the intensity and type of stress provide a clear benefit to microbial colonies. Results also demonstrate that the model may effectively predict qualitative patterns in microbial dynamics supported by empirical evidence, thereby improving our understanding of the effects of pore-scale physiological mechanisms on the soil macroscale phenomena.

Combined effects of antimony and sodium diethyldithiocarbamate on soil microbial activity and speciation change of heavy metals. Implications for contaminated lands hazardous material pollution in nonferrous metal mining areas.

Science.gov (United States)

Zhu, Xiaozhe; Yao, Jun; Wang, Fei; Yuan, Zhimin; Liu, Jianli; Jordan, Gyozo; Knudsen, Tatjana Šolević; Avdalović, Jelena

2018-05-05

The combined effects of antimony (Sb) and sodium diethyldithiocarbamate (DDTC), a common organic flotation reagent, on soil microbial activity and speciation changes of heavy metals were investigated for the first time. The results showed that the exchangeable fraction of Sb was transformed to a stable residual fraction during the incubation period, and the addition of DDTC promoted the transformation compared with single Sb pollution, probably because DDTC can react with heavy metals to form a complex. In addition, the presence of DDTC and Sb inhibited the soil microbial activity to varying degrees. The growth rate constant k of different interaction systems was in the following order on the 28th day: control group ≥ single DDTC pollution > combined pollution > single Sb pollution. A correlation analysis showed that the concentration of exchangeable Sb was the primary factor that affected the toxic reaction under combined pollution conditions, and it significantly affected the characteristics of the soil microorganisms. All the observations provide useful information for a better understanding of the toxic effects and potential risks of combined Sb and DDTC pollution in antimony mining areas. Copyright © 2018 Elsevier B.V. All rights reserved.

Modeling microbial community structure and functional diversity across time and space.

Science.gov (United States)

Larsen, Peter E; Gibbons, Sean M; Gilbert, Jack A

2012-07-01

Microbial communities exhibit exquisitely complex structure. Many aspects of this complexity, from the number of species to the total number of interactions, are currently very difficult to examine directly. However, extraordinary efforts are being made to make these systems accessible to scientific investigation. While recent advances in high-throughput sequencing technologies have improved accessibility to the taxonomic and functional diversity of complex communities, monitoring the dynamics of these systems over time and space - using appropriate experimental design - is still expensive. Fortunately, modeling can be used as a lens to focus low-resolution observations of community dynamics to enable mathematical abstractions of functional and taxonomic dynamics across space and time. Here, we review the approaches for modeling bacterial diversity at both the very large and the very small scales at which microbial systems interact with their environments. We show that modeling can help to connect biogeochemical processes to specific microbial metabolic pathways. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Nanoparticles within WWTP sludges have minimal impact on leachate quality and soil microbial community structure and function

International Nuclear Information System (INIS)

Durenkamp, Mark; Pawlett, Mark; Ritz, Karl; Harris, Jim A.; Neal, Andrew L.; McGrath, Steve P.

2016-01-01

One of the main pathways by which engineered nanoparticles (ENPs) enter the environment is through land application of waste water treatment plant (WWTP) sewage sludges. WWTP sludges, enriched with Ag and ZnO ENPs or their corresponding soluble metal salts during anaerobic digestion and subsequently mixed with soil (targeting a final concentration of 1400 and 140 mg/kg for Zn and Ag, respectively), were subjected to 6 months of ageing and leaching in lysimeter columns outdoors. Amounts of Zn and Ag leached were very low, accounting for <0.3% and <1.4% of the total Zn and Ag, respectively. No differences in total leaching rates were observed between treatments of Zn or Ag originally input to WWTP as ENP or salt forms. Phospholipid fatty acid profiling indicated a reduction in the fungal component of the soil microbial community upon metal exposure. However, overall, the leachate composition and response of the soil microbial community following addition of sewage sludge enriched either with ENPs or metal salts was very similar. - Highlights: • Adding nanoparticles (NPs) to influent of a WWTP provides a realistic exposure route. • ZnO and Ag NP and metal salt soil/sludges were aged 6 months in outdoor columns. • Amounts of Zn and Ag leached were very low in NP and metal salt treatments. • Both types of metal exposure reduced the fungal component of the soil microbial community. • Responses in NP and metal salt soil/sludges were very similar overall. - The fate and effects of ENPs are studied under realistic conditions: ENPs were added to the influent of a Waste Water Treatment Plant and the resulting sewage sludges mixed with soil in lysimeters.

In Situ Microbial Community Control of the Stability of Bio-reduced Uranium

International Nuclear Information System (INIS)

Baldwin, Brett R.; Peacock, Aaron D.; Resch, Charles T.; Arntzen, Evan; Smithgall, Amanda N.; Pfiffner, Susan; Gan, M.; McKinley, James P.; Long, Philip E.; White, David C.

2008-01-01

In aerobic aquifers typical of many Department of Energy (DOE) legacy waste sites, uranium is present in the oxidized U(VI) form which is more soluble and thus more mobile. Field experiments at the Old Rifle UMTRA site have demonstrated that biostimulation by electron donor addition (acetate) promotes biological U(VI) reduction (2). However, U(VI) reduction is reversible and oxidative dissolution of precipitated U(IV) after the cessation of electron donor addition remains a critical issue for the application of biostimulation as a treatment technology. Despite the potential for oxidative dissolution, field experiments at the Old Rifle site have shown that rapid reoxidation of bio-reduced uranium does not occur and U(VI) concentrations can remain at approximately 20% of background levels for more than one year. The extent of post-amendment U(VI) removal and the maintenance of bioreduced uranium may result from many factors including U(VI) sorption to iron-containing mineral phases, generation of H2S or FeS0.9, or the preferential sorption of U(VI) by microbial cells or biopolymers, but the processes controlling the reduction and in situ reoxidation rates are not known. To investigate the role of microbial community composition in the maintenance of bioreduced uranium, in-well sediment incubators (ISIs) were developed allowing field deployment of amended and native sediments during on-going experiments at the site. Field deployment of the ISIs allows expedient interrogation of microbial community response to field environmental perturbations and varying geochemical conditions.

In Situ Microbial Community Control of the Stability of Bio-reduced Uranium

Energy Technology Data Exchange (ETDEWEB)

Baldwin, Brett, R.; Peacock, Aaron, D.; Resch, Charles, T.; Arntzen, Evan; Smithgall, Amanda, N.; Pfiffner, Susan; Gan, M.; McKinley, James, P.; Long, Philip, E.; White, David, C.

2008-03-28

In aerobic aquifers typical of many Department of Energy (DOE) legacy waste sites, uranium is present in the oxidized U(VI) form which is more soluble and thus more mobile. Field experiments at the Old Rifle UMTRA site have demonstrated that biostimulation by electron donor addition (acetate) promotes biological U(VI) reduction (2). However, U(VI) reduction is reversible and oxidative dissolution of precipitated U(IV) after the cessation of electron donor addition remains a critical issue for the application of biostimulation as a treatment technology. Despite the potential for oxidative dissolution, field experiments at the Old Rifle site have shown that rapid reoxidation of bio-reduced uranium does not occur and U(VI) concentrations can remain at approximately 20% of background levels for more than one year. The extent of post-amendment U(VI) removal and the maintenance of bioreduced uranium may result from many factors including U(VI) sorption to iron-containing mineral phases, generation of H2S or FeS0.9, or the preferential sorption of U(VI) by microbial cells or biopolymers, but the processes controlling the reduction and in situ reoxidation rates are not known. To investigate the role of microbial community composition in the maintenance of bioreduced uranium, in-well sediment incubators (ISIs) were developed allowing field deployment of amended and native sediments during on-going experiments at the site. Field deployment of the ISIs allows expedient interrogation of microbial community response to field environmental perturbations and varying geochemical conditions.

Microbial corrosion of metallic materials in a deep nuclear-waste repository

Directory of Open Access Journals (Sweden)

Stoulil J.

2016-06-01

Full Text Available The study summarises current knowledge on microbial corrosion in a deep nuclear-waste repository. The first part evaluates the general impact of microbial activity on corrosion mechanisms. Especially, the impact of microbial metabolism on the environment and the impact of biofilms on the surface of structure materials were evaluated. The next part focuses on microbial corrosion in a deep nuclear-waste repository. The study aims to suggest the development of the repository environment and in that respect the viability of bacteria, depending on the probable conditions of the environment, such as humidity of bentonite, pressure in compact bentonite, the impact of ionizing radiation, etc. The last part is aimed at possible techniques for microbial corrosion mechanism monitoring in the conditions of a deep repository. Namely, electrochemical and microscopic techniques were discussed.

Reduced work function of graphene by metal adatoms

Energy Technology Data Exchange (ETDEWEB)

Legesse, Merid; Mellouhi, Fedwa El; Bentria, El Tayeb; Madjet, Mohamed E. [Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, Doha (Qatar); Fisher, Timothy S. [School of Mechanical Engineering and Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907 (United States); Kais, Sabre [Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, Doha (Qatar); Department of Chemistry and Physics, Purdue University, West Lafayette, IN 46323 (United States); College of Science and Engineering, Hamad Bin Khalifa University, Doha (Qatar); Alharbi, Fahhad H., E-mail: falharbi@qf.org.qa [Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, Doha (Qatar); College of Science and Engineering, Hamad Bin Khalifa University, Doha (Qatar)

2017-02-01

Highlights: • Using DFT, the maximum reduction of graphene workfunction is investigated. This is important for many applications. • The calculations show that the adatoms prefer to relax at hollow sites. • The transfer of electrons from the adatoms to graphene shifts up the Fermi level. So, graphene becomes metallic. • For those dopants that have been used experimentally, the calculations agree with the experimental data. • We found that 8% doping by Cs reduces the work function to 2.05 eV. - Abstract: In this paper, the work function of graphene doped by different metal adatoms and at different concentrations is investigated. Density functional theory is used to maximize the reduction of the work function. In general, the work function drops significantly before reaching saturation. For example in the case of Cs doping, the work function saturates at 2.05 eV with a modest 8% doping. The adsorption of different concentrations on metal adatoms on graphene is also studied. Our calculations show that the adatoms prefer to relax at hollow sites. The transfer of electron from metallic dopants to the graphene for all the studied systems shifts the Fermi energy levels above the Dirac-point and the doped graphenes become metallic. The value of Fermi energy shifts depends on the type of metallic dopants and its concentrations. A detail analysis of the electronic structure in terms of band structure and density of states, absorption energy, and charge transfer for each adatom-graphene system is presented.

Reduced work function of graphene by metal adatoms

International Nuclear Information System (INIS)

Legesse, Merid; Mellouhi, Fedwa El; Bentria, El Tayeb; Madjet, Mohamed E.; Fisher, Timothy S.; Kais, Sabre; Alharbi, Fahhad H.

2017-01-01

Highlights: • Using DFT, the maximum reduction of graphene workfunction is investigated. This is important for many applications. • The calculations show that the adatoms prefer to relax at hollow sites. • The transfer of electrons from the adatoms to graphene shifts up the Fermi level. So, graphene becomes metallic. • For those dopants that have been used experimentally, the calculations agree with the experimental data. • We found that 8% doping by Cs reduces the work function to 2.05 eV. - Abstract: In this paper, the work function of graphene doped by different metal adatoms and at different concentrations is investigated. Density functional theory is used to maximize the reduction of the work function. In general, the work function drops significantly before reaching saturation. For example in the case of Cs doping, the work function saturates at 2.05 eV with a modest 8% doping. The adsorption of different concentrations on metal adatoms on graphene is also studied. Our calculations show that the adatoms prefer to relax at hollow sites. The transfer of electron from metallic dopants to the graphene for all the studied systems shifts the Fermi energy levels above the Dirac-point and the doped graphenes become metallic. The value of Fermi energy shifts depends on the type of metallic dopants and its concentrations. A detail analysis of the electronic structure in terms of band structure and density of states, absorption energy, and charge transfer for each adatom-graphene system is presented.

A microbial biogeochemistry network for soil carbon and nitrogen cycling and methane flux: model structure and application to Asia

Science.gov (United States)

Xu, X.; Song, C.; Wang, Y.; Ricciuto, D. M.; Lipson, D.; Shi, X.; Zona, D.; Song, X.; Yuan, F.; Oechel, W. C.; Thornton, P. E.

2017-12-01

A microbial model is introduced for simulating microbial mechanisms controlling soil carbon and nitrogen biogeochemical cycling and methane fluxes. The model is built within the CN (carbon-nitrogen) framework of Community Land Model 4.5, named as CLM-Microbe to emphasize its explicit representation of microbial mechanisms to biogeochemistry. Based on the CLM4.5, three new pools were added: bacteria, fungi, and dissolved organic matter. It has 11 pools and 34 transitional processes, compared with 8 pools and 9 transitional flow in the CLM4.5. The dissolve organic carbon was linked with a new microbial functional group based methane module to explicitly simulate methane production, oxidation, transport and their microbial controls. Comparing with CLM4.5-CN, the CLM-Microbe model has a number of new features, (1) microbial control on carbon and nitrogen flows between soil carbon/nitrogen pools; (2) an implicit representation of microbial community structure as bacteria and fungi; (3) a microbial functional-group based methane module. The model sensitivity analysis suggests the importance of microbial carbon allocation parameters on soil biogeochemistry and microbial controls on methane dynamics. Preliminary simulations validate the model's capability for simulating carbon and nitrogen dynamics and methane at a number of sites across the globe. The regional application to Asia has verified the model in simulating microbial mechanisms in controlling methane dynamics at multiple scales.

Microbial Diversity in Sulfate-Reducing Marine Sediment Enrichment Cultures Associated with Anaerobic Biotransformation of Coastal Stockpiled Phosphogypsum (Sfax, Tunisia

Directory of Open Access Journals (Sweden)

Hana Zouch

2017-08-01

Full Text Available Anaerobic biotechnology using sulfate-reducing bacteria (SRB is a promising alternative for reducing long-term stockpiling of phosphogypsum (PG, an acidic (pH ~3 by-product of the phosphate fertilizer industries containing high amounts of sulfate. The main objective of this study was to evaluate, for the first time, the diversity and ability of anaerobic marine microorganisms to convert sulfate from PG into sulfide, in order to look for marine SRB of biotechnological interest. A series of sulfate-reducing enrichment cultures were performed using different electron donors (i.e., acetate, formate, or lactate and sulfate sources (i.e., sodium sulfate or PG as electron acceptors. Significant sulfide production was observed from enrichment cultures inoculated with marine sediments, collected near the effluent discharge point of a Tunisian fertilizer industry (Sfax, Tunisia. Sulfate sources impacted sulfide production rates from marine sediments as well as the diversity of SRB species belonging to Deltaproteobacteria. When PG was used as sulfate source, Desulfovibrio species dominated microbial communities of marine sediments, while Desulfobacter species were mainly detected using sodium sulfate. Sulfide production was also affected depending on the electron donor used, with the highest production obtained using formate. In contrast, low sulfide production (acetate-containing cultures was associated with an increase in the population of Firmicutes. These results suggested that marine Desulfovibrio species, to be further isolated, are potential candidates for bioremediation of PG by immobilizing metals and metalloids thanks to sulfide production by these SRB.

Modeling Logistic Performance in Quantitative Microbial Risk Assessment

NARCIS (Netherlands)

Rijgersberg, H.; Tromp, S.O.; Jacxsens, L.; Uyttendaele, M.

2010-01-01

In quantitative microbial risk assessment (QMRA), food safety in the food chain is modeled and simulated. In general, prevalences, concentrations, and numbers of microorganisms in media are investigated in the different steps from farm to fork. The underlying rates and conditions (such as storage

A dynamic mathematical model for microbial removal of pyritic sulfur from coal.

Science.gov (United States)

Kargi, F; Weissman, J G

1984-06-01

A dynamic mathematical model has been developed to describe microbial desulfurization of coal by Thiobacillus ferrooxidans. The model considers adsorption and desorption of cells on coal particles and microbial oxidation of pyritic sulfur on particle surfaces. The influence of certain parameters, such as microbial growth rate constants, adsorption-description constants, pulp density, coal particle size, initial cell and solid phase substrate concentration on the maximum rate of pyritic sulfur removal, have been elucidated. The maximum rate of pyritic sulfur removal was strongly dependent upon the number of attached cells per coal particle. At sufficiently high initial cell concentrations, the surfaces of coal particles are nearly saturated by the cells and the maximum leaching rate is limited either by total external surface area of coal particles or by the concentration of pyritic sulfur in the coal phase. The maximum volumetric rate of pyritic sulfur removal (mg S/h cm(3) mixture) increases with the pulp density of coal and reaches a saturation level at high pulp densities (e.g. 45%). The maximum rate also increases with decreasing particle diameter in a hyperbolic form. Increases in adsorption coefficient or decreases in the desorption coefficient also result in considerable improvements in this rate. The model can be applied to other systems consisting of suspended solid substrate particles in liquid medium with microbial oxidation occurring on the particle surfaces (e.g., bacterial ore leaching). The results obtained from this model are in good agreement with published experimental data on microbial desulfurization of coal and bacterial ore leaching.

X-ray spectroscopic studies of uranium transformations in microbial cultures

International Nuclear Information System (INIS)

Dodge, C.J.; Francis, A.J.; Clayton, C.R.

1995-01-01

Microbial transformations of uranyl nitrate, U:citric acid, and mixed metal U:Fe:citric acid complex were investigated. X-ray photoelectron spectroscopy (XPS) and X-ray absorption near edge structure (XANES) analyses showed that soluble U 6+ was reduced to insoluble U 4+ by Clostridium sp. and was associated with the bacterial surface, whereas U 3+ was observed within the biomass. Uranium forms a binuclear complex with citric acid involving two carboxylic acid groups and the hydroxyl group. Biodegradation studies of U:citric acid and U:Fe:citric acid complexes using Pseudomonas fluorescens showed they were recalcitrant. The lack of biodegradation was due to the nature of the metal-citrate complex species and not due to toxicity. Characterization of the mixed metal U:Fe:citric acid complex by extended X-ray absorption fine structure (EXAFS) indicated that Fe was associated with the U and citric acid, resulting in formation of a bionuclear mixed metal citrate complex

Treatment and electricity harvesting from sulfate/sulfide-containing wastewaters using microbial fuel cell with enriched sulfate-reducing mixed culture

International Nuclear Information System (INIS)

Lee, Duu-Jong; Lee, Chin-Yu; Chang, Jo-Shu

2012-01-01

Highlights: ► We started up microbial fuel cell (MFC) using enriched sulfate-reducing mixed culture. ► Sulfate-reducing bacteria and anode-respiring bacteria were enriched in anodic biofilms. ► The MFC effectively remove sulfate to elementary sulfur in the presence of lactate. ► The present device can treat sulfate laden wastewaters with electricity harvesting. - Abstract: Anaerobic treatment of sulfate-laden wastewaters can produce excess sulfide, which is corrosive to pipelines and is toxic to incorporated microorganisms. This work started up microbial fuel cell (MFC) using enriched sulfate-reducing mixed culture as anodic biofilms and applied the so yielded MFC for treating sulfate or sulfide-laden wastewaters. The sulfate-reducing bacteria in anodic biofilm effectively reduced sulfate to sulfide, which was then used by neighboring anode respiring bacteria (ARB) as electron donor for electricity production. The presence of organic carbons enhanced MFC performance since the biofilm ARB were mixotrophs that need organic carbon to grow. The present device introduces a route for treating sulfate laden wastewaters with electricity harvesting.

Treatment and electricity harvesting from sulfate/sulfide-containing wastewaters using microbial fuel cell with enriched sulfate-reducing mixed culture

Energy Technology Data Exchange (ETDEWEB)

Lee, Duu-Jong, E-mail: cedean@mail.ntust.edu.tw [Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan (China); Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan (China); Lee, Chin-Yu [Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan (China); Chang, Jo-Shu [Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan (China); Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan (China); Research Center for Energy Technology and Strategy, National Cheng Kung University, Tainan, Taiwan (China)

2012-12-15

Highlights: Black-Right-Pointing-Pointer We started up microbial fuel cell (MFC) using enriched sulfate-reducing mixed culture. Black-Right-Pointing-Pointer Sulfate-reducing bacteria and anode-respiring bacteria were enriched in anodic biofilms. Black-Right-Pointing-Pointer The MFC effectively remove sulfate to elementary sulfur in the presence of lactate. Black-Right-Pointing-Pointer The present device can treat sulfate laden wastewaters with electricity harvesting. - Abstract: Anaerobic treatment of sulfate-laden wastewaters can produce excess sulfide, which is corrosive to pipelines and is toxic to incorporated microorganisms. This work started up microbial fuel cell (MFC) using enriched sulfate-reducing mixed culture as anodic biofilms and applied the so yielded MFC for treating sulfate or sulfide-laden wastewaters. The sulfate-reducing bacteria in anodic biofilm effectively reduced sulfate to sulfide, which was then used by neighboring anode respiring bacteria (ARB) as electron donor for electricity production. The presence of organic carbons enhanced MFC performance since the biofilm ARB were mixotrophs that need organic carbon to grow. The present device introduces a route for treating sulfate laden wastewaters with electricity harvesting.

Microbial processes in radioactive waste disposal

International Nuclear Information System (INIS)

Pedersen, Karsten

2000-04-01

Independent scientific work has unambiguously demonstrated life to be present in most deep geological formations investigated, down to depths of several kilometres. Microbial processes have consequently become an integral part of the performance safety assessment of high-level radioactive waste (HLW) repositories. This report presents the research record from the last decade of the microbiology research programme of the Swedish Nuclear Fuel and Waste Management Company (SKB) and gives current perspectives of microbial processes in HLW disposal. The goal of the microbiology programme is to understand how microbes may interact with the performance of a future HLW repository. First, for those who are not so familiar with microbes and their ways of living, the concept of 'microbe' is briefly defined. Then, the main characteristics of recognised microbial assemblage and microbial growth, activity and survival are given. The main part of the report summarises data collected during the research period of 1987-1999 and interpretations of these data. Short summaries introduce the research tasks, followed by reviews of the results and insight gained. Sulphate-reducing bacteria (SRB) produce sulphide and have commonly been observed in groundwater environments typical of Swedish HLW repositories. Consequently, the potential for sulphide corrosion of the copper canisters surrounding the HLW must be considered. The interface between the copper canister and the buffer is of special concern. Despite the fact that nowhere are the environmental constraints for life as strong as here, it has been suggested that SRB could survive and locally produce sulphide in concentrations large enough to cause damage to the canister. Experiments conducted thus far have indicated the opposite. Early studies in the research programme revealed previously unknown microbial ecosystems in igneous rock aquifers at depths exceeding 1000 m. This discovery triggered a thorough exploration of the

Microbial processes in radioactive waste disposal

Energy Technology Data Exchange (ETDEWEB)

Pedersen, Karsten [Goeteborg Univ. (Sweden). Dept. of Cell and Molecular Biology, Microbiology

2000-04-15

Independent scientific work has unambiguously demonstrated life to be present in most deep geological formations investigated, down to depths of several kilometres. Microbial processes have consequently become an integral part of the performance safety assessment of high-level radioactive waste (HLW) repositories. This report presents the research record from the last decade of the microbiology research programme of the Swedish Nuclear Fuel and Waste Management Company (SKB) and gives current perspectives of microbial processes in HLW disposal. The goal of the microbiology programme is to understand how microbes may interact with the performance of a future HLW repository. First, for those who are not so familiar with microbes and their ways of living, the concept of 'microbe' is briefly defined. Then, the main characteristics of recognised microbial assemblage and microbial growth, activity and survival are given. The main part of the report summarises data collected during the research period of 1987-1999 and interpretations of these data. Short summaries introduce the research tasks, followed by reviews of the results and insight gained. Sulphate-reducing bacteria (SRB) produce sulphide and have commonly been observed in groundwater environments typical of Swedish HLW repositories. Consequently, the potential for sulphide corrosion of the copper canisters surrounding the HLW must be considered. The interface between the copper canister and the buffer is of special concern. Despite the fact that nowhere are the environmental constraints for life as strong as here, it has been suggested that SRB could survive and locally produce sulphide in concentrations large enough to cause damage to the canister. Experiments conducted thus far have indicated the opposite. Early studies in the research programme revealed previously unknown microbial ecosystems in igneous rock aquifers at depths exceeding 1000 m. This discovery triggered a thorough exploration of the

Microbial Biotransformation of a Polyphenol-Rich Potato Extract Affects Antioxidant Capacity in a Simulated Gastrointestinal Model

Directory of Open Access Journals (Sweden)

Joelle Khairallah

2018-03-01

Full Text Available A multistage human gastrointestinal model was used to digest a polyphenol-rich potato extract containing chlorogenic acid, caffeic acid, ferulic acid, and rutin as the primary polyphenols, to assess for their microbial biotransformation and to measure changes in antioxidant capacity in up to 24 h of digestion. The biotransformation of polyphenols was assessed by liquid chromatography–mass spectrometry. Antioxidant capacity was measured by the ferric reducing antioxidant power (FRAP assay. Among the colonic reactors, parent (polyphenols were detected in the ascending (AC, but not the transverse (TC or descending (DC colons. The most abundant microbial phenolic metabolites in all colonic reactors included derivatives of propionic acid, acetic acid, and benzoic acid. As compared to the baseline, an earlier increase in antioxidant capacity (T = 8 h was seen in the stomach and small intestine vessels as compared to the AC (T = 16 h and TC and DC (T = 24 h. The increase in antioxidant capacity observed in the DC and TC can be linked to the accumulation of microbial smaller-molecular-weight phenolic catabolites, as the parent polyphenolics had completely degraded in those vessels. The colonic microbial digestion of potato-based polyphenols could lead to improved colonic health, as this generates phenolic metabolites with significant antioxidant potential.

Remediation of soil co-contaminated with petroleum and heavy metals by the integration of electrokinetics and biostimulation.

Science.gov (United States)

Dong, Zhi-Yong; Huang, Wen-Hui; Xing, Ding-Feng; Zhang, Hong-Feng

2013-09-15

Successful remediation of soil co-contaminated with high levels of organics and heavy metals is a challenging task, because that metal pollutants in soil can partially or completely suppress normal heterotrophic microbial activity and thus hamper biodegradation of organics. In this study, the benefits of integrating electrokinetic (EK) remediation with biodegradation for decontaminating soil co-contaminated with crude oil and Pb were evaluated in laboratory-scale experiments lasting for 30 days. The treated soil contained 12,500 mg/kg of total petroleum hydrocarbons (TPH) and 450 mg/kg Pb. The amendments of EDTA and Tween 80, together with a regular refreshing of electrolyte showed the best performance to remediate this contaminated soil. An important function of EDTA-enhanced EK treatment was to eliminate heavy metal toxicity from the soil, thus activating microbial degradation of oil. Although Tween 80 reduced current, it could serve as a second substrate for enhancing microbial growth and biodegradation. It was found that oil biodegradation degree and microbial numbers increased toward the anode and cathode. Microbial metabolism was found to be beneficial to metal release from the soil matrix. Under the optimum conditions, the soil Pb and TPH removal percentages after 30 days of running reached 81.7% and 88.3%, respectively. After treatment, both the residual soil Pb and TPH concentrations met the requirement of the Chinese soil environmental quality standards. Copyright © 2013 Elsevier B.V. All rights reserved.

Decontamination of acid mine water from Ronneburg/Thueringen which is high in sulfates and metals using sulfate-reducing bacteria. Final report of the preliminary phase

International Nuclear Information System (INIS)

Hard, B.; Friedrich, S.

1995-01-01

The mining in Eastern Europe, particularly in East-Germany, is a major source of pollution to the surrounding areas of the mines. With the end of the cold war the demand for uranium has drastically declined. Many of the pits have therefore been closed down or are in the process of closure such as the uranium mine in Ronneburg in Thueringen. One major problem is the safe-making of the pits and dumps as they are highly radioactive through naturally occurring uranium and other radioactive elements. Because of the leaching process through bacteria, drainage water is very acidic, with pH-values between 1-2. The water is very rich in magnesium, iron and aluminium sulfate. Here the application of a microbial process to decontaminate acid mine drainage was investigated. Decontamination of the water includes: - Increase in pH - decrease in sulfate concentrations - minimization of the metal and radionuclide load. Sulfate-reducing bacteria seem suitable for this process. In order for such a microbial process to be economically viable a cheap and widely available electron donar has to be used eg. methanol. The work carried out reports on the isolation, characterization and physiology of sulfate-reducing methylotrophic bacteria and their suitability for a decontamination process of sulfuric acid uranium mine water. (orig.) [de

Microbial transformation of uranium in wastes

International Nuclear Information System (INIS)

Francis, A.J.; Dodge, C.J.; Gillow, J.B.; Cline, J.E.

1989-01-01

Contamination of soils, water, and sediments by radionuclides and toxic metals from the disposal of uranium processing wastes is a major national concern. Although much is known about the physico- chemical aspects of U, we have little information on the effects of aerobic and anaerobic microbial activities on the mobilization or immobilization of U and other toxic metals in mixed wastes. In order to understand the mechanisms of microbial transformations of uranium, we examined a contaminated pond sediment and a sludge sample from the uranium processing facility at Y-12 Plant, Oak Ridge, TN. The uranium concentration in the sediment and sludge samples was 923 and 3080 ug/g dry wt, respectively. In addition to U, the sediment and sludge samples contained high levels of toxic metals such as Cd, Cr, Cu, Hg, Pb, Ni, and Zn. The association of uranium with the various mineral fractions of the sediment and sludge was determined by selective chemical extraction techniques. Uranium was associated to varying degrees with the exchangeable carbonate, iron oxide, organic, and inert fractions in both samples. Initial results in samples amended with carbon and nitrogen indicate immobilization of U due to enhanced indigenous microbial activity under anaerobic conditions. 23 refs., 4 figs., 5 tabs

Development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium

International Nuclear Information System (INIS)

Teixeira, Catarina; Almeida, C. Marisa R.; Nunes da Silva, Marta; Bordalo, Adriano A.; Mucha, Ana P.

2014-01-01

Microbial assisted phytoremediation is a promising, though yet poorly explored, new remediation technique. The aim of this study was to develop autochthonous microbial consortia resistant to cadmium that could enhance phytoremediation of salt-marsh sediments contaminated with this metal. The microbial consortia were selectively enriched from rhizosediments colonized by Juncus maritimus and Phragmites australis. The obtained consortia presented similar microbial abundance but a fairly different community structure, showing that the microbial community was a function of the sediment from which the consortia were enriched. The effect of the bioaugmentation with the developed consortia on cadmium uptake, and the microbial community structure associated to the different sediments were assessed using a microcosm experiment. Our results showed that the addition of the cadmium resistant microbial consortia increased J. maritimus metal phytostabilization capacity. On the other hand, in P. australis, microbial consortia amendment promoted metal phytoextraction. The addition of the consortia did not alter the bacterial structure present in the sediments at the end of the experiments. This study provides new evidences that the development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium might be a simple, efficient, and environmental friendly remediation procedure. Capsule abstract: Development of autochthonous microbial consortia resistant to cadmium that enhanced phytoremediation by salt-marsh plants, without a long term effect on sediment bacterial diversity. - Highlights: • Cd resistant microbial consortia were developed and applied to salt-marsh sediments. • In Phragmites australis the consortia amendment promoted metal phytoextraction. • The consortia addition increased Juncus maritimus phytostabilization capacity. • No long term changes on the rhizosediment bacterial structure were observed

Development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium

Energy Technology Data Exchange (ETDEWEB)

Teixeira, Catarina [Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto (Portugal); Laboratório de Hidrobiologia e Ecologia, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto (Portugal); Almeida, C. Marisa R.; Nunes da Silva, Marta [Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto (Portugal); Bordalo, Adriano A. [Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto (Portugal); Laboratório de Hidrobiologia e Ecologia, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto (Portugal); Mucha, Ana P., E-mail: amucha@ciimar.up.pt [Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto (Portugal)

2014-09-15

Microbial assisted phytoremediation is a promising, though yet poorly explored, new remediation technique. The aim of this study was to develop autochthonous microbial consortia resistant to cadmium that could enhance phytoremediation of salt-marsh sediments contaminated with this metal. The microbial consortia were selectively enriched from rhizosediments colonized by Juncus maritimus and Phragmites australis. The obtained consortia presented similar microbial abundance but a fairly different community structure, showing that the microbial community was a function of the sediment from which the consortia were enriched. The effect of the bioaugmentation with the developed consortia on cadmium uptake, and the microbial community structure associated to the different sediments were assessed using a microcosm experiment. Our results showed that the addition of the cadmium resistant microbial consortia increased J. maritimus metal phytostabilization capacity. On the other hand, in P. australis, microbial consortia amendment promoted metal phytoextraction. The addition of the consortia did not alter the bacterial structure present in the sediments at the end of the experiments. This study provides new evidences that the development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium might be a simple, efficient, and environmental friendly remediation procedure. Capsule abstract: Development of autochthonous microbial consortia resistant to cadmium that enhanced phytoremediation by salt-marsh plants, without a long term effect on sediment bacterial diversity. - Highlights: • Cd resistant microbial consortia were developed and applied to salt-marsh sediments. • In Phragmites australis the consortia amendment promoted metal phytoextraction. • The consortia addition increased Juncus maritimus phytostabilization capacity. • No long term changes on the rhizosediment bacterial structure were observed.

Factors affecting microbial activity in compacted clay-based sealing materials proposed for use in a deep geologic repository for used nuclear fuel

International Nuclear Information System (INIS)

Stroes-Gascoyne, S.; Hamon, C.J.; Dixon, D.A.; Kjartanson, B.K.

2006-01-01

Microbial activity in clay-based barriers immediately adjacent to metal used-fuel containers in a repository could affect the longevity of such containers. The current emphasis is, therefore, on reducing or minimizing microbial activity in such clay-based barriers through material composition design. Factors affecting microbial activity in clay-based materials were studied in large-scale and smaller-scale experiments. Results suggested that keeping water activity (a w ) values below ∼0.95 may minimize microbial activity in clay-based barrier materials. A considerably higher effective montmorillonite dry density (EMDD), which partially controls a w , is achievable for 100% bentonite than for previously proposed reference buffer materials, which contain only 50% bentonite. (author)

The Application of Sulphate-Reducing Bacteria for the Heavy Metals Elimination from Acid Mine Drainage

Directory of Open Access Journals (Sweden)

Alena Luptáková

2004-12-01

Full Text Available One of the most important problems affecting mining companies around the world is the treatment of acid mine drainage (AMD. AMD is characterised by its high acidity, high concentration of metals (Cu, Zn, Cd,… and high concentration of dissolved sulphates. The techniques traditionally used for the treatment of AMD have been based on chemical methods of neutralization and precipitation. A possible alternative to the chemical treatment of AMD is bioremediation using anaerobic sulphate-reducing bacteria (SRB. The treatment of AMD by SRB is based on the ability of SRB to reduce sulphates to hydrogen sulphide, which binds readily with metals to form sparingly soluble precipitates. In this study we have attempted to investigate the feasibility of anaerobic biotreatment of the copper contaminated model solution and a real effluent AMD from the shaft Pech (the locality Smolnik using SRB. This method involves three stages: The H2S production by sulphate-reducing bacteria, the metals precipitation by the biologically produced H2S and the metal sulphides filtration. The studies confirm that copper was effectively recovered from the solution using bacterial produced H2S. An initial copper concentration 10 mg.l-1 was decreased to less than 0.05 mg.l-1 after 3 hours. The most adequate pH value for cooper precipitation was 2.5. Results of the copper precipitation from the areal effluent indicates that the optimal pH value for the copper precipitation is 3.5, but the created precipitates contain a mixture of copper and iron sulphides.

Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests

Science.gov (United States)

He, Yujie; Yang, Jinyan; Zhuang, Qianlai; Harden, Jennifer W.; McGuire, A. David; Liu, Yaling; Wang, Gangsheng; Gu, Lianhong

2015-01-01

Soil carbon dynamics of terrestrial ecosystems play a significant role in the global carbon cycle. Microbial-based decomposition models have seen much growth recently for quantifying this role, yet dormancy as a common strategy used by microorganisms has not usually been represented and tested in these models against field observations. Here we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of microbial dormancy at six temperate forest sites of different forest types. We then extrapolated the model to global temperate forest ecosystems to investigate biogeochemical controls on soil heterotrophic respiration and microbial dormancy dynamics at different temporal-spatial scales. The dormancy model consistently produced better match with field-observed heterotrophic soil CO2 efflux (RH) than the no dormancy model. Our regional modeling results further indicated that models with dormancy were able to produce more realistic magnitude of microbial biomass (analysis showed that soil organic carbon content was the dominating factor (correlation coefficient = 0.4–0.6) in the simulated spatial pattern of soil RHwith both models. In contrast to strong temporal and local controls of soil temperature and moisture on microbial dormancy, our modeling results showed that soil carbon-to-nitrogen ratio (C:N) was a major regulating factor at regional scales (correlation coefficient = −0.43 to −0.58), indicating scale-dependent biogeochemical controls on microbial dynamics. Our findings suggest that incorporating microbial dormancy could improve the realism of microbial-based decomposition models and enhance the integration of soil experiments and mechanistically based modeling.

Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation

Energy Technology Data Exchange (ETDEWEB)

Xu, M.; Wu, W.-M.; Wu, L.; He, Z.; Van Nostrand, J.D.; Deng, Y.; Luo, J.; Carley, J.; Ginder-Vogel, M.; Gentry, T.J.; Gu, B.; Watson, D.; Jardine, P.M.; Marsh, T.L.; Tiedje, J.M.; Hazen, T.C.; Criddle, C.S.; Zhou, J.

2010-02-15

A pilot-scale field test system with an inner loop nested within an outer loop was constructed for in situ U(VI) bioremediation at a US Department of Energy site, Oak Ridge, TN. The outer loop was used for hydrological protection of the inner loop where ethanol was injected for biostimulation of microorganisms for U(VI) reduction/immobilization. After 2 years of biostimulation with ethanol, U(VI) levels were reduced to below drinking water standard (<30 {micro}gl{sup -1}) in the inner loop monitoring wells. To elucidate the microbial community structure and functions under in situ uranium bioremediation conditions, we used a comprehensive functional gene array (GeoChip) to examine the microbial functional gene composition of the sediment samples collected from both inner and outer loop wells. Our study results showed that distinct microbial communities were established in the inner loop wells. Also, higher microbial functional gene number, diversity and abundance were observed in the inner loop wells than the outer loop wells. In addition, metal-reducing bacteria, such as Desulfovibrio, Geobacter, Anaeromyxobacter and Shewanella, and other bacteria, for example, Rhodopseudomonas and Pseudomonas, are highly abundant in the inner loop wells. Finally, the richness and abundance of microbial functional genes were highly correlated with the mean travel time of groundwater from the inner loop injection well, pH and sulfate concentration in groundwater. These results suggest that the indigenous microbial communities can be successfully stimulated for U bioremediation in the groundwater ecosystem, and their structure and performance can be manipulated or optimized by adjusting geochemical and hydrological conditions.

Genome-scale modelling of microbial metabolism with temporal and spatial resolution.

Science.gov (United States)

Henson, Michael A

2015-12-01

Most natural microbial systems have evolved to function in environments with temporal and spatial variations. A major limitation to understanding such complex systems is the lack of mathematical modelling frameworks that connect the genomes of individual species and temporal and spatial variations in the environment to system behaviour. The goal of this review is to introduce the emerging field of spatiotemporal metabolic modelling based on genome-scale reconstructions of microbial metabolism. The extension of flux balance analysis (FBA) to account for both temporal and spatial variations in the environment is termed spatiotemporal FBA (SFBA). Following a brief overview of FBA and its established dynamic extension, the SFBA problem is introduced and recent progress is described. Three case studies are reviewed to illustrate the current state-of-the-art and possible future research directions are outlined. The author posits that SFBA is the next frontier for microbial metabolic modelling and a rapid increase in methods development and system applications is anticipated. © 2015 Authors; published by Portland Press Limited.

Reductive immobilization of U(VI) in Fe(III) oxide-reducing subsurface sediments: Analysis of coupled microbial-geochemical processes in experimental reactive transport systems. Final Scientific/Technical Report-EMSP 73914

International Nuclear Information System (INIS)

Eric E. Roden Matilde M. Urrutia Mark O. Barnett Clifford R. Lange

2005-01-01

The purpose of this research was to provide information to DOE on microbiological and geochemical processes underlying the potential use of dissimilatory metal-reducing bacteria (DMRB) to create subsurface redox barriers for immobilization of uranium and other redox-sensitive metal/radionuclide contaminants that were released to the environment in large quantities during Cold War nuclear weapons manufacturing operations. Several fundamental scientific questions were addressed in order to understand and predict how such treatment procedures would function under in situ conditions in the subsurface. These questions revolved the coupled microbial-geochemical phenomena which are likely to occur within a redox barrier treatment zone, and on the dynamic interactions between hydrologic flux and biogeochemical process rates. First, we assembled a robust conceptual understanding and numerical framework for modeling the kinetics of microbial Fe(III) oxide reduction and associated DMRB growth in sediments. Development of this framework is a critical prerequisite for predicting the potential effectiveness of DMRB-promoted subsurface bioremediation, since Fe(III) oxides are expected to be the primary source of electron-accepting capacity for growth and maintenance of DMRB in subsurface environments. We also defined in detail the kinetics of microbial (enzymatic) versus abiotic, ferrous iron-promoted reduction of U(VI) in the presence and absence of synthetic and natural Fe(III) oxide materials. The results of these studies suggest that (i) the efficiency of dissolved U(VI) scavenging may be influenced by the kinetics of enzymatic U(VI) reduction in systems with relative short fluid residence times; (2) association of U(VI) with diverse surface sites in natural soils and sediments has the potential to limit the rate and extent of microbial U(VI) reduction, and in turn modulate the effectiveness of in situ U(VI) bioremediation; and (3) abiotic, ferrous iron (Fe(II)) drive n U

Interactions between plant and rhizosphere microbial communities in a metalliferous soil

International Nuclear Information System (INIS)

Epelde, Lur; Becerril, Jose M.; Barrutia, Oihana; Gonzalez-Oreja, Jose A.; Garbisu, Carlos

2010-01-01

In the present work, the relationships between plant consortia, consisting of 1-4 metallicolous pseudometallophytes with different metal-tolerance strategies (Thlaspi caerulescens: hyperaccumulator; Jasione montana: accumulator; Rumex acetosa: indicator; Festuca rubra: excluder), and their rhizosphere microbial communities were studied in a mine soil polluted with high levels of Cd, Pb and Zn. Physiological response and phytoremediation potential of the studied pseudometallophytes were also investigated. The studied metallicolous populations are tolerant to metal pollution and offer potential for the development of phytoextraction and phytostabilization technologies. T. caerulescens appears very tolerant to metal stress and most suitable for metal phytoextraction; the other three species enhance soil functionality. Soil microbial properties had a stronger effect on plant biomass rather than the other way around (35.2% versus 14.9%). An ecological understanding of how contaminants, ecosystem functions and biological communities interact in the long-term is needed for proper management of these fragile metalliferous ecosystems. - Rhizosphere microbial communities in highly polluted mine soils are determinant for the growth of pseudometallophytes.

Interactions between plant and rhizosphere microbial communities in a metalliferous soil

Energy Technology Data Exchange (ETDEWEB)

Epelde, Lur [NEIKER-Tecnalia, Department of Ecosystems, c/Berreaga 1, E-48160 Derio (Spain); Becerril, Jose M.; Barrutia, Oihana [Department of Plant Biology and Ecology, University of the Basque Country, UPV/EHU, P.O. Box 644, E-48080 Bilbao (Spain); Gonzalez-Oreja, Jose A. [NEIKER-Tecnalia, Department of Ecosystems, c/Berreaga 1, E-48160 Derio (Spain); Garbisu, Carlos, E-mail: cgarbisu@neiker.ne [NEIKER-Tecnalia, Department of Ecosystems, c/Berreaga 1, E-48160 Derio (Spain)

2010-05-15

In the present work, the relationships between plant consortia, consisting of 1-4 metallicolous pseudometallophytes with different metal-tolerance strategies (Thlaspi caerulescens: hyperaccumulator; Jasione montana: accumulator; Rumex acetosa: indicator; Festuca rubra: excluder), and their rhizosphere microbial communities were studied in a mine soil polluted with high levels of Cd, Pb and Zn. Physiological response and phytoremediation potential of the studied pseudometallophytes were also investigated. The studied metallicolous populations are tolerant to metal pollution and offer potential for the development of phytoextraction and phytostabilization technologies. T. caerulescens appears very tolerant to metal stress and most suitable for metal phytoextraction; the other three species enhance soil functionality. Soil microbial properties had a stronger effect on plant biomass rather than the other way around (35.2% versus 14.9%). An ecological understanding of how contaminants, ecosystem functions and biological communities interact in the long-term is needed for proper management of these fragile metalliferous ecosystems. - Rhizosphere microbial communities in highly polluted mine soils are determinant for the growth of pseudometallophytes.

Influence of platinum group metal-free catalyst synthesis on microbial fuel cell performance

Science.gov (United States)

Santoro, Carlo; Rojas-Carbonell, Santiago; Awais, Roxanne; Gokhale, Rohan; Kodali, Mounika; Serov, Alexey; Artyushkova, Kateryna; Atanassov, Plamen

2018-01-01

Platinum group metal-free (PGM-free) ORR catalysts from the Fe-N-C family were synthesized using sacrificial support method (SSM) technique. Six experimental steps were used during the synthesis: 1) mixing the precursor, the metal salt, and the silica template; 2) first pyrolysis in hydrogen rich atmosphere; 3) ball milling; 4) etching the silica template using harsh acids environment; 5) the second pyrolysis in ammonia rich atmosphere; 6) final ball milling. Three independent batches were fabricated following the same procedure. The effect of each synthetic parameters on the surface chemistry and the electrocatalytic performance in neutral media was studied. Rotating ring disk electrode (RRDE) experiment showed an increase in half wave potential and limiting current after the pyrolysis steps. The additional improvement was observed after etching and performing the second pyrolysis. A similar trend was seen in microbial fuel cells (MFCs), in which the power output increased from 167 ± 2 μW cm-2 to 214 ± 5 μW cm-2. X-ray Photoelectron Spectroscopy (XPS) was used to evaluate surface chemistry of catalysts obtained after each synthetic step. The changes in chemical composition were directly correlated with the improvements in performance. We report outstanding reproducibility in both composition and performance among the three different batches.

Effectiveness of stress release geometries on reducing residual stress in electroforming metal microstructure

Science.gov (United States)

Song, Chang; Du, Liqun; Zhao, Wenjun; Zhu, Heqing; Zhao, Wen; Wang, Weitai

2018-04-01

Micro electroforming, as a mature micromachining technology, is widely used to fabricate metal microdevices in micro electro mechanical systems (MEMS). However, large residual stress in the local positions of the micro electroforming layer often leads to non-uniform residual stress distributions, dimension accuracy defects and reliability issues during fabrication of the metal microdevice. To solve this problem, a novel design method of presetting stress release geometries in the topological structure of the metal microstructure is proposed in this paper. First, the effect of stress release geometries (circular shape, annular groove shape and rivet shape) on the residual stress in the metal microstructure was investigated by finite element modeling (FEM) analysis. Two evaluation parameters, stress concentration factor K T and stress non-uniformity factor δ were calculated. The simulation results show that presetting stress release geometries can effectively reduce and homogenize the residual stress in the metal microstructures were measured metal microstructure. By combined use with stress release geometries of annular groove shape and rivet shape, the stress concentration factor K T and the stress non-uniformity factor δ both decreased at a maximum of 49% and 53%, respectively. Meanwhile, the average residual stress σ avg decreased at a maximum of 20% from  -292.4 MPa to  -232.6 MPa. Then, micro electroforming experiments were carried out corresponding to the simulation models. The residual stresses in the metal microstructures were measured by micro Raman spectroscopy (MRS) method. The results of the experiment proved that the stress non-uniformity factor δ and the average residual stress σ avg also decreased at a maximum with the combination use of annular groove shape and rivet shape stress release geometries, which is in agreement with the results of FEM analysis. The stress non-uniformity factor δ has a maximum decrease of 49% and the

Microbial biosensors for environmental monitoring

Directory of Open Access Journals (Sweden)

David VOGRINC

2015-12-01

Full Text Available Microbial biosensors are analytical devices capable of sensing substances in the environment due to the specific biological reaction of the microorganism or its parts. Construction of a microbial biosensor requires knowledge of microbial response to the specific analyte. Linking this response with the quantitative data, using a transducer, is the crucial step in the construction of a biosensor. Regarding the transducer type, biosensors are divided into electrochemical, optical biosensors and microbial fuel cells. The use of the proper configuration depends on the selection of the biosensing element. With the use of transgenic E. coli strains, bioluminescence or fluorescence based biosensors were developed. Microbial fuel cells enable the use of the heterogeneous microbial populations, isolated from wastewater. Different microorganisms are used for different pollutants – pesticides, heavy metals, phenolic compounds, organic waste, etc. Biosensing enables measurement of their concentration and their toxic or genotoxic effects on the microbes. Increasing environmental awareness has contributed to the increase of interest for biomonitoring. Although technologies, such as bioinformatics and genetic engineering, allow us to design complex and efficient microbial biosensors for environmental pollutants, the transfer of the laboratory work to the field still remains a problem to solve.

Modelling gas generation in radioactive waste repositories

International Nuclear Information System (INIS)

Agg, P.J.

1993-02-01

In a repository containing low- and intermediate-level waste, gas generation will occur principally by the coupled processes of metal corrosion and microbial degradation of cellulosic waste. This Paper describes a mathematical model design to address gas generation by these mechanisms. The metal corrosion model incorporates a three-stage process encompassing both aerobic and anaerobic corrosion regimes; the microbial degradation model simulates the activities of eight different microbial populations, which are maintained as functions both of pH and of the concentrations of particular chemical species. Gas concentrations have been measured over a period of three years in large-scale drum experiments designed to simulate repository conditions. Model predictions are confirmed against the experimental measurements, and a prediction is then made of gas concentrations and generation rates over an assessment period of one million years in a radioactive waste repository. (author)

Modelling gas generation in radioactive waste repositories

International Nuclear Information System (INIS)

Agg, P.J.

1992-07-01

In a repository containing low- and intermediate-level waste, gas generation will occur principally by the coupled processes of metal corrosion and microbial degradation of cellulosic waste. This paper describes a mathematical model designed to address gas generation by these mechanisms. The metal corrosion model incorporates a three-stage process encompassing both aerobic and anaerobic corrosion regimes; the microbial degradation model simulates the activities of eight different microbial populations, which are maintained as functions both of pH and of the concentrations of particular chemical species. Gas concentrations have been measured over a period of three years in large-scale drum experiments designed to simulate repository conditions. Model predictions are confirmed against the experimental measurements, and a prediction is then made of gas concentrations and generation rates over an assessment period of one million years in a radioactive waste repository. (Author)

Antibiotic Resistance Genes and Correlations with Microbial Community and Metal Resistance Genes in Full-Scale Biogas Reactors As Revealed by Metagenomic Analysis

DEFF Research Database (Denmark)

Luo, Gang; Li, Bing; Li, Li-Guan

2017-01-01

resistance genes (MRGs). The total abundance of ARGs in all the samples varied from 7 × 10-3 to 1.08 × 10-1 copy of ARG/copy of 16S-rRNA gene, and the samples obtained from thermophilic biogas reactors had a lower total abundance of ARGs, indicating the superiority of thermophilic anaerobic digestion......Digested residues from biogas plants are often used as biofertilizers for agricultural crops cultivation. The antibiotic resistance genes (ARGs) in digested residues pose a high risk to public health due to their potential spread to the disease-causing microorganisms and thus reduce...... the susceptibility of disease-causing microorganisms to antibiotics in medical treatment. A high-throughput sequencing (HTS)-based metagenomic approach was used in the present study to investigate the variations of ARGs in full-scale biogas reactors and the correlations of ARGs with microbial communities and metal...

Constraint-based modeling in microbial food biotechnology

Science.gov (United States)

Rau, Martin H.

2018-01-01

Genome-scale metabolic network reconstruction offers a means to leverage the value of the exponentially growing genomics data and integrate it with other biological knowledge in a structured format. Constraint-based modeling (CBM) enables both the qualitative and quantitative analyses of the reconstructed networks. The rapid advancements in these areas can benefit both the industrial production of microbial food cultures and their application in food processing. CBM provides several avenues for improving our mechanistic understanding of physiology and genotype–phenotype relationships. This is essential for the rational improvement of industrial strains, which can further be facilitated through various model-guided strain design approaches. CBM of microbial communities offers a valuable tool for the rational design of defined food cultures, where it can catalyze hypothesis generation and provide unintuitive rationales for the development of enhanced community phenotypes and, consequently, novel or improved food products. In the industrial-scale production of microorganisms for food cultures, CBM may enable a knowledge-driven bioprocess optimization by rationally identifying strategies for growth and stability improvement. Through these applications, we believe that CBM can become a powerful tool for guiding the areas of strain development, culture development and process optimization in the production of food cultures. Nevertheless, in order to make the correct choice of the modeling framework for a particular application and to interpret model predictions in a biologically meaningful manner, one should be aware of the current limitations of CBM. PMID:29588387

Drosophila melanogaster Models of Metal-Related Human Diseases and Metal Toxicity.

Science.gov (United States)

Calap-Quintana, Pablo; González-Fernández, Javier; Sebastiá-Ortega, Noelia; Llorens, José Vicente; Moltó, María Dolores

2017-07-06

Iron, copper and zinc are transition metals essential for life because they are required in a multitude of biological processes. Organisms have evolved to acquire metals from nutrition and to maintain adequate levels of each metal to avoid damaging effects associated with its deficiency, excess or misplacement. Interestingly, the main components of metal homeostatic pathways are conserved, with many orthologues of the human metal-related genes having been identified and characterized in Drosophila melanogaster . Drosophila has gained appreciation as a useful model for studying human diseases, including those caused by mutations in pathways controlling cellular metal homeostasis. Flies have many advantages in the laboratory, such as a short life cycle, easy handling and inexpensive maintenance. Furthermore, they can be raised in a large number. In addition, flies are greatly appreciated because they offer a considerable number of genetic tools to address some of the unresolved questions concerning disease pathology, which in turn could contribute to our understanding of the metal metabolism and homeostasis. This review recapitulates the metabolism of the principal transition metals, namely iron, zinc and copper, in Drosophila and the utility of this organism as an experimental model to explore the role of metal dyshomeostasis in different human diseases. Finally, a summary of the contribution of Drosophila as a model for testing metal toxicity is provided.

Microbial Energy Conversion

Energy Technology Data Exchange (ETDEWEB)

Buckley, Merry [American Society for Microbiology (ASM), Washington, DC (United States); Wall, Judy D. [Univ. of Missouri, Columbia, MO (United States)

2006-10-01

The American Academy of Microbiology convened a colloquium March 10-12, 2006, in San Francisco, California, to discuss the production of energy fuels by microbial conversions. The status of research into various microbial energy technologies, the advantages and disadvantages of each of these approaches, research needs in the field, and education and training issues were examined, with the goal of identifying routes for producing biofuels that would both decrease the need for fossil fuels and reduce greenhouse gas emissions. Currently, the choices for providing energy are limited. Policy makers and the research community must begin to pursue a broader array of potential energy technologies. A diverse energy portfolio that includes an assortment of microbial energy choices will allow communities and consumers to select the best energy solution for their own particular needs. Funding agencies and governments alike need to prepare for future energy needs by investing both in the microbial energy technologies that work today and in the untested technologies that will serve the world’s needs tomorrow. More mature bioprocesses, such as ethanol production from starchy materials and methane from waste digestors, will find applications in the short term. However, innovative techniques for liquid fuel or biohydrogen production are among the longer term possibilities that should also be vigorously explored, starting now. Microorganisms can help meet human energy needs in any of a number of ways. In their most obvious role in energy conversion, microorganisms can generate fuels, including ethanol, hydrogen, methane, lipids, and butanol, which can be burned to produce energy. Alternatively, bacteria can be put to use in microbial fuel cells, where they carry out the direct conversion of biomass into electricity. Microorganisms may also be used some day to make oil and natural gas technologies more efficient by sequestering carbon or by assisting in the recovery of oil and

Synthesis and Antibacterial Activity of Metal(loid Nanostructures by Environmental Multi-Metal(loid Resistant Bacteria and Metal(loid-Reducing Flavoproteins

Directory of Open Access Journals (Sweden)

Maximiliano Figueroa

2018-05-01

Full Text Available Microbes are suitable candidates to recover and decontaminate different environments from soluble metal ions, either via reduction or precipitation to generate insoluble, non-toxic derivatives. In general, microorganisms reduce toxic metal ions generating nanostructures (NS, which display great applicability in biotechnological processes. Since the molecular bases of bacterial reduction are still unknown, the search for new -environmentally safe and less expensive- methods to synthesize NS have made biological systems attractive candidates. Here, 47 microorganisms isolated from a number of environmental samples were analyzed for their tolerance or sensitivity to 19 metal(loids. Ten of them were highly tolerant to some of them and were assessed for their ability to reduce these toxicants in vitro. All isolates were analyzed by 16S rRNA gene sequencing, fatty acids composition, biochemical tests and electron microscopy. Results showed that they belong to the Enterobacter, Staphylococcus, Acinetobacter, and Exiguobacterium genera. Most strains displayed metal(loid-reducing activity using either NADH or NADPH as cofactor. While Acinetobacter schindleri showed the highest tellurite (TeO32- and tetrachloro aurate (AuCl4- reducing activity, Staphylococcus sciuri and Exiguobacterium acetylicum exhibited selenite (SeO32- and silver (Ag+ reducing activity, respectively. Based on these results, we used these bacteria to synthetize, in vivo and in vitro Te, Se, Au, and Ag-containing nanostructures. On the other hand, we also used purified E. cloacae glutathione reductase to synthesize in vitro Te-, Ag-, and Se-containing NS, whose morphology, size, composition, and chemical composition were evaluated. Finally, we assessed the putative anti-bacterial activity exhibited by the in vitro synthesized NS: Te-containing NS were more effective than Au-NS in inhibiting Escherichia coli and Listeria monocytogenes growth. Aerobically synthesized TeNS using MF09 crude

MICROBIAL REMOVAL OF HEAVY METALS FROM WASTEWATER

Directory of Open Access Journals (Sweden)

Justyna Koc-Jurczyk

2014-10-01

Full Text Available Industrialization and urbanization result in increase of heavy metals released into the environment (soil, lakes, rivers, seas, oceans, groundwater. Studies on biosorption of heavy metals are aimed to specify types of microorganisms which could efficiently bind metals. This approach has a very important significance for both slowing down metals exploitation by recovery, and also reduction of environmental pollution by decrease of their excessive concentration. Recent studies have reported about the capabilities of fungi, algae, yeasts, bacteria, waste and agricultural residues or materials containing chitosan derived from crustacean shells as a biosorbents. Biohydrometallurgy could be considered as a new “green” technology of heavy metals removal from wastewater.

Modelling chelate-Induced phytoextraction: functional models predicting bioavailability of metals in soil, metal uptake and shoot biomass

Directory of Open Access Journals (Sweden)

Pasqualina Sacco

2006-06-01

Full Text Available Chelate-induced phytoextraction of heavy metals from contaminated soils requires special care to determine, a priori, the best method of chelate application, in terms of both dose and timing. In fact, the chelate dose must assure the bioavailability of the metal to the plant without increasing leaching risk and giving toxic effects. Three mathematical models are here proposed for usefully interpreting the processes taking place: a increased soil bioavailability of metals by chelants; b metal uptake by plants; c variation in plant biomass. The models are implemented and validated using data from pot and lysimeter trials. Both the chelate dose and the time elapsed since its application affected metal bioavailability and plant response. Contrariwise, the distribution strategy (single vs. split application seems to produce significant differences both in plant growth and metal uptake, but not in soil metal bioavailability. The proposed models may help to understand and predict the chelate dose – effect relationship with less experimental work.

Modelling chelate-Induced phytoextraction: functional models predicting bioavailability of metals in soil, metal uptake and shoot biomass

Directory of Open Access Journals (Sweden)

Pasqualina Sacco

Full Text Available Chelate-induced phytoextraction of heavy metals from contaminated soils requires special care to determine, a priori, the best method of chelate application, in terms of both dose and timing. In fact, the chelate dose must assure the bioavailability of the metal to the plant without increasing leaching risk and giving toxic effects. Three mathematical models are here proposed for usefully interpreting the processes taking place: a increased soil bioavailability of metals by chelants; b metal uptake by plants; c variation in plant biomass. The models are implemented and validated using data from pot and lysimeter trials. Both the chelate dose and the time elapsed since its application affected metal bioavailability and plant response. Contrariwise, the distribution strategy (single vs. split application seems to produce significant differences both in plant growth and metal uptake, but not in soil metal bioavailability. The proposed models may help to understand and predict the chelate dose – effect relationship with less experimental work.

Effects of copper particles on a model septic system's function and microbial community.

Science.gov (United States)

Taylor, Alicia A; Walker, Sharon L

2016-03-15

There is concern surrounding the addition of nanoparticles into consumer products due to toxicity potential and the increased risk of human and environmental exposures to these particles. Copper nanoparticles are found in many common consumer goods; therefore, the disposal and subsequent interactions between potentially toxic Cu-based nanoparticles and microbial communities may have detrimental impacts on wastewater treatment processes. This study investigates the effects of three copper particles (micron- and nano-scale Cu particles, and a nano-scale Cu(OH)2-based fungicide) on the function and operation of a model septic tank. Septic system analyses included water quality evaluations and microbial community characterizations to detect changes in and relationships between the septic tank function and microbial community phenotype/genotype. As would be expected for optimal wastewater treatment, biological oxygen demand (BOD5) was reduced by at least 63% during nano-scale Cu exposure, indicating normal function. pH was reduced to below the optimum anaerobic fermentation range during the micro Cu exposure, suggesting incomplete degradation of organic waste may have occurred. The copper fungicide, Cu(OH)2, caused a 57% increase in total organic carbon (TOC), which is well above the typical range for septic systems and also corresponded to increased BOD5 during the majority of the Cu(OH)2 exposure. The changes in TOC and BOD5 demonstrate that the system was improperly treating waste. Overall, results imply individual exposures to the three Cu particles caused distinct disruptions in septic tank function. However, it was observed that the system was able to recover to typical operating conditions after three weeks post-exposure. These results imply that during periods of Cu introduction, there are likely pulses of improper removal of total organic carbon and significant changes in pH not in the optimal range for the system. Copyright © 2016 Elsevier Ltd. All rights

Sulfate Reduction Remediation of a Metals Plume Through Organic Injection

International Nuclear Information System (INIS)

Phifer, M.A.

2003-01-01

Laboratory testing and a field-scale demonstration for the sulfate reduction remediation of an acidic/metals/sulfate groundwater plume at the Savannah River Site has been conducted. The laboratory testing consisted of the use of anaerobic microcosms to test the viability of three organic substrates to promote microbially mediated sulfate reduction. Based upon the laboratory testing, soybean oil and sodium lactate were selected for injection during the subsequent field-scale demonstration. The field-scale demonstration is currently ongoing. Approximately 825 gallons (3,123 L) of soybean oil and 225 gallons (852 L) of 60 percent sodium lactate have been injected into an existing well system within the plume. Since the injections, sulfate concentrations in the injection zone have significantly decreased, sulfate-reducing bacteria concentrations have significantly increased, the pH has increased, the Eh has decreased, and the concentrations of many metals have decreased. Microbially mediated sulfate reduction has been successfully promoted for the remediation of the acidic/metals/sulfate plume by the injection of soybean oil and sodium lactate within the plume

Microbial processes in coastal pollution

International Nuclear Information System (INIS)

Capone, D.G.; Bauer, J.E.

1992-01-01

In this chapter, the authors describe the nature and range of some of the interactions that can occur between the microbiota and environmental contaminants in coastal areas. The implications of such interactions are also discussed. Pollutant types include inorganic nutrients, heavy metals, bulk organics, organic contaminants, pathogenic microorganisms and microbial pollutants. Both the effects of pollutants such as petroleum hydrocarbons on natural microbial populations and the mitigation of contaminant effects by complexation and biodegradation are considered. Finally, several areas of emerging concerns are presented that involve a confluence of biogeochemistry, microbial ecology and applied and public health microbiology. These concerns range in relevance from local/regional to oceanic/global scales. 308 ref

Selenite reduction by anaerobic microbial aggregates: Microbial community structure, and proteins associated to the produced selenium spheres.

Directory of Open Access Journals (Sweden)

Graciela eGonzalez-Gil

2016-04-01

Full Text Available Certain types of anaerobic granular sludge, which consists of microbial aggregates, can reduce selenium oxyanions. To envisage strategies for removing those oxyanions from wastewater and recovering the produced elemental selenium (Se0, insights into the microbial community structure and synthesis of Se0 within these microbial aggregates are required. High-throughput sequencing showed that Veillonellaceae (c.a. 20 % and Pseudomonadaceae (c.a.10 % were the most abundant microbial phylotypes in selenite reducing microbial aggregates. The majority of the Pseudomonadaceae sequences were affiliated to the genus Pseudomonas. A distinct outer layer (~200 m of selenium deposits indicated that bioreduction occurred in the outer zone of the microbial aggregates. In that outer layer, SEM analysis showed abundant intracellular and extracellular Se0 (nano spheres, with some cells having high numbers of intracellular Se0 spheres. Electron tomography showed that microbial cells can harbor a single large intracellular sphere that stretches the cell body. The Se0 spheres produced by the microorganisms were capped with organic material. X-ray photoelectron spectroscopy (XPS analysis of extracted Se0 spheres, combined with a mathematical approach to analyzing XPS spectra from biological origin, indicated that proteins and lipids were components of the capping material associated to the Se0 spheres. The most abundant proteins associated to the spheres were identified by proteomic analysis. Most of the proteins or peptide sequences capping the Se0 spheres were identified as periplasmic outer membrane porins and as the cytoplasmic elongation factor Tu protein, suggesting an intracellular formation of the Se0 spheres. In view of these and previous findings, a schematic model for the synthesis of Se0 spheres by the microorganisms inhabiting the granular sludge is proposed.

Selenite Reduction by Anaerobic Microbial Aggregates: Microbial Community Structure, and Proteins Associated to the Produced Selenium Spheres

KAUST Repository

Gonzalez-Gil, Graciela

2016-04-26

Certain types of anaerobic granular sludge, which consists of microbial aggregates, can reduce selenium oxyanions. To envisage strategies for removing those oxyanions from wastewater and recovering the produced elemental selenium (Se0), insights into the microbial community structure and synthesis of Se0 within these microbial aggregates are required. High-throughput sequencing showed that Veillonellaceae (c.a. 20%) and Pseudomonadaceae (c.a.10%) were the most abundant microbial phylotypes in selenite reducing microbial aggregates. The majority of the Pseudomonadaceae sequences were affiliated to the genus Pseudomonas. A distinct outer layer (∼200 μm) of selenium deposits indicated that bioreduction occurred in the outer zone of the microbial aggregates. In that outer layer, SEM analysis showed abundant intracellular and extracellular Se0 (nano)spheres, with some cells having high numbers of intracellular Se0 spheres. Electron tomography showed that microbial cells can harbor a single large intracellular sphere that stretches the cell body. The Se0 spheres produced by the microorganisms were capped with organic material. X-ray photoelectron spectroscopy (XPS) analysis of extracted Se0 spheres, combined with a mathematical approach to analyzing XPS spectra from biological origin, indicated that proteins and lipids were components of the capping material associated to the Se0 spheres. The most abundant proteins associated to the spheres were identified by proteomic analysis. Most of the proteins or peptide sequences capping the Se0 spheres were identified as periplasmic outer membrane porins and as the cytoplasmic elongation factor Tu protein, suggesting an intracellular formation of the Se0 spheres. In view of these and previous findings, a schematic model for the synthesis of Se0 spheres by the microorganisms inhabiting the granular sludge is proposed.

Metal recovery by microbial electro-metallurgy

NARCIS (Netherlands)

Dominguez-Benetton, Xochitl; Varia, Jeet Chandrakant; Pozo, Guillermo; Modin, Oskar; Heijne, Ter Annemiek; Fransaer, Jan; Rabaey, Korneel

2018-01-01

Raw metals are fundamental to the global economy as they are essential to maintain the quality of our life as well as industrial performance. A number of metal-bearing aqueous matrices are appealing as alternative supplies to conventional mining, like solid industrial and urban waste leachates,

Development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium.

Science.gov (United States)

Teixeira, Catarina; Almeida, C Marisa R; Nunes da Silva, Marta; Bordalo, Adriano A; Mucha, Ana P

2014-09-15

Microbial assisted phytoremediation is a promising, though yet poorly explored, new remediation technique. The aim of this study was to develop autochthonous microbial consortia resistant to cadmium that could enhance phytoremediation of salt-marsh sediments contaminated with this metal. The microbial consortia were selectively enriched from rhizosediments colonized by Juncus maritimus and Phragmites australis. The obtained consortia presented similar microbial abundance but a fairly different community structure, showing that the microbial community was a function of the sediment from which the consortia were enriched. The effect of the bioaugmentation with the developed consortia on cadmium uptake, and the microbial community structure associated to the different sediments were assessed using a microcosm experiment. Our results showed that the addition of the cadmium resistant microbial consortia increased J. maritimus metal phytostabilization capacity. On the other hand, in P. australis, microbial consortia amendment promoted metal phytoextraction. The addition of the consortia did not alter the bacterial structure present in the sediments at the end of the experiments. This study provides new evidences that the development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium might be a simple, efficient, and environmental friendly remediation procedure. Development of autochthonous microbial consortia resistant to cadmium that enhanced phytoremediation by salt-marsh plants, without a long term effect on sediment bacterial diversity. Copyright © 2014 Elsevier B.V. All rights reserved.

Reducing the leachability of nitrate, phosphorus and heavy metals from soil using waste material

Directory of Open Access Journals (Sweden)

Faridullah

Full Text Available Abstract Contaminants like nitrate (NO3, phosphorus (P and heavy metals in water are often associated with agricultural activities. Various soil and water remediation techniques have been employed to reduce the risk associated with these contaminants. A study was conducted to examine the extent of leaching of heavy metals (Cd, Ni, Pb and Cr, NO3 and P. For this purpose sandy and silt loam soils were amended with different waste materials, namely wood ash, solid waste ash, vegetable waste, charcoal, and sawdust. The soils were saturated with wastewater. Irrespective of the waste applied, the pH and EC of the amended soils were found to be greater than the control. Charcoal, sawdust and wood ash significantly decreased heavy metals, nitrate and phosphorus concentrations in the leachate. Treatments were more efficient for reducing Ni than other heavy metals concentrations. Waste amendments differed for heavy metals during the process of leaching. Heavy metals in the soil were progressively depleted due to the successive leaching stages. This research suggests that waste material may act as an adsorbent for the above contaminants and can reduce their leachability in soils.

Chlorhexidine-releasing implant coating on intramedullary nail reduces infection in a rat model

Directory of Open Access Journals (Sweden)

SM Shiels

2018-03-01

Full Text Available The use of internal intramedullary nails for long bone fracture fixation is a common practice among surgeons. Bacteria naturally attach to these devices, increasing the risk for wound infection, which can result in non- or malunion, additional surgical procedures and extended hospital stays. Intramedullary nail surface properties can be modified to reduce bacterial colonisation and potentially infectious complications. In the current study, a coating combining a non-fouling property with leaching chlorhexidine for orthopaedic implantation was tested. Coating stability and chlorhexidine release were evaluated in vitro. Using a rat model of intramedullary fixation and infection, the effect of the coating on microbial colonisation and fracture healing was evaluated in vivo by quantitative microbiology, micro-computed tomography, plain radiography, three-point bending and/or histology. Low dose systemic cefazolin was administered to increase the similarities to clinical practice, without overshadowing the effect of the anti-infective coating. When introduced into a contaminated wound, the non-fouling chlorhexidine-coated implant reduced the overall bacteria colonisation within the bone and on the implant, reduced the osteolysis and increased the radiographic union, confirming its potential for reducing complications in wounds at high risk of infection. However, when implanted into a sterile wound, non-union increased. Further studies are required to best optimise the anti-microbial effectiveness, while not sacrificing fracture union.

Microbial processes relevant for the long-term performance of radioactive waste repositories in clays

International Nuclear Information System (INIS)

Meleshyn, Artur

2012-01-01

Document available in extended abstract form only. A number of investigations on occurrence and viability of microbes in compacted clays have been aimed at studying possible microbial effects on long-term performance of a deep geological repository (DGR) for high-level radioactive waste (HLW) and spent nuclear fuel (SF). Compacted clays are considered in current DGR designs either as a buffer material or as a host rock. The primary purpose of the present work was to qualitatively evaluate the relevance of microbial activity for the long-term performance of a DGR and to identify which safety-relevant processes and properties can be potentially influenced by this activity. The present analysis identified eight clay properties essential for maintaining safety functions of containment and retardation of the disposal system - swelling pressure, specific surface area, cation exchange capacity, anion sorption capacity, porosity, permeability, fluid pressure, plasticity - which can potentially be influenced by microbial processes in clay buffer and Clay-stone within a DGR for HLW/SF. Iron(III)- and sulphate-reducing, fermentative, methane-producing and oxidizing microbes can be considered to be present in any clay formation. Each habitat includes a massive number of microbial niches with perhaps only a small proportion of the species being metabolically active at the habitat's conditions, the remainder becoming not extinct. Moreover, clays contain electron donors and electron acceptors in amounts sufficient for these microbes to remain active during very long periods of time. Additional sources of electron donors or electron acceptors will inevitably be added to the repository system as a result of DGR excavation, placement of radioactive waste as well as backfilling and sealing of the DGR. In no case should the potential impact of microbes be underestimated based on a possible argument of comparably low biomass of the microbes in contact with metal surfaces or dissolved

Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests

Energy Technology Data Exchange (ETDEWEB)

He, Yujie [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Yang, Jinyan [Univ. of Georgia, Athens, GA (United States). Warnell School of Forestry and Natural Resources; Northeast Forestry Univ., Harbin (China). Center for Ecological Research; Zhuang, Qianlai [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Purdue Univ., West Lafayette, IN (United States). Dept. of Agronomy; Harden, Jennifer W. [U.S. Geological Survey, Menlo Park, CA (United States); McGuire, Anthony D. [Alaska Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, Univ. of Alaska, Fairbanks, AK (United States). U.S. Geological Survey, Alaska Cooperative Fish and Wildlife Research Unit; Liu, Yaling [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Wang, Gangsheng [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Climate Change Science Inst. and Environmental Sciences Division; Gu, Lianhong [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division

2015-11-20

Soil carbon dynamics of terrestrial ecosystems play a significant role in the global carbon cycle. Microbial-based decomposition models have seen much growth recently for quantifying this role, yet dormancy as a common strategy used by microorganisms has not usually been represented and tested in these models against field observations. Here in this study we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of microbial dormancy at six temperate forest sites of different forest types. We then extrapolated the model to global temperate forest ecosystems to investigate biogeochemical controls on soil heterotrophic respiration and microbial dormancy dynamics at different temporal-spatial scales. The dormancy model consistently produced better match with field-observed heterotrophic soil CO₂ efflux (R_H) than the no dormancy model. Our regional modeling results further indicated that models with dormancy were able to produce more realistic magnitude of microbial biomass (<2% of soil organic carbon) and soil R_H (7.5 ± 2.4 PgCyr^-1). Spatial correlation analysis showed that soil organic carbon content was the dominating factor (correlation coefficient = 0.4-0.6) in the simulated spatial pattern of soil R_H with both models. In contrast to strong temporal and local controls of soil temperature and moisture on microbial dormancy, our modeling results showed that soil carbon-to-nitrogen ratio (C:N) was a major regulating factor at regional scales (correlation coefficient = -0.43 to -0.58), indicating scale-dependent biogeochemical controls on microbial dynamics. Our findings suggest that incorporating microbial dormancy could improve the realism of microbial-based decomposition models and enhance the integration of soil experiments and mechanistically based modeling.

Microbial removal of Fe(III) impurities from clay using dissimilatory iron reducers.

Science.gov (United States)

Lee, E Y; Cho, K S; Ryu, H W; Chang, Y K

1999-01-01

Fe(III) impurities, which detract refractoriness and whiteness from porcelain and pottery, could be biologically removed from low-quality clay by indigenous dissimilatory Fe(III)-reducing microorganisms. Insoluble Fe(III) in clay particles was leached out as soluble Fe(II), and the Fe(III) reduction reaction was coupled to the oxidation of sugars such as glucose, maltose and sucrose. A maximum removal of 44-45% was obtained when the relative amount of sugar was 5% (w/w; sugar/clay). By the microbial treatment, the whiteness of the clay was increased from 63.20 to 79.64, whereas the redness was clearly decreased from 13.47 to 3.55.

A preliminary assessment of the chemical and microbial water ...

African Journals Online (AJOL)

A preliminary assessment of the chemical and microbial water quality of the Chunies River - Limpopo: short communication. ... For this purpose sampling was undertaken on 25 and 26 May 2002, and a range of chemical (macro-elements, micro-elements and heavy metals) and microbial variables (HPC, total coliforms and ...

Microbial treatment of heavy metal leachates

International Nuclear Information System (INIS)

Alvarez Aliaga, M. T.

2009-01-01

Ore-mining metallurgy and other industrial activities represent the source of heavy metal and radionuclide contamination in terrestrial and aquatic environments. Physico-chemical processes are employed for heavy metal removal from industrial wastewaters. However, limitations due to the cost-effectiveness and use of contaminating reagents make these processes not environmentally friendly. (Author)

Evaluation of chemical immersion treatments to reduce microbial populations in fresh beef.

Science.gov (United States)

Kassem, Ahmed; Meade, Joseph; Gibbons, James; McGill, Kevina; Walsh, Ciara; Lyng, James; Whyte, Paul

2017-11-16

The aim of the current study was to assess the ability of a number of chemicals (acetic Acid (AA), citric acid (CA) lactic acid (LA), sodium decanoate (SD) and trisodium phosphate (TSP)) to reduce microbial populations (total viable count, Campylobacter jejuni, Escherichia coli, Salmonella typhimurium and Listeria monocytogenes) on raw beef using an immersion system. The following concentrations of each chemical were used: 3 & 5% for AA, CA, LA, SD and 10 &12% for TSP. Possible synergistic effects of using combinations of two chemicals sequentially (LA+CA and LA+AA) were also investigated. L*, a* and b* values were measured before and after treatments and ΔE* values were calculated in order to determine any changes in the color of meat due to the use of these chemicals. In general, all chemical treatments resulted in significantly (p0.05). The application of combinations of chemical immersion treatments (LA3%+AA3% and LA3%+CA3%) did not result in further significant reductions in microbial populations when compared to single chemical treatments (P3 immediately after treatment and after 24h storage. The remaining treatments did not result in significant changes to the color of raw beef. Copyright © 2017 Elsevier B.V. All rights reserved.

Literature review on the use of bioaccumulation for heavy metal removal and recovery

International Nuclear Information System (INIS)

Benemann, J.R.; Wilde, E.W.

1991-02-01

Bioaccumulation of metals by microbes -- '' bioremoval'' -- is a powerful new technology for the concentration, recovery, and removal of toxic heavy metals and radionuclides from waste streams and contaminated environments. Algae are particularly well suited for metal bioremoval. A recent commercial application of bioremoval utilizes inert (dead) immobilized microalgae biomass as ion exchange materials for the removal of heavy metals from industrial waste waters. Also, living microalgal cultures have been used to remove metals from mine effluents. Microbial cells and biomass can bioaccumulate metals and radionuclides by a large variety of mechanisms, both dependent and independent of cell metabolism. Microbial cell walls can act as ion exchange and metal complexation agents. Heavy metals can precipitate and even crystallize on cell surfaces. Metabolically produced hydrogen sulfide or other metabolic products can bioprecipitate heavy metals. Many microbes produce both intra- and extracellular metal complexing agents which could be considered in practical metal removal processes. Bioremoval processes are greatly affected by the microbial species and even strain used, pH, redox potential, temperature, and other conditions under which the microbes are grown. Development of practical applications of bioremoval requires applies research using the particular waste solutions to be treated, or close simulations thereof. From a practical perspective, the selection of the microbial biomass and the process for contacting the microbial biomass with the metal containing solutions are the key issues. Much of the recent commercial R ampersand D has emphasized commercially available, inert, microbial biomass sources as these can be acquired in sufficient quantities at affordable costs. The fundamental research and practical applications of bioaccumulation by microalgae suggests these organisms warrant a high priority in the development of advanced bioremoval processes

Literature review on the use of bioaccumulation for heavy metal removal and recovery

Energy Technology Data Exchange (ETDEWEB)

Benemann, J.R. (Benemann (J.R.), Pinole, CA (United States)); Wilde, E.W. (Westinghouse Savannah River Co., Aiken, SC (United States))

1991-02-01

Bioaccumulation of metals by microbes -- bioremoval'' -- is a powerful new technology for the concentration, recovery, and removal of toxic heavy metals and radionuclides from waste streams and contaminated environments. Algae are particularly well suited for metal bioremoval. A recent commercial application of bioremoval utilizes inert (dead) immobilized microalgae biomass as ion exchange materials for the removal of heavy metals from industrial waste waters. Also, living microalgal cultures have been used to remove metals from mine effluents. Microbial cells and biomass can bioaccumulate metals and radionuclides by a large variety of mechanisms, both dependent and independent of cell metabolism. Microbial cell walls can act as ion exchange and metal complexation agents. Heavy metals can precipitate and even crystallize on cell surfaces. Metabolically produced hydrogen sulfide or other metabolic products can bioprecipitate heavy metals. Many microbes produce both intra- and extracellular metal complexing agents which could be considered in practical metal removal processes. Bioremoval processes are greatly affected by the microbial species and even strain used, pH, redox potential, temperature, and other conditions under which the microbes are grown. Development of practical applications of bioremoval requires applies research using the particular waste solutions to be treated, or close simulations thereof. From a practical perspective, the selection of the microbial biomass and the process for contacting the microbial biomass with the metal containing solutions are the key issues. Much of the recent commercial R D has emphasized commercially available, inert, microbial biomass sources as these can be acquired in sufficient quantities at affordable costs. The fundamental research and practical applications of bioaccumulation by microalgae suggests these organisms warrant a high priority in the development of advanced bioremoval processes.

Microbial biomass carbon and enzyme activities of urban soils in Beijing.

Science.gov (United States)

Wang, Meie; Markert, Bernd; Shen, Wenming; Chen, Weiping; Peng, Chi; Ouyang, Zhiyun

2011-07-01

To promote rational and sustainable use of soil resources and to maintain the urban soil quality, it is essential to assess urban ecosystem health. In this study, the microbiological properties of urban soils in Beijing and their spatial distribution patterns across the city were evaluated based on measurements of microbial biomass carbon and urease and invertase activities of the soils for the purpose of assessing the urban ecosystem health of Beijing. Grid sampling design, normal Kriging technique, and the multiple comparisons among different land use types were used in soil sampling and data treatment. The inherent chemical characteristics of urban soils in Beijing, e.g., soil pH, electronic conductivity, heavy metal contents, total N, P and K contents, and soil organic matter contents were detected. The size and diversity of microbial community and the extent of microbial activity in Beijing urban soils were measured as the microbial biomass carbon content and the ratio of microbial biomass carbon content to total soil organic carbon. The microbial community health measured in terms of microbial biomass carbon, urease, and invertase activities varied with the organic substrate and nutrient contents of the soils and were not adversely affected by the presence of heavy metals at p urban soils influenced the nature and activities of the microbial communities.

Role of metal/silicon semiconductor contact engineering for enhanced output current in micro-sized microbial fuel cells

KAUST Repository

Mink, Justine E.

2013-11-25

We show that contact engineering plays an important role to extract the maximum performance from energy harvesters like microbial fuel cells (MFCs). We experimented with Schottky and Ohmic methods of fabricating contact areas on silicon in an MFC contact material study. We utilized the industry standard contact material, aluminum, as well as a metal, whose silicide has recently been recognized for its improved performance in smallest scale integration requirements, cobalt. Our study shows that improvements in contact engineering are not only important for device engineering but also for microsystems. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ferrihydrite-associated organic matter (OM stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortia

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R. E. Cooper

2017-11-01

Full Text Available The formation of Fe(III oxides in natural environments occurs in the presence of natural organic matter (OM, resulting in the formation of OM–mineral complexes that form through adsorption or coprecipitation processes. Thus, microbial Fe(III reduction in natural environments most often occurs in the presence of OM–mineral complexes rather than pure Fe(III minerals. This study investigated to what extent does the content of adsorbed or coprecipitated OM on ferrihydrite influence the rate of Fe(III reduction by Shewanella oneidensis MR-1, a model Fe(III-reducing microorganism, in comparison to a microbial consortium extracted from the acidic, Fe-rich Schlöppnerbrunnen fen. We found that increased OM content led to increased rates of microbial Fe(III reduction by S. oneidensis MR-1 in contrast to earlier findings with the model organism Geobacter bremensis. Ferrihydrite–OM coprecipitates were reduced slightly faster than ferrihydrites with adsorbed OM. Surprisingly, the complex microbial consortia stimulated by a mixture of electrons donors (lactate, acetate, and glucose mimics S. oneidensis under the same experimental Fe(III-reducing conditions suggesting similar mechanisms of electron transfer whether or not the OM is adsorbed or coprecipitated to the mineral surfaces. We also followed potential shifts of the microbial community during the incubation via 16S rRNA gene sequence analyses to determine variations due to the presence of adsorbed or coprecipitated OM–ferrihydrite complexes in contrast to pure ferrihydrite. Community profile analyses showed no enrichment of typical model Fe(III-reducing bacteria, such as Shewanella or Geobacter sp., but an enrichment of fermenters (e.g., Enterobacteria during pure ferrihydrite incubations which are known to use Fe(III as an electron sink. Instead, OM–mineral complexes favored the enrichment of microbes including Desulfobacteria and Pelosinus sp., both of which can utilize lactate and

Ferrihydrite-associated organic matter (OM) stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortia

Science.gov (United States)

Cooper, Rebecca Elizabeth; Eusterhues, Karin; Wegner, Carl-Eric; Totsche, Kai Uwe; Küsel, Kirsten

2017-11-01

The formation of Fe(III) oxides in natural environments occurs in the presence of natural organic matter (OM), resulting in the formation of OM-mineral complexes that form through adsorption or coprecipitation processes. Thus, microbial Fe(III) reduction in natural environments most often occurs in the presence of OM-mineral complexes rather than pure Fe(III) minerals. This study investigated to what extent does the content of adsorbed or coprecipitated OM on ferrihydrite influence the rate of Fe(III) reduction by Shewanella oneidensis MR-1, a model Fe(III)-reducing microorganism, in comparison to a microbial consortium extracted from the acidic, Fe-rich Schlöppnerbrunnen fen. We found that increased OM content led to increased rates of microbial Fe(III) reduction by S. oneidensis MR-1 in contrast to earlier findings with the model organism Geobacter bremensis. Ferrihydrite-OM coprecipitates were reduced slightly faster than ferrihydrites with adsorbed OM. Surprisingly, the complex microbial consortia stimulated by a mixture of electrons donors (lactate, acetate, and glucose) mimics S. oneidensis under the same experimental Fe(III)-reducing conditions suggesting similar mechanisms of electron transfer whether or not the OM is adsorbed or coprecipitated to the mineral surfaces. We also followed potential shifts of the microbial community during the incubation via 16S rRNA gene sequence analyses to determine variations due to the presence of adsorbed or coprecipitated OM-ferrihydrite complexes in contrast to pure ferrihydrite. Community profile analyses showed no enrichment of typical model Fe(III)-reducing bacteria, such as Shewanella or Geobacter sp., but an enrichment of fermenters (e.g., Enterobacteria) during pure ferrihydrite incubations which are known to use Fe(III) as an electron sink. Instead, OM-mineral complexes favored the enrichment of microbes including Desulfobacteria and Pelosinus sp., both of which can utilize lactate and acetate as an electron

Biochemical parameters and bacterial species richness in soils contaminated by sludge-borne metals and remediated with inorganic soil amendments

International Nuclear Information System (INIS)

Mench, Michel; Renella, Giancarlo; Gelsomino, Antonio; Landi, Loretta; Nannipieri, Paolo

2006-01-01

The effectiveness of two amendments for the in situ remediation of a Cd- and Ni-contaminated soil in the Louis Fargue long-term field experiment was assessed. In April 1995, one replicate plot (S1) was amended with 5% w/w of beringite (B), a coal fly ash (treatment S1 + B), and a second plot with 1% w/w zerovalent-Fe iron grit (SS) (treatment S1+SS), with the aim of increasing metal sorption and attenuating metal impacts. Long-term responses of daily respiration rates, microbial biomass, bacterial species richness and the activities of key soil enzymes (acid and alkaline phosphatase, arylsulfatase, β-glucosidase, urease and protease activities) were studied in relation to soil metal extractability. Seven years after initial amendments, the labile fractions of Cd and Ni in both the S1 + B and S1 + SS soils were reduced to various extents depending on the metal and fractions considered. The soil microbial biomass and respiration rate were not affected by metal contamination and amendments in the S1 + B and S1 + SS soils, whereas the activity of different soil enzymes was restored. The SS treatment was more effective in reducing labile pools of Cd and Ni and led to a greater recovery of soil enzyme activities than the B treatment. Bacterial species richness in the S1 soil did not alter with either treatment. It was concluded that monitoring of the composition and activity of the soil microbial community is important in evaluating the effectiveness of soil remediation practices. - Amendments (coal fly ash, zerovalent-Fe iron grit), reduced labile fractions of Cd and Ni in contaminated soils and restored the activity of key soil hydrolases

Anaerobic digestion of nitrogen rich poultry manure: Impact of thermophilic biogas process on metal release and microbial resistances.

Science.gov (United States)

Anjum, Reshma; Grohmann, Elisabeth; Krakat, Niclas

2017-02-01

Poultry manure is a nitrogen rich fertilizer, which is usually recycled and spread on agricultural fields. Due to its high nutrient content, chicken manure is considered to be one of the most valuable animal wastes as organic fertilizer. However, when chicken litter is applied in its native form, concerns are raised as such fertilizers also include high amounts of antibiotic resistant pathogenic Bacteria and heavy metals. We studied the impact of an anaerobic thermophilic digestion process on poultry manure. Particularly, microbial antibiotic resistance profiles, mobile genetic elements promoting the resistance dissemination in the environment as well as the presence of heavy metals were focused in this study. The initiated heat treatment fostered a community shift from pathogenic to less pathogenic bacterial groups. Phenotypic and molecular studies demonstrated a clear reduction of multiple resistant pathogens and self-transmissible plasmids in the heat treated manure. That treatment also induced a higher release of metals and macroelements. Especially, Zn and Cu exceeded toxic thresholds. Although the concentrations of a few metals reached toxic levels after the anaerobic thermophilic treatment, the quality of poultry manure as organic fertilizer may raise significantly due to the elimination of antibiotic resistance genes (ARG) and self-transmissible plasmids. Copyright © 2016 Elsevier Ltd. All rights reserved.

Functional diversity of microbial decomposers facilitates plant coexistence in a plant-microbe-soil feedback model.

Science.gov (United States)

Miki, Takeshi; Ushio, Masayuki; Fukui, Shin; Kondoh, Michio

2010-08-10

Theory and empirical evidence suggest that plant-soil feedback (PSF) determines the structure of a plant community and nutrient cycling in terrestrial ecosystems. The plant community alters the nutrient pool size in soil by affecting litter decomposition processes, which in turn shapes the plant community, forming a PSF system. However, the role of microbial decomposers in PSF function is often overlooked, and it remains unclear whether decomposers reinforce or weaken litter-mediated plant control over nutrient cycling. Here, we present a theoretical model incorporating the functional diversity of both plants and microbial decomposers. Two fundamental microbial processes are included that control nutrient mineralization from plant litter: (i) assimilation of mineralized nutrient into the microbial biomass (microbial immobilization), and (ii) release of the microbial nutrients into the inorganic nutrient pool (net mineralization). With this model, we show that microbial diversity may act as a buffer that weakens plant control over the soil nutrient pool, reversing the sign of PSF from positive to negative and facilitating plant coexistence. This is explained by the decoupling of litter decomposability and nutrient pool size arising from a flexible change in the microbial community composition and decomposition processes in response to variations in plant litter decomposability. Our results suggest that the microbial community plays a central role in PSF function and the plant community structure. Furthermore, the results strongly imply that the plant-centered view of nutrient cycling should be changed to a plant-microbe-soil feedback system, by incorporating the community ecology of microbial decomposers and their functional diversity.

Imaging microbial metal metabolism in situ under conditions of the deep-sea hydrothermal vents

Science.gov (United States)

Oger, P. M.; Daniel, I.; Simionovici, A.; Picard, A.

2006-12-01

High-pressure biotopes are the most widely spread biotopes on Earth. They represent one possible location for the origin of life. They also share striking similarities with extraterrestrial biotopes such as those postulated for Europe or Mars. In absence of light, dissimilatory reduction of metals (DMR) is fueling the ecosystem. Monitoring the metabolism of the deep-sea hydrothermal vent microbial fauna under P, T and chemical conditions relevant to their isolation environment can be difficult because of the confinement and because most spectroscopic probes do not sense metallic ions in solution. We demonstrated the possibility to use Xray spectroscopy to monitor the speciation of metallic species in solution. Experiments were performed at The ESRF using Selenium (Se) detoxification by Agrobacterium tumefaciens as an analog of DMR. The reduction of Se from selenite to the metal was monitored by a combiantion of two Xray spectroscopic techniques (XANES and μXRF). Cells were incubated in the low pressure DAC in growth medium supplemented with 5mM Selenite and incubated under pressures up to 60 Mpa at 30°C for 24h. The evolution of the speciation can be easily monitored and the concentration of each Se species determined from the Xray spectra by linear combinations of standard spectra. Selenite is transformed by the bacterium into a mixture of metal Se and methylated Se after 24 hours. Se detoxification is observed in situ up to at least 25 MPa. The technique, developped for Se can be adapted to monitor other elements more relevant to DMR such as As, Fe or S, which should allow to monitor in situ under controlled pressure and temperature the metabolism of vent organisms. It is also amenable to the monitoring of toxic metals. Xray spectroscopy and the lpDAC are compatible with other spectroscopic techniques, such as Raman, UV or IR spectroscopies, allowing to probe other metabolic activities. Hence, enlarging the range of metabolic information that can be obtained in

Different Mechanisms of Soil Microbial Response to Global Change Result in Different Outcomes in the MIMICS-CN Model

Science.gov (United States)

Kyker-Snowman, E.; Wieder, W. R.; Grandy, S.

2017-12-01

Microbial-explicit models of soil carbon (C) and nitrogen (N) cycling have improved upon simulations of C and N stocks and flows at site-to-global scales relative to traditional first-order linear models. However, the response of microbial-explicit soil models to global change factors depends upon which parameters and processes in a model are altered by those factors. We used the MIcrobial-MIneral Carbon Stabilization Model with coupled N cycling (MIMICS-CN) to compare modeled responses to changes in temperature and plant inputs at two previously-modeled sites (Harvard Forest and Kellogg Biological Station). We spun the model up to equilibrium, applied each perturbation, and evaluated 15 years of post-perturbation C and N pools and fluxes. To model the effect of increasing temperatures, we independently examined the impact of decreasing microbial C use efficiency (CUE), increasing the rate of microbial turnover, and increasing Michaelis-Menten kinetic rates of litter decomposition, plus several combinations of the three. For plant inputs, we ran simulations with stepwise increases in metabolic litter, structural litter, whole litter (structural and metabolic), or labile soil C. The cumulative change in soil C or N varied in both sign and magnitude across simulations. For example, increasing kinetic rates of litter decomposition resulted in net releases of both C and N from soil pools, while decreasing CUE produced short-term increases in respiration but long-term accumulation of C in litter pools and shifts in soil C:N as microbial demand for C increased and biomass declined. Given that soil N cycling constrains the response of plant productivity to global change and that soils generate a large amount of uncertainty in current earth system models, microbial-explicit models are a critical opportunity to advance the modeled representation of soils. However, microbial-explicit models must be improved by experiments to isolate the physiological and stoichiometric

Metal Oxide Nanomaterial QNAR Models: Available Structural Descriptors and Understanding of Toxicity Mechanisms

Directory of Open Access Journals (Sweden)

Jiali Ying

2015-10-01

Full Text Available Metal oxide nanomaterials are widely used in various areas; however, the divergent published toxicology data makes it difficult to determine whether there is a risk associated with exposure to metal oxide nanomaterials. The application of quantitative structure activity relationship (QSAR modeling in metal oxide nanomaterials toxicity studies can reduce the need for time-consuming and resource-intensive nanotoxicity tests. The nanostructure and inorganic composition of metal oxide nanomaterials makes this approach different from classical QSAR study; this review lists and classifies some structural descriptors, such as size, cation charge, and band gap energy, in recent metal oxide nanomaterials quantitative nanostructure activity relationship (QNAR studies and discusses the mechanism of metal oxide nanomaterials toxicity based on these descriptors and traditional nanotoxicity tests.

Evaluation of two iterative techniques for reducing metal artifacts in computed tomography.

Science.gov (United States)

Boas, F Edward; Fleischmann, Dominik

2011-06-01

To evaluate two methods for reducing metal artifacts in computed tomography (CT)--the metal deletion technique (MDT) and the selective algebraic reconstruction technique (SART)--and compare these methods with filtered back projection (FBP) and linear interpolation (LI). The institutional review board approved this retrospective HIPAA-compliant study; informed patient consent was waived. Simulated projection data were calculated for a phantom that contained water, soft tissue, bone, and iron. Clinical projection data were obtained retrospectively from 11 consecutively identified CT scans with metal streak artifacts, with a total of 178 sections containing metal. Each scan was reconstructed using FBP, LI, SART, and MDT. The simulated scans were evaluated quantitatively by calculating the average error in Hounsfield units for each pixel compared with the original phantom. Two radiologists who were blinded to the reconstruction algorithms used qualitatively evaluated the clinical scans, ranking the overall severity of artifacts for each algorithm. P values for comparisons of the image quality ranks were calculated from the binomial distribution. The simulations showed that MDT reduces artifacts due to photon starvation, beam hardening, and motion and does not introduce new streaks between metal and bone. MDT had the lowest average error (76% less than FBP, 42% less than LI, 17% less than SART). Blinded comparison of the clinical scans revealed that MDT had the best image quality 100% of the time (95% confidence interval: 72%, 100%). LI had the second best image quality, and SART and FBP had the worst image quality. On images from two CT scans, as compared with images generated by the scanner, MDT revealed information of potential clinical importance. For a wide range of scans, MDT yields reduced metal streak artifacts and better-quality images than does FBP, LI, or SART. http://radiology.rsna.org/lookup/suppl/doi:10.1148/radiol.11101782/-/DC1. RSNA, 2011

Comparison of Two Mechanistic Microbial Growth Models to Estimate Shelf Life of Perishable Food Package under Dynamic Temperature Conditions

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Dong Sun Lee

2014-01-01

Full Text Available Two mechanistic microbial growth models (Huang’s model and model of Baranyi and Roberts given in differential and integrated equation forms were compared in predicting the microbial growth and shelf life under dynamic temperature storage and distribution conditions. Literatures consistently reporting the microbial growth data under constant and changing temperature conditions were selected to obtain the primary model parameters, set up the secondary models, and apply them to predict the microbial growth and shelf life under fluctuating temperatures. When evaluated by general estimation behavior, bias factor, accuracy factor, and root-mean-square error, Huang’s model was comparable to Baranyi and Roberts’ model in the capability to estimate microbial growth under dynamic temperature conditions. Its simple form of single differential equation incorporating directly the growth rate and lag time may work as an advantage to be used in online shelf life estimation by using the electronic device.

In-Drift Microbial Communities

Energy Technology Data Exchange (ETDEWEB)

D. Jolley

2000-11-09

As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999). This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses.

In-Drift Microbial Communities

International Nuclear Information System (INIS)

Jolley, D.

2000-01-01

As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999). This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses

Effect of hydraulic retention time on metal precipitation in sulfate reducing inverse fluidized bed reactors

KAUST Repository

Villa-Gómez, Denys Kristalia

2014-02-13

BACKGROUND: Metal sulfide recovery in sulfate reducing bioreactors is a challenge due to the formation of small precipitates with poor settling properties. The size of the metal sulfide precipitates with the change in operational parameters such as pH, sulfide concentration and reactor configuration has been previously studied. The effect of the hydraulic retention time (HRT) on the metal precipitate characteristics such as particle size for settling has not yet been addressed. RESULTS: The change in size of the metal (Cu, Zn, Pb and Cd) sulfide precipitates as a function of the HRT was studied in two sulfate reducing inversed fluidized bed (IFB) reactors operating at different chemical oxygen demand concentrations to produce high and low sulfide concentrations. The decrease of the HRT from 24 to 9h in both IFB reactors affected the contact time of the precipitates formed, thus making differences in aggregation and particle growth regardless of the differences in sulfide concentration. Further HRT decrease to 4.5h affected the sulfate reducing activity for sulfide production and hence, the supersaturation level and solid phase speciation. Metal sulfide precipitates affected the sulfate reducing activity and community in the biofilm, probably because of the stronger local supersaturation causing metal sulfides accumulation in the biofilm. CONCLUSIONS: This study shows that the HRT is an important factor determining the size and thus the settling rate of the metal sulfides formed in bioreactors.

The large-scale process of microbial carbonate precipitation for nickel remediation from an industrial soil.

Science.gov (United States)

Zhu, Xuejiao; Li, Weila; Zhan, Lu; Huang, Minsheng; Zhang, Qiuzhuo; Achal, Varenyam

2016-12-01

Microbial carbonate precipitation is known as an efficient process for the remediation of heavy metals from contaminated soils. In the present study, a urease positive bacterial isolate, identified as Bacillus cereus NS4 through 16S rDNA sequencing, was utilized on a large scale to remove nickel from industrial soil contaminated by the battery industry. The soil was highly contaminated with an initial total nickel concentration of approximately 900 mg kg -1 . The soluble-exchangeable fraction was reduced to 38 mg kg -1 after treatment. The primary objective of metal stabilization was achieved by reducing the bioavailability through immobilizing the nickel in the urease-driven carbonate precipitation. The nickel removal in the soils contributed to the transformation of nickel from mobile species into stable biominerals identified as calcite, vaterite, aragonite and nickelous carbonate when analyzed under XRD. It was proven that during precipitation of calcite, Ni 2+ with an ion radius close to Ca 2+ was incorporated into the CaCO 3 crystal. The biominerals were also characterized by using SEM-EDS to observe the crystal shape and Raman-FTIR spectroscopy to predict responsible bonding during bioremediation with respect to Ni immobilization. The electronic structure and chemical-state information of the detected elements during MICP bioremediation process was studied by XPS. This is the first study in which microbial carbonate precipitation was used for the large-scale remediation of metal-contaminated industrial soil. Copyright © 2016 Elsevier Ltd. All rights reserved.

Reducing nitrogen crossover in microbial reverse-electrodialysis cells by using adjacent anion exchange membranes and anion exchange resin

KAUST Repository

Wallack, Maxwell J.; Geise, Geoffrey M.; Hatzell, Marta C.; Hickner, Michael A.; Logan, Bruce E.

2015-01-01

Microbial reverse electrodialysis cells (MRECs) combine power generation from salinity gradient energy using reverse electrodialysis (RED), with power generation from organic matter using a microbial fuel cell. Waste heat can be used to distill ammonium bicarbonate into high (HC) and low salt concentration (LC) solutions for use in the RED stack, but nitrogen crossover into the anode chamber must be minimized to avoid ammonia loses, and foster a healthy microbial community. To reduce nitrogen crossover, an additional low concentration (LC) chamber was inserted before the anode using an additional anion exchange membrane (AEM) next to another AEM, and filled with different amounts of anion or cation ion exchange resins. Addition of the extra AEM increased the ohmic resistance of the test RED stack from 103 Ω cm2 (1 AEM) to 295 Ω cm2 (2 AEMs). However, the use of the anion exchange resin decreased the solution resistance of the LC chamber by 74% (637 Ω cm2, no resin; 166 Ω cm2 with resin). Nitrogen crossover into the anode chamber was reduced by up to 97% using 50% of the chamber filled with an anion exchange resin compared to the control (no additional chamber). The added resistance contributed by the use of the additional LC chamber could be compensated for by using additional LC and HC membrane pairs in the RED stack.

A Stochastic Multi-Media Model of Microbial Transport in Watersheds

Science.gov (United States)

Yeghiazarian, L.; Safwat, A.; Whiteaker, T.; Teklitz, A.; Nietch, C.; Maidment, D. R.; Best, E. P.

2012-12-01

Fecal contamination is the leading cause of surface-water impairment in the US, and fecal pathogens are capable of triggering massive outbreaks of gastrointestinal disease. The difficulty in prediction of water contamination has its roots in the stochastic variability of fecal pathogens in the environment, and in the complexity of microbial dynamics and interactions on the soil surface and in water. To address these challenges, we have developed a stochastic model whereby the transport of microorganisms in watersheds is considered in two broad categories: microorganisms that are attached to mineral or organic substrates in suspended sediment; and unattached microorganisms suspended in overland flow. The interactions of microorganisms with soil particles on the soil surface and in the overland flow lead to transitions of microorganisms between solid and aqueous media. The strength of attachment of microorganisms to soil particles is determined by the chemical characteristics of soils which are highly correlated with the particle size. The particle size class distribution in the suspended sediment is predicted by the Water Erosion Prediction Project (WEPP). The model is integrated with ArcGIS, resulting in a general transport-modeling framework applicable to a variety of biological and chemical surface water contaminants. Simulations are carried out for a case study of contaminant transport in the East Fork Little Miami River Watershed in Ohio. Model results include the spatial probability distribution of microbes in the watershed and can be used for assessment of (1) mechanisms dominating microbial transport, and (2) time and location of highest likelihood of microbial occurrence, thus yielding information on best water sampling strategies.

Mtr Extracellular Electron Transfer Pathways in Fe(III)-reducing or Fe(II)-oxidizing Bacteria: A Genomic Perspective

Energy Technology Data Exchange (ETDEWEB)

Shi, Liang; Rosso, Kevin M.; Zachara, John M.; Fredrickson, Jim K.

2012-12-01

Originally discovered in the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 (MR-1), the Mtr (i.e., metal-reducing) pathway exists in all characterized strains of metal-reducing Shewanella. The protein components identified to date for the Mtr pathway of MR-1 include four multi-heme c-type cytochromes (c-Cyts), CymA, MtrA, MtrC and OmcA, and a porin-like, outer membrane protein MtrB. They are strategically positioned along the width of the MR-1 cell envelope to mediate electron transfer from the quinone/quinol pool in the inner-membrane to the Fe(III)-containing minerals external to the bacterial cells. A survey of microbial genomes revealed homologues of the Mtr pathway in other dissimilatory Fe(III)-reducing bacteria, including Aeromonas hydrophila, Ferrimonas balearica and Rhodoferax ferrireducens, and in the Fe(II)-oxidizing bacteria Dechloromonas aromatica RCB, Gallionella capsiferriformans ES-2 and Sideroxydans lithotrophicus ES-1. The widespread distribution of Mtr pathways in Fe(III)-reducing or Fe(II)-oxidizing bacteria emphasizes the importance of this type of extracellular electron transfer pathway in microbial redox transformation of Fe. Their distribution in these two different functional groups of bacteria also emphasizes the bi-directional nature of electron transfer reactions carried out by the Mtr pathways. The characteristics of the Mtr pathways may be shared by other pathways used by microorganisms for exchanging electrons with their extracellular environments.

An analysis of harmful factors to storage stability of the reduced metallic spent fuel

International Nuclear Information System (INIS)

Joo, Z. S.; Yoo, K. S.; Cho, I. J.; Kook, D. H.; Lee, J. C.; Lee, E. P.

2002-01-01

To analyze harmful factors for the reduced uranium metal, which was mainly composed of uranium, several basic properties such as microstructure, immiscibility, thermal, fission product effects were surveyed. And the oxidation properties of metal uranium and uranium alloys were also studied to select alloying elements for producing a stable uranium metal

Bioaccumulation of radionuclides and metals by microorganisms: Potential role in the separation of inorganic contaminants and for the in situ treatment of the subsurface

International Nuclear Information System (INIS)

Bolton, H. Jr.; Wildung, R.E.

1993-01-01

Radionuclide, metal and organic contaminants are present in relatively inaccessible subsurface environments at many U.S Department of Energy (DOE) sites. Subsurface contamination is of concern to DOE because the migration of these contaminants into relatively deep subsurface zones indicates that they exist in a mobile chemical form and thus could potentially enter domestic groundwater supplies. Currently, economic approaches to stabilize or remediate these deep contaminated zones are limited, because these systems are not well characterized and there is a lack of understanding of how geochemical, microbial, and hydrological processes interact to influence contaminant behavior. Microorganisms offer a potential means for radionuclide and metal immobilization or mobilization for subsequent surface treatment. Bioaccumulation is a specific microbial sequestering mechanism wherein mobile radionuclides and metals become associated with the microbial biomass by both intra- and extracellular sequestering ligands. Since most of the microorganism in the subsurface are associated with the stationary strata, bioaccumulation of mobile radionuclides and metals would initially result in a decrease in the transport of inorganic contaminants. How long the inorganic contaminants would remain immobilized, the selectivity of the bioaccumulation process for specific inorganic contaminants, the mechanism involved, and how the geochemistry and growth conditions of the subsurface environment influence bioaccumulation are not currently known. This presentation focuses on the microbial process of immobilizing radionuclides and metals and using this process to reduce inorganic contaminant migration at DOE sites. Background research with near-surface microorganisms will be presented to demonstrate this process and show its potential to reduce inorganic contaminant migration. Future research needs and approaches in this relatively new research area will also be discussed