Black Carbon Facilitated Dechlorination of DDT and its Metabolites by Sulfide.

PubMed

Ding, Kai; Xu, Wenqing

2016-12-06

1,1-trichloro-2,2-di(4-chlorophenyl)ethane (DDT) and its metabolites 1,1-dichloro-2,2-bis(4-chlorophenyl)ethane (DDD) and 1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene (DDE), are often detected in soils and sediments containing high concentrations of black carbon. Sulfide (∼5 mM) from biological sulfate reduction often coexists with black carbon and serves as both a strong reductant and a nucleophile for the abiotic transformation of contaminants. In this study, we found that the abiotic transformation of DDT, DDD, and DDE (collectively referred to as DDX) require both sulfide and black carbon. 89.3 ± 1.8% of DDT, 63.2 ± 1.9% of DDD, and 50.9 ± 1.6% of DDE were degraded by sulfide (5 mM) in the presence of graphite powder (21 g/L) after 28 days at pH 7. Chloride was a product of DDX degradation. To better understand the reaction pathways, electrochemical cells and batch reactor experiments with sulfide-pretreated graphite powder were used to differentiate the involvement of black carbon materials in DDX transformation by sulfide. Our results suggest that DDT and DDD are transformed by surface intermediates formed from the reaction between sulfide and black carbon, while DDE degradation involves reductive dechlorination. This research lays the groundwork for developing an alternative in situ remediation technique for rapidly decontaminating soils and sediments to lower toxic products under environmentally relevant conditions.

Influence of Dissolved Organic Matter and Fe (II) on the Abiotic Reduction of Pentachloronitrobenzene

EPA Science Inventory

Nitroaromatic pesticides (NAPs) are hydrophobic contaminants that can accumulate in sediments by the deposition of suspended solids from surface waters. Fe(II) and dissolved organic matter (DOM), present in suboxic and anoxic zones of freshwater sediments, can transform NAPs in n...

Investigation of In-situ Biogeochemical Reduction of Chlorinated Solvents in Groundwater by Reduced Iron Minerals

EPA Science Inventory

Biogeochemical transformation is a process in which chlorinated solvents are degraded abiotically by reactive minerals formed by, at least in part or indirectly from, anaerobic biological processes. Five mulch biowall and/or vegetable oil-based bioremediation applications for tr...

Reduction of jarosite by Shewanella oneidensis MR-1 and secondary mineralization

NASA Astrophysics Data System (ADS)

Bingjie, Ouyang; Xiancai, Lu; Huan, Liu; Juan, Li; Tingting, Zhu; Xiangyu, Zhu; Jianjun, Lu; Rucheng, Wang

2014-01-01

Jarosite is a common mineral in a variety of environments formed by the oxidation of iron sulfide normally accompanying with the generation of acid mine drainage (AMD) in mining areas or acid rock drainages (ARD) in many localities. Decomposition of jarosite by dissimilatory iron reducing bacteria (DIRB) influences the mobility of many heavy metals generally accommodated in natural jarosite. This study examined the anaerobic reduction of synthesized jarosite by Shewanella oneidensis strain MR-1, a typical facultative bacteria. The release of ferrous and ferric ion, as well as sulfate and potassium, in the inoculated experimental group lasting 80 days is much higher than that in abiotic control groups. The detection of bicarbonate and acetate in experimental solution further confirms the mechanism of microbial reduction of jarosite, in which lactate acts as the electron donor. The produced ferrous iron stimulates the subsequent secondary mineralization, leading to precipitation and transformation of various iron-containing minerals. Green rust and goethite are the intermediate minerals of the microbial reduction process under anoxic conditions, and the end products include magnetite and siderite. In aerobic environments, goethite, magnetite and siderite were also detected, but the contents were relatively lower. While in abiotic experiments, only goethite has been detected as a product. Thus, the microbial reduction and subsequent mineral transformation can remarkably influence the geochemical cycling of iron and sulfur in supergene environments, as well as the mobility of heavy metals commonly accommodated in jarosite.

Transformation of benzalkonium chloride under nitrate reducing conditions.

PubMed

Tezel, Ulas; Pavlostathis, Spyros G

2009-03-01

The effect and transformation potential of benzalkonium chlorides (BAC) under nitrate reducing conditions were investigated at concentrations up to 100 mg/L in batch assays using a mixed, mesophilic (35 degrees C) methanogenic culture. Glucose was used as the carbon and energy source and the initial nitrate concentration was 70 mg N/L Dissimilatory nitrate reduction to ammonia (DNRA) and to dinitrogen (DNRN) were observed at BAC concentrations up to 25 mg/L At and above 50 mg BAC/L, DNRA was inhibited and DNRN was incomplete resulting in accumulation of nitrous oxide. Long-term inhibition of methanogenesis and accumulation of volatile fatty acids were observed at and above 50 mg BAC/L Over 99% of the added BAC was recovered from all cultures except the one amended with 100 mg BAC/L where 37% of the initially added BAC was transformed during the 100 day incubation period. Abiotic and biotic assays performed with 100 mg/L of BAC and 5 mM (in the liquid phase) of either nitrate, nitrite, or nitric oxide demonstrated that BAC transformation was abiotic and followed the modified Hofmann degradation pathway, i.e., bimolecular nucleophilic substitution with nitrite. Alkyl dimethyl amines (tertiary amines) were produced at equamolar levels to BAC transformed, but were not further degraded. This is the first report demonstrating the transformation of BAC under nitrate reducing conditions and elucidating the BAC transformation pathway.

Chemical Transformation System: Cloud Based ...

EPA Pesticide Factsheets

Integrated Environmental Modeling (IEM) systems that account for the fate/transport of organics frequently require physicochemical properties as well as transformation products. A myriad of chemical property databases exist but these can be difficult to access and often do not contain the proprietary chemicals that environmental regulators must consider. We are building the Chemical Transformation System (CTS) to facilitate model parameterization and analysis. CTS integrates a number of physicochemical property calculators into the system including EPI Suite, SPARC, TEST and ChemAxon. The calculators are heterogeneous in their scientific methodologies, technology implementations and deployment stacks. CTS also includes a chemical transformation processing engine that has been loaded with reaction libraries for human biotransformation, abiotic reduction and abiotic hydrolysis. CTS implements a common interface for the disparate calculators accepting molecular identifiers (SMILES, IUPAC, CAS#, user-drawn molecule) before submission for processing. To make the system as accessible as possible and provide a consistent programmatic interface, we wrapped the calculators in a standardized RESTful Application Programming Interface (API) which makes it capable of servicing a much broader spectrum of clients without constraints to interoperability such as operating system or programming language. CTS is hosted in a shared cloud environment, the Quantitative Environmental

(Bio)transformation of 2,4-dinitroanisole (DNAN) in Soils

PubMed Central

Olivares, Christopher I.; Abrell, Leif; Khatiwada, Raju; Chorover, Jon; Sierra-Alvarez, Reyes; Field, Jim A.

2015-01-01

Recent studies have begun to assess the environmental fate and toxicity of 2,4-dinitroanisole (DNAN), an insensitive munition compound of interest to defense agencies. Aerobic and anaerobic DNAN biotransformation in soils was evaluated in this study. Under aerobic conditions, there was little evidence of transformation; most observed removal was attributed to adsorption and subsequent slow chemical reactions. Under anaerobic conditions, DNAN was reductively (bio)transformed and the rate of the transformation was positively correlated with soil organic carbon (OC) up to a threshold of 2.07% OC. H2 addition enhanced the nitroreduction rate compared to endogenous treatments lacking H2. Heat-killed treatments provided rates similar to the endogenous treatment, suggesting that abiotic factors play a role in DNAN reduction. Ten (bio)transformation products were detected by high-resolution mass spectrometry. The proposed transformation pathway involves reduction of DNAN to aromatic amines, with putative reactive nitroso-intermediates coupling with the amines to form azo dimers. Secondary reactions include N-alkyl substitution, O-demethylation (sometimes followed by dehydroxylation), and removal of an N-containing group. Globally, our results suggest that the main reaction DNAN undergoes in anaerobic soils is nitroreduction to 2-methoxy-5-nitroaniline (MENA) and 2,4-diaminoanisole (DAAN), followed by anaerobic coupling reactions yielding azo-dimers. The dimers were subsequently subject to further (bio)transformations. PMID:26551225

Transformations of TNT and related aminotoluenes in groundwater aquifer slurries under different electron-accepting conditions

USGS Publications Warehouse

Krumholz, L.R.; Li, J.; Clarkson, W.W.; Wilber, G.G.; Suflita, J.M.

1997-01-01

The transport and fate of pollutants is often governed by both their tendency to sorb as well as their susceptibility to biodegradation. We have evaluated these parameters for 2,4,6-trinitrotoluene (TNT) and several biodegradation products. Slurries of aquifer sediment and groundwater depleted TNT at rates of 27, 7.7 and 5.9 μM day−1 under methanogenic, sulfate-reducing and nitrate-reducing conditions, respectively. Abiotic losses of TNT were determined in autoclaved controls. Abiotic TNT loss and subsequent transformation of the products was also observed. These transformations were especially important during the first step in the reduction of TNT. Subsequent abiotic reactions could account for all of the transformations observed in bottles which were initially nitrate-reducing. Other controls removed TNT reduction products at much slower rates than slurries containing live organisms. 2-Amino-4,6-dinitrotoluene was produced in all slurries but disappeared in methanogenic and in sulfate-reducing slurries within several weeks. This compound was converted to 2,4-diamino-6-nitrotoluene in all slurries with subsequent removal of the latter from methanogenic and sulfate-reducing slurries, while it persisted in autoclaved controls and in the nitrate-reducing slurries. Aquifer slurries incubated with either 2,4- or 2,6-diaminotoluene showed losses of these compounds relative to autoclaved controls under nitrate-reducing conditions but not under sulfate-reducing or methanogenic conditions. These latter compounds are important as reduced intermediates in the biodegradation of dinitrotoluenes and as industrial chemicals. In experiments to examine sorption, exposure to landfill sediment resulted in losses of approximately 15% of diaminotoluene isomers and 25% of aminodinitrotoluene isomers from initial solution concentrations within 24 h. Isotherms confirmed that the diaminotoluenes were least strongly sorbed and the amino-dinitrotoluenes most strongly sorbed to this sediment, while TNT sorption capacity was intermediate. In our studies, 2,4,6-triaminotoluene sorption capacity was indeterminate due to its chemical instability. Coupled with biodegradation information, isotherms help describe the likelihood of contaminant removal, persistence, and movement at impacted sites.

Mechanism of Uranium Reduction and Immobilization in Desulfovibrio vulgaris Biofilms.

PubMed

Stylo, Malgorzata; Neubert, Nadja; Roebbert, Yvonne; Weyer, Stefan; Bernier-Latmani, Rizlan

2015-09-01

The prevalent formation of noncrystalline U(IV) species in the subsurface and their enhanced susceptibility to reoxidation and remobilization, as compared to crystalline uraninite, raise concerns about the long-term sustainability of the bioremediation of U-contaminated sites. The main goal of this study was to resolve the remaining uncertainty concerning the formation mechanism of noncrystalline U(IV) in the environment. Controlled laboratory biofilm systems (biotic, abiotic, and mixed biotic-abiotic) were probed using a combination of U isotope fractionation and X-ray absorption spectroscopy (XAS). Regardless of the mechanism of U reduction, the presence of a biofilm resulted in the formation of noncrystalline U(IV). Our results also show that biotic U reduction is the most effective way to immobilize and reduce U. However, the mixed biotic-abiotic system resembled more closely an abiotic system: (i) the U(IV) solid phase lacked a typically biotic isotope signature and (ii) elemental sulfur was detected, which indicates the oxidation of sulfide coupled to U(VI) reduction. The predominance of abiotic U reduction in our systems is due to the lack of available aqueous U(VI) species for direct enzymatic reduction. In contrast, in cases where bicarbonate is present at a higher concentration, aqueous U(VI) species dominate, allowing biotic U reduction to outcompete the abiotic processes.

Anaerobic aquifer transformations of 2,4-Dinitrophenol under different terminal electron accepting conditions

USGS Publications Warehouse

Krumholz, L.R.; Suflita, J.M.

1997-01-01

We evaluated the susceptibility of 2,4-dinitrophenol (2,4-DNP) and 2,4-diaminophenol to anaerobic biodegradation in aquifer slurries. Aquifer microorganisms depleted 2,4-DNP at rates of 25, 9 and 0.4 μM/day under methanogenic, sulfate-reducing and nitrate-reducing conditions, respectively. Rates of abiotic, 2,4-DNP loss in autoclaved control incubations were 7.2, 6.2 and 0.95 μM/day respectively. Abiotic, 2,4-DNP reduction was especially important as the first step in its transformation. 2-Amino-4-nitrophenol was produced by this process, but this compound was further metabolized in methanogenic and sulfate-reducing aquifer slurries. This partially reduced compound persisted in autoclaved controls and in the nitrate-reducing aquifer slurries. Aquifer slurries incubated with either 2,4-DNP or 2,4-diaminophenol produced methane when incubated with no other electron acceptor suggesting that mineralization had occurred under these conditions. In parallel experiments, aquifer slurries amended with 2,6-dinitrophenol or picric acid did not produce methane at levels above the substrate unamended controls.

Uranium isotopes fingerprint biotic reduction.

PubMed

Stylo, Malgorzata; Neubert, Nadja; Wang, Yuheng; Monga, Nikhil; Romaniello, Stephen J; Weyer, Stefan; Bernier-Latmani, Rizlan

2015-05-05

Knowledge of paleo-redox conditions in the Earth's history provides a window into events that shaped the evolution of life on our planet. The role of microbial activity in paleo-redox processes remains unexplored due to the inability to discriminate biotic from abiotic redox transformations in the rock record. The ability to deconvolute these two processes would provide a means to identify environmental niches in which microbial activity was prevalent at a specific time in paleo-history and to correlate specific biogeochemical events with the corresponding microbial metabolism. Here, we demonstrate that the isotopic signature associated with microbial reduction of hexavalent uranium (U), i.e., the accumulation of the heavy isotope in the U(IV) phase, is readily distinguishable from that generated by abiotic uranium reduction in laboratory experiments. Thus, isotope signatures preserved in the geologic record through the reductive precipitation of uranium may provide the sought-after tool to probe for biotic processes. Because uranium is a common element in the Earth's crust and a wide variety of metabolic groups of microorganisms catalyze the biological reduction of U(VI), this tool is applicable to a multiplicity of geological epochs and terrestrial environments. The findings of this study indicate that biological activity contributed to the formation of many authigenic U deposits, including sandstone U deposits of various ages, as well as modern, Cretaceous, and Archean black shales. Additionally, engineered bioremediation activities also exhibit a biotic signature, suggesting that, although multiple pathways may be involved in the reduction, direct enzymatic reduction contributes substantially to the immobilization of uranium.

Abiotic Transformation Of Estrogens In Synthetic Municipal Wastewater: An Alternative For Treatment?

EPA Science Inventory

The abiotic transformation of estrogens, including estrone (E1), estradiol (E2), estriol (E3) and ethinylestradiol (EE2), in the presence of model vegetable matter was confirmed in this study. Batch experiments were performed to model the catalytic conversion of E1, E2, E3, and ...

Interactions between Biological and Abiotic Pathways in the Reduction of Chlorinated Solvents

EPA Science Inventory

While biologically mediated reductive dechlorination continues to be a significant focus of chlorinated solvent remediation, there has been an increased interest in abiotic reductive processes for the remediation of chlorinated solvents. In situ chemical reduction (ISCR) uses zer...

Coupled Abiotic-Biotic Degradation of Bisphenol A

NASA Astrophysics Data System (ADS)

Im, J.; Prevatte, C.; Campagna, S. R.; Loeffler, F.

2014-12-01

Bisphenol A (BPA) is a ubiquitous environmental contaminant with weak estrogenic activity. BPA is readily biodegradable with oxygen available, but is recalcitrant to microbial degradation under anoxic conditions. However, BPA is susceptible to abiotic transformation under anoxic conditions. To better understand the fate of BPA in anoxic environments, the kinetics of BPA transformation by manganese oxide (d-MnO2) were investigated. BPA was rapidly transformed by MnO2 with a pseudo-first-order rate constant of 0.413 min-1. NMR and LC-MS analyses identified 4-hydroxycumyl alcohol (HCA) as a major intermediate. Up to 64% of the initial amount of BPA was recovered as HCA within 5 min, but the conversion efficiency decreased with time, suggesting that HCA was further degraded by MnO2. Further experiments confirmed that HCA was also susceptible to transformation by MnO2, albeit at 5-fold lower rates than BPA transformation. Mass balance approaches suggested that HCA was the major BPA transformation intermediate, but other compounds may also be formed. The abiotic transformation of BPA by MnO2 was affected by pH, and 10-fold higher transformation rates were observed at pH 4.5 than at pH 10. Compared to BPA, HCA has a lower octanol-water partitioning coefficient (Log Kow) of 0.76 vs 2.76 for BPA and a higher aqueous solubility of 2.65 g L-1 vs 0.31 g L-1 for BPA, suggesting higher mobility of HCA in the environment. Microcosms established with freshwater sediment materials collected from four geographically distinct locations and amended with HCA demonstrated rapid HCA biodegradation under oxic, but not under anoxic conditions. These findings suggest that BPA is not inert under anoxic conditions and abiotic reactions with MnO2 generate HCA, which has increased mobility and is susceptible to aerobic degradation. Therefore, coupled abiotic-biotic processes can affect the fate and longevity of BPA in terrestrial environments.

Uranium isotopes fingerprint biotic reduction

DOE PAGES

Stylo, Malgorzata; Neubert, Nadja; Wang, Yuheng; ...

2015-04-20

Knowledge of paleo-redox conditions in the Earth’s history provides a window into events that shaped the evolution of life on our planet. The role of microbial activity in paleo-redox processes remains unexplored due to the inability to discriminate biotic from abiotic redox transformations in the rock record. The ability to deconvolute these two processes would provide a means to identify environmental niches in which microbial activity was prevalent at a specific time in paleo-history and to correlate specific biogeochemical events with the corresponding microbial metabolism. Here, we demonstrate that the isotopic signature associated with microbial reduction of hexavalent uranium (U),more » i.e., the accumulation of the heavy isotope in the U(IV) phase, is readily distinguishable from that generated by abiotic uranium reduction in laboratory experiments. Thus, isotope signatures preserved in the geologic record through the reductive precipitation of uranium may provide the sought-after tool to probe for biotic processes. Because uranium is a common element in the Earth’s crust and a wide variety of metabolic groups of microorganisms catalyze the biological reduction of U(VI), this tool is applicable to a multiplicity of geological epochs and terrestrial environments. The findings of this study indicate that biological activity contributed to the formation of many authigenic U deposits, including sandstone U deposits of various ages, as well as modern, Cretaceous, and Archean black shales. In addition, engineered bioremediation activities also exhibit a biotic signature, suggesting that, although multiple pathways may be involved in the reduction, direct enzymatic reduction contributes substantially to the immobilization of uranium.« less

Abiotic CO2 reduction during geologic carbon sequestration facilitated by Fe(II)-bearing minerals

NASA Astrophysics Data System (ADS)

Nielsen, L. C.; Maher, K.; Bird, D. K.; Brown, G. E.; Thomas, B.; Johnson, N. C.; Rosenbauer, R. J.

2012-12-01

Redox reactions involving subsurface minerals and fluids and can lead to the abiotic generation of hydrocarbons from CO2 under certain conditions. Depleted oil reservoirs and saline aquifers targeted for geologic carbon sequestration (GCS) can contain significant quantities of minerals such as ferrous chlorite, which could facilitate the abiotic reduction of carbon dioxide to n-carboxylic acids, hydrocarbons, and amorphous carbon (C0). If such reactions occur, the injection of supercritical CO2 (scCO2) could significantly alter the oxidation state of the reservoir and cause extensive reorganization of the stable mineral assemblage via dissolution and reprecipitation reactions. Naturally occurring iron oxide minerals such as magnetite are known to catalyze CO2 reduction, resulting in the synthesis of organic compounds. Magnetite is thermodynamically stable in Fe(II) chlorite-bearing mineral assemblages typical of some reservoir formations. Thermodynamic calculations demonstrate that GCS reservoirs buffered by the chlorite-kaolinite-carbonate(siderite/magnesite)-quartz assemblage favor the reduction of CO2 to n-carboxylic acids, hydrocarbons, and C0, although the extent of abiotic CO2 reduction may be kinetically limited. To investigate the rates of abiotic CO2 reduction in the presence of magnetite, we performed batch abiotic CO2 reduction experiments using a Dickson-type rocking hydrothermal apparatus at temperatures (373 K) and pressures (100 bar) within the range of conditions relevant to GCS. Blank experiments containing CO2 and H2 were used to rule out the possibility of catalytic activity of the experimental apparatus. Reaction of brine-suspended magnetite nanoparticles with scCO2 at H2 partial pressures typical of reservoir rocks - up to 100 and 0.1 bars respectively - was used to investigate the kinetics of magnetite-catalyzed abiotic CO2 reduction. Later experiments introducing ferrous chlorite (ripidolite) were carried out to determine the potential for heterogeneous catalysis in GCS systems.

Reductive Dechlorination of Carbon Tetrachloride by Tetrachloroethene and Trichloroethene Respiring Anaerobic Mixed Cultures

NASA Astrophysics Data System (ADS)

Vickstrom, K. E.; Azizian, M.; Semprini, L.

2015-12-01

Carbon tetrachloride (CT) is a toxic and recalcitrant groundwater contaminant with the potential to form a broad range of transformation products. Of the possible biochemical pathways through which CT can be degraded, reductive dehalogenation to less chlorinated compounds and mineralization to carbon dioxide (CO2) appear to be the most frequently utilized pathways by anaerobic organisms. Results will be presented from batch experiments of CT degradation by the Evanite (EV), Victoria Strain (VS) and Point Mugu (PM) anaerobic dechlorinating cultures. The cultures are grown in chemostats and are capable of transforming tetrachloroethene (PCE) or trichloroethene (TCE) to ethene by halorespiration via reductive dehalogenase enzymes. For the batch CT transformation tests, the cells along with supernatant were harvested from chemostats fed PCE or TCE, but never CT. The batch reactors were initially fed 0.0085 mM CT and an excess of formate (EV and VS) or lactate (PM) as electron donor. Transformation of CT was 100% with about 20% converted to chloroform (CF) and undetected products. Multiple additions of CT showed a slowing of pseudo first-order CT transformation rates across all cultures. Batch reactors were then established and fed 0.085 mM CT with an excess of electron donor in order to better quantify the reductive pathway. CT was transformed to CF and dichloromethane (DCM), with trace amounts of chloromethane (CM) detected. Between 60-90% of the mass added to the system was accounted for, showing that the majority of the carbon tetrachloride present is being reductively dehalogenated. Results from batch reactors that were poisoned using sodium azide, and from reactors not provided electron donor will be presented to distinguish between biotic and abiotic reactions. Furthermore, results from reactors prepared with acetylene (a potent, reversible inhibitor of reductive dehalogenases (1)) will be presented as a means of identifying the enzymes involved in the transformation of CT. The results clearly demonstrate that reductive dechlorination of CT can be promoted by anaerobic cultures not previously acclimated to CT. 1. G. Pon, M. R. Hyman, L. Semprini, Environ. Sci. Technol. 37, 3181-3188 (2003).

Transformation of soil organics under extreme climate events: a project description

NASA Astrophysics Data System (ADS)

Blagodatskaya, Evgenia

2017-04-01

Recent climate scenarios predict not only continued global warming but also an increased frequency and intensity of extreme climatic events such as strong changes in temperature and precipitation with unusual regional dynamics. Weather anomalies at European territory of Russia are currently revealed as long-term drought and strong showers in summer and as an increased frequency of soil freezing-thawing cycles. Climate extremes totally change biogeochemical processes and elements cycling both at the ecosystem level and at the level of soil profile mainly affecting soil biota. Misbalance in these processes can cause a reduction of soil carbon stock and an increase of greenhouse gases emission. Our project aims to reveal the transformation mechanisms of soil organic matter caused by extreme weather events taking into consideration the role of biotic-abiotic interactions in regulation of formation, maintenance and turnover of soil carbon stock. Our research strategy is based on the novel concept considering extreme climatic events (showers after long-term droughts, soil flooding, freezing-thawing) as abiotic factors initiating a microbial succession. Study on stoichiometric flexibility of plants under climate extremes as well as on resulting response of soil heterotrophs on stoichiometric changes in substrate will be used for experimental prove and further development of the theory of ecological stoichiometry. The results enable us to reveal the mechanisms of biotic - abiotic interactions responsible for the balance between mobilization and stabilization of soil organic matter. Identified mechanisms will form the basis of an ecosystem model enabled to predict the effects of extreme climatic events on biogenic carbon cycle in the biosphere.

U. S. EPA’S APPROACH FOR CHLORINATED SOLVENTS

EPA Science Inventory

The approach for chlorinated solvents is similar to the approach for petroleum hydrocarbons. However, there are more mechanisms of removal, including reductive dechlorination (biotic or abiotic), dehydrochloroelimination (abiotic), and hydrolysis (biotic or abiotic). As a resul...

Mineral transformations during the dissolution of uranium ore minerals by dissimilatory metal-reducing bacteria

NASA Astrophysics Data System (ADS)

Glasauer, S.; Weidler, P.; Fakra, S.; Tyliszczak, T.; Shuh, D.

2011-12-01

Carnotite minerals [X2(UO2)2(VO4)2]; X = K, Ca, Ba, Mn, Na, Cu or Pb] form the major ore of uranium in the Colorado Plateau. These deposits are highly oxidized and contain U(VI) and V(IV). The biotransformation of U(VI) bound in carnotite by bacteria during dissimilatory metal reduction presents a complex puzzle in mineral chemistry. Both U(VI) and V(V) can be respired by metal reducing bacteria, and the mineral structure can change depending on the associated counterion. We incubated anaerobic cultures of S. putrefaciens CN32 with natural carnotite minerals from southeastern Utah in a nutrient-limited defined medium. Strain CN32 is a gram negative bacterium and a terrestrial isolate from New Mexico. The mineral and metal transformations were compared to a system that contained similar concentrations of soluble U(VI) and V(V). Electron (SEM, TEM) microscopies and x-ray spectromicroscopy (STXM) were used in conjunction with XRD to track mineral changes, and bacterial survival was monitored throughout the incubations. Slow rates of metal reduction over 10 months for the treatment with carnotite minerals revealed distinct biotic and abiotic processes, providing insight on mineral transformation and bacteria-metal interactions. The bacteria existed as small flocs or individual cells attached to the mineral phase, but did not adsorb soluble U or V, and accumulated very little of the biominerals. Reduction of mineral V(V) necessarily led to a dismantling of the carnotite structure. Bioreduction of V(V) by CN32 contributed small but profound changes to the mineral system, resulting in new minerals. Abiotic cation exchange within the carnotite group minerals induced the rearrangement of the mineral structures, leading to further mineral transformation. In contrast, bacteria survival was poor for treatments with soluble U(VI) and V(V), although both metals were reduced completely and formed solid UO2 and VO2; we also detected V(III). For these treatments, the bacteria formed extensive biofilms or flocs that contained U and V in the exopolymer, but excluded these metals from the bacteria. This suggests a specific mechanism to inhibit metal sorption to cell wall components. The example illustrates the interplay between bacteria and minerals under conditions that model oligotrophic survival, and provides insight on U mobilization from common uranium ore minerals.

Effect of abiotic factors on the mercury reduction process by humic acids in aqueous systems

USDA-ARS?s Scientific Manuscript database

Mercury (Hg) in the environment can have serious toxic effects on a variety of living organisms, and is a pollutant of concern worldwide. The reduction of mercury from the toxic Hg2+ form to Hg0 is especially important. One pathway for this reduction to occur is through an abiotic process with humic...

Model-based Analysis of Mixed Uranium(VI) Reduction by Biotic and Abiotic Pathways During in Situ Bioremediation

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

Zhao, Jiao; Scheibe, Timothy D.; Mahadevan, Radhakrishnan

2013-10-24

Uranium bioremediation has emerged as a potential strategy of cleanup of radionuclear contamination worldwide. An integrated geochemical & microbial community model is a promising approach to predict and provide insights into the bioremediation of a complicated natural subsurface. In this study, an integrated column-scale model of uranium bioremediation was developed, taking into account long-term interactions between biotic and abiotic processes. It is also combined with a comprehensive thermodynamic analysis to track the fate and cycling of biogenic species. As compared with other bioremediation models, the model increases the resolution of the connection of microbial community to geochemistry and establishes directmore » quantitative correlation between overall community evolution and geochemical variation, thereby accurately predicting the community dynamics under different sedimentary conditions. The thermodynamic analysis examined a recently identified homogeneous reduction of U(VI) by Fe(II) under dynamic sedimentary conditions across time and space. It shows that the biogenic Fe(II) from Geobacter metabolism can be removed rapidly by the biogenic sulphide from sulfate reducer metabolism, hence constituting one of the reasons that make the abiotic U(VI) reduction thermodynamically infeasible in the subsurface. Further analysis indicates that much higher influent concentrations of both Fe(II) and U(VI) than normal are required to for abiotic U(VI) reduction to be thermodynamically feasible, suggesting that the abiotic reduction cannot be an alternative to the biotic reduction in the remediation of uranium contaminated groundwater.« less

Using biotechnology and genomics to improve biotic and abiotic stress in apple

USDA-ARS?s Scientific Manuscript database

Genomic sequencing, molecular biology, and transformation technologies are providing valuable tools to better understand the complexity of how plants develop, function, and respond to biotic and abiotic stress. These approaches should complement but not replace a solid understanding of whole plant ...

Reduction of Chlorate by Iron Mediated Processes: Implications for Oxy-Chlorine Species on Mars and Earth

NASA Astrophysics Data System (ADS)

Brundrett, M.; Yan, W.; Jackson, W. A.

2017-12-01

Studies have confirmed the presence of chlorate (ClO3-) and perchlorate (ClO4-) in terrestrial systems, lunar regolith, Martian surface soils, and meteorites [1, 2, 4]. A roughly equimolar ratio of ClO3- : ClO4- has been observed for most systems with the only major exceptions the Antarctica dry valley soils (MDV) and Martian surface material, where the ClO3- : ClO4- ratios are significantly less than 1 [3, 4]. All known ClO4- production mechanisms produce molar ratios of ClO3-: ClO4- equal to or greater than 1 [5]. Post depositional processes may explain the potential reduction of ClO3-. The objective of this study was to determine the potential abiotic transformation of ClO3- by Fe (II)-bearing minerals, similar to known reactions between NO3- and Fe (II) minerals. The presence of iron-derived minerals has been established in the MDV, Martian soils, and chondrite meteorites. Batch experiments were conducted by reacting four Fe (II)-bearing minerals (wustite, siderite, magnetite, and green rust) with ClO3- at various pH (4.5, 6.5, 8.9). Chlorate reduction was rapid (half-life on the order of hours to days) and generally ClO3- was quantitatively converted to Cl-. Results of this study will increase our understanding of surface reactions that produced and transformed oxy-chlorine compounds on Mars elucidating past and present Martian surface conditions. The study also has implications into the understanding of the evolutionary processes that previously or currently dictate the abiotic geochemical processing of oxy-chlorine anions through terrestrial systems. [1] Jackson et al. (2015) EPSL 430, 470-476. [2] Rao et al. (2010) ES&T 44, 8429-8434. [3] Jackson et al. (2010) ES&T 44, 4869-4876. [4] Hecht et al. (2009) SCI 325, 64-67. [5] Rao et al. (2010) ES&T 44, 2961-2967.

Enhanced transformation of tetrabromobisphenol a by nitrifiers in nitrifying activated sludge.

PubMed

Li, Fangjie; Jiang, Bingqi; Nastold, Peter; Kolvenbach, Boris Alexander; Chen, Jianqiu; Wang, Lianhong; Guo, Hongyan; Corvini, Philippe François-Xavier; Ji, Rong

2015-04-07

The fate of the most commonly used brominated flame retardant, tetrabromobisphenol A (TBBPA), in wastewater treatment plants is obscure. Using a (14)C-tracer, we studied TBBPA transformation in nitrifying activated sludge (NAS). During the 31-day incubation, TBBPA transformation (half-life 10.3 days) was accompanied by mineralization (17% of initial TBBPA). Twelve metabolites, including those with single benzene ring, O-methyl TBBPA ether, and nitro compounds, were identified. When allylthiourea was added to the sludge to completely inhibit nitrification, TBBPA transformation was significantly reduced (half-life 28.9 days), formation of the polar and single-ring metabolites stopped, but O-methylation was not significantly affected. Abiotic experiments confirmed the generation of mono- and dinitro-brominated forms of bisphenol A in NAS by the abiotic nitration of TBBPA by nitrite, a product of ammonia-oxidizing microorganisms (AOMs). Three biotic (type II ipso-substitution, oxidative skeletal cleavage, and O-methylation) and one abiotic (nitro-debromination) pathways were proposed for TBBPA transformation in NAS. Apart from O-methylation, AOMs were involved in three other pathways. Our results are the first to provide information about the complex metabolism of TBBPA in NAS, and they are consistent with a determining role for nitrifiers in TBBPA degradation by initiating its cleavage into single-ring metabolites that are substrates for the growth of heterotrophic bacteria.

Technetium Reduction and Permanent Sequestration by Abiotic and Biotic Formation of Low-Solubility Sulfide Mineral Phases

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

Tratnyek, Paul G.; Tebo, Bradley M.; Fan, Dimin

One way to minimize the mobility of the Tc VII oxyanion pertechnetate (TcO 4 -) is to effect reduction under sulfidogenic conditions (generated abiotically by Fe 0 or biotically) to form TcS x, which is significantly slower to oxidize than Tc IVO 2. In sediment systems, TcS x and other precipitates may oxidize more slowly due to oxygen diffusion limitations to these low permeability precipitate zones. In addition, the TcO 4 - reduction rate may be more rapid in the presence of sediment because of additional reductive surface phases. This project aims to provide a fundamental understanding of the feasibilitymore » of immobilization of TcO 4 - as TcS x in the vadose zone or groundwater by application nano zero-valent iron (nZVI), and sulfide or sulfate. Biotic batch experiments have used the sulfate-reducing bacterium (SRB) Desulfotomaculum reducens. The iron sulfide mineral mackinawite was generated under these conditions, while vivianite was formed in nZVI only controls. The sulfide/bacteria-containing system consistently reduced aqueous pertechnetate rapidly (> 95% in the first hour), a rate similar to that for the sulfide-free, nZVI only system. Reduced Tc (aged for 3 months) generated in both SRB/nZVI systems was highly resistant to reoxidation. In reduced samples, Tc was found associated with solid phases containing Fe and S (D. reducens/nZVI) or Fe (nZVI only). Experiments using D. reducens without nZVI provided some additional insights. Firstly, stationary phase cultures were able to slowly reduce pertechnetate. Secondly, addition of pertechnetate at the beginning of cell growth (lag phase) resulted in a faster rate of Tc reduction, possibly indicating a direct (e.g. enzymatic) role for D. reducens in Tc reduction. Abiotic batch experiments were conducted with Na 2S as the sulfide source. Pertechnetate reduction was rapid in the presence of sulfide and nZVI, although the rate was suppressed at the higher S/Fe ratios tested. This suppression appeared to be due to the formation of Tc-containing colloids. As with the biotic experiments, pertechnetate reduced under sulfidic conditions was highly resistant to reoxidation. The microscopic morphology of abiotically-transformed nZVI particles varied significantly with those in the biotic experiment, although mackinawite was formed in both systems (as indicated by μXRD and Mössbauer spectroscopy). Preliminary XAS analysis pointed to a mixture of Tc-O and Tc-S binding in the abiotic sulfide/nZVI system, while the major reduced solids under non-sulfidic conditions were TcO 2•nH 2O. The presence of sediment and advective flow to the TcO 4 -/nZVI/sulfide system results in additional processes occurring. Although the natural Hanford sediment used has sufficient available ferrous iron to slowly reduce TcO 4 -, under anaerobic conditions, that rate is orders of magnitude slower than reduction by nZVI/sulfide. Batch and 1-D column experiments showed that the TcO 4 - reduction rate increased with the sediment surface area (with the same nZVI mass). As in batch systems, column studies showed that the presence of sulfide with TcO 4 - at low (2-5 mM) concentrations increased the TcO 4 - reduction rate and high (10-30 mM) sulfide decreased the rate. This change is attributed to the formation of sulfide precipitates on the nZVI and sediment surfaces. Injection of low and high sulfide (i.e. pretreatment) prior to TcO 4 -/sulfide injection also greatly decreased the TcO 4 - reduction rate, likely decreasing the generation of ferrous iron from the nZVI. Although the high sulfide systems have slower Tc reduction rates, 190 times more Tc mass precipitated than in the low sulfide systems and the highest fraction of Tc mass remained immobilized.« less

Coupled biotic-abiotic oxidation of organic matter by biogenic MnO_{2}

NASA Astrophysics Data System (ADS)

Gonzalez, Julia; Peña, Jasquelin

2016-04-01

Some reactive soil minerals are strongly implicated in stabilising organic matter. However, others can play an active role in the oxidation of organic molecules. In natural systems, layer-type manganese oxide minerals (MnO2) typically occur as biomineral assemblages consisting of mineral particles and microbial biomass. Both the mineral and biological fractions of the assemblage can be powerful oxidants of organic C. The biological compartment relies on a set of enzymes to drive oxidative transformations of reduced C-substrates, whereas MnO2 minerals are strong, less specific abiotic oxidants that are assumed to rely on interfacial interactions between C-substrates and the mineral surface. This project aims to understand the coupling between microbial C mineralization and abiotic C oxidation mediated by MnO2 in bacterial-MnO2 assemblages. Specifically, under conditions of high C turnover, microbial respiration can significantly alter local pH, dissolved oxygen and pool of available reductants, which may modify rates and mechanism of C oxidation by biotic and abiotic components. We first investigated changes in the solution chemistry of Pseudomonas putida suspensions exposed to varying concentrations of glucose, chosen to represent readily bioavailable substrates in soils. Glucose concentrations tested ranged between 0 and 5.5mM and changes in pH, dissolved oxygen and dissolved organic and inorganic carbon were tracked over 48h. We then combined literature review and wet-chemical experiments to compile the pH dependence of rates of organic substrate oxidation by MnO2, including glucose. Our results demonstrate a strong pH dependence for these abiotic reactions. In assemblages of P. putida - MnO2, kinetic limitations for abiotic C oxidation by MnO2 are overcome by changes in biogeochemical conditions that result from bacterial C metabolism. When extrapolated to a soil solution confronted to an input of fresh dissolved organic matter, bacterial C metabolism of the labile fraction may lower solution pH into a regime that favours abiotic oxidation of recalcitrant C by MnO2. This project demonstrates that the co-occurrence of mineral particles with metabolically active cells provides a direct link between the C and Mn cycles.

Cheminformatics and Computational Chemistry: A Powerful ...

EPA Pesticide Factsheets

The registration of new chemicals under the Toxicological Substances Control Act (TSCA) and new pesticides under the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) requires knowledge of the process science underlying the transformation of organic chemicals in natural ecosystems. The purpose of this presentation is to demonstrate how cheminformatics using chemical terms language in combination with the output of physicochemical property calculators can be employed to encode this knowledge and make it available to the appropriate decision makers. The encoded process science is realized through the execution of reaction libraries in simulators such as EPA’s Chemical Transformation Simulator (CTS). In support of the CTS, reaction libraries have or are currently being developed for a number of transformation processes including hydrolysis, abiotic reduction, photolysis and disinfection by-product formation. Examples of how the process science available in the peer-reviewed literature is being encoded will be presented. Presented at the 252nd American Chemical Society National Meeting:Aquatic Chemistry: Symposium in Honor of Professor Alan T. Stone

Abiotic gene transfer: rare or rampant?

PubMed Central

Kotnik, Tadej; Weaver, James C.

2016-01-01

Phylogenetic studies reveal that horizontal gene transfer (HGT) plays a prominent role in evolution and genetic variability of life. Five biotic mechanisms of HGT among prokaryotic organisms have been extensively characterized: conjugation, competence, transduction, gene-transfer-agent (GTA) particles, and transitory fusion with recombination, but it is not known whether they can account for all natural HGT. It is even less clear how HGT could have occurred before any of these mechanisms had developed. Here, we consider contemporary conditions and experiments on microorganisms to estimate possible roles of abiotic HGT – currently and throughout evolution. Candidate mechanisms include freeze-and-thaw, microbeads-agitation, and electroporation-based transformation, and we posit that these laboratory techniques have analogues in nature acting as mechanisms of abiotic HGT: freeze-and-thaw cycles in polar waters, sand-agitation at foreshores and riverbeds, and lightning-triggered electroporation in near-surface aqueous habitats. We derive conservative order-of-magnitude estimates for rates of microorganisms subjected to freeze-and-thaw cycles, sand-agitation, and lightning-triggered electroporation, at 1024, 1019, and 1017 per year, respectively. Considering the yield of viable transformants, which is by far the highest in electroporation, we argue this may still favor lightning-triggered transformation over the other two mechanisms. Electroporation-based gene transfer also appears to be the most general of these abiotic candidates, and perhaps even of all known HGT mechanisms. Future studies should provide improved estimates of gene transfer rates and cell viability, currently and in the past, but to assess the importance of abiotic HGT in nature, will likely require substantial progress – also in knowledge of biotic HGT. PMID:27067073

Pathways for abiotic organic synthesis at submarine hydrothermal fields.

PubMed

McDermott, Jill M; Seewald, Jeffrey S; German, Christopher R; Sylva, Sean P

2015-06-23

Arguments for an abiotic origin of low-molecular weight organic compounds in deep-sea hot springs are compelling owing to implications for the sustenance of deep biosphere microbial communities and their potential role in the origin of life. Theory predicts that warm H2-rich fluids, like those emanating from serpentinizing hydrothermal systems, create a favorable thermodynamic drive for the abiotic generation of organic compounds from inorganic precursors. Here, we constrain two distinct reaction pathways for abiotic organic synthesis in the natural environment at the Von Damm hydrothermal field and delineate spatially where inorganic carbon is converted into bioavailable reduced carbon. We reveal that carbon transformation reactions in a single system can progress over hours, days, and up to thousands of years. Previous studies have suggested that CH4 and higher hydrocarbons in ultramafic hydrothermal systems were dependent on H2 generation during active serpentinization. Rather, our results indicate that CH4 found in vent fluids is formed in H2-rich fluid inclusions, and higher n-alkanes may likely be derived from the same source. This finding implies that, in contrast with current paradigms, these compounds may form independently of actively circulating serpentinizing fluids in ultramafic-influenced systems. Conversely, widespread production of formate by ΣCO2 reduction at Von Damm occurs rapidly during shallow subsurface mixing of the same fluids, which may support anaerobic methanogenesis. Our finding of abiogenic formate in deep-sea hot springs has significant implications for microbial life strategies in the present-day deep biosphere as well as early life on Earth and beyond.

Pathways for abiotic organic synthesis at submarine hydrothermal fields

PubMed Central

McDermott, Jill M.; Seewald, Jeffrey S.; German, Christopher R.; Sylva, Sean P.

2015-01-01

Arguments for an abiotic origin of low-molecular weight organic compounds in deep-sea hot springs are compelling owing to implications for the sustenance of deep biosphere microbial communities and their potential role in the origin of life. Theory predicts that warm H2-rich fluids, like those emanating from serpentinizing hydrothermal systems, create a favorable thermodynamic drive for the abiotic generation of organic compounds from inorganic precursors. Here, we constrain two distinct reaction pathways for abiotic organic synthesis in the natural environment at the Von Damm hydrothermal field and delineate spatially where inorganic carbon is converted into bioavailable reduced carbon. We reveal that carbon transformation reactions in a single system can progress over hours, days, and up to thousands of years. Previous studies have suggested that CH4 and higher hydrocarbons in ultramafic hydrothermal systems were dependent on H2 generation during active serpentinization. Rather, our results indicate that CH4 found in vent fluids is formed in H2-rich fluid inclusions, and higher n-alkanes may likely be derived from the same source. This finding implies that, in contrast with current paradigms, these compounds may form independently of actively circulating serpentinizing fluids in ultramafic-influenced systems. Conversely, widespread production of formate by ΣCO2 reduction at Von Damm occurs rapidly during shallow subsurface mixing of the same fluids, which may support anaerobic methanogenesis. Our finding of abiogenic formate in deep-sea hot springs has significant implications for microbial life strategies in the present-day deep biosphere as well as early life on Earth and beyond. PMID:26056279

Arsenic behavior in river sediments under redox gradient: a review.

PubMed

Gorny, Josselin; Billon, Gabriel; Lesven, Ludovic; Dumoulin, David; Madé, Benoît; Noiriel, Catherine

2015-02-01

The fate of arsenic - a redox sensitive metalloid - in surface sediments is closely linked to early diagenetic processes. The review presents the main redox mechanisms and final products of As that have been evidenced over the last years. Oxidation of organic matter and concomitant reduction of oxidants by bacterial activity result in redox transformations of As species. The evolution of the sediment reactivity will also induce secondary abiotic reactions like complexation/de-complexation, sorption, precipitation/dissolution and biotic reactions that could, for instance, lead to the detoxification of some As species. Overall, abiotic redox reactions that govern the speciation of As mostly involve manganese (hydr)-oxides and reduced sulfur species produced by the sulfate-reducing bacteria. Bacterial activity is also responsible for the inter-conversion between As(V) and As(III), as well as for the production of methylated arsenic species. In surficial sediments, sorption processes also control the fate of inorganic As(V), through the formation of inner sphere complexes with iron (hydr)-oxides, that are biologically reduced in buried sediment. Arsenic species can also be bound to organic matter, either directly to functional groups or indirectly through metal complexes. Finally, even if the role of reduced sulfur species in the cycling of arsenic in sediments has been evidenced, some of the transformations remain hypothetical and deserve further investigation. Copyright © 2014 Elsevier B.V. All rights reserved.

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

Wu, Tao; Kukkadapu, Ravi K.; Griffin, Aron M.

Fe(III)-oxides and Fe(III)-bearing phyllosilicates are the two major iron sources utilized as electron acceptors by dissimilatory iron-reducing bacteria (DIRB) in anoxic soils and sediments. Although there have been many studies of microbial Fe(III)-oxide and Fe(III)-phyllosilicate reduction with both natural and specimen materials, no controlled experimental information is available on the interaction between these two phases when both are available for microbial reduction. In this study, the model DIRB Geobacter sulfurreducens was used to examine the pathways of Fe(III) reduction in Fe(III)-oxide stripped subsurface sediment that was coated with different amounts of synthetic high surface area goethite. Cryogenic (12K) 57Fe Mössbauermore » spectroscopy was used to determine changes in the relative abundances of Fe(III)-oxide, Fe(III)-phyllosilicate, and phyllosilicate-associated Fe(II) (Fe(II)-phyllosilicate) in bioreduced samples. Analogous Mössbauer analyses were performed on samples from abiotic Fe(II) sorption experiments in which sediments were exposed to a quantity of exogenous soluble Fe(II) (FeCl22H2O) comparable to the amount of Fe(II) produced during microbial reduction. A Fe partitioning model was developed to analyze the fate of Fe(II) and assess the potential for abiotic Fe(II)-catalyzed reduction of Fe(III)-phyllosilicatesilicates. The microbial reduction experiments indicated that although reduction of Fe(III)-oxide accounted for virtually all of the observed bulk Fe(III) reduction activity, there was no significant abiotic electron transfer between oxide-derived Fe(II) and Fe(III)-phyllosilicatesilicates, with 26-87% of biogenic Fe(II) appearing as sorbed Fe(II) in the Fe(II)-phyllosilicate pool. In contrast, the abiotic Fe(II) sorption experiments showed that 41 and 24% of the added Fe(II) engaged in electron transfer to Fe(III)-phyllosilicate surfaces in synthetic goethite-coated and uncoated sediment. Differences in the rate of Fe(II) addition and system redox potential may account for the microbial and abiotic reaction systems. Our experiments provide new insight into pathways for Fe(III) reduction in mixed Fe(III)-oxide/Fe(III)-phyllosilicate assemblages, and provide key mechanistic insight for interpreting microbial reduction experiments and field data from complex natural soils and sediments.« less

Riboflavin-mediated RDX transformation in the presence of Shewanella putrefaciens CN32 and lepidocrocite.

PubMed

Bae, Sungjun; Lee, Yoonhwa; Kwon, Man Jae; Lee, Woojin

2014-06-15

The potential of riboflavin for the reductive degradation of a cyclic nitramine, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), was investigated in the presence of lepidocrocite and/or Shewanella putrefaciens CN32. RDX reduction by CN32 alone or CN32 with lepidocrocite was insignificant, while 110 μM RDX was completely reduced by CN32 with riboflavin in 78 h. The transformation products identified included nitroso metabolites, formaldehyde, and ammonium, indicating the ring cleavage of RDX. UV and visible light analysis revealed that riboflavin was microbially reduced by CN32, and that the reduced riboflavin was linked to the complete degradation of RDX. In the presence of both CN32 and lepidocrocite (γ-FeOOH), 100 μM-riboflavin increased the rate and extent of Fe(II) production as well as RDX reduction. An abiotic study also showed that Fe(II)-riboflavin complex, and Fe(II) adsorbed on lepidocrocite, reduced RDX by 48% and 21%, respectively. The findings in this study suggest that riboflavin-mediated RDX degradation pathways in subsurface environments are diverse and complex. However, riboflavin, either from bacteria or exogenous sources, can significantly increase RDX degradation. This will provide a sustainable clean-up option for explosive-contaminated subsurface environments. Copyright © 2014 Elsevier B.V. All rights reserved.

Effect of H2 and redox condition on biotic and abiotic MTBE transformation

USGS Publications Warehouse

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

2006-01-01

Laboratory studies conducted with surface water sediment from a methyl tert-butyl ether (MTBE)-contaminated site in South Carolina demonstrated that, under methanogenic conditions, [U-14C] MTBE was transformed to 14C tert-butyl alcohol (TBA) with no measurable production of 14CO2. Production of TBA was not attributed to the activity of methanogenic microorganisms, however, because comparable transformation of [U-14C] MTBE to 14C-TBA also was observed in heat-sterilized controls with dissolved H2 concentrations > 5 nM. The results suggest that the transformation of MTBE to TBA may be an abiotic process that is driven by biologically produced H2 under in situ conditions. In contrast, mineralization of [U-14C] MTBE to 14CO2 was completely inhibited by heat sterilization and only observed in treatments characterized by dissolved H2 concentrations < 2 nM. These results suggest that the pathway of MTBE transformation is influenced by in situ H2 concentrations and that in situ H2 concentrations may be an useful indicator of MTBE transformation pathways in ground water systems.

Prediction of Hydrolysis Products of Organic Chemicals under Environmental pH Conditions

EPA Science Inventory

Cheminformatics-based software tools can predict the molecular structure of transformation products using a library of transformation reaction schemes. This paper presents the development of such a library for abiotic hydrolysis of organic chemicals under environmentally relevant...

Cheminformatics Applications and Physicochemical Property ...

EPA Pesticide Factsheets

The registration of new chemicals under the Toxic Substances Control Act (TSCA) and new pesticides under the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) requires knowledge of the process science underlying the transport and transformation of organic chemicals in natural ecosystems. The purpose of this presentation is to demonstrate how cheminformatics, using chemical terms language in combination with the output of physicochemical property calculators, can be employed to encode this knowledge and make it available to the appropriate decision makers. The encoded process science is realized through the execution of reaction libraries in simulators such as EPA’s Chemical Transformation Simulator (CTS). In support of the CTS, reaction libraries have, or are currently being developed for a number of transformation processes including hydrolysis, abiotic reduction, photolysis and disinfection by-product formation. Examples of how the process science in the peer-reviewed literature is being encoded will be presented. The purpose of this presentation is to demonstrate how cheminformatics, using chemical terms language in combination with the output of physicochemical property calculators, can be employed to encode this knowledge and make it available to the appropriate decision makers.

Constraints on hydrocarbon and organic acid abundances in hydrothermal fluids at the Von Damm vent field, Mid-Cayman Rise (Invited)

NASA Astrophysics Data System (ADS)

McDermott, J. M.; Seewald, J.; German, C. R.; Sylva, S. P.

2013-12-01

The generation of organic compounds in vent fluids has been of interest since the discovery of seafloor hydrothermal systems, due to implications for the sustenance of present-day microbial populations and their potential role in the origin of life on early Earth. Possible sources of organic compounds in hydrothermal systems include microbial production, thermogenic degradation of organic material, and abiotic synthesis. Abiotic organic synthesis reactions may occur during active circulation of seawater-derived fluids through the oceanic crust or within olivine-hosted fluid inclusions containing carbon-rich magmatic volatiles. H2-rich end-member fluids at the Von Damm vent field on the Mid-Cayman Rise, where fluid temperatures reach 226°C, provide an exciting opportunity to examine the extent of abiotic carbon transformations in a highly reducing system. Our results indicate multiple sources of carbon compounds in vent fluids at Von Damm. An ultramafic-influenced hydrothermal system located on the Mount Dent oceanic core complex at 2350 m depth, Von Damm vent fluids contain H2, CH4, and C2+ hydrocarbons in high abundance relative to basalt-hosted vent fields, and in similar abundance to other ultramafic-hosted systems, such as Rainbow and Lost City. The CO2 content and isotopic composition in end-member fluids are virtually identical to bottom seawater, suggesting that seawater DIC is unchanged during hydrothermal circulation of seawater-derived fluids. Accordingly, end-member CH4 that is present in slightly greater abundance than CO2 cannot be generated from reduction of aqueous CO2 during hydrothermal circulation. We postulate that CH4 and C2+ hydrocarbons that are abundantly present in Von Damm vent fluids reflect leaching of fluids from carbon- and H2-rich fluid inclusions hosted in plutonic rocks. Geochemical modeling of carbon speciation in the Von Damm fluids suggests that the relative abundances of CH4, C2+ hydrocarbons, and CO2 are consistent with thermodynamic equilibrium at higher temperatures and more reducing conditions than those observed in the Von Damm vent fluids. These findings are consistent with a scenario in which n-alkanes form abiotically within a high-H2, carbon-rich olivine-hosted fluid inclusion, and are subsequently liberated and transported to the seafloor during hydrothermal alteration of the lower crustal rocks exposed at the Mount Dent oceanic core complex. Mixed fluids at Von Damm show depletions in CO2 and H2, relative to conservative mixing. Multiple S isotope measurements indicate that the H2 sink cannot be attributed to sulfate reduction. Thermodynamic constraints indicate that high-H2 conditions support the active formation of formate via reduction of dissolved CO2 during hydrothermal circulation - a process that has also been described at the Lost City vent field - and could account for the concurrent depletions in CO2 and H2. The transformation of inorganic carbon to organic compounds via two distinct pathways in modern seafloor hydrothermal vents validates theoretical and experimental conceptual models regarding processes occurring in the crust and during hydrothermal circulation, and is relevant to supporting life in vent ecosystems.

DEMONSTRATION BULLETIN: METAL-ENHANCED ABIOTIC DEGRADATION TECHNOLOGY - ENVIROMETAL TECHNOLOGIES, INC.

EPA Science Inventory

EnviroMetal Technologies, Inc. (ETI), of Guelph, ON, Canada, has developed the metal-enhanced abiotic degradation technology to treat halogenated volatile organic compounds (VOC) in water. A reactive, zero-valent, granular iron medium causes reductive dehalogenation of VOCs yield...

Analysis of long-term bacterial vs. chemical Fe(III) oxide reduction kinetics

NASA Astrophysics Data System (ADS)

Roden, Eric E.

2004-08-01

Data from studies of dissimilatory bacterial (10 8 cells mL -1 of Shewanella putrefaciens strain CN32, pH 6.8) and ascorbate (10 mM, pH 3.0) reduction of two synthetic Fe(III) oxide coated sands and three natural Fe(III) oxide-bearing subsurface materials (all at ca. 10 mmol Fe(III) L -1) were analyzed in relation to a generalized rate law for mineral dissolution (J t/m 0 = k'(m/m 0) γ, where J t is the rate of dissolution and/or reduction at time t, m 0 is the initial mass of oxide, and m/m 0 is the unreduced or undissolved mineral fraction) in order to evaluate changes in the apparent reactivity of Fe(III) oxides during long-term biological vs. chemical reduction. The natural Fe(III) oxide assemblages demonstrated larger changes in reactivity (higher γ values in the generalized rate law) compared to the synthetic oxides during long-term abiotic reductive dissolution. No such relationship was evident in the bacterial reduction experiments, in which temporal changes in the apparent reactivity of the natural and synthetic oxides were far greater (5-10 fold higher γ values) than in the abiotic reduction experiments. Kinetic and thermodynamic considerations indicated that neither the abundance of electron donor (lactate) nor the accumulation of aqueous end-products of oxide reduction (Fe(II), acetate, dissolved inorganic carbon) are likely to have posed significant limitations on the long-term kinetics of oxide reduction. Rather, accumulation of biogenic Fe(II) on residual oxide surfaces appeared to play a dominant role in governing the long-term kinetics of bacterial crystalline Fe(III) oxide reduction. The experimental findings together with numerical simulations support a conceptual model of bacterial Fe(III) oxide reduction kinetics that differs fundamentally from established models of abiotic Fe(III) oxide reductive dissolution, and indicate that information on Fe(III) oxide reactivity gained through abiotic reductive dissolution techniques cannot be used to predict long-term patterns of reactivity toward enzymatic reduction at circumneutral pH.

Functional analysis of overexpressed PtDRS1 involved in abiotic stresses enhances growth in transgenic poplar.

PubMed

Mohammadi, Kourosh; Movahedi, Ali; Maleki, Samaneh Sadat; Sun, Weibo; Zhang, Jiaxin; Almasi Zadeh Yaghuti, Amir; Nourmohammadi, Saeed; Zhuge, Qiang

2018-05-01

Drought and salinity are two main abiotic stressors that can disrupt plant growth and survival. Various biotechnological approaches have been used to alleviate the problem of drought stress by improving water stress resistance in forestry and agriculture. The drought sensitive 1 (DRS1) gene acts as a regulator of drought stress, identified in human, yeast and some model plants, such as Arabidopsis thaliana, but there have been no reports of DRS1 transformation in poplar plants to date. In this study, we transformed the DRS1 gene from Populus trichocarpa into Populus deltoides × Populus euramericana 'Nanlin895' using Agrobacterium tumefaciens-mediated transformation. We confirmed that the DRS1 gene was transformed into 'Nanlin895' poplar genomes using reverse transcription polymerase chain reaction (PCR), multiplex PCR, real-time PCR, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. All transformed and wild-type (WT) plants were then transferred into a greenhouse for complementary experiments. We analyzed the physiological and biochemical responses of transgenic plants under drought and salt stresses in the greenhouse, and the results were compared with control WT plants. Responses to abiotic stress were greater in transgenic plants compared with WT. Based on our results, introduction of the DRS1 gene into poplar 'Nanlin895' plants significantly enhanced the resistance of those plants to water deficit and high salinity, allowing higher growth rates of roots and shoots in those plants. Additionally, the clawed root rate increased in transformed poplars grown in culture media or in soil, and improved survival under drought and salt stress conditions. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Non-enzymatic U(VI) interactions with biogenic mackinawite

NASA Astrophysics Data System (ADS)

Veeramani, H.; Qafoku, N. P.; Kukkadapu, R. K.; Murayama, M.; Hochella, M. F.

2011-12-01

Reductive immobilization of hexavalent uranium [U(VI)] by stimulation of dissimilatory metal and/or sulfate reducing bacteria (DMRB or DSRB) has been extensively researched as a remediation strategy for subsurface U(VI) contamination. These bacteria derive energy by reducing oxidized metals as terminal electron acceptors, often utilizing organic substrates as electron donors. Thus, when evaluating the potential for in-situ uranium remediation in heterogeneous subsurface media, it is important to understand how the presence of alternative electron acceptors such as Fe(III) and sulfate affect U(VI) remediation and the long term behavior and reactivity of reduced uranium. Iron, an abundant subsurface element, represents a substantial sink for electrons from DMRB, and the reduction of Fe(III) leads to the formation of dissolved Fe(II) or to reactive biogenic Fe(II)- and mixed Fe(II)/Fe(III)- mineral phases. Consequently, abiotic U(VI) reduction by reactive forms of biogenic Fe(II) minerals could be a potentially important process for uranium immobilization. In our study, the DMRB Shewanella putrefaciens CN32 was used to synthesize a biogenic Fe(II)-bearing sulfide mineral: mackinawite, that has been characterized by XRD, SEM, HRTEM and Mössbauer spectroscopy. Batch experiments involving treated biogenic mackinawite and uranium (50:1 molar ratio) were carried out at room temperature under strict anoxic conditions. Following complete removal of uranium from solution, the biogenic mackinawite was analyzed by a suite of analytical techniques including XAS, HRTEM and Mössbauer spectroscopy to determine the speciation of uranium and investigate concomitant Fe(II)-phase transformation. Determining the speciation of uranium is critical to success of a remediation strategy. The present work elucidates non-enzymatic/abiotic molecular scale redox interactions between biogenic mackinawite and uranium.

Microbial fuel cells: From fundamentals to applications. A review.

PubMed

Santoro, Carlo; Arbizzani, Catia; Erable, Benjamin; Ieropoulos, Ioannis

2017-07-15

In the past 10-15 years, the microbial fuel cell (MFC) technology has captured the attention of the scientific community for the possibility of transforming organic waste directly into electricity through microbially catalyzed anodic, and microbial/enzymatic/abiotic cathodic electrochemical reactions. In this review, several aspects of the technology are considered. Firstly, a brief history of abiotic to biological fuel cells and subsequently, microbial fuel cells is presented. Secondly, the development of the concept of microbial fuel cell into a wider range of derivative technologies, called bioelectrochemical systems, is described introducing briefly microbial electrolysis cells, microbial desalination cells and microbial electrosynthesis cells. The focus is then shifted to electroactive biofilms and electron transfer mechanisms involved with solid electrodes. Carbonaceous and metallic anode materials are then introduced, followed by an explanation of the electro catalysis of the oxygen reduction reaction and its behavior in neutral media, from recent studies. Cathode catalysts based on carbonaceous, platinum-group metal and platinum-group-metal-free materials are presented, along with membrane materials with a view to future directions. Finally, microbial fuel cell practical implementation, through the utilization of energy output for practical applications, is described.

Microbial fuel cells: From fundamentals to applications. A review

NASA Astrophysics Data System (ADS)

Santoro, Carlo; Arbizzani, Catia; Erable, Benjamin; Ieropoulos, Ioannis

2017-07-01

In the past 10-15 years, the microbial fuel cell (MFC) technology has captured the attention of the scientific community for the possibility of transforming organic waste directly into electricity through microbially catalyzed anodic, and microbial/enzymatic/abiotic cathodic electrochemical reactions. In this review, several aspects of the technology are considered. Firstly, a brief history of abiotic to biological fuel cells and subsequently, microbial fuel cells is presented. Secondly, the development of the concept of microbial fuel cell into a wider range of derivative technologies, called bioelectrochemical systems, is described introducing briefly microbial electrolysis cells, microbial desalination cells and microbial electrosynthesis cells. The focus is then shifted to electroactive biofilms and electron transfer mechanisms involved with solid electrodes. Carbonaceous and metallic anode materials are then introduced, followed by an explanation of the electro catalysis of the oxygen reduction reaction and its behavior in neutral media, from recent studies. Cathode catalysts based on carbonaceous, platinum-group metal and platinum-group-metal-free materials are presented, along with membrane materials with a view to future directions. Finally, microbial fuel cell practical implementation, through the utilization of energy output for practical applications, is described.

EIMS Fragmentation Pathways and MRM Quantification of 7α/β-Hydroxy-Dehydroabietic Acid TMS Derivatives

NASA Astrophysics Data System (ADS)

Rontani, Jean-François; Aubert, Claude; Belt, Simon T.

2015-09-01

EI mass fragmentation pathways of TMS derivatives οf 7α/β-hydroxy-dehydroabietic acids resulting from NaBH4-reduction of oxidation products of dehydroabietic acid (a component of conifers) were investigated and deduced by a combination of (1) low energy CID-GC-MS/MS, (2) deuterium labeling, (3) different derivatization methods, and (4) GC-QTOF accurate mass measurements. Having identified the main fragmentation pathways, the TMS-derivatized 7α/β-hydroxy-dehydroabietic acids could be quantified in multiple reaction monitoring (MRM) mode in sea ice and sediment samples collected from the Arctic. These newly characterized transformation products of dehydroabietic acid constitute potential tracers of biotic and abiotic degradation of terrestrial higher plants in the environment.

Abiotic methane formation during experimental serpentinization of olivine

PubMed Central

2016-01-01

Fluids circulating through actively serpentinizing systems are often highly enriched in methane (CH4). In many cases, the CH4 in these fluids is thought to derive from abiotic reduction of inorganic carbon, but the conditions under which this process can occur in natural systems remain unclear. In recent years, several studies have reported abiotic formation of CH4 during experimental serpentinization of olivine at temperatures at or below 200 °C. However, these results seem to contradict studies conducted at higher temperatures (300 °C to 400 °C), where substantial kinetic barriers to CH4 synthesis have been observed. Here, the potential for abiotic formation of CH4 from dissolved inorganic carbon during olivine serpentinization is reevaluated in a series of laboratory experiments conducted at 200 °C to 320 °C. A 13C-labeled inorganic carbon source was used to unambiguously determine the origin of CH4 generated in the experiments. Consistent with previous high-temperature studies, the results indicate that abiotic formation of CH4 from reduction of dissolved inorganic carbon during the experiments is extremely limited, with nearly all of the observed CH4 derived from background sources. The results indicate that the potential for abiotic synthesis of CH4 in low-temperature serpentinizing environments may be much more limited than some recent studies have suggested. However, more extensive production of CH4 was observed in one experiment performed under conditions that allowed an H2-rich vapor phase to form, suggesting that shallow serpentinization environments where a separate gas phase is present may be more favorable for abiotic synthesis of CH4. PMID:27821742

Abiotic methane formation during experimental serpentinization of olivine.

PubMed

McCollom, Thomas M

2016-12-06

Fluids circulating through actively serpentinizing systems are often highly enriched in methane (CH 4 ). In many cases, the CH 4 in these fluids is thought to derive from abiotic reduction of inorganic carbon, but the conditions under which this process can occur in natural systems remain unclear. In recent years, several studies have reported abiotic formation of CH 4 during experimental serpentinization of olivine at temperatures at or below 200 °C. However, these results seem to contradict studies conducted at higher temperatures (300 °C to 400 °C), where substantial kinetic barriers to CH 4 synthesis have been observed. Here, the potential for abiotic formation of CH 4 from dissolved inorganic carbon during olivine serpentinization is reevaluated in a series of laboratory experiments conducted at 200 °C to 320 °C. A 13 C-labeled inorganic carbon source was used to unambiguously determine the origin of CH 4 generated in the experiments. Consistent with previous high-temperature studies, the results indicate that abiotic formation of CH 4 from reduction of dissolved inorganic carbon during the experiments is extremely limited, with nearly all of the observed CH 4 derived from background sources. The results indicate that the potential for abiotic synthesis of CH 4 in low-temperature serpentinizing environments may be much more limited than some recent studies have suggested. However, more extensive production of CH 4 was observed in one experiment performed under conditions that allowed an H 2 -rich vapor phase to form, suggesting that shallow serpentinization environments where a separate gas phase is present may be more favorable for abiotic synthesis of CH 4 .

Hydroxylamine addition impact to Nitrosomonas europaea activity in the presence of monochloramine.

PubMed

Wahman, David G; Speitel, Gerald E

2015-01-01

In drinking water, monochloramine may promote ammonia–oxidizing bacteria (AOB) growth because of concurrent ammonia presence. AOB use (i) ammonia monooxygenase for biological ammonia oxidation to hydroxylamine and (ii) hydroxylamine oxidoreductase for biological hydroxylamine oxidation to nitrite. In addition, monochloramine and hydroxylamine abiotically react, providing AOB a potential benefit by removing the disinfectant (monochloramine) and releasing growth substrate (ammonia). Alternatively and because biological hydroxylamine oxidation supplies the electrons (reductant) required for biological ammonia oxidation, the monochloramine/hydroxylamine abiotic reaction represents a possible inactivation mechanism by consuming hydroxylamine and inhibiting reductant generation. To investigate the abiotic monochloramine and hydroxylamine reaction's impact on AOB activity, the current study used batch experiments with Nitrosomonas europaea (AOB pure culture), ammonia, monochloramine, and hydroxylamine addition. To decipher whether hydroxylamine addition benefitted N. europaea activity by (i) removing monochloramine and releasing free ammonia or (ii) providing an additional effect (possibly the aforementioned reductant source), a previously developed cometabolism model was coupled with an abiotic monochloramine and hydroxylamine model for data interpretation. N. europaea maintained ammonia oxidizing activity when hydroxylamine was added before complete ammonia oxidation cessation. The impact could not be accounted for by monochloramine removal and free ammonia release alone and was concentration dependent for both monochloramine and hydroxylamine. In addition, a preferential negative impact occurred for ammonia versus hydroxylamine oxidation. These results suggest an additional benefit of exogenous hydroxylamine addition beyond monochloramine removal and free ammonia release, possibly providing reductant generation.

Molecular Mechanisms of Bacterial Mercury Transformation

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

Summers, Anne O.; Smith, Jeremy C.

Hg is of special interest to DOE due to past intensive use in manufacture of nuclear weapons at the Oak Ridge Reservation (ORR). Because of its facile oxidation/reduction [Hg(II)/Hg(0)] chemistry, ability to bond to carbon [as in highly toxic methylmercury: MeHg(I)] and its unique physical properties [e.g., volatility of Hg(0)], Hg has a complex environmental cycle involving soils, sediments, waterways and the atmosphere and including biotic and abiotic chemical and physical transport and transformations. Understanding such processes well enough to design stewardship plans that minimize negative impacts in diverse ecological settings requires rich knowledge of the contributing abiotic and bioticmore » processes. Prokaryotes are major players in the global Hg cycle. Facultative and anaerobic bacteria can form MeHg(I) with consequent intoxication of wildlife and humans. Sustainable stewardship of Hg-contaminated sites requires eliminating not only MeHg(I) but also the Hg(II) substrate for methylation. Fortunately, a variety of mercury resistant (HgR) aerobic and facultative bacteria and archaea can do both things. Prokaryotes harboring narrow or broad Hg resistance (mer) loci detoxify Hg(II) or RHg(I), respectively, to relatively inert, less toxic, volatile Hg(0). HgR microbes are enriched in highly contaminated sites and extensive field data show they depress levels of MeHg >500-fold in such zones. So, enhancing the natural capacity of indigenous HgR microbes to remove Hg(II) and RHg(I) from soils, sediments and waterways is a logical component of a comprehensive plan for clean up and stewardship of contaminated sites.« less

Multiple abiotic stress tolerance of the transformants yeast cells and the transgenic Arabidopsis plants expressing a novel durum wheat catalase.

PubMed

Feki, Kaouthar; Kamoun, Yosra; Ben Mahmoud, Rihem; Farhat-Khemakhem, Ameny; Gargouri, Ali; Brini, Faiçal

2015-12-01

Catalases are reactive oxygen species scavenging enzymes involved in response to abiotic and biotic stresses. In this study, we described the isolation and functional characterization of a novel catalase from durum wheat, designed TdCAT1. Molecular Phylogeny analyses showed that wheat TdCAT1 exhibited high amino acids sequence identity to other plant catalases. Sequence homology analysis showed that TdCAT1 protein contained the putative calmodulin binding domain and a putative conserved internal peroxisomal targeting signal PTS1 motif around its C-terminus. Predicted three-dimensional structural model revealed the presence of four putative distinct structural regions which are the N-terminal arm, the β-barrel, the wrapping and the α-helical domains. TdCAT1 protein had the heme pocket that was composed by five essential residues. TdCAT1 gene expression analysis showed that this gene was induced by various abiotic stresses in durum wheat. The expression of TdCAT1 in yeast cells and Arabidopsis plants conferred tolerance to several abiotic stresses. Compared with the non-transformed plants, the transgenic lines maintained their growth and accumulated more proline under stress treatments. Furthermore, the amount of H2O2 was lower in transgenic lines, which was due to the high CAT and POD activities. Taken together, these data provide the evidence for the involvement of durum wheat catalase TdCAT1 in tolerance to multiple abiotic stresses in crop plants. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Mass Dependent and Mass Independent Fractionation of Hg Isotopes and Estimation of Photochemical Loss of Hg in Aquatic Systems

NASA Astrophysics Data System (ADS)

Bergquist, B. A.; Blum, J. D.

2007-12-01

Mercury is a globally distributed and highly toxic pollutant, the mobility and bioaccumulation of which is dependent on its redox cycling. Hg isotope analysis is an important new tool for identifying Hg sources and tracking Hg transformations in the environment. Most natural samples analyzed for Hg isotopes display mass-dependent isotope fractionation (MDF), but a small body of data suggests that some natural samples also display mass- independent isotope fractionation (MIF) of the odd Hg isotopes. Here we document MIF of Hg isotopes during an important natural process, constrain the potential mechanism of isotope fractionation, and apply the MIF observed in natural samples to quantify the photochemical reduction of Hg species in the environment. Reduction of Hg species to Hg0 vapor is an important pathway for removal of Hg from aqueous systems into the atmosphere and occurs by abiotic and biotic mechanisms. In laboratory experiments, we find that photochemical reduction Hg species by natural sunlight leads to large MIF of the odd isotopes. Also, the relationship between MIF for the two odd isotopes of Hg is significantly different for different photo-reduction pathways. In contrast, both biological reduction (Kritee et al., 2006) and dark abiotic organically-mediated reduction follow MDF. Natural samples from aquatic ecosystems preserve both MDF and MIF. In fish, MDF increases with the size and Hg concentration of fish suggesting MDF may be useful in understanding Hg bioaccumulation. Fish also display a large range in MIF (4‰), and the relationship between the MIF of the two odd isotopes in fish has a similar slope to the slope found for photo-reduction of CH3Hg+. Since fish bioaccumulate CH3Hg+, fish may be recording the extent to which CH3Hg+ is lost via photochemical reduction in an aquatic ecosystem. Fish populations from different locations have different MIF values, but mostly display similar MIF within a given locale. This suggests that MIF is preserved in the food web and could be used to quantify photo-reduction of CH3Hg+ in ecosystems. Both MDF and MIF of Hg isotopes will be useful for quantifying and understanding Hg biogeochemical cycling in the environment.

Transformation of carbon tetrachloride and chloroform by trichloroethene respiring anaerobic mixed cultures and supernatant.

PubMed

Vickstrom, Kyle E; Azizian, Mohammad F; Semprini, Lewis

2017-09-01

Carbon tetrachloride (CT) and chloroform (CF) were transformed in batch reactor experiments conducted with anaerobic dechlorinating cultures and supernatant (ADC + S) harvested from continuous flow reactors. The Evanite (EV) and Victoria/Stanford (VS) cultures, capable of respiring trichloroethene (TCE), 1,2-cis-dichloroethene (cDCE), and vinyl chloride (VC) to ethene (ETH), were grown in continuous flow reactors receiving an influent feed of saturated TCE (10 mM; 60 mEq) and formate (45 mM; 90 mEq) but no CT or CF. Cells and supernatant were harvested from the chemostats and inoculated into batch reactors at the onset of each experiment. CT transformation was complete following first order kinetics with CF, DCM and CS 2 as the measurable transformation products, representing 20-40% of the original mass of CT, with CO 2 likely the unknown transformation product. CF was transformed to DCM and likely CO 2 at an order of magnitude rate lower than CT, while DCM was not further transformed. An analytical first order model including multiple key reactions effectively simulated CT transformation, product formation and transformation, and provided reasonable estimates of transformation rate coefficients. Biotic and abiotic treatments indicated that CT was mainly transformed via abiotic processes. However, the presence of live cells was associated with the transformation of CF to DCM. In biotic tests both TCE and CT were simultaneously transformed, with TCE transformed to ETH and approximately 15-53% less CF formed via CT transformation. A 14-day exposure to CF (CF max  = 1.4 μM) reduced all rates of chlorinated ethene respiration by a factor of 10 or greater. Copyright © 2017 Elsevier Ltd. All rights reserved.

In situ characterization of green rust in the presence of arsenate and phosphate in simulated oxidized and reduced environments.

NASA Astrophysics Data System (ADS)

Root, R. A.; O'Day, P. A.

2008-12-01

Nano- to micron-scale particles of mixed-valent iron hydroxide, specifically green rust (GR [FeII6- x(OH)y FeIIIx(OH)12-y]x+[Anionx- + H2O]x-), have been identified and studied as corrosion products of steel, and recently rediscovered in hydromorphic soils and sediments. Green rusts are intermediate phases produced by biotic and abiotic reductive dissolution of ferric oxyhydroxides, or by oxidation of dissolved ferrous iron. Adsorbed oxyanions can stabilize GR phases and inhibit the formation of thermodynamically favored iron phases such as magnetite or lepidocrocite in subsurface environments. This study used synchrotron XRD to characterize iron (hydr)oxide minerals precipitated from solution and subsequent aging products under different environmental conditions of pH and Eh. Here we show the in situ abiotic development of green rust and its stabilization by the addition of adsorbed oxyanions or alternatively, subsequent rapid transformation to magnetite or lepidocrocite in the absence of added anions. A closed batch reactor with an in-line capillary was used to expose the reaction products to continuous synchrotron radiation. Laue patterns were collected at time intervals of 3-5 minutes and used to detect the formation of crystalline iron (hydr)oxide minerals that precipitate as a function time and chemical perturbations to the system, i.e. changing the pH, redox potential, ratio of Fe2+ to OH- , and addition of an oxyanion, arsenate or phosphate. The reactions were monitored by observing the development of diagnostic green rust XRD d-spacing peak at 10.9 Å (300), the 3.29 Å (210) d- spacing for lepidocrocite, and the 2.53 Å (100) d-spacing for magnetite, with continuous in-line measurement of pH and ORP. We found that green rust was stabilized by the adsorption of arsenate and phosphate. In the presence of arsenate or phosphate at pH =7, green rust transformed to lepidocrocite after several hours when anoxic controls were removed. When pH and Eh were constant, GR did not transform to magnetite or lepidocrocite. However, without arsenate or phosphate, the transformation occurred in less than 1 hour. At pH > 7.5, green rust transformed to magnetite within 1 hour. In the presence of phosphate or arsenate, the transformation was retarded and took up to 8 hours. The rates of transformation and meta- stability of iron (hydr)oxide phases in natural redoximorphic sediments play important roles in the cycling of contaminants and nutrients.

Final Report: Molecular mechanisms and kinetics of microbial anaerobic nitrate-dependent U(IV) and Fe(II) oxidation

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

O'Day, Peggy A.; Asta, Maria P.; Kanematsu, Masakazu

2015-02-27

In this project, we combined molecular genetic, spectroscopic, and microscopic techniques with kinetic and reactive transport studies to describe and quantify biotic and abiotic mechanisms underlying anaerobic, nitrate-dependent U(IV) and Fe(II) oxidation, which influences the long-term efficacy of in situ reductive immobilization of uranium at DOE sites. In these studies, Thiobacillus denitrificans, an autotrophic bacterium that catalyzes anaerobic U(IV) and Fe(II) oxidation, was used to examine coupled oxidation-reduction processes under either biotic (enzymatic) or abiotic conditions in batch and column experiments with biogenically produced UIVO2(s). Synthesis and quantitative analysis of coupled chemical and transport processes were done with the reactivemore » transport modeling code Crunchflow. Research focused on identifying the primary redox proteins that catalyze metal oxidation, environmental factors that influence protein expression, and molecular-scale geochemical factors that control the rates of biotic and abiotic oxidation.« less

Download Trim.Fate

EPA Pesticide Factsheets

TRIM.FaTE is a spatially explicit, compartmental mass balance model that describes the movement and transformation of pollutants over time, through a user-defined, bounded system that includes both biotic and abiotic compartments.

Overexpression of Bacterial mtlD Gene in Peanut Improves Drought Tolerance through Accumulation of Mannitol

PubMed Central

Bhauso, Tengale Dipak; Radhakrishnan, Thankappan; Kumar, Abhay; Mishra, Gyan Prakash; Dobaria, Jentilal Ramjibhai; Patel, Kirankumar; Rajam, Manchikatla Venkat

2014-01-01

In the changing global environmental scenarios, water scarcity and recurrent drought impose huge reductions to the peanut (Arachis hypogaea L.) crop yield. In plants, osmotic adjustments associated with efficient free radical scavenging ability during abiotic stress are important components of stress tolerance mechanisms. Mannitol, a compatible solute, is known to scavenge hydroxyl radicals generated during various abiotic stresses, thereby conferring tolerance to water-deficit stress in many plant species. However, peanut plant is not known to synthesize mannitol. Therefore, bacterial mtlD gene coding for mannitol 1-phosphate dehydrogenase under the control of constitutive promoter CaMV35S was introduced and overexpressed in the peanut cv. GG 20 using Agrobacterium tumefaciens-mediated transformation. A total of eight independent transgenic events were confirmed at molecular level by PCR, Southern blotting, and RT-PCR. Transgenic lines had increased amount of mannitol and exhibited enhanced tolerance in response to water-deficit stress. Improved performance of the mtlD transgenics was indicated by excised-leaf water loss assay and relative water content under water-deficit stress. Better performance of transgenics was due to the ability of the plants to synthesize mannitol. However, regulation of mtlD gene expression in transgenic plants remains to be elucidated. PMID:25436223

Thermodynamic Versus Surface Area Control of Microbial Fe(III) Oxide Reduction Kinetics

NASA Astrophysics Data System (ADS)

Roden, E. E.

2003-12-01

Recent experimental studies of synthetic and natural Fe(III) oxide reduction permit development of conceptual and quantitative models of enzymatic Fe(III) oxide reduction at circumneutral pH that can be compared to and contrasted with established models of abiotic mineral dissolution. The findings collectively support a model for controls on enzymatic reduction that differs fundamentally from those applied to abiotic reductive dissolution as a result of two basic phenomena: (1) the relatively minor influence of oxide mineralogical and thermodynamic properties on surface area-normalized rates of enzymatic reduction compared to abiotic reductive dissolution; and (2) the major limitation which sorption and/or surface precipitation of biogenic Fe(II) on residual oxide and Fe(III)-reducing bacterial cell surfaces poses to enzymatic electron transfer in the presence of excess electron donor. Parallel studies with two major Fe(III)-reducing bacteria genera (Shewanella and Geobacter) lead to common conclusions regarding the importance of these phenomena in regulating the rate and long-term extent of Fe(III) oxide reduction. Although the extent to which these phenomena can be traced to underlying kinetic vs. thermodynamic effects cannot be resolved with current information, models in which rates of enzymatic reduction are limited kinetically by the abundance of "available" oxide surface sites (as controlled by oxide surface area and the abundance of surface-bound Fe(II)) provide an adequate macroscopic description of controls on the initial rate and long-term extent of oxide reduction. In some instances, thermodynamic limitation posed by the accumulation of aqueous reaction end-products (i.e. Fe(II) and alkalinity) must also be invoked to explain observed long-term patterns of reduction. In addition, the abundance of Fe(III)-reducing microorganisms plays an important role in governing rates of reduction and needs to be considered in models of Fe(III) reduction in nonsteady-state systems, e.g. subsurface environments in which Fe(III) reduction is stimulated by contamination with organics or for the purposes of metal/radionuclide bioremediation.

MICROSCALE METABOLIC, REDOX AND ABIOTIC REACTIONS IN HANFORD 300 AREA SUBSURFACE SEDIMENTS

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

Beyenal, Haluk; McLEan, Jeff; Majors, Paul

2013-11-14

The Hanford 300 Area is a unique site due to periodic hydrologic influence of river water resulting in changes in groundwater elevation and flow direction. This area is also highly subject to uranium remobilization, the source of which is currently believed to be the region at the base of the vadose zone that is subject to period saturation due to the changes in the water levels in the Columbia River. We found that microbial processes and redox and abiotic reactions which operate at the microscale were critical to understanding factors controlling the macroscopic fate and transport of contaminants in themore » subsurface. The combined laboratory and field research showed how microscale conditions control uranium mobility and how biotic, abiotic and redox reactions relate to each other. Our findings extended the current knowledge to examine U(VI) reduction and immobilization using natural 300 Area communities as well as selected model organisms on redox-sensitive and redox-insensitive minerals. Using innovative techniques developed specifically to probe biogeochemical processes at the microscale, our research expanded our current understanding of the roles played by mineral surfaces, bacterial competition, and local biotic, abiotic and redox reaction rates on the reduction and immobilization of uranium.« less

Relating microbial community structure to functioning in forest soil organic carbon transformation and turnover.

PubMed

You, Yeming; Wang, Juan; Huang, Xueman; Tang, Zuoxin; Liu, Shirong; Sun, Osbert J

2014-03-01

Forest soils store vast amounts of terrestrial carbon, but we are still limited in mechanistic understanding on how soil organic carbon (SOC) stabilization or turnover is controlled by biotic and abiotic factors in forest ecosystems. We used phospholipid fatty acids (PLFAs) as biomarker to study soil microbial community structure and measured activities of five extracellular enzymes involved in the degradation of cellulose (i.e., β-1,4-glucosidase and cellobiohydrolase), chitin (i.e., β-1,4-N-acetylglucosaminidase), and lignin (i.e., phenol oxidase and peroxidase) as indicators of soil microbial functioning in carbon transformation or turnover across varying biotic and abiotic conditions in a typical temperate forest ecosystem in central China. Redundancy analysis (RDA) was performed to determine the interrelationship between individual PFLAs and biotic and abiotic site factors as well as the linkage between soil microbial structure and function. Path analysis was further conducted to examine the controls of site factors on soil microbial community structure and the regulatory pathway of changes in SOC relating to microbial community structure and function. We found that soil microbial community structure is strongly influenced by water, temperature, SOC, fine root mass, clay content, and C/N ratio in soils and that the relative abundance of Gram-negative bacteria, saprophytic fungi, and actinomycetes explained most of the variations in the specific activities of soil enzymes involved in SOC transformation or turnover. The abundance of soil bacterial communities is strongly linked with the extracellular enzymes involved in carbon transformation, whereas the abundance of saprophytic fungi is associated with activities of extracellular enzymes driving carbon oxidation. Findings in this study demonstrate the complex interactions and linkage among plant traits, microenvironment, and soil physiochemical properties in affecting SOC via microbial regulations.

Salicylic acid-induced abiotic stress tolerance and underlying mechanisms in plants

PubMed Central

Khan, M. Iqbal R.; Fatma, Mehar; Per, Tasir S.; Anjum, Naser A.; Khan, Nafees A.

2015-01-01

Abiotic stresses (such as metals/metalloids, salinity, ozone, UV-B radiation, extreme temperatures, and drought) are among the most challenging threats to agricultural system and economic yield of crop plants. These stresses (in isolation and/or combination) induce numerous adverse effects in plants, impair biochemical/physiological and molecular processes, and eventually cause severe reductions in plant growth, development and overall productivity. Phytohormones have been recognized as a strong tool for sustainably alleviating adverse effects of abiotic stresses in crop plants. In particular, the significance of salicylic acid (SA) has been increasingly recognized in improved plant abiotic stress-tolerance via SA-mediated control of major plant-metabolic processes. However, the basic biochemical/physiological and molecular mechanisms that potentially underpin SA-induced plant-tolerance to major abiotic stresses remain least discussed. Based on recent reports, this paper: (a) overviews historical background and biosynthesis of SA under both optimal and stressful environments in plants; (b) critically appraises the role of SA in plants exposed to major abiotic stresses; (c) cross-talks potential mechanisms potentially governing SA-induced plant abiotic stress-tolerance; and finally (d) briefly highlights major aspects so far unexplored in the current context. PMID:26175738

Transformation and Sorption of Illicit Drug Biomarkers in Sewer Systems: Understanding the Role of Suspended Solids in Raw Wastewater.

PubMed

Ramin, Pedram; Libonati Brock, Andreas; Polesel, Fabio; Causanilles, Ana; Emke, Erik; de Voogt, Pim; Plósz, Benedek Gy

2016-12-20

Sewer pipelines, although primarily designed for sewage transport, can also be considered as bioreactors. In-sewer processes may lead to significant variations of chemical loadings from source release points to the treatment plant influent. In this study, we assessed in-sewer utilization of growth substrates (primary metabolic processes) and transformation of illicit drug biomarkers (secondary metabolic processes) by suspended biomass. Sixteen drug biomarkers were targeted, including mephedrone, methadone, cocaine, heroin, codeine, and tetrahydrocannabinol (THC) and their major human metabolites. Batch experiments were performed under aerobic and anaerobic conditions using raw wastewater. Abiotic biomarker transformation and partitioning to suspended solids and reactor wall were separately investigated under both redox conditions. A process model was identified by combining and extending the Wastewater Aerobic/anaerobic Transformations in Sewers (WATS) model and Activated Sludge Model for Xenobiotics (ASM-X). Kinetic and stoichiometric model parameters were estimated using experimental data via the Bayesian optimization method DREAM (ZS) . Results suggest that biomarker transformation significantly differs from aerobic to anaerobic conditions, and abiotic conversion is the dominant mechanism for many of the selected substances. Notably, an explicit description of biomass growth during batch experiments was crucial to avoid significant overestimation (up to 385%) of aerobic biotransformation rate constants. Predictions of in-sewer transformation provided here can reduce the uncertainty in the estimation of drug consumption as part of wastewater-based epidemiological studies.

TRIM.FaTE Public Reference Library Documentation

EPA Pesticide Factsheets

TRIM.FaTE is a spatially explicit, compartmental mass balance model that describes the movement and transformation of pollutants over time, through a user-defined, bounded system that includes both biotic and abiotic compartments.

A significant abiotic pathway for the formation of unknown nitrogen in nature

NASA Astrophysics Data System (ADS)

Jokic, A.; Schulten, H.-R.; Cutler, J. N.; Schnitzer, M.; Huang, P. M.

2004-03-01

The global nitrogen cycle is of prime importance in natural ecosystems. However, the origin and nature of up to one-half of total soil N remains obscure despite all attempts at elucidation. Our data provide, for the first time, unequivocal evidence that the promoting action of Mn (IV) oxide on the Maillard reaction (sugar-amino acid condensation) under ambient conditions results in the abiotic formation of heterocyclic N compounds, which are often referred to as unknown nitrogen, and of amides which are apparently the dominant N moieties in nature. The information presented is of fundamental significance in understanding the role of mineral colloids in abiotic transformations of organic N moieties, the incorporation of N in the organic matrix of fossil fuels, and the global N cycle.

Total Risk Integrated Methodology (TRIM) - TRIM.FaTE

EPA Pesticide Factsheets

TRIM.FaTE is a spatially explicit, compartmental mass balance model that describes the movement and transformation of pollutants over time, through a user-defined, bounded system that includes both biotic and abiotic compartments.

Microbially mediated transformations of phosphorus in the sea: new views of an old cycle.

PubMed

Karl, David M

2014-01-01

Phosphorus (P) is a required element for life. Its various chemical forms are found throughout the lithosphere and hydrosphere, where they are acted on by numerous abiotic and biotic processes collectively referred to as the P cycle. In the sea, microorganisms are primarily responsible for P assimilation and remineralization, including recently discovered P reduction-oxidation bioenergetic processes that add new complexity to the marine microbial P cycle. Human-induced enhancement of the global P cycle via mining of phosphate-bearing rock will likely influence the pace of P-cycle dynamics, especially in coastal marine habitats. The inextricable link between the P cycle and cycles of other bioelements predicts future impacts on, for example, nitrogen fixation and carbon dioxide sequestration. Additional laboratory and field research is required to build a comprehensive understanding of the marine microbial P cycle.

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

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

Kostka, Joel E.; Prakash, Om; Green, Stefan J.

2012-05-01

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

Arsenic Mobilization Influenced By Iron Reduction And Sulfidogenesis Under Dynamic Flow

NASA Astrophysics Data System (ADS)

Kocar, B. D.; Stewart, B. D.; Herbel, M.; Fendorf, S.

2004-12-01

Sulfidogenesis and iron reduction are ubiquitous processes that occur in a variety of anoxic subsurface and surface environments, which profoundly impact the cycling of arsenic. Of the iron (hydr)oxides, ferrihydrite possesses one of the highest capacities to retain arsenic, and is globally distributed within soils and sediments. Upon dissimilatory iron reduction, ferrihydrite may transform to lower surface area minerals, such as goethite and magnetite, which decreases arsenic retention, thus enhancing its transport. Here we examine how arsenic retained on ferrihydrite is mobilized under dynamic flow in the presence of Sulfurosprillum barnesii strain SES-3, a bacteria capable of reducing both As(V) and Fe(III). Ferrihydrite coated sands, loaded with 150 mg kg-1 As(V), were inoculated with S. barnesii, packed into a column and reacted with a synthetic groundwater solution. Within several days after initiation of flow, the concentration of arsenic in the column effluent increased dramatically coincident with the mineralogical transformation of ferrihydrite and As(V) reduction to As(III). Following the initial pulse of arsenic, effluent concentration then declined to less than 10 μ M. Thus, arsenic release into the aqueous phase is contingent upon the incongruent reduction of As(V) and Fe(III) as mediated by biological activity. Reaction of abiotically or biotically generated dissolved sulfide with iron (hydr)oxides may have a dramatic influence on the fate of arsenic within surface and subsurface environments. Accordingly, we examined the reaction of dissolved bisulfide and iron (hydr)oxide complexed with arsenic in both batch and column systems. Low ratios of sulfide to iron in batch reaction systems result in the formation of elemental sulfur and concomitant arsenic release from the iron (hydr)oxide surface. High sulfide to iron ratios, in contrast, appear to favor the formation of iron and arsenic sulfides. Our findings demonstrate that iron (hydr)oxides may quench reactions between sulfide and constituents sorbed to iron (hydr)oxide surfaces, forming elemental sulfur as opposed to sulfide-arsenic complexes. In addition, reductive transformation of iron (hydr)oxide by dissolved sulfide may release sorbed constituents. Hence, moderate to low concentrations of dissolved sulfide in association with iron (hydr)oxides may inhibit sequestration of important contaminants that are attenuated by Fe(III) and/or S(-II) bearing phases.

Responses of transgenic Arabidopsis plants and recombinant yeast cells expressing a novel durum wheat manganese superoxide dismutase TdMnSOD to various abiotic stresses.

PubMed

Kaouthar, Feki; Ameny, Farhat-Khemakhem; Yosra, Kamoun; Walid, Saibi; Ali, Gargouri; Faiçal, Brini

2016-07-01

In plant cells, the manganese superoxide dismutase (Mn-SOD) plays an elusive role in the response to oxidative stress. In this study, we describe the isolation and functional characterization of a novel Mn-SOD from durum wheat (Triticum turgidum L. subsp. Durum), named TdMnSOD. Molecular phylogeny analysis showed that the durum TdMnSOD exhibited high amino acids sequence identity with other Mn-SOD plants. The three-dimensional structure showed that TdMnSOD forms a homotetramer and each subunit is composed of a predominantly α-helical N-terminal domain and a mixed α/β C-terminal domain. TdMnSOD gene expression analysis showed that this gene was induced by various abiotic stresses in durum wheat. The expression of TdMnSOD enhances tolerance of the transformed yeast cells to salt, osmotic, cold and H2O2-induced oxidative stresses. Moreover, the analysis of TdMnSOD transgenic Arabidopsis plants subjected to different environmental stresses revealed low H2O2 and high proline levels as compared to the wild-type plants. Compared with the non-transformed plants, an increase in the total SOD and two other antioxidant enzyme activities including catalase (CAT) and peroxidases (POD) was observed in the three transgenic lines subjected to abiotic stress. Taken together, these data provide evidence for the involvement of durum wheat TdMnSOD in tolerance to multiple abiotic stresses in crop plants. Copyright © 2016 Elsevier GmbH. All rights reserved.

Biotechnological advancement in genetic improvement of broccoli (Brassica oleracea L. var. italica), an important vegetable crop.

PubMed

Kumar, Pankaj; Srivastava, Dinesh Kumar

2016-07-01

With the advent of molecular biotechnology, plant genetic engineering techniques have opened an avenue for the genetic improvement of important vegetable crops. Vegetable crop productivity and quality are seriously affected by various biotic and abiotic stresses which destabilize rural economies in many countries. Moreover, absence of proper post-harvest storage and processing facilities leads to qualitative and quantitative losses. In the past four decades, conventional breeding has significantly contributed to the improvement of vegetable yields, quality, post-harvest life, and resistance to biotic and abiotic stresses. However, there are many constraints in conventional breeding, which can only be overcome by advancements made in modern biology. Broccoli (Brassica oleracea L. var. italica) is an important vegetable crop, of the family Brassicaceae; however, various biotic and abiotic stresses cause enormous crop yield losses during the commercial cultivation of broccoli. Thus, genetic engineering can be used as a tool to add specific characteristics to existing cultivars. However, a pre-requisite for transferring genes into plants is the availability of efficient regeneration and transformation techniques. Recent advances in plant genetic engineering provide an opportunity to improve broccoli in many aspects. The goal of this review is to summarize genetic transformation studies on broccoli to draw the attention of researchers and scientists for its further genetic advancement.

Potential of isotope analysis (C, Cl) to identify dechlorination mechanisms

NASA Astrophysics Data System (ADS)

Cretnik, Stefan; Thoreson, Kristen; Bernstein, Anat; Ebert, Karin; Buchner, Daniel; Laskov, Christine; Haderlein, Stefan; Shouakar-Stash, Orfan; Kliegman, Sarah; McNeill, Kristopher; Elsner, Martin

2013-04-01

Chloroethenes are commonly used in industrial applications, and detected as carcinogenic contaminants in the environment. Their dehalogenation is of environmental importance in remediation processes. However, a detailed understanding frequently accounted problem is the accumulation of toxic degradation products such as cis-dichloroethylene (cis-DCE) at contaminated sites. Several studies have addressed the reductive dehalogenation reactions using biotic and abiotic model systems, but a crucial question in this context has remained open: Do environmental transformations occur by the same mechanism as in their corresponding in vitro model systems? The presented study shows the potential to close this research gap using the latest developments in compound specific chlorine isotope analysis, which make it possible to routinely measure chlorine isotope fractionation of chloroethenes in environmental samples and complex reaction mixtures.1,2 In particular, such chlorine isotope analysis enables the measurement of isotope fractionation for two elements (i.e., C and Cl) in chloroethenes. When isotope values of both elements are plotted against each other, different slopes reflect different underlying mechanisms and are remarkably insensitive towards masking. Our results suggest that different microbial strains (G. lovleyi strain SZ, D. hafniense Y51) and the isolated cofactor cobalamin employ similar mechanisms of reductive dechlorination of TCE. In contrast, evidence for a different mechanism was obtained with cobaloxime cautioning its use as a model for biodegradation. The study shows the potential of the dual isotope approach as a tool to directly compare transformation mechanisms of environmental scenarios, biotic transformations, and their putative chemical lab scale systems. Furthermore, it serves as an essential reference when using the dual isotope approach to assess the fate of chlorinated compounds in the environment.

Phytoplankton dynamics of a subtropical reservoir controlled by the complex interplay among hydrological, abiotic, and biotic variables.

PubMed

Kuo, Yi-Ming; Wu, Jiunn-Tzong

2016-12-01

This study was conducted to identify the key factors related to the spatiotemporal variations in phytoplankton abundance in a subtropical reservoir from 2006 to 2010 and to assist in developing strategies for water quality management. Dynamic factor analysis (DFA), a dimension-reduction technique, was used to identify interactions between explanatory variables (i.e., environmental variables) and abundance (biovolume) of predominant phytoplankton classes. The optimal DFA model significantly described the dynamic changes in abundances of predominant phytoplankton groups (including dinoflagellates, diatoms, and green algae) at five monitoring sites. Water temperature, electrical conductivity, water level, nutrients (total phosphorus, NO 3 -N, and NH 3 -N), macro-zooplankton, and zooplankton were the key factors affecting the dynamics of aforementioned phytoplankton. Therefore, transformations of nutrients and reactions between water quality variables and aforementioned processes altered by hydrological conditions may also control the abundance dynamics of phytoplankton, which may represent common trends in the DFA model. The meandering shape of Shihmen Reservoir and its surrounding rivers caused a complex interplay between hydrological conditions and abiotic and biotic variables, resulting in phytoplankton abundance that could not be estimated using certain variables. Additional water quality and hydrological variables at surrounding rivers and monitoring plans should be executed a few days before and after reservoir operations and heavy storm, which would assist in developing site-specific preventive strategies to control phytoplankton abundance.

ABIOTIC REACTIONS MAY BE THE MOST IMPORTANT MECHANISM IN NATURAL ATTENUATION OF CHLORINATED SOLVENTS

EPA Science Inventory

The EPA Technical Protocol for Evaluating Natural Attenuation of Chlorinated Solvents in Ground Water was developed with the assumption that natural biological reductive dechlorination was the only important mechanism for destruction of chlorinated solvents and their reduction ...

QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS FOR CHEMICAL REDUCTIONS OF ORGANIC CONTAMINANTS

EPA Science Inventory

Sufficient kinetic data on abiotic reduction reactions involving organic contaminants are now available that quantitative structure-activity relationships (QSARs) for these reactions can be developed. Over 50 QSARs have been reported, most in just the last few years, and they ar...

A meta-analysis of soil microbial biomass responses to forest disturbances

PubMed Central

Holden, Sandra R.; Treseder, Kathleen K.

2013-01-01

Climate warming is likely to increase the frequency and severity of forest disturbances, with uncertain consequences for soil microbial communities and their contribution to ecosystem C dynamics. To address this uncertainty, we conducted a meta-analysis of 139 published soil microbial responses to forest disturbances. These disturbances included abiotic (fire, harvesting, storm) and biotic (insect, pathogen) disturbances. We hypothesized that soil microbial biomass would decline following forest disturbances, but that abiotic disturbances would elicit greater reductions in microbial biomass than biotic disturbances. In support of this hypothesis, across all published studies, disturbances reduced soil microbial biomass by an average of 29.4%. However, microbial responses differed between abiotic and biotic disturbances. Microbial responses were significantly negative following fires, harvest, and storms (48.7, 19.1, and 41.7% reductions in microbial biomass, respectively). In contrast, changes in soil microbial biomass following insect infestation and pathogen-induced tree mortality were non-significant, although biotic disturbances were poorly represented in the literature. When measured separately, fungal and bacterial responses to disturbances mirrored the response of the microbial community as a whole. Changes in microbial abundance following disturbance were significantly positively correlated with changes in microbial respiration. We propose that the differential effect of abiotic and biotic disturbances on microbial biomass may be attributable to differences in soil disruption and organic C removal from forests among disturbance types. Altogether, these results suggest that abiotic forest disturbances may significantly decrease soil microbial abundance, with corresponding consequences for microbial respiration. Further studies are needed on the effect of biotic disturbances on forest soil microbial communities and soil C dynamics. PMID:23801985

Abiotic Bromination of Soil Organic Matter

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

Leri, Alessandra C.; Ravel, Bruce

Biogeochemical transformations of plant-derived soil organic matter (SOM) involve complex abiotic and microbially mediated reactions. One such reaction is halogenation, which occurs naturally in the soil environment and has been associated with enzymatic activity of decomposer organisms. Building on a recent finding that naturally produced organobromine is ubiquitous in SOM, we hypothesized that inorganic bromide could be subject to abiotic oxidations resulting in bromination of SOM. Through lab-based degradation treatments of plant material and soil humus, we have shown that abiotic bromination of particulate organic matter occurs in the presence of a range of inorganic oxidants, including hydrogen peroxide andmore » assorted forms of ferric iron, producing both aliphatic and aromatic forms of organobromine. Bromination of oak and pine litter is limited primarily by bromide concentration. Fresh plant material is more susceptible to bromination than decayed litter and soil humus, due to a labile pool of mainly aliphatic compounds that break down during early stages of SOM formation. As the first evidence of abiotic bromination of particulate SOM, this study identifies a mechanistic source of the natural organobromine in humic substances and the soil organic horizon. Formation of organobromine through oxidative treatments of plant material also provides insights into the relative stability of aromatic and aliphatic components of SOM.« less

Abiotic Bromination of Soil Organic Matter.

PubMed

Leri, Alessandra C; Ravel, Bruce

2015-11-17

Biogeochemical transformations of plant-derived soil organic matter (SOM) involve complex abiotic and microbially mediated reactions. One such reaction is halogenation, which occurs naturally in the soil environment and has been associated with enzymatic activity of decomposer organisms. Building on a recent finding that naturally produced organobromine is ubiquitous in SOM, we hypothesized that inorganic bromide could be subject to abiotic oxidations resulting in bromination of SOM. Through lab-based degradation treatments of plant material and soil humus, we have shown that abiotic bromination of particulate organic matter occurs in the presence of a range of inorganic oxidants, including hydrogen peroxide and assorted forms of ferric iron, producing both aliphatic and aromatic forms of organobromine. Bromination of oak and pine litter is limited primarily by bromide concentration. Fresh plant material is more susceptible to bromination than decayed litter and soil humus, due to a labile pool of mainly aliphatic compounds that break down during early stages of SOM formation. As the first evidence of abiotic bromination of particulate SOM, this study identifies a mechanistic source of the natural organobromine in humic substances and the soil organic horizon. Formation of organobromine through oxidative treatments of plant material also provides insights into the relative stability of aromatic and aliphatic components of SOM.

Enhanced abiotic reduction of Cr(VI) in a soil slurry system by natural biomaterial addition.

PubMed

Park, Donghee; Ahn, Chi Kyu; Kim, Young Mi; Yun, Yeoung-Sang; Park, Jong Moon

2008-12-30

Among various plant-based natural biomaterials, pine bark was chosen as an efficient biomaterial capable of removing toxic Cr(VI) from aqueous solution. XPS spectra indicated that Cr(VI) was abiotically reduced to Cr(III) in both liquid and solid phases. The Cr(VI)-reducing capacity of pine bark was determined as 545 (+/-1.3)mg-Cr(VI)g(-1) of it, which was 8.7 times higher than that of a common chemical Cr(VI)-reductant, FeSO4 x 7H2O. Because pine bark could completely reduce toxic Cr(VI) to less toxic or nontoxic Cr(III) even at neutral pH, it was used as an organic reductant to remediate Cr(VI)-contaminated soil in this study. Soil slurry system using a bottle roller was applied to ex situ slurry-phase remediation experiments. In the soil slurry system, pine bark completely reduced Cr(VI) to Cr(III) and adsorbed the reduced-Cr(III) on its surface. Abiotic remediation rate of Cr(VI)-contaminated soil increased with the increase of pine bark dosage and with the decreases of Cr(VI) and water contents. In conclusion, pine bark can be used to remediate Cr(VI)-contaminated soil efficiently and environmentally friendly.

GEOCHEMICAL FACTORS GOVERNING METHYL MERCURY PRODUCTION IN MERCURY CONTAMINATED SEDIMENTS

EPA Science Inventory

Bench scale experiments were conducted to improve our understanding of aquatic mercury transformation processes (biotic and abiotic), specifically those factors which govern the production of methyl mercury (MeHg) in sedimentary environments. The greatest cause for concern regar...

Mercury Isotopes in Earth and Environmental Sciences

NASA Astrophysics Data System (ADS)

Blum, Joel D.; Sherman, Laura S.; Johnson, Marcus W.

2014-05-01

Virtually all biotic, dark abiotic, and photochemical transformations of mercury (Hg) produce Hg isotope fractionation, which can be either mass dependent (MDF) or mass independent (MIF). The largest range in MDF is observed among geological materials and rainfall impacted by anthropogenic sources. The largest positive MIF of Hg isotopes (odd-mass excess) is caused by photochemical degradation of methylmercury in water. This signature is retained through the food web and measured in all freshwater and marine fish. The largest negative MIF of Hg isotopes (odd-mass deficit) is caused by photochemical reduction of inorganic Hg and has been observed in Arctic snow and plant foliage. Ratios of MDF to MIF and ratios of 199Hg MIF to 201Hg MIF are often diagnostic of biogeochemical reaction pathways. More than a decade of research demonstrates that Hg isotopes can be used to trace sources, biogeochemical cycling, and reactions involving Hg in the environment.

Natural and induced reduction of hexavalent chromium in soil

NASA Astrophysics Data System (ADS)

Leita, Liviana; Margon, Alja; Sinicco, Tania; Mondini, Claudio; Valentini, Massimiliano; Cantone, Pierpaolo

2013-04-01

Even though naturally elevated levels of chromium can be found naturally in some soils, distressing amounts of the hexavalent form (CrVI) are largely restricted to sites contaminated by anthropogenic activities. In fact, the widespread use of chromium in various industries and the frequently associated inadequate disposal of its by-products and wastes have created serious environmental pollution problems in many parts of the world. CrVI is toxic to plants, animals and humans and exhibits also mutagenic effects. However, being a strong oxidant, CrVI can be readily reduced to the much less harmful trivalent form (CrIII) when suitable electron donors are present in the environment. CrIII is relatively insoluble, less available for biological uptake, and thus definitely less toxic for web-biota. Various electron donors in soil can be involved in CrVI reduction in soil. The efficiency of CrVI reducing abiotic agents such as ferrous iron and sulphur compounds is well documented. Furthermore, CrVI reduction is also known to be significantly enhanced by a wide variety of cell-produced monosaccharides, including glucose. In this study we evaluated the dynamics of hexavalent chromium (CrVI) reduction in contaminated soil amended or not with iron sulphate or/and glucose and assessed the effects of CrVI on native or glucose-induced soil microbial biomass size and activity. CrVI negatively affected both soil microbial activity and the size of the microbial biomass. During the incubation period, the concentration of CrVI in soil decreased over time whether iron sulphate or/and glucose was added or not, but with different reduction rates. Soil therefore displayed a natural attenuation capacity towards chromate reduction. Addition of iron sulphate or/and glucose, however, increased the reduction rate by both abiotic and biotic mechanisms. Our data suggest that glucose is likely to have exerted an indirect role in the increased rate of CrVI reduction by promoting growth of indigenous microbial biomass, while iron sulphate exerted a direct abiotic role.

Massive production of abiotic methane during subduction evidenced in metamorphosed ophicarbonates from the Italian Alps

PubMed Central

Vitale Brovarone, Alberto; Martinez, Isabelle; Elmaleh, Agnès; Compagnoni, Roberto; Chaduteau, Carine; Ferraris, Cristiano; Esteve, Imène

2017-01-01

Alteration of ultramafic rocks plays a major role in the production of hydrocarbons and organic compounds via abiotic processes on Earth and beyond and contributes to the redistribution of C between solid and fluid reservoirs over geological cycles. Abiotic methanogenesis in ultramafic rocks is well documented at shallow conditions, whereas natural evidence at greater depths is scarce. Here we provide evidence for intense high-pressure abiotic methanogenesis by reduction of subducted ophicarbonates. Protracted (≥0.5–1 Ma), probably episodic infiltration of reduced fluids in the ophicarbonates and methanogenesis occurred from at least ∼40 km depth to ∼15–20 km depth. Textural, petrological and isotopic data indicate that methane reached saturation triggering the precipitation of graphitic C accompanied by dissolution of the precursor antigorite. Continuous infiltration of external reducing fluids caused additional methane production by interaction with the newly formed graphite. Alteration of high-pressure carbonate-bearing ultramafic rocks may represent an important source of abiotic methane, with strong implications for the mobility of deep C reservoirs. PMID:28223715

Microbial Sulfate Reduction Enhances Arsenic Mobility Downstream of Zerovalent-Iron-Based Permeable Reactive Barrier.

PubMed

Kumar, Naresh; Couture, Raoul-Marie; Millot, Romain; Battaglia-Brunet, Fabienne; Rose, Jérôme

2016-07-19

We assessed the potential of zerovalent-iron- (Fe(0)) based permeable reactive barrier (PRB) systems for arsenic (As) remediation in the presence or absence of microbial sulfate reduction. We conducted long-term (200 day) flow-through column experiments to investigate the mechanisms of As transformation and mobility in aquifer sediment (in particular, the PRB downstream linkage). Changes in As speciation in the aqueous phase were monitored continuously. Speciation in the solid phase was determined at the end of the experiment using X-ray absorption near-edge structure (XANES) spectroscopy analysis. We identified thio-As species in solution and AsS in solid phase, which suggests that the As(V) was reduced to As(III) and precipitated as AsS under sulfate-reducing conditions and remained as As(V) under abiotic conditions, even with low redox potential and high Fe(II) content (4.5 mM). Our results suggest that the microbial sulfate reduction plays a key role in the mobilization of As from Fe-rich aquifer sediment under anoxic conditions. Furthermore, they illustrate that the upstream-downstream linkage of PRB affects the speciation and mobility of As in downstream aquifer sediment, where up to 47% of total As initially present in the sediment was leached out in the form of mobile thio-As species.

Natural dissolved organic matter dynamics in karstic aquifer: O'Leno Sink-Rise system, Florida, USA

NASA Astrophysics Data System (ADS)

Jin, J.; Zimmerman, A. R.

2010-12-01

Natural dissolved organic matter (NDOM) dynamics in karstic aquifer remain poorly understood due to the inaccessibility and heterogeneity of the subsurface. Because the Santa Fe River sinks into the Floridan Aquifer and emerges 6 km down gradient, the O'Leno Sink-Rise system in Northern Florida provides an ideal setting to study NDOM transformation in groundwater. Water samples were collected at both high and low temporal resolutions over 3 years from the River Sink, Rise, and a series of shallow and deep wells. Analyses of dissolved organic and inorganic carbon, stable isotopic, and spectrophotometry (excitation-emission matrix or EEM) show that reversals of hydrologic head gradient in the conduit and matrix are closely related to the delivery of NDOM to the aquifer. In addition, the relative influence of biotic and abiotic processes varies along spatiotemporal gradients; regions of the aquifer with greatest connectivity to surface water (new NDOM and terminal electron acceptor supply) see the most microbial transformation of NDOM, while those with least connectivity see relatively greater abiotic transformation of NDOM. A source water mixing model was established for the Sink-Rise system using Mg2+ and SO42- concentrations from three end-members identified as allogenic recharge, upwelling deep water, and shallow groundwater of the Upper Floridan Aquifer. Biogeochemical processes were quantified after accounting for changes that occurred due to source water mixing, according to the model. In addition to NDOM remineralization by subsurface microbes which occurred mostly during wet periods, adsorption of NDOM onto aquifer materials as well as release of NDOM from aquifer materials was also observed. During wet periods when DOC-rich conduit water entered the matrix, progressive NDOM remineralization was found along the preferential flow paths from the conduits into the matrices. Both biotic and abiotic NDOM transformation processes were found to control channel dissolution and thus the subsurface geomorphology, all of which are linked to hydrology and climate patterns.

Fluctuation Analysis of Redox Potential to Distinguish Microbial Fe(II) Oxidation.

PubMed

Enright, A M L; Ferris, F G

2016-11-01

We developed a novel method for distinguishing abiotic and biological iron oxidation in liquid media using oxidation-reduction (redox) potential time series data. The instrument and processing algorithm were tested by immersing the tip of a Pt electrode with an Ag-AgCl reference electrode into an active iron-oxidizing biofilm in a groundwater discharge zone, as well as in two abiotic systems: a killed sample and a chemical control from the same site. We used detrended fluctuation analysis to characterize average root mean square fluctuation behavior, which was distinct in the live system. The calculated α value scaling exponents determined by detrended fluctuation analysis were significantly different at p < 0.001. This indicates that time series of electrode response data may be used to distinguish live and abiotic chemical reaction pathways. Due to the simplicity, portability, and small size, it may be suitable for characterization of extraterrestrial environments where water has been observed, such as Mars and Europa. Key Words: Oxidation-reduction potential-Detrended fluctuation analysis-Iron-oxidizing bacteria. Astrobiology 16, 846-852.

ABIOTIC REDOX TRANSFORMATION OF ORGANIC COMPOUNDS AT THE CLAY-WATER INTERFACE

EPA Science Inventory

The interactions of clay, water and organic compounds considerably modify the structural and physico-chemical properties of all components and create a unique domain for biological and chemical species in environments. Previous research indicates that the nature and properties of...

Abiotic Transformations Of 17α-Estradiol In Simulated Wastewater Influent

EPA Science Inventory

Scientists from various disciplines have been studying the fate, impact and transport of estrogens in natural and engineered systems. Emphasis is mostly focused on natural and synthetic estrogens affiliated with humans and animals. It is widely accepted that Wastewater Treatmen...

Biotic and abiotic transformations of methyl tertiary butyl ether (MTBE).

PubMed

Fischer, Axel; Oehm, Claudia; Selle, Michael; Werner, Peter

2005-11-01

Methyl tertiary butyl ether (MTBE) is a fuel additive which is used all over the world. In recent years it has often been found in groundwater, mainly in the USA, but also in Europe. Although MTBE seems to be a minor toxic, it affects the taste and odour of water at concentrations of < 30 microg/L. Although MTBE is often a recalcitrant compound, it is known that many ethers can be degraded by abiotic means. The aim of this study was to examine biotic and abiotic transformations of MTBE with respect to the particular conditions of a contaminated site (former refinery) in Leuna, Germany. Groundwater samples from wells of a contaminated site were used for aerobic and anaerobic degradation experiments. The abiotic degradation experiment (hydrolysis) was conducted employing an ion-exchange resin and MTBE solutions in distilled water. MTBE, tertiary butyl formate (TBF) and tertiary butyl alcohol (TBA) were measured by a gas chromatograph with flame ionisation detector (FID). Aldehydes and organic acids were respectively analysed by a gas chromatograph with electron capture detector (ECD) and high-performance ion chromatography (HPIC). Under aerobic conditions, MTBE was degraded in laboratory experiments. Only 4 of a total of 30 anaerobic experiments exhibited degradation, and the process was very slow. In no cases were metabolites detected, but a few degradation products (TBF, TBA and formic acid) were found on the site, possibly due to the lower temperatures in groundwater. The abiotic degradation of MTBE with an ion-exchange resin as a catalyst at pH 3.5 was much faster than hydrolysis in diluted hydrochloric acid (pH 1.0). Although the aerobic degradation of MTBE in the environment seems to be possible, the specific conditions responsible are widely unknown. Successful aerobic degradation only seems to take place if there is a lack of other utilisable compounds. However, MTBE is often accompanied by other fuel compounds on contaminated sites and anaerobic conditions prevail. MTBE is often recalcitrant under anaerobic conditions, at least in the presence of other carbon sources. The abiotic hydrolysis of MTBE seems to be of secondary importance (on site), but it might be possible to enhance it with catalysts. MTBE only seems to be recalcitrant under particular conditions. In some cases, the degradation of MTBE on contaminated sites could be supported by oxygen. Enhanced hydrolysis could also be an alternative.

Fenton process on single and mixture components of phenothiazine pharmaceuticals: Assessment of intermediaries, fate, and preliminary ecotoxicity.

PubMed

Wilde, Marcelo L; Schneider, Mandy; Kümmerer, Klaus

2017-04-01

Pharmaceuticals do not occur isolated in the environment but in multi-component mixtures and may exhibit antagonist, synergistic or additive behavior. Knowledge on this is still scarce. The situation is even more complicated if effluents or potable water is treated by oxidative processes or such transformations occur in the environment. Thus, determining the fate and effects of parent compounds, metabolites and transformation products (TPs) formed by transformation and degradation processes in the environment is needed. This study investigated the fate and preliminary ecotoxicity of the phenothiazine pharmaceuticals, Promazine (PRO), Promethazine (PRM), Chlorpromazine (CPR), and Thioridazine (THI) as single and as components of the resulting mixtures obtained from their treatment by Fenton process. The Fenton process was carried out at pH7 and by using 0.5-2mgL -1 of [Fe 2+ ] 0 and 1-12.5mgL -1 of [H 2 O 2 ] 0 at the fixed ratio [Fe 2+ ] 0 :[H 2 O 2 ] 0 of 1:10 (w:w). No complete mineralization was achieved. Constitutional isomers and some metabolite-like TPs formed were suggested based on their UHPLC-HRMS n data. A degradation pathway was proposed considering interconnected mechanisms such as sulfoxidation, hydroxylation, N-dealkylation, and dechlorination steps. Aerobic biodegradation tests (OECD 301 D and OECD 301 F) were applied to the parent compounds separately, to the mixture of parent compounds, and for the cocktail of TPs present after the treatment by Fenton process. The samples were not readily biodegradable. However, LC-MS analysis revealed that abiotic transformations, such hydrolysis, and autocatalytic transformations occurred. The initial ecotoxicity tested towards Vibrio fischeri as individual compounds featured a reduction in toxicity of PRM and CPR by the treatment process, whereas PRO showed an increase in acute luminescence inhibition and THI a stable luminescence inhibition. Concerning effects of the mixture components, reduction in toxicity by the Fenton process was predicted by concentration addition and independent action models. Copyright © 2017 Elsevier B.V. All rights reserved.

Virus induced gene silencing in Lolium temulentum

USDA-ARS?s Scientific Manuscript database

Lolium temulentum L. is valuable as a model species for studying abiotic stress in closely related forage and turf grasses, many of which are polyploid outcrossing species. As with most monocot species, Agrobacterium-mediated transformation of L. temulentum is still challenging, time consuming and n...

FRACTIONATION OF STABLE CARBON ISOTOPES DURING ABIOTIC TRANSFORMATION OF TCE

EPA Science Inventory

At a Superfund Site in Minnesota, ground water is contaminated with trichloroethylene (TCE) with the contaminant plume stretching over five miles long. The ground water is iron and manganese reducing, and the complete absence of dichloroethylene, vinyl chloride, and ethene in th...

Micropropagation, genetic engineering, and molecular biology of Populus

Treesearch

N. B. Klopfenstein; Y. W. Chun; M. -S. Kim; M. A. Ahuja; M. C. Dillon; R. C. Carman; L. G. Eskew

1997-01-01

Thirty-four Populus biotechnology chapters, written by 85 authors, are comprised in 5 sections: 1) in vitro culture (micropropagation, somatic embryogenesis, protoplasts, somaclonal variation, and germplasm preservation); 2) transformation and foreign gene expression; 3) molecular biology (molecular/genetic characterization); 4) biotic and abiotic resistance (disease,...

Transformation of Chlorpyrifos and Chlorpyrifos-Methyl in Prairie Pothole Porewaters

NASA Astrophysics Data System (ADS)

Anderson, R. M.; Chin, Y. P.

2014-12-01

The prairie pothole region (PPR) extends over approximately 700,000 km2 in the Great Plains region in United States and Canada and is a critical breeding ground for migratory waterfowl, as well as an important ecosystem for diverse invertebrates and aquatic plants (van der Valk, 2003). Consisting of up to 12 million permanent and temporary depressional wetlands, the PPR is negatively impacted by non-point source pesticide pollution due to extensive agricultural development in the region. Recent studies have shown that high (mM) levels of sulfate in the pothole lakes are capable of abiotically reducing dinitroaniline and chloroacetanilide pesticides (Zeng, 2011; Zeng, 2012). In this study the transformation of the organophosphorus pesticide chlorpyrifos (CP) and its analog chlorpyrifos-methyl (CPM) was studied using pore waters sampled from two pothole lakes. CP and CPM have been found to react in the laboratory with sulfur species via a SN2 mechanism, with degradation by sulfur compounds occurring faster than hydrolysis at high pH (Wu, 2006). To date the reaction of CP and CPM in natural environments with sulfur species has not been studied. Chlorpyrifos-methyl underwent rapid degradation in the presence of reduced sulfur species in pore water, while chlorpyrifos degradation occurred at significantly slower rates. Both CP and CPM degradation occurred at comparable rates to what has been previously observed in the laboratory (Wu, 2006). References van der Valk, Arnold G., and Roger L. Pederson. "The SWANCC decision and its implications for prairie potholes." Wetlands 23.3 (2003): 590-596. Wu, Tong, Qiu Gan, and Urs Jans. "Nucleophilic Substitution of Phosphorothionate Ester Pesticides with Bisulfide (HS-) and Polysulfides (Sn2-)." Environmental science & technology 40.17 (2006): 5428-5434. Zeng, Teng, et al. "Pesticide processing potential in prairie pothole porewaters."Environmental science & technology 45.16 (2011): 6814-6822. Zeng, Teng, Yu-Ping Chin, and William A. Arnold. "Potential for abiotic reduction of pesticides in prairie pothole porewaters." Environmental science & technology 46.6 (2012): 3177-3187.

Comparative physiological, metabolomic, and transcriptomic analyses reveal mechanisms of improved abiotic stress resistance in bermudagrass [Cynodon dactylon (L). Pers.] by exogenous melatonin

PubMed Central

Shi, Haitao; Jiang, Chuan; Ye, Tiantian; Tan, Dun-xian; Reiter, Russel J.; Zhang, Heng; Liu, Renyi; Chan, Zhulong

2015-01-01

Melatonin (N-acetyl-5-methoxytryptamine), a well-known animal hormone, is also involved in plant development and abiotic stress responses. In this study, it is shown that exogenous application of melatonin conferred improved salt, drought, and cold stress resistances in bermudagrass. Moreover, exogenous melatonin treatment alleviated reactive oxygen species (ROS) burst and cell damage induced by abiotic stress; this involved activation of several antioxidants. Additionally, melatonin-pre-treated plants exhibited higher concentrations of 54 metabolites, including amino acids, organic acids, sugars, and sugar alcohols, than non-treated plants under abiotic stress conditions. Genome-wide transcriptomic profiling identified 3933 transcripts (2361 up-regulated and 1572 down-regulated) that were differentially expressed in melatonin-treated plants versus controls. Pathway and gene ontology (GO) term enrichment analyses revealed that genes involved in nitrogen metabolism, major carbohydrate metabolism, tricarboxylic acid (TCA)/org transformation, transport, hormone metabolism, metal handling, redox, and secondary metabolism were over-represented after melatonin pre-treatment. Taken together, this study provides the first evidence of the protective roles of exogenous melatonin in the bermudagrass response to abiotic stresses, partially via activation of antioxidants and modulation of metabolic homeostasis. Notably, metabolic and transcriptomic analyses showed that the underlying mechanisms of melatonin could involve major reorientation of photorespiratory and carbohydrate and nitrogen metabolism. PMID:25225478

Abiotic reduction of trifluralin and pendimethalin by sulfides in black-carbon-amended coastal sediments.

PubMed

Gong, Wenwen; Liu, Xinhui; Xia, Shuhua; Liang, Baocui; Zhang, Wei

2016-06-05

Dinitroaniline herbicides such as trifluralin and pendimethalin are persistent bioaccumulative toxins to aquatic organisms. Thus, in-situ remediation of contaminated sediments is desired. This study investigated whether black carbons (BCs), including apple wood charcoal (BC1), rice straw biochar (BC2), and activated carbon (BC3), could facilitate abiotic reduction of trifluralin and pendimethalin by sulfides of environmentally-relevant concentrations in anoxic coastal sediments. The reduction rates of trifluralin and pendimethalin increased substantially with increasing BC dosages in the sediments. This enhancing effect was dependent on BC type with the greatest for BC3 followed by BC1 and BC2, which well correlated with their specific surface area. The pseudo-first order reduction rate constants (kobs) for BC3-amended sediment (2%) were 13- and 14 times the rate constants in the BC-free sediment. The reduction rates increased with increasing temperature from 8 to 25°C in the BC-amended sediment, following the Arrhenius relationship. Finally, through molecular modeling by density functional theory and reaction species identification from mass spectra, molecular pathways of trifluralin and pendimethalin reduction were elucidated. In contrary to the separate sequential reduction of each nitro group to amine group, both nitro groups, first reduced to nitroso, then eventually to amine groups. Copyright © 2016 Elsevier B.V. All rights reserved.

Concentration effects on biotic and abiotic processes in the removal of 1,1,2-trichloroethane and vinyl chloride using carbon-amended ZVI

NASA Astrophysics Data System (ADS)

Patterson, Bradley M.; Lee, Matthew; Bastow, Trevor P.; Wilson, John T.; Donn, Michael J.; Furness, Andrew; Goodwin, Bryan; Manefield, Mike

2016-05-01

A permeable reactive barrier, consisting of both zero valent iron (ZVI) and a biodegradable organic carbon, was evaluated for the remediation of 1,1,2-trichloroethane (1,1,2-TCA) contaminated groundwater. During an 888 day laboratory column study, degradation rates initially stabilized with a degradation half-life of 4.4 ± 0.4 days. Based on the accumulation of vinyl chloride (VC) and limited production of 1,1-dichloroethene (1,1-DCE) and 1,2-dichloroethane (1,2-DCA), the dominant degradation pathway was likely abiotic dichloroelimination to form VC. Degradation of VC was not observed based on the accumulation of VC and limited ethene production. After a step reduction in the influent concentration of 1,1,2-TCA from 170 ± 20 mg L- 1 to 39 ± 11 mg L- 1, the degradation half-life decreased 5-fold to 0.83 ± 0.17 days. The isotopic enrichment factor of 1,1,2-TCA also changed after the step reduction from - 14.6 ± 0.7‰ to - 0.72 ± 0.12‰, suggesting a possible change in the degradation mechanism from abiotic reductive degradation to biodegradation. Microbiological data suggested a co-culture of Desulfitobacterium and Dehalococcoides was responsible for the biodegradation of 1,1,2-TCA to ethene.

Detection of Abiotic Methane in Terrestrial Continental Hydrothermal Systems: Implications for Methane on Mars

NASA Technical Reports Server (NTRS)

Socki, Richard A.; Niles, Paul B.; Gibson, Everett K., Jr.; Romanek, Christopher S.; Zhang, Chuanlun L.; Bissada, Kadry K.

2008-01-01

The recent detection of methane in the Martian atmosphere and the possibility that its origin could be attributed to biological activity, have highlighted the importance of understanding the mechanisms of methane formation and its usefulness as a biomarker. Much debate has centered on the source of the methane in hydrothermal fluids, whether it is formed biologically by microorganisms, diagenetically through the decomposition of sedimentary organic matter, or inorganically via reduction of CO2 at high temperatures. Ongoing research has now shown that much of the methane present in sea-floor hydrothermal systems is probably formed through inorganic CO2 reduction processes at very high temperatures (greater than 400 C). Experimental results have indicated that methane might form inorganically at temperatures lower still, however these results remain controversial. Currently, methane in continental hydrothermal systems is thought to be formed mainly through the breakdown of sedimentary organic matter and carbon isotope equilibrium between CO2 and CH4 is thought to be rarely present if at all. Based on isotopic measurements of CO2 and CH4 in two continental hydrothermal systems, we suggest that carbon isotope equilibration exists at temperatures as low as 155 C. This would indicate that methane is forming through abiotic CO2 reduction at lower temperatures than previously thought and could bolster arguments for an abiotic origin of the methane detected in the martian atmosphere.

Case Study: Microbial Ecology and Forensics of Chinese Drywall-Elemental Sulfur Disproportionation as Primary Generator of Hydrogen Sulfide.

PubMed

Tomei Torres, Francisco A

2017-06-21

Drywall manufactured in China released foul odors attributed to volatile sulfur compounds. These included hydrogen sulfide, methyl mercaptan, and sulfur dioxide. Given that calcium sulfate is the main component of drywall, one would suspect bacterial reduction of sulfate to sulfide as the primary culprit. However, when the forensics, i.e., the microbial and chemical signatures left in the drywall, are studied, the evidence suggests that, rather than dissimilatory sulfate reduction, disproportionation of elemental sulfur to hydrogen sulfide and sulfate was actually the primary cause of the malodors. Forensic evidence suggests that the transformation of elemental sulfur went through several abiological and microbial stages: (1) partial volatilization of elemental sulfur during the manufacture of plaster of Paris, (2) partial abiotic disproportionation of elemental sulfur to sulfide and thiosulfate during the manufacture of drywall, (3) microbial disproportionation of elemental sulfur to sulfide and sulfate resulting in neutralization of all alkalinity, and acidification below pH 4, (4) acidophilic microbial disproportionation of elemental sulfur to sulfide and sulfuric acid, and (5) hydrogen sulfide volatilization, coating of copper fixtures resulting in corrosion, and oxidation to sulfur dioxide.

SORPTION AND ABIOTIC REDOX TRANSFORMATION OF NITROBENZENE AT THE SMECTITE-WATER INTERFACE

EPA Science Inventory

The effect of the redox state of structural Fe on the surface reactivity of iron-bearing phyllosilicates in aqueous suspension was investigated using a molecular probe. For this purpose the structural Fe in montmorillonite and ferruginous smectite was chemically reduced by sodium...

Carbon and nitrogen isotope effects associated with the dioxygenation of aniline and diphenylamine.

PubMed

Pati, Sarah G; Shin, Kwanghee; Skarpeli-Liati, Marita; Bolotin, Jakov; Eustis, Soren N; Spain, Jim C; Hofstetter, Thomas B

2012-11-06

Dioxygenation of aromatic rings is frequently the initial step of biodegradation of organic subsurface pollutants. This process can be tracked by compound-specific isotope analysis to assess the extent of contaminant transformation, but the corresponding isotope effects, especially for dioxygenation of N-substituted, aromatic contaminants, are not well understood. We investigated the C and N isotope fractionation associated with the biodegradation of aniline and diphenylamine using pure cultures of Burkholderia sp. strain JS667, which can biodegrade both compounds, each by a distinct dioxygenase enzyme. For diphenylamine, the C and N isotope enrichment was normal with ε(C)- and ε(N)-values of -0.6 ± 0.1‰ and -1.0 ± 0.1‰, respectively. In contrast, N isotopes of aniline were subject to substantial inverse fractionation (ε(N) of +13 ± 0.5‰), whereas the ε(C)-value was identical to that of diphenylamine. A comparison of the apparent kinetic isotope effects for aniline and diphenylamine dioxygenation with those from abiotic oxidation by manganese oxide (MnO(2)) suggest that the oxidation of a diarylamine system leads to distinct C-N bonding changes compared to aniline regardless of reaction mechanism and oxidant involved. Combined evaluation of the C and N isotope signatures of the contaminants reveals characteristic Δδ(15)N/Δδ(13)C-trends for the identification of diphenylamine and aniline oxidation in contaminated subsurfaces and for the distinction of aniline oxidation from its formation by microbial and/or abiotic reduction of nitrobenzene.

COMPARISON OF TRICHLOROETHYLENE REDUCTIVE DEHALOGENATION BY MICROBIAL COMMUNITIES STIMULATED ON SILICON-BASED ORGANIC COMPOUNDS AS SLOW-RELEASE ANAEROBIC SUBSTRATES. (R828772C001)

EPA Science Inventory

Microcosm studies were conducted to demonstrate the effectiveness of tetrabutoxysilane (TBOS) as a slow-release anaerobic substrate to promote reductive dehalogenation of trichloroethylene (TCE). The abiotic hydrolysis of TBOS and tetrakis(2-ethylbutoxy)silane (TKEBS), and the...

CARBON TETRACHLORIDE TRANSFORMATION IN A MODEL IRON-REDUCING CULTURE: RELATIVE KINETICS OF BIOTIC AND ABIOTIC REACTIONS. (R825958)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Abiotic and Biotic Transformation of TCE under Sulfate Reducing Conditions: the Role of Spatial Heterogeneity

EPA Science Inventory

At a number of sites in the USA, passive reactive barriers built with shredded plant mulch have been constructed to treat ground water contaminated with TCE. These barriers are called biowalls because anaerobic biodegradation of the plant mulch is expected to provide substrates...

Interacting effects of sunlight, agriculturally derived dissolved organic matter and reactive oxygen species on fecal indicator bacteria growth dynamics

EPA Science Inventory

Bacterial survival in agriculturally impacted surface waters is dependent on resource availability and also on potential resource transformations, mediated by biotic and abiotic processes. In this study, we focused on the effect of sunlight irradiated cattle fecal extract (CFE) a...

Authentic Research Experience and "Big Data" Analysis in the Classroom: Maize Response to Abiotic Stress

ERIC Educational Resources Information Center

Makarevitch, Irina; Frechette, Cameo; Wiatros, Natalia

2015-01-01

Integration of inquiry-based approaches into curriculum is transforming the way science is taught and studied in undergraduate classrooms. Incorporating quantitative reasoning and mathematical skills into authentic biology undergraduate research projects has been shown to benefit students in developing various skills necessary for future…

Bromate Reduction by Rhodococcus sp. Br-6 in the Presence of Multiple Redox Mediators.

PubMed

Tamai, Naoko; Ishii, Takahiro; Sato, Yusuke; Fujiya, Hiroko; Muramatsu, Yasuyuki; Okabe, Nobuaki; Amachi, Seigo

2016-10-04

A bromate (BrO 3 - )-reducing bacterium, designated Rhodococcus sp. strain Br-6, was isolated from soil. The strain reduced 250 μM bromate completely within 4 days under growth conditions transitioning from aerobic to anaerobic conditions, while no reduction was observed under aerobic and anaerobic growth conditions. Bromate was reduced to bromide (Br - ) stoichiometrically, and acetate was required as an electron donor. Interestingly, bromate reduction by strain Br-6 was significantly dependent on both ferric iron and a redox dye 2,6-dichloroindophenol (DCIP). Cell free extract of strain Br-6 showed a dicumarol-sensitive diaphorase activity, which catalyzes the reduction of DCIP in the presence of NADH. Following abiotic experiments showed that the reduced form of DCIP was reoxidized by ferric iron, and that the resulting ferrous iron reduced bromate abiotically. Furthermore, activity staining of the cell free extract revealed that one of diaphorase isoforms possessed a bromate-reducing activity. Our results demonstrate that strain Br-6 utilizes multiple redox mediators, that is, DCIP and ferric iron, for bromate reduction. Since the apparent rate of bromate reduction by this strain (60 μM day -1 ) was 3 orders of magnitude higher than that of known bromate-reducing bacteria, it could be applicable to removal of this probable human carcinogen from drinking water.

Biological versus mineralogical chromium reduction: potential for reoxidation by manganese oxide.

PubMed

Butler, Elizabeth C; Chen, Lixia; Hansel, Colleen M; Krumholz, Lee R; Elwood Madden, Andrew S; Lan, Ying

2015-11-01

Hexavalent chromium (Cr(vi), present predominantly as CrO4(2-) in water at neutral pH) is a common ground water pollutant, and reductive immobilization is a frequent remediation alternative. The Cr(iii) that forms upon microbial or abiotic reduction often co-precipitates with naturally present or added iron (Fe), and the stability of the resulting Fe-Cr precipitate is a function of its mineral properties. In this study, Fe-Cr solids were formed by microbial Cr(vi) reduction using Desulfovibrio vulgaris strain RCH1 in the presence of the Fe-bearing minerals hematite, aluminum substituted goethite (Al-goethite), and nontronite (NAu-2, Clay Minerals Society), or by abiotic Cr(vi) reduction by dithionite reduced NAu-2 or iron sulfide (FeS). The properties of the resulting Fe-Cr solids and their behavior upon exposure to the oxidant manganese (Mn) oxide (birnessite) differed significantly. In microcosms containing strain RCH1 and hematite or Al-goethite, there was significant initial loss of Cr(vi) in a pattern consistent with adsorption, and significant Cr(vi) was found in the resulting solids. The solid formed when Cr(vi) was reduced by FeS contained a high proportion of Cr(iii) and was poorly crystalline. In microcosms with strain RCH1 and hematite, Cr precipitates appeared to be concentrated in organic biofilms. Reaction between birnessite and the abiotically formed Cr(iii) solids led to production of significant dissolved Cr(vi) compared to the no-birnessite controls. This pattern was not observed in the solids generated by microbial Cr(vi) reduction, possibly due to re-reduction of any Cr(vi) generated upon oxidation by birnessite by active bacteria or microbial enzymes. The results of this study suggest that Fe-Cr precipitates formed in groundwater remediation may remain stable only in the presence of active anaerobic microbial reduction. If exposed to environmentally common Mn oxides such as birnessite in the absence of microbial activity, there is the potential for rapid (re)formation of dissolved Cr(vi) above regulatory levels.

Enantioselective reductive transformation of climbazole: A concept towards quantitative biodegradation assessment in anaerobic biological treatment processes.

PubMed

Brienza, Monica; Chiron, Serge

2017-06-01

An efficient chiral method-based using liquid chromatography-high resolution-mass spectrometry analytical method has been validated for the determination of climbazole (CBZ) enantiomers in wastewater and sludge with quantification limits below the 1 ng/L and 2 ng/g range, respectively. On the basis of this newly developed analytical method, the stereochemistry of CBZ was investigated over time in sludge biotic and sterile batch experiments under anoxic dark and light conditions and during wastewater biological treatment by subsurface flow constructed wetlands. CBZ stereoselective degradation was exclusively observed under biotic conditions, confirming the specificity of enantiomeric fraction variations to biodegradation processes. Abiotic CBZ enantiomerization was insignificant at circumneutral pH and CBZ was always biotransformed into CBZ-alcohol due to the specific and enantioselective reduction of the ketone function of CBZ into a secondary alcohol function. This transformation was almost quantitative and biodegradation gave good first order kinetic fit for both enantiomers. The possibility to apply the Rayleigh equation to enantioselective CBZ biodegradation processes was investigated. The results of enantiomeric enrichment allowed for a quantitative assessment of in situ biodegradation processes due to a good fit (R 2  > 0.96) of the anoxic/anaerobic CBZ biodegradation to the Rayleigh dependency in all the biotic microcosms and was also applied in subsurface flow constructed wetlands. This work extended the concept of applying the Rayleigh equation towards quantitative biodegradation assessment of organic contaminants to enantioselective processes operating under anoxic/anaerobic conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Kinetics of abiotic nitrous oxide production via oxidation of hydroxylamine by particulate metals in seawater

NASA Astrophysics Data System (ADS)

Cavazos, A. R.; Taillefert, M.; Glass, J. B.

2016-12-01

The oceans are a significant of nitrous oxide (N2O) to the atmosphere. Current models of global oceanic N2­O flux focus on microbial N2O cycling and often ignore abiotic reactions, such as the thermodynamically favorable oxidation of the nitrification intermediate hydroxylamine (NH2OH) by Mn(IV) or Fe(III). At circumneutral pH, NH2OH oxidation is more thermodynamically favorable via Mn(IV) than Fe(III) reduction. We characterized the kinetics of NH2OH oxidation in synthetic ocean water at pH 5.1-8.8 using microsensor electrodes to measure real-time N2O production. N2O production rates and yield were greater when NH2OH was oxidized by Mn(IV) than Fe(III). Accordingly, the reduction of Mn(IV) was first order with respect to NH2OH whereas the reduction of Fe(III) was zero order with respect to NH2OH. Interestingly, the order of the reaction with respect to Mn(IV) appears to be negative whereas the reaction is second order with respect to Fe(III). The inverse order with respect to Mn(IV) may be due to the aggregation of particles in seawater, which decreases their surface area and changes their reactivity. Finally, the reaction is first order with respect to protons with Fe(III) as the oxidant but zero order with Mn(IV). The stronger effect of the pH on the reaction with Fe(III) as the oxidant compared to Mn(IV) reflects the stoichiometry of these two reactions, as each mole of N2O produced by Fe(III) reduction consumes eight protons while each mole of N2O produced with Mn(IV) as the oxidant requires only four protons. Our data show that abiotic NH2OH oxidation by Mn(IV) or Fe(III) particles may represent a significant source of N2O in seawater. These findings suggest that abiotic N2O production in marine waters may be significant in areas of the oceans where particulate metals originating from aerosols, dust, or rivers may react with NH2OH released from ammonia-oxidizing microorganisms.

Biotic and abiotic retention, recycling and remineralization of metals in the ocean

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

Boyd, Philip W.; Ellwood, Michael J.; Tagliabue, Alessandro

Trace metals shape both the biogeochemical functioning and biological structure of oceanic provinces. Trace metal biogeochemistry has primarily focused on modes of external supply of metals from aeolian, hydrothermal, sedimentary and other sources. However, metals also undergo internal transformations such as abiotic and biotic retention, recycling and remineralization. The role of these internal transformations in metal biogeochemical cycling is now coming into focus. First, the retention of metals by biota in the surface ocean for days, weeks or months depends on taxon-specific metal requirements of phytoplankton, and on their ultimate fate: that is, viral lysis, senescence, grazing and/or export tomore » depth. Rapid recycling of metals in the surface ocean can extend seasonal productivity by maintaining higher levels of metal bioavailability compared to the influence of external metal input alone. As metal-containing organic particles are exported from the surface ocean, different metals exhibit distinct patterns of remineralization with depth. These patterns are mediated by a wide range of physicochemical and microbial processes such as the ability of particles to sorb metals, and are influenced by the mineral and organic characteristics of sinking particles. We conclude that internal metal transformations play an essential role in controlling metal bioavailability, phytoplankton distributions and the subsurface resupply of metals.« less

Genome-wide analysis of the GH3 family in apple (Malus × domestica).

PubMed

Yuan, Huazhao; Zhao, Kai; Lei, Hengjiu; Shen, Xinjie; Liu, Yun; Liao, Xiong; Li, Tianhong

2013-05-02

Auxin plays important roles in hormone crosstalk and the plant's stress response. The auxin-responsive Gretchen Hagen3 (GH3) gene family maintains hormonal homeostasis by conjugating excess indole-3-acetic acid (IAA), salicylic acid (SA), and jasmonic acids (JAs) to amino acids during hormone- and stress-related signaling pathways. With the sequencing of the apple (Malus × domestica) genome completed, it is possible to carry out genomic studies on GH3 genes to indentify candidates with roles in abiotic/biotic stress responses. Malus sieversii Roem., an apple rootstock with strong drought tolerance and the ancestral species of cultivated apple species, was used as the experimental material. Following genome-wide computational and experimental identification of MdGH3 genes, we showed that MdGH3s were differentially expressed in the leaves and roots of M. sieversii and that some of these genes were significantly induced after various phytohormone and abiotic stress treatments. Given the role of GH3 in the negative feedback regulation of free IAA concentration, we examined whether phytohormones and abiotic stresses could alter the endogenous auxin level. By analyzing the GUS activity of DR5::GUS-transformed Arabidopsis seedlings, we showed that ABA, SA, salt, and cold treatments suppressed the auxin response. These findings suggest that other phytohormones and abiotic stress factors might alter endogenous auxin levels. Previous studies showed that GH3 genes regulate hormonal homeostasis. Our study indicated that some GH3 genes were significantly induced in M. sieversii after various phytohormone and abiotic stress treatments, and that ABA, SA, salt, and cold treatments reduce the endogenous level of axuin. Taken together, this study provides evidence that GH3 genes play important roles in the crosstalk between auxin, other phytohormones, and the abiotic stress response by maintaining auxin homeostasis.

Transgenic banana plants overexpressing a native plasma membrane aquaporin MusaPIP1;2 display high tolerance levels to different abiotic stresses.

PubMed

Sreedharan, Shareena; Shekhawat, Upendra K S; Ganapathi, Thumballi R

2013-10-01

Water transport across cellular membranes is regulated by a family of water channel proteins known as aquaporins (AQPs). As most abiotic stresses like suboptimal temperatures, drought or salinity result in cellular dehydration, it is imperative to study the cause-effect relationship between AQPs and the cellular consequences of abiotic stress stimuli. Although plant cells have a high isoform diversity of AQPs, the individual and integrated roles of individual AQPs in optimal and suboptimal physiological conditions remain unclear. Herein, we have identified a plasma membrane intrinsic protein gene (MusaPIP1;2) from banana and characterized it by overexpression in transgenic banana plants. Cellular localization assay performed using MusaPIP1;2::GFP fusion protein indicated that MusaPIP1;2 translocated to plasma membrane in transformed banana cells. Transgenic banana plants overexpressing MusaPIP1;2 constitutively displayed better abiotic stress survival characteristics. The transgenic lines had lower malondialdehyde levels, elevated proline and relative water content and higher photosynthetic efficiency as compared to equivalent controls under different abiotic stress conditions. Greenhouse-maintained hardened transgenic plants showed faster recovery towards normal growth and development after cessation of abiotic stress stimuli, thereby underlining the importance of these plants in actual environmental conditions wherein the stress stimuli is often transient but severe. Further, transgenic plants where the overexpression of MusaPIP1;2 was made conditional by tagging it with a stress-inducible native dehydrin promoter also showed similar stress tolerance characteristics in in vitro and in vivo assays. Plants developed in this study could potentially enable banana cultivation in areas where adverse environmental conditions hitherto preclude commercial banana cultivation. © 2013 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Comparative physiological, metabolomic, and transcriptomic analyses reveal mechanisms of improved abiotic stress resistance in bermudagrass [Cynodon dactylon (L). Pers.] by exogenous melatonin.

PubMed

Shi, Haitao; Jiang, Chuan; Ye, Tiantian; Tan, Dun-Xian; Reiter, Russel J; Zhang, Heng; Liu, Renyi; Chan, Zhulong

2015-02-01

Melatonin (N-acetyl-5-methoxytryptamine), a well-known animal hormone, is also involved in plant development and abiotic stress responses. In this study, it is shown that exogenous application of melatonin conferred improved salt, drought, and cold stress resistances in bermudagrass. Moreover, exogenous melatonin treatment alleviated reactive oxygen species (ROS) burst and cell damage induced by abiotic stress; this involved activation of several antioxidants. Additionally, melatonin-pre-treated plants exhibited higher concentrations of 54 metabolites, including amino acids, organic acids, sugars, and sugar alcohols, than non-treated plants under abiotic stress conditions. Genome-wide transcriptomic profiling identified 3933 transcripts (2361 up-regulated and 1572 down-regulated) that were differentially expressed in melatonin-treated plants versus controls. Pathway and gene ontology (GO) term enrichment analyses revealed that genes involved in nitrogen metabolism, major carbohydrate metabolism, tricarboxylic acid (TCA)/org transformation, transport, hormone metabolism, metal handling, redox, and secondary metabolism were over-represented after melatonin pre-treatment. Taken together, this study provides the first evidence of the protective roles of exogenous melatonin in the bermudagrass response to abiotic stresses, partially via activation of antioxidants and modulation of metabolic homeostasis. Notably, metabolic and transcriptomic analyses showed that the underlying mechanisms of melatonin could involve major reorientation of photorespiratory and carbohydrate and nitrogen metabolism. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Sedimentary reservoir oxidation during geologic CO2 sequestration

NASA Astrophysics Data System (ADS)

Lammers, Laura N.; Brown, Gordon E.; Bird, Dennis K.; Thomas, Randal B.; Johnson, Natalie C.; Rosenbauer, Robert J.; Maher, Katharine

2015-04-01

Injection of carbon dioxide into subsurface geologic reservoirs during geologic carbon sequestration (GCS) introduces an oxidizing supercritical CO2 phase into a subsurface geologic environment that is typically reducing. The resulting redox disequilibrium provides the chemical potential for the reduction of CO2 to lower free energy organic species. However, redox reactions involving carbon typically require the presence of a catalyst. Iron oxide minerals, including magnetite, are known to catalyze oxidation and reduction reactions of C-bearing species. If the redox conditions in the reservoir are modified by redox transformations involving CO2, such changes could also affect mineral stability, leading to dissolution and precipitation reactions and alteration of the long-term fate of CO2 in GCS reservoirs. We present experimental evidence that reservoirs with reducing redox conditions are favorable environments for the relatively rapid abiotic reduction of CO2 to organic molecules. In these experiments, an aqueous suspension of magnetite nanoparticles was reacted with supercritical CO2 under pressure and temperature conditions relevant to GCS in sedimentary reservoirs (95-210 °C and ∼100 bars of CO2). Hydrogen production was observed in several experiments, likely caused by Fe(II) oxidation either at the surface of magnetite or in the aqueous phase. Heating of the Fe(II)-rich system resulted in elevated PH2 and conditions favorable for the reduction of CO2 to acetic acid. Implications of these results for the long-term fate of CO2 in field-scale systems were explored using reaction path modeling of CO2 injection into reservoirs containing Fe(II)-bearing primary silicate minerals, with kinetic parameters for CO2 reduction obtained experimentally. The results of these calculations suggest that the reaction of CO2 with reservoir constituents will occur in two primary stages (1) equilibration of CO2 with organic acids resulting in mineral-fluid disequilibrium, and (2) gradual dissolution of primary minerals promoting significant CO2 reduction through the release of Fe(II). The reduction of CO2 is identified as a new trapping mechanism that could significantly enhance the long-term stability of GCS reservoirs. Identification of reservoir characteristics that promote CO2 redox transformations could be used as an additional factor in screening geologic reservoirs for GCS.

The Promoter of AtUSP Is Co-regulated by Phytohormones and Abiotic Stresses in Arabidopsis thaliana.

PubMed

Bhuria, Monika; Goel, Parul; Kumar, Sanjay; Singh, Anil K

2016-01-01

Universal stress proteins (USPs) are known to be expressed in response to various abiotic stresses in a wide variety of organisms, such as bacteria, archaebacteria, protists, algae, fungi, plants, and animals. However, in plants, biological function of most of the USPs still remains obscure. In the present study, Arabidopsis USP gene ( AtUSP ) showed induction in response to abscisic acid (ABA) and various abiotic stresses viz . heat, dehydration, salt, osmotic, and cold stresses. Additionally, in silico analysis of AtUSP promoter identified several cis -elements responsive to phytohormones and abiotic stresses such as ABRE, ERE, DRE, and HSE, etc. To functionally validate the AtUSP promoter, the 1115 bp region of promoter was characterized under phytohormone and abiotic stress treatments. Deletion analysis of promoter was carried out by cloning the full length promoter (D0) and its three 5' deletion derivatives, D1 (964 bp), D2 (660 bp), and D3 (503 bp) upstream of the β-glucuronidase (GUS) reporter gene, which were then stably transformed in Arabidopsis plants. The AtUSP promoter (D0) showed minimal activity under non-stress conditions which was enhanced in response to phytohormone treatments (ABA and ACC) and abiotic stresses such as dehydration, heat, cold, salt, and osmotic stresses. The seedlings harboring D1 and D2 deletion fragments showed constitutive GUS expression even under control condition with increased activity almost under all the treatments. However, D3 seedlings exhibited complete loss of activity under control condition with induction under ACC treatment, dehydration, heat, oxidative, salt, and osmotic stresses. Thus, present study clearly showed that AtUSP promoter is highly inducible by phytohormones and multiple abiotic stresses and it can be exploited as stress inducible promoter to generate multi-stress tolerant crops with minimal effects on their other important traits.

Unravelling chemical priming machinery in plants: the role of reactive oxygen-nitrogen-sulfur species in abiotic stress tolerance enhancement.

PubMed

Antoniou, Chrystalla; Savvides, Andreas; Christou, Anastasis; Fotopoulos, Vasileios

2016-10-01

Abiotic stresses severely limit crop yield and their detrimental effects are aggravated by climate change. Chemical priming is an emerging field in crop stress management. The exogenous application of specific chemical agents before stress events results in tolerance enhancement and reduction of stress impacts on plant physiology and growth. However, the molecular mechanisms underlying the remarkable effects of chemical priming on plant physiology remain to be elucidated. Reactive oxygen, nitrogen and sulfur species (RONSS) are molecules playing a vital role in the stress acclimation of plants. When applied as priming agents, RONSS improve stress tolerance. This review summarizes the recent knowledge on the role of RONSS in cell signalling and gene regulation contributing to abiotic stress tolerance enhancement. Copyright © 2016 Elsevier Ltd. All rights reserved.

Chemical formation of hybrid di-nitrogen calls fungal codenitrification into question

PubMed Central

Phillips, Rebecca L.; Song, Bongkeun; McMillan, Andrew M. S.; Grelet, Gwen; Weir, Bevan S.; Palmada, Thilak; Tobias, Craig

2016-01-01

Removal of excess nitrogen (N) can best be achieved through denitrification processes that transform N in water and terrestrial ecosystems to di-nitrogen (N2) gas. The greenhouse gas nitrous oxide (N2O) is considered an intermediate or end-product in denitrification pathways. Both abiotic and biotic denitrification processes use a single N source to form N2O. However, N2 can be formed from two distinct N sources (known as hybrid N2) through biologically mediated processes of anammox and codenitrification. We questioned if hybrid N2 produced during fungal incubation at neutral pH could be attributed to abiotic nitrosation and if N2O was consumed during N2 formation. Experiments with gas chromatography indicated N2 was formed in the presence of live and dead fungi and in the absence of fungi, while N2O steadily increased. We used isotope pairing techniques and confirmed abiotic production of hybrid N2 under both anoxic and 20% O2 atmosphere conditions. Our findings question the assumptions that (1) N2O is an intermediate required for N2 formation, (2) production of N2 and N2O requires anaerobiosis, and (3) hybrid N2 is evidence of codenitrification and/or anammox. The N cycle framework should include abiotic production of N2. PMID:27976694

Chemical formation of hybrid di-nitrogen calls fungal codenitrification into question.

PubMed

Phillips, Rebecca L; Song, Bongkeun; McMillan, Andrew M S; Grelet, Gwen; Weir, Bevan S; Palmada, Thilak; Tobias, Craig

2016-12-15

Removal of excess nitrogen (N) can best be achieved through denitrification processes that transform N in water and terrestrial ecosystems to di-nitrogen (N 2 ) gas. The greenhouse gas nitrous oxide (N 2 O) is considered an intermediate or end-product in denitrification pathways. Both abiotic and biotic denitrification processes use a single N source to form N 2 O. However, N 2 can be formed from two distinct N sources (known as hybrid N 2 ) through biologically mediated processes of anammox and codenitrification. We questioned if hybrid N 2 produced during fungal incubation at neutral pH could be attributed to abiotic nitrosation and if N 2 O was consumed during N 2 formation. Experiments with gas chromatography indicated N 2 was formed in the presence of live and dead fungi and in the absence of fungi, while N 2 O steadily increased. We used isotope pairing techniques and confirmed abiotic production of hybrid N 2 under both anoxic and 20% O 2 atmosphere conditions. Our findings question the assumptions that (1) N 2 O is an intermediate required for N 2 formation, (2) production of N 2 and N 2 O requires anaerobiosis, and (3) hybrid N 2 is evidence of codenitrification and/or anammox. The N cycle framework should include abiotic production of N 2 .

Abiotic and Biotic Transformation of TCE under Sulfate Reducing Conditions: the Role of Spatial Heterogeneity (Monterey, CA)

EPA Science Inventory

At a number of sites in the USA, passive reactive barriers built with shredded plant mulch have been constructed to treat ground water contaminated with TCE. These barriers are called biowalls because anaerobic biodegradation of the plant mulch is expected to provide substrates ...

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

Chaurasia, Neha; Mishra, Yogesh; Rai, Lal Chand

Phytochelatin synthase (PCS) is involved in the synthesis of phytochelatins (PCs), plays role in heavy metal detoxification. The present study describes for first time the functional expression and characterization of pcs gene of Anabaena sp. PCC 7120 in Escherichia coli in terms of offering protection against heat, salt, carbofuron (pesticide), cadmium, copper, and UV-B stress. The involvement of pcs gene in tolerance to above abiotic stresses was investigated by cloning of pcs gene in expression vector pGEX-5X-2 and its transformation in E. coli BL21 (DE3). The E. coli cells transformed with pGEX-5X-pcs showed better growth than control cells (pGEX-5X-2) undermore » temperature (47 deg. C), NaCl (6% w/v), carbofuron (0.025 mg ml{sup -1}), CdCl{sub 2} (4 mM), CuCl{sub 2} (1 mM), and UV-B (10 min) exposure. The enhanced expression of pcs gene revealed by RT-PCR analysis under above stresses at different time intervals further advocates its role in tolerance against above abiotic stresses.« less

Co-transforming bar and CsALDH Genes Enhanced Resistance to Herbicide and Drought and Salt Stress in Transgenic Alfalfa (Medicago sativa L.)

PubMed Central

Duan, Zhen; Zhang, Daiyu; Zhang, Jianquan; Di, Hongyan; Wu, Fan; Hu, Xiaowen; Meng, Xuanchen; Luo, Kai; Zhang, Jiyu; Wang, Yanrong

2015-01-01

Drought and high salinity are two major abiotic factors that restrict the productivity of alfalfa. By application of the Agrobacterium-mediated transformation method, an oxidative responsive gene, CsALDH12A1, from the desert grass Cleistogenes songorica together with the bar gene associated with herbicide resistance, were co-transformed into alfalfa (Medicago sativa L.). From the all 90 transformants, 16 were positive as screened by spraying 1 mL L-1 10% Basta solution and molecularly diagnosis using PCR. Real-time PCR analysis indicated that drought and salt stress induced high CsALDH expression in the leaves of the transgenic plants. The CsALDH expression levels under drought (15 d) and salt stress (200 mM NaCl) were 6.11 and 6.87 times higher than in the control plants, respectively. In comparison to the WT plants, no abnormal phenotypes were observed among the transgenic plants, which showed significant enhancement of tolerance to 15 d of drought and 10 d of salinity treatment. Evaluation of the physiological and biochemical indices during drought and salt stress of the transgenic plants revealed relatively lower Na+ content and higher K+ content in the leaves relative to the WT plants, a reduction of toxic on effects and maintenance of osmotic adjustment. In addition, the transgenic plants could maintain a higher relative water content level, higher shoot biomass, fewer changes in the photosystem, decreased membrane injury, and a lower level of osmotic stress. These results indicate that the co-expression of the introduced bar and CsALDH genes enhanced the herbicide, drought and salt tolerance of alfalfa and therefore can potentially be used as a novel genetic resource for the future breeding programs to develop new cultivars. PMID:26734025

The long-term legacy of geomorphic and riparian vegetation feedbacks on the dammed Bill Williams River, Arizona, USA

USGS Publications Warehouse

Kui, Li; Stella, John C.; Shafroth, Patrick B.; House, P. Kyle; Wilcox, Andrew C.

2017-01-01

On alluvial rivers, fluvial landforms and riparian vegetation communities codevelop as a result of feedbacks between plants and abiotic processes. The influence of vegetation on river channel and floodplain geomorphology can be particularly strong on dammed rivers with altered hydrology and reduced flood disturbance. We used a 56-year series of aerial photos on the dammed Bill Williams River (Arizona, USA) to investigate how (a) different woody riparian vegetation types influence river channel planform and (b) how different fluvial landforms drive the composition of riparian plant communities over time. We mapped vegetation types and geomorphic surfaces and quantified how relations between fluvial and biotic processes covaried over time using linear mixed models. In the decades after the dam was built, woody plant cover within the river's bottomland nearly doubled, narrowing the active channel by 60% and transforming its planform from wide and braided to a single thread and more sinuous channel. Compared with native cottonwood–willow vegetation, nonnative tamarisk locally induced a twofold greater reduction in channel braiding. Vegetation expanded at different rates depending on the type of landform, with tamarisk cover on former high-flow channels increasing 17% faster than cottonwood–willow. Former low-flow channels with frequent inundation supported a greater increase in cottonwood–willow relative to tamarisk. These findings give insight into how feedbacks between abiotic and biotic processes in river channels accelerate and fortify changes triggered by dam construction, creating river systems increasingly distinct from predam ecological communities and landforms, and progressively more resistant to restoration of predam forms and processes.

Defining the Molecular-Cellular-Field Continuum of Mercury Detoxification

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

Summers, Anne O.

Hg is of special interest to DOE due to past intensive use in manufacture of nuclear weapons at the Oak Ridge Reservation (ORR). Because of its facile oxidation/reduction [Hg(II)/Hg(0)] chemistry, ability to bond to carbon [as in highly toxic methylmercury: MeHg(I)] and its unique physical properties [e.g., volatility of Hg(0)], Hg has a complex environmental cycle involving soils, sediments, waterways and the atmosphere and including biotic and abiotic chemical and physical transport and transformations.1 Understanding such processes well enough to design stewardship plans that minimize negative impacts in diverse ecological settings requires rich knowledge of the contributing abiotic and bioticmore » processes. Prokaryotes are major players in the global Hg cycle. Facultative and anaerobic bacteria can form MeHg(I) with consequent intoxication of wildlife and humans. Sustainable stewardship of Hg-contaminated sites requires eliminating not only MeHg(I) but also the Hg(II) substrate for methylation. Fortunately, a variety of mercury resistant (HgR) aerobic and facultative bacteria and archaea can do both things. Prokaryotes harboring narrow or broad Hg resistance (mer) loci detoxify Hg(II) or RHg(I), respectively, to relatively inert, less toxic, volatile Hg(0). HgR microbes are enriched in highly contaminated sites and extensive field data show they depress levels of MeHg >500-fold in such zones2. So, enhancing the natural capacity of indigenous HgR microbes to remove Hg(II) and RHg(I) from soils, sediments and waterways is a logical component of a comprehensive plan for clean up and stewardship of contaminated sites.« less

Studies of biominerals relevant to the search for life on Mars.

PubMed

Blanco, Armando; D'Elia, Marcella; Licchelli, Domenico; Orofino, Vincenzo; Fonti, Sergio

2006-12-01

The evidence of the water erosion on Mars is particularly interesting since present climatic conditions are such that liquid water cannot exist at the surface. But, if water was present on the planet in the past, there may have been life, too. Since the discovery of carbonates on Mars also may have very important implications on the possibility that life developed there, we are studying minerals that can have biotic or abiotic origin: calcite (CaCO(3)) and aragonite, a metastable state of calcite.We have analysed biomineral aragonite, in the form of recent sea shells, as well as crystals of mineral aragonite. Infrared spectroscopy in the 2-25 mum wavelength range reveals that, after thermal processing, the biotic samples have a different spectral behaviour from the abiotic ones. As a result, it is possible to distinguish abiotic mineral aragonite from aragonite of recent biological origin.Obviously, if life existed in the past on the Red Planet, we could expect to find "ancient" biotic carbonates, which should therefore be investigated, in order to search for a way of discriminating them from abiotic minerals. For this reason, at the beginning we have considered samples of crushed fossil shells of aragonite composition. Afterwards, in order to take into account that fossilization processes almost always produce a transformation of metastable form (aragonite) into more stable form (calcite), we also studied samples of mineral calcite and different types of fossils completely transformed into calcite. All these biotic fossil samples show the same spectral behaviour as the fresh biotic material after thermal annealing at 485 degrees C. Instead, the calcite behaves like abiotic aragonite.Furthermore, it is known that seashells and other biominerals are formed through an intimate association of inorganic materials with organic macromolecules. The macromolecules control the nucleation, structure, morphology, crystal orientation and spatial confinement of the inorganic phase: this differentiates biominerals from minerals. Analysing the aragonite or calcite fossils with a Scanning Electron Microscope, we found that the fossilization process did not modify the structure of the biominerals which maintain their microscopic characteristics. Looking at the morphology of fossil biominerals, it is evident that the crystals are arranged in complex architectures compared with the compact structure of the mineral crystals. In conclusion, the properties and structure of the biominerals are different from those of the minerals. The rapid increase of the crystalline structure developed under biotic conditions makes these minerals less resistant to thermal treatments, compared with samples of abiotic origin. This result holds both for recent shells as well as all fossil samples. The spectroscopic behaviour of all analysed calcium carbonates of biotic origin is different from that of the abiotic one. Therefore, the infrared spectroscopy is a valid technique to discern the origin of the samples and a powerful tool for analysing in-situ and "sample-return" Mars missions specimens. Also Optical and Scanning Electron Microscopy can be useful to support this type of studies.

Evidence for photolytic and microbial degradation processes in the dissipation of leptospermone, a natural β-triketone herbicide.

PubMed

Romdhane, Sana; Devers-Lamrani, Marion; Martin-Laurent, Fabrice; Jrad, Amani Ben; Raviglione, Delphine; Salvia, Marie-Virginie; Besse-Hoggan, Pascale; Dayan, Franck E; Bertrand, Cédric; Barthelmebs, Lise

2017-07-17

Bioherbicides appear as an ecofriendly alternative to synthetic herbicides, generally used for weed management, because they are supposed to have low side on human health and ecosystems. In this context, our work aims to study abiotic (i.e., photolysis) and biotic (i.e,. biodegradation) processes involved in the fate of leptospermone, a natural β-triketone herbicide, by combining chemical and microbiological approaches. Under controlled conditions, the photolysis of leptospermone was sensitive to pH. Leptospermone has a half-life of 72 h under simulated solar light irradiations. Several transformation products, including hydroxy-leptospermone, were identified. For the first time, a bacterial strain able to degrade leptospermone was isolated from an arable soil. Based on its 16S ribosomal RNA (rRNA) gene sequence, it was affiliated to the Methylophilus group and was accordingly named as Methylophilus sp. LS1. Interestingly, we report that the abundance of OTUs, similar to the 16S rRNA gene sequence of Methylophilus sp. LS1, was strongly increased in soil treated with leptospermone. The leptospermone was completely dissipated by this bacteria, with a half-life time of 6 days, allowing concomitantly its growth. Hydroxy-leptospermone was identified in the bacterial culture as a major transformation product, allowing us to propose a pathway of transformation of leptospermone including both abiotic and biotic processes.

Progress of tissue culture and genetic transformation research in pigeon pea [Cajanus cajan (L.) Millsp.].

PubMed

Krishna, Gaurav; Reddy, P Sairam; Ramteke, P W; Bhattacharya, P S

2010-10-01

Pigeon pea [Cajanus cajan (L.) Millsp.] (Family: Fabaceae) is an important legume crop cultivated across 50 countries in Asia, Africa, and the Americas; and ranks fifth in area among pulses after soybean, common bean, peanut, and chickpea. It is consumed as a major source of protein (21%) to the human population in many developing countries. In India, it is the second important food legume contributing to 80% of the global production. Several biotic and abiotic stresses are posing a big threat to its production and productivity. Attempts to address these problems through conventional breeding methods have met with partial success. This paper reviews the chronological progress made in tissue culture through organogenesis and somatic embryogenesis, including the influence of factors such as genotypes, explant sources, and culture media including the supplementation of plant growth regulators. Comprehensive lists of morphogenetic pathways involved in in vitro regeneration through organogenesis and somatic embryogenesis using different explant tissues of diverse pigeon pea genotypes are presented. Similarly, the establishment of protocols for the production of transgenics via particle bombardment and Agrobacterium-mediated transformation using different explant tissues, Agrobacterium strains, Ti plasmids, and plant selectable markers, as well as their interactions on transformation efficiency have been discussed. Future research thrusts on the use of different promoters and stacking of genes for various biotic and abiotic stresses in pigeon pea are suggested.

Stable expression of mtlD gene imparts multiple stress tolerance in finger millet.

PubMed

Hema, Ramanna; Vemanna, Ramu S; Sreeramulu, Shivakumar; Reddy, Chandrasekhara P; Senthil-Kumar, Muthappa; Udayakumar, Makarla

2014-01-01

Finger millet is susceptible to abiotic stresses, especially drought and salinity stress, in the field during seed germination and early stages of seedling development. Therefore developing stress tolerant finger millet plants combating drought, salinity and associated oxidative stress in these two growth stages is important. Cellular protection through osmotic adjustment and efficient free radical scavenging ability during abiotic stress are important components of stress tolerance mechanisms in plants. Mannitol, an osmolyte, is known to scavenge hydroxyl radicals generated during various abiotic stresses and thereby minimize stress damage in several plant species. In this study transgenic finger millet plants expressing the mannitol biosynthetic pathway gene from bacteria, mannitol-1-phosphate dehydrogenase (mtlD), were developed through Agrobacterium tumefaciens-mediated genetic transformation. mtlD gene integration in the putative transgenic plants was confirmed by Southern blot. Further, performance of transgenic finger millet under drought, salinity and oxidative stress was studied at plant level in T1 generation and in T1 and T2 generation seedlings. Results from these experiments showed that transgenic finger millet had better growth under drought and salinity stress compared to wild-type. At plant level, transgenic plants showed better osmotic adjustment and chlorophyll retention under drought stress compared to the wild-type. However, the overall increase in stress tolerance of transgenics for the three stresses, especially for oxidative stress, was only marginal compared to other mtlD gene expressing plant species reported in the literature. Moreover, the Agrobacterium-mediated genetic transformation protocol developed for finger millet in this study can be used to introduce diverse traits of agronomic importance in finger millet.

Biological and Abiotic Transformations of Ethylene Dibromide and 1,2-Dichloroethane in Ground Water at Leaded Gasoline Spill Sites

EPA Science Inventory

Tetra-ethyl lead was widely used in leaded automobile gasoline from 1923 until 1987. To prevent lead deposits from fouling the engine, 1,2-dibromoethane (EDB) and 1,2-dichloroethane (1,2-DCA) were added to the gasoline to act as lead scavengers. The Maximum Contaminant Levels...

Simultaneous influence of indigenous microorganism along with abiotic factors controlling arsenic mobilization in Brahmaputra floodplain, India

NASA Astrophysics Data System (ADS)

Sathe, Sandip S.; Mahanta, Chandan; Mishra, Pushpanjali

2018-06-01

In the dynamic cycling of oxic and anoxic aqueous alluvial aquifer environments, varying Arsenic (As) concentrations are controlled by both abiotic and biotic factors. Studies have shown a significant form of toxic As (III) being released through the reductive dissolution of iron-oxy/hydroxide minerals and microbial reduction mechanisms, which leads to a serious health concern. The present study was performed in order to assess the abiotic and biotic factors influencing As release into the alluvial aquifer groundwater in Brahmaputra floodplain, India. The groundwater chemistry, characterization of the sediments, isolation, identification and characterization of prominent As releasing indigenous bacterium were conducted. The measured solid and liquid phases of total As concentration were ranged between 0.02 and 17.2 mg kg-1 and 8 to 353 μg L-1, respectively. The morphology and mineralogy showed the presence of detrital and authigenic mineral assemblages whereas primary and secondary As bearing Realgar and Claudetite minerals were identified, respectively. Furthermore, significant non-labile As fraction was found associated with the amorphous oxides of Fe, Mn and Al. The observed groundwater chemistry and sediment color, deduced a sub-oxic reducing aquifer conditions in As-contaminated regions. In addition, 16S rDNA sequencing results of the isolated bacterium showed the prominent Pseudomonas aeruginosa responsible for the mobilization of As, reducing condition, biomineralization and causing grey color to the sediments at the shallower and deeper aquifers in the study area. These findings suggest that microbial metabolic activities are equally responsible in iron-oxy/hydroxide reductive dissolution, controlling As mobilization in dynamic fluvial flood plains.

SERDP ER-1421 Abiotic and Biotic Mechanisms Controlling In Situ Remediation of NDMA: Final Report

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

Szecsody, James E.; McKinley, James P.; Crocker, Fiona H.

This laboratory-scale project was initiated to investigate in situ abiotic/biotic mineralization of NDMA. Under iron-reducing conditions, aquifer sediments showed rapid abiotic NDMA degradation to dimethylamine (DMA), nitrate, formate, and finally, CO2. These are the first reported experiments of abiotic NDMA mineralization. The NDMA reactivity of these different iron phases showed that adsorbed ferrous iron was the dominant reactive phase that promoted NDMA reduction, and other ferrous phases present (siderite, iron sulfide, magnetite, structural ferrous iron in 2:1 clays) did not promote NDMA degradation. In contrast, oxic sediments that were biostimulated with propane promoted biomineralization of NDMA by a cometabolic monooxygenasemore » enzyme process. Other monooxygenase enzyme processes were not stimulated with methane or toluene additions, and acetylene addition did not block mineralization. Although NDMA mineralization extent was the highest in oxic, biostimulated sediments (30 to 82%, compared to 10 to 26% for abiotic mineralization in reduced sediments), large 1-D column studies (high sediment/water ratio of aquifers) showed 5.6 times higher NDMA mineralization rates in reduced sediment (half-life 410 ± 147 h) than oxic biomineralization (half life 2293 ± 1866 h). Sequential reduced/oxic biostimulated sediment mineralization (half-life 3180 ± 1094 h) was also inefficient compared to reduced sediment. These promising laboratory-scale results for NDMA mineralization should be investigated at field scale. Future studies of NDMA remediation should focus on the comparison of this in situ abiotic NDMA mineralization (iron-reducing environments) to ex situ biomineralization, which has been shown successful in other studies.« less

Comparative in Silico Analysis of Ferric Reduction Oxidase (FRO) Genes Expression Patterns in Response to Abiotic Stresses, Metal and Hormone Applications.

PubMed

Muhammad, Izhar; Jing, Xiu-Qing; Shalmani, Abdullah; Ali, Muhammad; Yi, Shi; Gan, Peng-Fei; Li, Wen-Qiang; Liu, Wen-Ting; Chen, Kun-Ming

2018-05-12

The ferric reduction oxidase (FRO) gene family is involved in various biological processes widely found in plants and may play an essential role in metal homeostasis, tolerance and intricate signaling networks in response to a number of abiotic stresses. Our study describes the identification, characterization and evolutionary relationships of FRO genes families. Here, total 50 FRO genes in Plantae and 15 ‘FRO like’ genes in non-Plantae were retrieved from 16 different species. The entire FRO genes have been divided into seven clades according to close similarity in biological and functional behavior. Three conserved domains were common in FRO genes while in two FROs sub genome have an extra NADPH-Ox domain, separating the function of plant FROs. OsFRO1 and OsFRO7 genes were expressed constitutively in rice plant. Real-time RT-PCR analysis demonstrated that the expression of OsFRO1 was high in flag leaf, and OsFRO7 gene expression was maximum in leaf blade and flag leaf. Both genes showed vigorous expressions level in response to different abiotic and hormones treatments. Moreover, the expression of both genes was also substantial under heavy metal stresses. OsFRO1 gene expression was triggered following 6 h under Zn, Pb, Co and Ni treatments, whereas OsFRO7 gene expression under Fe, Pb and Ni after 12 h, Zn and Cr after 6 h, and Mn and Co after 3 h treatments. These findings suggest the possible involvement of both the genes under abiotic and metal stress and the regulation of phytohormones. Therefore, our current work may provide the foundation for further functional characterization of rice FRO genes family.

Contribution of microorganisms to non-extractable residue formation from biodegradable organic contaminants in soil

NASA Astrophysics Data System (ADS)

Nowak, K. M.; Girardi, C.; Miltner, A.; Schäffer, A.; Kästner, M.

2012-04-01

Biodegradation of organic contaminants in soil is actually understood as their transformation into various primary metabolites, microbial biomass, mineralisation products and non-extractable residues (NER). NER are generally considered to be composed of parent compounds or primary metabolites with hazardous potential. Up to date, however, their chemical composition remains still unclear. Studies on NER formation are limited to quantitative analyses in soils or to simple humic acids-contaminant systems. However, in the case of biodegradable organic compounds, NER may also contain microbial biomass components, e.g. fatty acids (FA) and amino acids (AA). After cell death, these biomolecules are incorporated into soil organic matter (SOM) and stabilised, ultimately forming biogenic residues which are not any more extractable. We investigated the incorporation of the 13C-label into FA and AA and their fate during biodegradation experiments in soil with isotope-labelled 2,4-dichlorophenoxyacetic acid (13C6-2,4-D) and ibuprofen (13C6-ibu) as model organic contaminants. Our study proved for the first time that nearly all NER formed from 13C6-2,4-D and 13C6-ibu in soil derived from harmless microbial biomass components stabilised in SOM. 13C-FA and 13C-AA contents in the living microbial biomass fraction decreased over time and these components were continuously incorporated into the non-living SOM pool in biotic experiments with 13C6-2,4-D and 13C6-ibu. The 13C-AA in the non-living SOM were surprisingly stable from day 32 (13C6-2,4-D) and 58 (13C6-ibu) until the end of incubation. We also studied the transformation of 13C6-2,4-D and 13C6-ibu into NER in the abiotic soil experiments. In these experiments, the total NER contents were much lower than in the corresponding biotic experiments. The absence of labelled biomolecules in the NER fraction in abiotic soils demonstrated that they consist of the potentially hazardous parent compounds and / or their metabolites. Biogenic residue formation is relevant during biodegradation of organic contaminants, whereas abiotic NER are formed from the non-biodegraded residual contaminants. Abiotic NER and biogenic residue formation are competitive processes and do not occur in a similar extent. In the biotic treatment, the rapid mineralisation of an organic compound reduces the extent of abiotic NER formation via physico-chemical interactions between a parent compound and / or its primary metabolites with SOM. Therefore, in order to properly assess the potential risks of a target contaminant in soil to humans and the environment, it is necessary to distinguish between abiotic NER and biogenic residue formation in the mass balances of contaminants.

Genome-wide analysis of the GH3 family in apple (Malus × domestica)

PubMed Central

2013-01-01

Background Auxin plays important roles in hormone crosstalk and the plant’s stress response. The auxin-responsive Gretchen Hagen3 (GH3) gene family maintains hormonal homeostasis by conjugating excess indole-3-acetic acid (IAA), salicylic acid (SA), and jasmonic acids (JAs) to amino acids during hormone- and stress-related signaling pathways. With the sequencing of the apple (Malus × domestica) genome completed, it is possible to carry out genomic studies on GH3 genes to indentify candidates with roles in abiotic/biotic stress responses. Results Malus sieversii Roem., an apple rootstock with strong drought tolerance and the ancestral species of cultivated apple species, was used as the experimental material. Following genome-wide computational and experimental identification of MdGH3 genes, we showed that MdGH3s were differentially expressed in the leaves and roots of M. sieversii and that some of these genes were significantly induced after various phytohormone and abiotic stress treatments. Given the role of GH3 in the negative feedback regulation of free IAA concentration, we examined whether phytohormones and abiotic stresses could alter the endogenous auxin level. By analyzing the GUS activity of DR5::GUS-transformed Arabidopsis seedlings, we showed that ABA, SA, salt, and cold treatments suppressed the auxin response. These findings suggest that other phytohormones and abiotic stress factors might alter endogenous auxin levels. Conclusion Previous studies showed that GH3 genes regulate hormonal homeostasis. Our study indicated that some GH3 genes were significantly induced in M. sieversii after various phytohormone and abiotic stress treatments, and that ABA, SA, salt, and cold treatments reduce the endogenous level of axuin. Taken together, this study provides evidence that GH3 genes play important roles in the crosstalk between auxin, other phytohormones, and the abiotic stress response by maintaining auxin homeostasis. PMID:23638690

Regulation of nitrogen mineralization and nitrification in Southern Appalachian ecosystems: separating the relative importance of biotic vs. abiotic controls

Treesearch

Jennifer d. Knoepp; James M. Vose

2007-01-01

Long-term measurements of soil nitrogen (N) transformations along an environmental gradient within the Coweeta Hydrologic Laboratory basin in western North Carolina showed a strong seasonal pattern and suggested that vegetation community type through its influence on soil properties-was an important regulating factor. Our objective was to determine the relative effects...

Current achievements and future directions in genetic engineering of European plum (Prunus domestica L.).

PubMed

Petri, Cesar; Alburquerque, Nuria; Faize, Mohamed; Scorza, Ralph; Dardick, Chris

2018-06-01

In most woody fruit species, transformation and regeneration are difficult. However, European plum (Prunus domestica) has been shown to be amenable to genetic improvement technologies from classical hybridization, to genetic engineering, to rapid cycle crop breeding ('FasTrack' breeding). Since the first report on European plum transformation with marker genes in the early 90 s, numerous manuscripts have been published reporting the generation of new clones with agronomically interesting traits, such as pests, diseases and/or abiotic stress resistance, shorter juvenile period, dwarfing, continuous flowering, etc. This review focuses on the main advances in genetic transformation of European plum achieved to date, and the lines of work that are converting genetic engineering into a contemporary breeding tool for this species.

Stable Expression of mtlD Gene Imparts Multiple Stress Tolerance in Finger Millet

PubMed Central

Hema, Ramanna; Vemanna, Ramu S.; Sreeramulu, Shivakumar; Reddy, Chandrasekhara P.; Senthil-Kumar, Muthappa; Udayakumar, Makarla

2014-01-01

Finger millet is susceptible to abiotic stresses, especially drought and salinity stress, in the field during seed germination and early stages of seedling development. Therefore developing stress tolerant finger millet plants combating drought, salinity and associated oxidative stress in these two growth stages is important. Cellular protection through osmotic adjustment and efficient free radical scavenging ability during abiotic stress are important components of stress tolerance mechanisms in plants. Mannitol, an osmolyte, is known to scavenge hydroxyl radicals generated during various abiotic stresses and thereby minimize stress damage in several plant species. In this study transgenic finger millet plants expressing the mannitol biosynthetic pathway gene from bacteria, mannitol-1-phosphate dehydrogenase (mtlD), were developed through Agrobacterium tumefaciens-mediated genetic transformation. mtlD gene integration in the putative transgenic plants was confirmed by Southern blot. Further, performance of transgenic finger millet under drought, salinity and oxidative stress was studied at plant level in T1 generation and in T1 and T2 generation seedlings. Results from these experiments showed that transgenic finger millet had better growth under drought and salinity stress compared to wild-type. At plant level, transgenic plants showed better osmotic adjustment and chlorophyll retention under drought stress compared to the wild-type. However, the overall increase in stress tolerance of transgenics for the three stresses, especially for oxidative stress, was only marginal compared to other mtlD gene expressing plant species reported in the literature. Moreover, the Agrobacterium-mediated genetic transformation protocol developed for finger millet in this study can be used to introduce diverse traits of agronomic importance in finger millet. PMID:24922513

Methane clumped isotopes in the Songliao Basin (China): New insights into abiotic vs. biotic hydrocarbon formation

NASA Astrophysics Data System (ADS)

Shuai, Yanhua; Etiope, Giuseppe; Zhang, Shuichang; Douglas, Peter M. J.; Huang, Ling; Eiler, John M.

2018-01-01

Abiotic hydrocarbon gas, typically generated in serpentinized ultramafic rocks and crystalline shields, has important implications for the deep biosphere, petroleum systems, the carbon cycle and astrobiology. Distinguishing abiotic gas (produced by chemical reactions like Sabatier synthesis) from biotic gas (produced from degradation of organic matter or microbial activity) is sometimes challenging because their isotopic and molecular composition may overlap. Abiotic gas has been recognized in numerous locations on the Earth, although there are no confirmed instances where it is the dominant source of commercially valuable quantities in reservoir rocks. The deep hydrocarbon reservoirs of the Xujiaweizi Depression in the Songliao Basin (China) have been considered to host significant amounts of abiotic methane. Here we report methane clumped-isotope values (Δ18) and the isotopic composition of C1-C3 alkanes, CO2 and helium of five gas samples collected from those Xujiaweizi deep reservoirs. Some geochemical features of these samples resemble previously suggested identifiers of abiotic gas (13C-enriched CH4; decrease in 13C/12C ratio with increasing carbon number for the C1-C4 alkanes; abundant, apparently non-biogenic CO2; and mantle-derived helium). However, combining these constraints with new measurements of the clumped-isotope composition of methane and careful consideration of the geological context, suggests that the Xujiaweizi depression gas is dominantly, if not exclusively, thermogenic and derived from over-mature source rocks, i.e., from catagenesis of buried organic matter at high temperatures. Methane formation temperatures suggested by clumped-isotopes (167-213 °C) are lower than magmatic gas generation processes and consistent with the maturity of local source rocks. Also, there are no geological conditions (e.g., serpentinized ultramafic rocks) that may lead to high production of H2 and thus abiotic production of CH4 via CO2 reduction. We propose that the Songliao gas is representative of an atypical type of thermogenic gas that can be mistaken for abiotic gas. Such gases may be encountered more frequently in future exploration of deep or over-mature petroleum systems.

Abiotic versus biotic controls on soil nitrogen cycling in drylands along a 3200 km transect

NASA Astrophysics Data System (ADS)

Liu, Dongwei; Zhu, Weixing; Wang, Xiaobo; Pan, Yuepeng; Wang, Chao; Xi, Dan; Bai, Edith; Wang, Yuesi; Han, Xingguo; Fang, Yunting

2017-03-01

Nitrogen (N) cycling in drylands under changing climate is not well understood. Our understanding of N cycling over larger scales to date relies heavily on the measurement of bulk soil N, and the information about internal soil N transformations remains limited. The 15N natural abundance (δ15N) of ammonium and nitrate can serve as a proxy record for the N processes in soils. To better understand the patterns and mechanisms of N cycling in drylands, we collected soils along a 3200 km transect at about 100 km intervals in northern China, with mean annual precipitation (MAP) ranging from 36 to 436 mm. We analyzed N pools and δ15N of ammonium, dual isotopes (15N and 18O) of nitrate, and the microbial gene abundance associated with soil N transformations. We found that N status and its driving factors were different above and below a MAP threshold of 100 mm. In the arid zone with MAP below 100 mm, soil inorganic N accumulated, with a large fraction being of atmospheric origin, and ammonia volatilization was strong in soils with high pH. In addition, the abundance of microbial genes associated with soil N transformations was low. In the semiarid zone with MAP above 100 mm, soil inorganic N concentrations were low and were controlled mainly by biological processes (e.g., plant uptake and denitrification). The preference for soil ammonium over nitrate by the dominant plant species may enhance the possibility of soil nitrate losses via denitrification. Overall, our study suggests that a shift from abiotic to biotic controls on soil N biogeochemistry under global climate changes would greatly affect N losses, soil N availability, and other N transformation processes in these drylands in China.

Biotransformation of gabapentin in surface water matrices under different redox conditions and the occurrence of one major TP in the aquatic environment.

PubMed

Henning, Nina; Kunkel, Uwe; Wick, Arne; Ternes, Thomas A

2018-06-15

Laboratory-scale incubation experiments in water/sediment systems were conducted to test the transformation behavior of the anticonvulsant gabapentin (GBP) under different environmental conditions (aerobic, anaerobic, with abiotic controls). GBP was transformed by biological processes as it was eliminated quickly under aerobic conditions (dissipation time 50% of initial concentration (DT 50 ): 2-7 days) whereas no decrease was observed under anaerobic conditions. Measurements via high resolution mass spectrometry (LC-Orbitrap-MS) revealed eight biological transformation products (TPs). Three of them were identified with reference standards (GBP-Lactam, TP186, TP213), while for the other five TPs tentative structures were proposed from information by MS 2 /MS 3 experiments. Furthermore, the quantitatively most relevant TP GBP-Lactam was formed via intramolecular amidation (up to 18% of initial GBP concentration). Incubation experiments with GBP-Lactam revealed a higher stability against biotic degradation (DT 50 : 12 days) in contrast to GBP, while it was stable under anaerobic and abiotic conditions. Besides GBP, GBP-Lactam was detected in surface water in the μg L -1 range. Finally, GBP and GBP-Lactam were found in potable water with concentrations up to 0.64 and 0.07 μg L -1 , respectively. According to the elevated environmental persistence of GBP-Lactam compared to GBP and its presumed enhanced toxicity, we recommend to involve GBP-Lactam into monitoring programs. Copyright © 2018 Elsevier Ltd. All rights reserved.

An alternative pathway for marine nitrous oxide production at oxic-anoxic interfaces from coupled biotic-abiotic reactions

NASA Astrophysics Data System (ADS)

Glass, J. B.; Stanton, C. L.; Ochoa, H.; Haslun, J. A.; Gandhi, H.; Taillefert, M.; Dichristina, T. J.; Stewart, F. J.; Klotz, M. G.; Ostrom, N. E.

2016-02-01

Marine emissions of nitrous oxide (N2O), a potent greenhouse gas, comprise approximately a third of global sources. Recent evidence suggests that the dominant source of N2O in seawater is the activity of ammonia-oxidizing Thaumarchaeota that lack characterized N2O-generating enzymes. Nitrous oxide may arise from a novel enzyme and/or abiotic reactions between nitrification intermediates, hydroxylamine (NH2OH) and nitric oxide (NO), and redox-active metals in seawater. Isotopic site preference, or difference in δ15N between the two nitrogen atoms in N2O, has been used as tracer for microbial N2O production pathways (-10 to 0‰ for nitrifier-denitrification and denitrification vs. 30-37‰ for nitrification via NH2OH oxidation). Seawater N2O site preference falls in between these two characterized end members, suggesting simultaneous production via a combination of both microbial pathways or via a novel mechanism with intermediate site preference. Here we show significant N2O production in abiotic experiments after addition of iron to seawater containing NH2OH and NO. The N2O produced from chemical reduction of NO by Fe(II) had a site preference of 16‰ whereas N2O produced from abiotic NH2OH oxidation had a site preference of 31‰. We propose that coupled biotic-abiotic N2O production pathways could contribute significant sources of N2O at marine oxic-anoxic interfaces.

ABIOTIC REDUCTION AND DETOXIFICATION OF CHROMATE PRESENT IN SOILS

EPA Science Inventory

Theoretical and experimental research has supported the assertion that Cr(III) species are the most stable, immobile, and nontoxic forms of chromium and that they may form rapidly when adequate reducing agents are introduced in an oxidized soil environment. The objective of this ...

Abiotic degradation of hexahydro-l,3,5-trinitro-1,3,5-triazine in the presence of hydrogen sulfide and black carbon.

PubMed

Kemper, Jerome M; Ammar, Emaan; Mitch, William A

2008-03-15

We report that hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) was rapidly destroyed by sulfides in the presence of black carbon, forming nitrite and formaldehyde, rather than toxic nitrosated reduction products. Although traditionally viewed as inactive sorbents, black carbons have been noted to participate in the destruction of certain contaminants, such as azo dyes, via quinonoid groups. However, in our experiments sulfide modification of quinones did not seem to be involved. Although at least 1.2 mM sulfides were needed for the reaction to proceed, abiotic natural attenuation of RDX in marine sediments may occur, because these concentrations are found in certain marine sediments, together with black carbon. In the absence of natural black carbons, synthetic black carbons, such as activated carbon, may be added to sediments. As compared with other in situ techniques, such as bioremediation and zero-valent iron cutoff trenches, which often generate nitrosated byproducts, this in situ, abiotic technique may be an attractive alternative.

Elicitation Based Enhancement of Secondary Metabolites in Rauwolfia serpentina and Solanum khasianum Hairy Root Cultures.

PubMed

Srivastava, Mrinalini; Sharma, Swati; Misra, Pratibha

2016-05-01

Rauwolfia serpentina and Solanum khasianum are well-known medicinally important plants contained important alkaloids in their different parts. Elicitation of these alkaloids is important because of associated pharmaceutical properties. Targeted metabolites were ajmaline and ajmalicine in R. serpentina; solasodine and α-solanine in S. khasianum. Enhancement of secondary metabolites through biotic and abiotic elicitors in hairy root cultures of R. serpentina and S. khasianum. In this report, hairy root cultures of these two plants were established through Agrobacterium rhizogenes mediated transformation by optimizing various parameters as age of explants, duration of preculture, and co-cultivation period. NaCl was used as abiotic elicitors in these two plants. Cellulase from Aspergillus niger was used as biotic elicitor in S. khasianum and mannan from Saccharomyces cerevisiae was used in R. serpentina. First time we have reported the effect of biotic and abiotic elicitors on the production of important metabolites in hairy root cultures of these two plants. Ajmalicine production was stimulated up to 14.8-fold at 100 mM concentration of NaCl after 1 week of treatment. Ajmaline concentration was also increased 2.9-fold at 100 mg/l dose of mannan after 1 week. Solasodine content was enhanced up to 4.0-fold and 3.6-fold at 100 mM and 200 mM NaCl, respectively, after 6 days of treatments. This study explored the potential of the elicitation strategy in A. rhizogenes transformed cell cultures and this potential further used for commercial production of these pharmaceutically important secondary metabolites. Hairy roots of Rauwolfia serpentina were subjected to salt (abiotic stress) and mannan (biotic stress) treatment for 1 week. Ajmaline and ajmalicine secondary metabolites were quantified before and after stress treatmentAjmalicine yield was enhanced up to 14.8-fold at 100 mM concentration of NaCl. Ajmaline content was also stimulated 2.9-fold at 100 mg/l dose of mannan after 1 weekHairy roots of Solanum khasianum were treated with cellulase (biotic elicitor) and salt (abiotic stress)Solasodine content was improved up to 4.0-fold and 3.6-fold at 100 mM and 200 mM NaCl, respectively, after 6.days of treatmentsThe α-solanine content increased to 1.6-fold after 24 h of treatment at 100 μg/mL cellulase concentration. Abbreviations used: MS medium: Murashige and Skoog medium, B5 medium: Gamborg B5 medium, OD: Optical Density, NaCl: Sodium Chloride.

Elicitation Based Enhancement of Secondary Metabolites in Rauwolfia serpentina and Solanum khasianum Hairy Root Cultures

PubMed Central

Srivastava, Mrinalini; Sharma, Swati; Misra, Pratibha

2016-01-01

Background: Rauwolfia serpentina and Solanum khasianum are well-known medicinally important plants contained important alkaloids in their different parts. Elicitation of these alkaloids is important because of associated pharmaceutical properties. Targeted metabolites were ajmaline and ajmalicine in R. serpentina; solasodine and α-solanine in S. khasianum. Objective: Enhancement of secondary metabolites through biotic and abiotic elicitors in hairy root cultures of R. serpentina and S. khasianum. Materials and Methods: In this report, hairy root cultures of these two plants were established through Agrobacterium rhizogenes mediated transformation by optimizing various parameters as age of explants, duration of preculture, and co-cultivation period. NaCl was used as abiotic elicitors in these two plants. Cellulase from Aspergillus niger was used as biotic elicitor in S. khasianum and mannan from Saccharomyces cerevisiae was used in R. serpentina. Results: First time we have reported the effect of biotic and abiotic elicitors on the production of important metabolites in hairy root cultures of these two plants. Ajmalicine production was stimulated up to 14.8-fold at 100 mM concentration of NaCl after 1 week of treatment. Ajmaline concentration was also increased 2.9-fold at 100 mg/l dose of mannan after 1 week. Solasodine content was enhanced up to 4.0-fold and 3.6-fold at 100 mM and 200 mM NaCl, respectively, after 6 days of treatments. Conclusion: This study explored the potential of the elicitation strategy in A. rhizogenes transformed cell cultures and this potential further used for commercial production of these pharmaceutically important secondary metabolites. SUMMARY Hairy roots of Rauwolfia serpentina were subjected to salt (abiotic stress) and mannan (biotic stress) treatment for 1 week. Ajmaline and ajmalicine secondary metabolites were quantified before and after stress treatmentAjmalicine yield was enhanced up to 14.8-fold at 100 mM concentration of NaCl. Ajmaline content was also stimulated 2.9-fold at 100 mg/l dose of mannan after 1 weekHairy roots of Solanum khasianum were treated with cellulase (biotic elicitor) and salt (abiotic stress)Solasodine content was improved up to 4.0-fold and 3.6-fold at 100 mM and 200 mM NaCl, respectively, after 6.days of treatmentsThe α-solanine content increased to 1.6-fold after 24 h of treatment at 100 μg/mL cellulase concentration. Abbreviations used: MS medium: Murashige and Skoog medium, B5 medium: Gamborg B5 medium, OD: Optical Density, NaCl: Sodium Chloride. PMID:27563218

Dual element (CCl) isotope approach to distinguish abiotic reactions of chlorinated methanes by Fe(0) and by Fe(II) on iron minerals at neutral and alkaline pH.

PubMed

Rodríguez-Fernández, Diana; Heckel, Benjamin; Torrentó, Clara; Meyer, Armin; Elsner, Martin; Hunkeler, Daniel; Soler, Albert; Rosell, Mònica; Domènech, Cristina

2018-05-07

A dual element CCl isotopic study was performed for assessing chlorinated methanes (CMs) abiotic transformation reactions mediated by iron minerals and Fe(0) to further distinguish them in natural attenuation monitoring or when applying remediation strategies in polluted sites. Isotope fractionation was investigated during carbon tetrachloride (CT) and chloroform (CF) degradation in anoxic batch experiments with Fe(0), with FeCl 2 (aq), and with Fe-bearing minerals (magnetite, Mag and pyrite, Py) amended with FeCl 2 (aq), at two different pH values (7 and 12) representative of field and remediation conditions. At pH 7, only CT batches with Fe(0) and Py underwent degradation and CF accumulation evidenced hydrogenolysis. With Py, thiolytic reduction was revealed by CS 2 yield and is a likely reason for different Λ value (Δδ 13 C/Δδ 37 Cl) comparing with Fe(0) experiments at pH 7 (2.9 ± 0.5 and 6.1 ± 0.5, respectively). At pH 12, all CT experiments showed degradation to CF, again with significant differences in Λ values between Fe(0) (5.8 ± 0.4) and Fe-bearing minerals (Mag, 2 ± 1, and Py, 3.7 ± 0.9), probably evidencing other parallel pathways (hydrolytic and thiolytic reduction). Variation of pH did not significantly affect the Λ values of CT degradation by Fe(0) nor Py. CF degradation by Fe(0) at pH 12 showed a Λ (8 ± 1) similar to that reported at pH 7 (8 ± 2), suggesting CF hydrogenolysis as the main reaction and that CF alkaline hydrolysis (13.0 ± 0.8) was negligible. Our data establish a base for discerning the predominant or combined pathways of CMs natural attenuation or for assessing the effectiveness of remediation strategies using recycled minerals or Fe(0). Copyright © 2018 Elsevier Ltd. All rights reserved.

Overexpression of WsSGTL1 Gene of Withania somnifera Enhances Salt Tolerance, Heat Tolerance and Cold Acclimation Ability in Transgenic Arabidopsis Plants

PubMed Central

Mishra, Manoj K.; Chaturvedi, Pankaj; Singh, Ruchi; Singh, Gaurav; Sharma, Lokendra K.; Pandey, Vibha; Kumari, Nishi; Misra, Pratibha

2013-01-01

Background Sterol glycosyltrnasferases (SGT) are enzymes that glycosylate sterols which play important role in plant adaptation to stress and are medicinally important in plants like Withania somnifera. The present study aims to find the role of WsSGTL1 which is a sterol glycosyltransferase from W. somnifera, in plant’s adaptation to abiotic stress. Methodology The WsSGTL1 gene was transformed in Arabidopsis thaliana through Agrobacterium mediated transformation, using the binary vector pBI121, by floral dip method. The phenotypic and physiological parameters like germination, root length, shoot weight, relative electrolyte conductivity, MDA content, SOD levels, relative electrolyte leakage and chlorophyll measurements were compared between transgenic and wild type Arabidopsis plants under different abiotic stresses - salt, heat and cold. Biochemical analysis was done by HPLC-TLC and radiolabelled enzyme assay. The promoter of the WsSGTL1 gene was cloned by using Genome Walker kit (Clontech, USA) and the 3D structures were predicted by using Discovery Studio Ver. 2.5. Results The WsSGTL1 transgenic plants were confirmed to be single copy by Southern and homozygous by segregation analysis. As compared to WT, the transgenic plants showed better germination, salt tolerance, heat and cold tolerance. The level of the transgene WsSGTL1 was elevated in heat, cold and salt stress along with other marker genes such as HSP70, HSP90, RD29, SOS3 and LEA4-5. Biochemical analysis showed the formation of sterol glycosides and increase in enzyme activity. When the promoter of WsSGTL1 gene was cloned from W. somnifera and sequenced, it contained stress responsive elements. Bioinformatics analysis of the 3D structure of the WsSGTL1 protein showed functional similarity with sterol glycosyltransferase AtSGT of A. thaliana. Conclusions Transformation of WsSGTL1 gene in A. thaliana conferred abiotic stress tolerance. The promoter of the gene in W.somnifera was found to have stress responsive elements. The 3D structure showed functional similarity with sterol glycosyltransferases. PMID:23646175

[Interaction of clay minerals with microorganisms: a review of experimental data].

PubMed

Naĭmark, E B; Eroshchev-Shak, V A; Chizhikova, N P; Kompantseva, E I

2009-01-01

A review of publications containing results of experiments on the interaction of microorganisms with clay minerals is presented. Bacteria are shown to be involved in all processes related to the transformation of clay minerals: formation of clays from metamorphic and sedimentary rocks, formation of clays from solutions, reversible transitions of different types of clay minerals, and consolidation of clay minerals into sedimentary rocks. Integration of these results allows to conclude that bacteria reproduced all possible abiotic reactions associated with the clay minerals, these reactions proceed much faster with the bacteria being involved. Thus, bacteria act as a living catalyst in the geochemical cycle of clay minerals. The ecological role of bacteria can be considered as a repetition of a chemical process of the abiotic world, but with the use of organic catalytic innovation.

Contribution of biotic and abiotic factors in the natural attenuation of sulfamethoxazole: A path analysis approach.

PubMed

Li, Yan; Rashid, Azhar; Wang, Hongjie; Hu, Anyi; Lin, Lifeng; Yu, Chang-Ping; Chen, Meng; Sun, Qian

2018-08-15

Sulfamethoxazole (SMX) is a sulfonamide antibiotic, widely used as curative and preventive drug for human, animal, and aquaculture bacterial infections. Its residues have been ubiquitously detected in the surface waters and sediments. In the present study, SMX dissipation and kinetics was studied in the natural water samples from Jiulong River under simulated complex natural conditions as well as conditions to mimic various biotic and abiotic environmental conditions in isolation. Structural equation modeling (SEM) by employing partial least square technique in path coefficient analysis was used to investigate the direct and indirect contributions of different environmental factors in the natural attenuation of SMX. The model explained 81% of the variability in natural attenuation as a dependent variable under the influence of sole effects of direct photo-degradation, indirect photo-degradation, hydrolysis, microbial degradation and bacterial degradation. The results of SEM suggested that the direct and indirect photo-degradation were the major pathways in the SMX natural attenuation. However, other biotic and abiotic factors also play a mediatory role during the natural attenuation and other processes. Furthermore, the potential transformation products of SMX were identified and their toxicity was evaluated. Copyright © 2018 Elsevier B.V. All rights reserved.

Biotic conversion of sulphate to sulphide and abiotic conversion of sulphide to sulphur in a microbial fuel cell using cobalt oxide octahedrons as cathode catalyst.

PubMed

Chatterjee, Pritha; Ghangrekar, M M; Rao, Surampalli; Kumar, Senthil

2017-05-01

Varying chemical oxygen demand (COD) and sulphate concentrations in substrate were used to determine reaction kinetics and mass balance of organic matter and sulphate transformation in a microbial fuel cell (MFC). MFC with anodic chamber volume of 1 L, fed with wastewater having COD of 500 mg/L and sulphate of 200 mg/L, could harvest power of 54.4 mW/m 2 , at a Coulombic efficiency of 14%, with respective COD and sulphate removals of 90 and 95%. Sulphide concentration, even up to 1500 mg/L, did not inhibit anodic biochemical reactions, due to instantaneous abiotic oxidation to sulphur, at high inlet sulphate. Experiments on abiotic oxidation of sulphide to sulphur revealed maximum oxidation taking place at an anodic potential of -200 mV. More than 99% sulphate removal could be achieved in a MFC with inlet COD/sulphate of 0.75, giving around 1.33 kg/m 3  day COD removal. Bioelectrochemical conversion of sulphate facilitating sulphur recovery in a MFC makes it an interesting pollution abatement technique.

Simulation of dual carbon-bromine stable isotope fractionation during 1,2-dibromoethane degradation.

PubMed

Jin, Biao; Nijenhuis, Ivonne; Rolle, Massimo

2018-06-01

We performed a model-based investigation to simultaneously predict the evolution of concentration, as well as stable carbon and bromine isotope fractionation during 1,2-dibromoethane (EDB, ethylene dibromide) transformation in a closed system. The modelling approach considers bond-cleavage mechanisms during different reactions and allows evaluating dual carbon-bromine isotopic signals for chemical and biotic reactions, including aerobic and anaerobic biological transformation, dibromoelimination by Zn(0) and alkaline hydrolysis. The proposed model allowed us to accurately simulate the evolution of concentrations and isotope data observed in a previous laboratory study and to successfully identify different reaction pathways. Furthermore, we illustrated the model capabilities in degradation scenarios involving complex reaction systems. Specifically, we examined (i) the case of sequential multistep transformation of EDB and the isotopic evolution of the parent compound, the intermediate and the reaction product and (ii) the case of parallel competing abiotic pathways of EDB transformation in alkaline solution.

Light and abiotic stresses regulate the expression of GDP-L-galactose phosphorylase and levels of ascorbic acid in two kiwifruit genotypes via light-responsive and stress-inducible cis-elements in their promoters.

PubMed

Li, Juan; Liang, Dong; Li, Mingjun; Ma, Fengwang

2013-09-01

Ascorbic acid (AsA) plays an essential role in plants by protecting cells against oxidative damage. GDP-L-galactose phosphorylase (GGP) is the first committed gene for AsA synthesis. Our research examined AsA levels, regulation of GGP gene expression, and how these are related to abiotic stresses in two species of Actinidia (kiwifruit). When leaves were subjected to continuous darkness or light, ABA or MeJA, heat, or a hypoxic environment, we found some correlation between the relative levels of GGP mRNA and AsA concentrations. In transformed tobacco plants, activity of the GGP promoter was induced by all of these treatments. However, the degree of inducibility in the two kiwifruit species differed among the GGP promoter deletions. We deduced that the G-box motif, a light-responsive element, may have an important function in regulating GGP transcripts under various light conditions in both A. deliciosa and A. eriantha. Other elements such as ABRE, the CGTCA motif, and HSE might also control the promoter activities of GGP in kiwifruit. Altogether, these data suggest that GGP expression in the two kiwifruit species is regulated by light or abiotic stress via the relative cis-elements in their promoters. Furthermore, GGP has a critical role in modulating AsA concentrations in kiwifruit species under abiotic stresses.

Abiotic synthesis of organic compounds from carbon disulfide under hydrothermal conditions.

PubMed

Rushdi, Ahmed I; Simoneit, Bernd R T

2005-12-01

Abiotic formation of organic compounds under hydrothermal conditions is of interest to bio, geo-, and cosmochemists. Oceanic sulfur-rich hydrothermal systems have been proposed as settings for the abiotic synthesis of organic compounds. Carbon disulfide is a common component of magmatic and hot spring gases, and is present in marine and terrestrial hydrothermal systems. Thus, its reactivity should be considered as another carbon source in addition to carbon dioxide in reductive aqueous thermosynthesis. We have examined the formation of organic compounds in aqueous solutions of carbon disulfide and oxalic acid at 175 degrees C for 5 and 72 h. The synthesis products from carbon disulfide in acidic aqueous solutions yielded a series of organic sulfur compounds. The major compounds after 5 h of reaction included dimethyl polysulfides (54.5%), methyl perthioacetate (27.6%), dimethyl trithiocarbonate (6.8%), trithianes (2.7%), hexathiepane (1.4%), trithiolanes (0.8%), and trithiacycloheptanes (0.3%). The main compounds after 72 h of reaction consisted of trithiacycloheptanes (39.4%), pentathiepane (11.6%), tetrathiocyclooctanes (11.5%), trithiolanes (10.6%), tetrathianes (4.4%), trithianes (1.2%), dimethyl trisulfide (1.1%), and numerous minor compounds. It is concluded that the abiotic formation of aliphatic straight-chain and cyclic polysulfides is possible under hydrothermal conditions and warrants further studies.

Abiotic Reductive Dechlorination of Tetrachloroethylene and Trichloroethylene in Anaerobic Environments

DTIC Science & Technology

2009-01-15

Measurement of Henry’s Law Constant for methyl tert-butyl ether Using Solid-phase Microextraction. Environmental Toxicology and Chemistry 2001, 20, 1625...and Environmental Microbiology 2005, 71, 3413-3419. Nirmalakhandan, N. N., R. E. Speece. QSAR Model for Predicting Henry’s Constant. Environmental

REDUCTIVE DEHALOGENATION OF ORGANIC CONTAMINANTS IN SOILS AND GROUND WATER

EPA Science Inventory

Introduction and large scale production of synthetic halogenated organic chemicals over the last 50 years has resulted in a group of contaminants which tend to persist in the environment and resist both biotic and abiotic degradation. The low solubility of these types of contamin...

REDUCTIVE DEHALOGENATION OF ORGANIC CONTAMINANTS IN SOILS AND GROUND WATER

EPA Science Inventory

Introduction and large-scale production of synthetic halogenated organic chemicals over the last fifty years has resulted in a group of contaminants that tend to persist in the environment and resist both biotic and abiotic degradation. The low solubility of these types of contam...

Combined abiotic and biotic in-situ reduction of hexavalent chromium in groundwater using nZVI and whey: A remedial pilot test.

PubMed

Němeček, Jan; Pokorný, Petr; Lacinová, Lenka; Černík, Miroslav; Masopustová, Zuzana; Lhotský, Ondřej; Filipová, Alena; Cajthaml, Tomáš

2015-12-30

The paper describes a pilot remediation test combining two Cr(VI) geofixation methods - chemical reduction by nanoscale zero-valent iron (nZVI) and subsequent biotic reduction supported by whey. Combination of the methods exploited the advantages of both - a rapid decrease in Cr(VI) concentrations by nZVI, which prevented further spreading of the contamination and facilitated subsequent use of the cheaper biological method. Successive application of whey as an organic substrate to promote biotic reduction of Cr(VI) after application of nZVI resulted in a further and long-term decrease in the Cr(VI) contents in the groundwater. The effect of biotic reduction was observed even in a monitoring well located at a distance of 22 m from the substrate injection wells after 10 months. The results indicated a reciprocal effect of both the phases - nZVI oxidized to Fe(III) during the abiotic phase was microbially reduced back to Fe(II) and acted as a reducing agent for Cr(VI) even when the microbial density was already low due to the consumed substrate. Community analysis with pyrosequencing of the 16S rRNA genes further confirmed partial recycling of nZVI in the form of Fe(II), where the results showed that the Cr(VI) reducing process was mediated mainly by iron-reducing and sulfate-reducing bacteria. Copyright © 2015 Elsevier B.V. All rights reserved.

Presumed magnetic biosignatures observed in magnetite derived from abiotic reductive alteration of nanogoethite

NASA Astrophysics Data System (ADS)

Till, Jessica L.; Guyodo, Yohan; Lagroix, France; Morin, Guillaume; Menguy, Nicolas; Ona-Nguema, Georges

2017-03-01

The oriented chains of nanoscale Fe-oxide particles produced by magnetotactic bacteria are a striking example of biomineralization. Several distinguishing features of magnetite particles that comprise bacterial magnetosomes have been proposed to collectively constitute a biosignature of magnetotactic bacteria (Thomas-Keprta et al., 2001). These features include high crystallinity, chemical purity, a single-domain magnetic structure, well-defined crystal morphology, and arrangement of particles in chain structures. Here, we show that magnetite derived from the inorganic breakdown of nanocrystalline goethite exhibits magnetic properties and morphologies remarkably similar to those of biogenic magnetite from magnetosomes. During heating in reducing conditions, oriented nanogoethite aggregates undergo dehydroxylation and transform into stoichiometric magnetite. We demonstrate that highly crystalline single-domain magnetite with euhedral grain morphologies produced abiogenically from goethite meets several of the biogenicity criteria commonly used for the identification of magnetofossils. Furthermore, the suboxic conditions necessary for magnetofossil preservation in sediments are conducive to the reductive alteration of nanogoethite, as well as the preservation of detrital magnetite originally formed from goethite. The findings of this study have potential implications for the identification of biogenic magnetite, particularly in older sediments where diagenesis commonly disrupts the chain structure of magnetosomes. Our results indicate that isolated magnetofossils cannot be positively distinguished from inorganic magnetite on the basis of their magnetic properties and morphology, and that intact chain structures remain the only reliable distinguishing feature of fossil magnetosomes.

In situ and laboratory studies on the fate of specific organic compounds in an anaerobic landfill leachate plume, 1. Experimental conditions and fate of phenolic compounds

NASA Astrophysics Data System (ADS)

Nielsen, Per H.; Albrechtsen, Hans-Jørgen; Heron, Gorm; Christensen, Thomas H.

1995-11-01

The transformation of specific organic compounds was investigated by in situ and laboratory experiments in an anaerobic landfill leachate pollution plume at four different distances from the landfill. This paper presents the experimental conditions in the in situ microcosm and laboratory batch microcosm experiments performed and the results on the fate of 7 phenolic compounds. Part 2 of this series of papers, also published in this issue, presents the results on the fate of 8 aromatic compounds and 4 chlorinated aliphatic compounds. The redox conditions in the plume were characterized as methanogenic, Fe(III)-reducing and NO 3--reducing by the redox sensitive species present in groundwater and sediment and by bioassays. With a few exceptions the aquifer redox conditions were maintained throughout the experiments as monitored by redox sensitive species present in groundwater during the experiments, by redox sensitive species present in the sediment after the experiments and by bioassays performed after the experiments. Transformation of nitrophenol was very fast close to the landfill in strongly reducing conditions, while transformation was slower in the more oxidized part of the plume. Lag phases for the nitrophenols were short (maximum 10 days). Phenol was only transformed in the more distant part of the plume in experiments where NO 3-, Fe(III) and Mn(IV) reduction was dominant. Lag phases for phenol were either absent or lasted up to 2 months. Dichlorophenols were only transformed in experiments representing strongly reducing, presumably methanogenic, redox conditions close to the landfill after lag phases of up to 3 months. Transformation of o-cresol was not observed in any of the experiments throughout the plume. Generally, there was good accordance between the results obtained by in situ and laboratory experiments, both concerning redox conditions and the fate of the phenolic compounds. However, for phenol and 2,4-dichlorophenol, transformation was observed in some in situ experiments but not in the corresponding laboratory experiments. In some experiments, this coul be explained by differences in the redox conditions developing during the experiments. Nitrophenols were apparently transformed abiotically in the most reduced part of the plume, at 2 m from the landfill.

Reduction of adsorbed As(V) on nano-TiO2 by sulfate-reducing bacteria.

PubMed

Luo, Ting; Ye, Li; Ding, Cheng; Yan, Jinlong; Jing, Chuanyong

2017-11-15

Reduction of surface-bound arsenate [As(V)] and subsequent release into the aqueous phase contribute to elevated As in groundwater. However, this natural process is not fully understood, especially in the presence of sulfate-reducing bacteria (SRB). Gaining mechanistic insights into solid-As(V)-SRB interactions motivated our molecular level study on the fate of nano-TiO 2 bound As(V) in the presence of Desulfovibrio vulgaris DP4, a strain of SRB, using incubation and in situ ATR-FTIR experiments. The incubation results clearly revealed the reduction of As(V), either adsorbed on nano-TiO 2 or dissolved, in the presence of SRB. In contrast, this As(V) reduction was not observed in abiotic control experiments where sulfide was used as the reductant. Moreover, the reduction was faster for surface-bound As(V) than for dissolved As(V), as evidenced by the appearance of As(III) at 45h and 75h, respectively. ATR-FTIR results provided direct evidence that the surface-bound As(V) was reduced to As(III) on TiO 2 surfaces in the presence of SRB. In addition, the As(V) desorption from nano-TiO 2 was promoted by SRB relative to abiotic sulfide, due to the competition between As(V) and bacterial phosphate groups for TiO 2 surface sites. This competition was corroborated by the ATR-FTIR analysis, which showed inner-sphere surface complex formation by bacterial phosphate groups on TiO 2 surfaces. The results from this study highlight the importance of indirect bacteria-mediated As(V) reduction and release in geochemical systems. Copyright © 2017 Elsevier B.V. All rights reserved.

Abiotic nitrogen fixation on terrestrial planets: reduction of NO to ammonia by FeS.

PubMed

Summers, David P; Basa, Ranor C B; Khare, Bishun; Rodoni, David

2012-02-01

Understanding the abiotic fixation of nitrogen and how such fixation can be a supply of prebiotic nitrogen is critical for understanding both the planetary evolution of, and the potential origin of life on, terrestrial planets. As nitrogen is a biochemically essential element, sources of biochemically accessible nitrogen, especially reduced nitrogen, are critical to prebiotic chemistry and the origin of life. Loss of atmospheric nitrogen can result in loss of the ability to sustain liquid water on a planetary surface, which would impact planetary habitability and hydrological processes that shape the surface. It is known that NO can be photochemically converted through a chain of reactions to form nitrate and nitrite, which can be subsequently reduced to ammonia. Here, we show that NO can also be directly reduced, by FeS, to ammonia. In addition to removing nitrogen from the atmosphere, this reaction is particularly important as a source of reduced nitrogen on an early terrestrial planet. By converting NO directly to ammonia in a single step, ammonia is formed with a higher product yield (~50%) than would be possible through the formation of nitrate/nitrite and subsequent conversion to ammonia. In conjunction with the reduction of NO, there is also a catalytic disproportionation at the mineral surface that converts NO to NO₂ and N₂O. The NO₂ is then converted to ammonia, while the N₂O is released back in the gas phase, which provides an abiotic source of nitrous oxide.

Dual isotope plots reflect transformation pathways of pesticides: Potential to assess pesticide fate and elucidate transformation mechanisms

NASA Astrophysics Data System (ADS)

Meyer, Armin; Penning, Holger; Sorensen, Sebastian; Aamand, Jens; Elsner, Martin

2010-05-01

The degradation of pesticides in deeper soil layers and groundwater is of growing interest, because they have repeatedly been found in drinking water supply wells and may pose a risk to future water resources. Current assessment schemes face a common problem, however: natural degradation often cannot be reliably assessed by concentration measurements alone, since mass balances are difficult to establish and transformation cannot be distinguished from sorption or dilution. Even detection of metabolites may only give an incomplete picture. When several transformation pathways occur, some metabolites may be degraded or form bound residues so that the associated pathways may be missed. Our research shows that dual isotope plots derived from compound specific isotope analysis offer a novel approach to give additional, complementary insight into the natural degradation of pesticides. Detection of metabolites is not required, since the isotope fractionation can be fully observed in the pesticide itself. Specifically, different initial biotransformation reactions of the phenylurea herbicide isoproturon (3-(4-isopropylphenyl)-1,1-dimethylurea) in pure culture experiments with bacterial and fungal strains showed strongly pathway-dependent isotope fractionation. When analyzing isotopic changes in different parts of the isoproturon molecule, hydroxylation of the isopropyl group by fungi was found to be associated with C and H isotope fractionation. In contrast, hydrolysis by Arthrobacter globiformis D47 caused strong C and N isotope fractionation, albeit in a different manner than abiotic hydrolysis so that isotope measurements can distinguish between both modes of transformation. Likewise, we observed highly pathway-dependent C and N isotope fractionation of atrazine (1-chloro-3-ethylamino-5-isopropylamino-2,4,6-triazine). Desalkylation of atrazine by Rhodococcus sp. strain NI86/21 resulted in enrichment of both 13-C and 15-N in atrazine, whereas hydrolysis to hydroxyatrazine by Chelatobacter heintzii, Pseudomonas sp. ADP and Arthrobacter aurescens TC1 gave enrichment of 13-C, but depletion of 15-N. Comparison with abiotic reference experiments provided novel insight into the underlying enzymatic transformation mechanisms. Our investigations show how characteristic isotope patterns may significantly add to the present understanding of the environmental fate of pesticides.

C, N, and H isotope fractionation of the herbicide isoproturon reflects different microbial transformation pathways.

PubMed

Penning, Holger; Sørensen, Sebastian R; Meyer, Armin H; Aamand, Jens; Elsner, Martin

2010-04-01

The fate of pesticides in the subsurface is of great interest to the public, industry, and regulatory authorities. Compound-specific isotope analysis (CSIA) is a promising tool complementary to existing methods for elucidating pesticide degradation reactions. Here, we address three different initial biotransformation reactions of the phenylurea herbicide isoproturon (3-(4-isopropylphenyl)-1,1-dimethylurea) in pure culture experiments with bacterial and fungal strains. When analyzing isotopic changes in different parts of the isoproturon molecule, hydroxylation of the isopropyl group by fungi was found to be associated with C and H isotope fractionation. In contrast, hydrolysis by Arthrobacter globiformis D47 caused strong C and N isotope fractionation, albeit in a different manner than abiotic hydrolysis so that isotope measurements can distinguish between both modes of transformation. No significant isotope fractionation was observed during N-demethylation by Sphingomonas sp. SRS2. The observed isotope fractionation patterns were in agreement with the type of reactions and elements involved. Moreover, their substantially different nature suggests that isotope changes in natural samples may be uniquely attributed to either pathway, allowing even to distinguish the abiotic versus biotic nature of hydrolysis. Our investigations show how characteristic isotope patterns may significantly add to the present understanding of the environmental fate of pesticides.

Abiotic degradation of glyphosate into aminomethylphosphonic acid in the presence of metals.

PubMed

Ascolani Yael, J; Fuhr, J D; Bocan, G A; Daza Millone, A; Tognalli, N; Dos Santos Afonso, M; Martiarena, M L

2014-10-08

Glyphosate [N-phosphono-methylglycine (PMG)] is the most used herbicide worldwide, particularly since the development of transgenic glyphosate-resistant (GR) crops. Aminomethylphosphonic acid (AMPA) is the main glyphosate metabolite, and it may be responsible for GR crop damage upon PMG application. PMG degradation into AMPA has hitherto been reckoned mainly as a biological process, produced by soil microorganisms (bacteria and fungi) and plants. In this work, we use density functional calculations to identify the vibrational bands of PMG and AMPA in surface-enhanced Raman spectroscopy (SERS) and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectra experiments. SERS shows the presence of AMPA after glyphosate is deposited from aqueous solution on different metallic surfaces. AMPA is also detected in ATR-FTIR experiments when PMG interacts with metallic ions in aqueous solution. These results reveal an abiotic degradation process of glyphosate into AMPA, where metals play a crucial role.

Antagonistic, overlapping and distinct responses to biotic stress in rice (Oryza sativa) and interactions with abiotic stress

PubMed Central

2013-01-01

Background Every year, substantial crop loss occurs globally, as a result of bacterial, fungal, parasite and viral infections in rice. Here, we present an in-depth investigation of the transcriptomic response to infection with the destructive bacterial pathogen Xanthomonas oryzae pv. oryzae(Xoo) in both resistant and susceptible varieties of Oryza sativa. A comparative analysis to fungal, parasite and viral infection in rice is also presented. Results Within 24 h of Xoo inoculation, significant reduction of cell wall components and induction of several signalling components, membrane bound receptor kinases and specific WRKY and NAC transcription factors was prominent, providing a framework for how the presence of this pathogen was signalled and response mounted. Extensive comparative analyses of various other pathogen responses, including in response to infection with another bacterium (Xoc), resistant and susceptible parasite infection, fungal, and viral infections, led to a proposed model for the rice biotic stress response. In this way, a conserved induction of calcium signalling functions, and specific WRKY and NAC transcription factors, was identified in response to all biotic stresses. Comparison of these responses to abiotic stress (cold, drought, salt, heat), enabled the identification of unique genes responsive only to bacterial infection, 240 genes responsive to both abiotic and biotic stress, and 135 genes responsive to biotic, but not abiotic stresses. Functional significance of a number of these genes, using genetic inactivation or over-expression, has revealed significant stress-associated phenotypes. While only a few antagonistic responses were observed between biotic and abiotic stresses, e.g. for a number of endochitinases and kinase encoding genes, some of these may be crucial in explaining greater pathogen infection and damage under abiotic stresses. Conclusions The analyses presented here provides a global view of the responses to multiple stresses, further validates known resistance-associated genes, and highlights new potential target genes, some lineage specific to rice, that play important roles in response to stress, providing a roadmap to develop varieties of rice that are more resistant to multiple biotic and abiotic stresses, as encountered in nature. PMID:23398910

Banana NAC transcription factor MusaNAC042 is positively associated with drought and salinity tolerance.

PubMed

Tak, Himanshu; Negi, Sanjana; Ganapathi, T R

2017-03-01

Banana is an important fruit crop and its yield is hampered by multiple abiotic stress conditions encountered during its growth. The NAC (NAM, ATAF, and CUC) transcription factors are involved in plant response to biotic and abiotic stresses. In the present study, we studied the induction of banana NAC042 transcription factor in drought and high salinity conditions and its overexpression in transgenic banana to improve drought and salinity tolerance. MusaNAC042 expression was positively associated with stress conditions like salinity and drought and it encoded a nuclear localized protein. Transgenic lines of banana cultivar Rasthali overexpressing MusaNAC042 were generated by Agrobacterium-mediated transformation of banana embryogenic cells and T-DNA insertion was confirmed by PCR and Southern blot analysis. Our results using leaf disc assay indicated that transgenic banana lines were able to tolerate drought and high salinity stress better than the control plants and retained higher level of total chlorophyll and lower level of MDA content (malondialdehyde). Transgenic lines analyzed for salinity (250 mM NaCl) and drought (Soil gravimetric water content 0.15) tolerance showed higher proline content, better Fv/Fm ratio, and lower levels of MDA content than control suggesting that MusaNAC042 may be involved in responses to higher salinity and drought stresses in banana. Expression of several abiotic stress-related genes like those coding for CBF/DREB, LEA, and WRKY factors was altered in transgenic lines indicating that MusaNAC042 is an efficient modulator of abiotic stress response in banana.

Transgenic Alfalfa Plants Expressing the Sweetpotato Orange Gene Exhibit Enhanced Abiotic Stress Tolerance

PubMed Central

Wang, Zhi; Ke, Qingbo; Kim, Myoung Duck; Kim, Sun Ha; Ji, Chang Yoon; Jeong, Jae Cheol; Lee, Haeng-Soon; Park, Woo Sung; Ahn, Mi-Jeong; Li, Hongbing; Xu, Bingcheng; Deng, Xiping; Lee, Sang-Hoon; Lim, Yong Pyo; Kwak, Sang-Soo

2015-01-01

Alfalfa (Medicago sativa L.), a perennial forage crop with high nutritional content, is widely distributed in various environments worldwide. We recently demonstrated that the sweetpotato Orange gene (IbOr) is involved in increasing carotenoid accumulation and enhancing resistance to multiple abiotic stresses. In this study, in an effort to improve the nutritional quality and environmental stress tolerance of alfalfa, we transferred the IbOr gene into alfalfa (cv. Xinjiang Daye) under the control of an oxidative stress-inducible peroxidase (SWPA2) promoter through Agrobacterium tumefaciens-mediated transformation. Among the 11 transgenic alfalfa lines (referred to as SOR plants), three lines (SOR2, SOR3, and SOR8) selected based on their IbOr transcript levels were examined for their tolerance to methyl viologen (MV)-induced oxidative stress in a leaf disc assay. The SOR plants exhibited less damage in response to MV-mediated oxidative stress and salt stress than non-transgenic plants. The SOR plants also exhibited enhanced tolerance to drought stress, along with higher total carotenoid levels. The results suggest that SOR alfalfa plants would be useful as forage crops with improved nutritional value and increased tolerance to multiple abiotic stresses, which would enhance the development of sustainable agriculture on marginal lands. PMID:25946429

Transgenic alfalfa plants expressing the sweetpotato Orange gene exhibit enhanced abiotic stress tolerance.

PubMed

Wang, Zhi; Ke, Qingbo; Kim, Myoung Duck; Kim, Sun Ha; Ji, Chang Yoon; Jeong, Jae Cheol; Lee, Haeng-Soon; Park, Woo Sung; Ahn, Mi-Jeong; Li, Hongbing; Xu, Bingcheng; Deng, Xiping; Lee, Sang-Hoon; Lim, Yong Pyo; Kwak, Sang-Soo

2015-01-01

Alfalfa (Medicago sativa L.), a perennial forage crop with high nutritional content, is widely distributed in various environments worldwide. We recently demonstrated that the sweetpotato Orange gene (IbOr) is involved in increasing carotenoid accumulation and enhancing resistance to multiple abiotic stresses. In this study, in an effort to improve the nutritional quality and environmental stress tolerance of alfalfa, we transferred the IbOr gene into alfalfa (cv. Xinjiang Daye) under the control of an oxidative stress-inducible peroxidase (SWPA2) promoter through Agrobacterium tumefaciens-mediated transformation. Among the 11 transgenic alfalfa lines (referred to as SOR plants), three lines (SOR2, SOR3, and SOR8) selected based on their IbOr transcript levels were examined for their tolerance to methyl viologen (MV)-induced oxidative stress in a leaf disc assay. The SOR plants exhibited less damage in response to MV-mediated oxidative stress and salt stress than non-transgenic plants. The SOR plants also exhibited enhanced tolerance to drought stress, along with higher total carotenoid levels. The results suggest that SOR alfalfa plants would be useful as forage crops with improved nutritional value and increased tolerance to multiple abiotic stresses, which would enhance the development of sustainable agriculture on marginal lands.

Multiple sulfur isotopes fractionations associated with abiotic sulfur transformations in Yellowstone National Park geothermal springs

PubMed Central

2014-01-01

Background The paper presents a quantification of main (hydrogen sulfide and sulfate), as well as of intermediate sulfur species (zero-valent sulfur (ZVS), thiosulfate, sulfite, thiocyanate) in the Yellowstone National Park (YNP) hydrothermal springs and pools. We combined these measurements with the measurements of quadruple sulfur isotope composition of sulfate, hydrogen sulfide and zero-valent sulfur. The main goal of this research is to understand multiple sulfur isotope fractionation in the system, which is dominated by complex, mostly abiotic, sulfur cycling. Results Water samples from six springs and pools in the Yellowstone National Park were characterized by pH, chloride to sulfate ratios, sulfide and intermediate sulfur species concentrations. Concentrations of sulfate in pools indicate either oxidation of sulfide by mixing of deep parent water with shallow oxic water, or surface oxidation of sulfide with atmospheric oxygen. Thiosulfate concentrations are low (<6 μmol L-1) in the pools with low pH due to fast disproportionation of thiosulfate. In the pools with higher pH, the concentration of thiosulfate varies, depending on different geochemical pathways of thiosulfate formation. The δ34S values of sulfate in four systems were close to those calculated using a mixing line of the model based on dilution and boiling of a deep hot parent water body. In two pools δ34S values of sulfate varied significantly from the values calculated from this model. Sulfur isotope fractionation between ZVS and hydrogen sulfide was close to zero at pH < 4. At higher pH zero-valent sulfur is slightly heavier than hydrogen sulfide due to equilibration in the rhombic sulfur–polysulfide – hydrogen sulfide system. Triple sulfur isotope (32S, 33S, 34S) fractionation patterns in waters of hydrothermal pools are more consistent with redox processes involving intermediate sulfur species than with bacterial sulfate reduction. Small but resolved differences in ∆33S among species and between pools are observed. Conclusions The variation of sulfate isotopic composition, the origin of differences in isotopic composition of sulfide and zero–valent sulfur, as well as differences in ∆33S of sulfide and sulfate are likely due to a complex network of abiotic redox reactions, including disproportionation pathways. PMID:24959098

Poaceae vs. Abiotic Stress: Focus on Drought and Salt Stress, Recent Insights and Perspectives

PubMed Central

Landi, Simone; Hausman, Jean-Francois; Guerriero, Gea; Esposito, Sergio

2017-01-01

Poaceae represent the most important group of crops susceptible to abiotic stress. This large family of monocotyledonous plants, commonly known as grasses, counts several important cultivated species, namely wheat (Triticum aestivum), rice (Oryza sativa), maize (Zea mays), and barley (Hordeum vulgare). These crops, notably, show different behaviors under abiotic stress conditions: wheat and rice are considered sensitive, showing serious yield reduction upon water scarcity and soil salinity, while barley presents a natural drought and salt tolerance. During the green revolution (1940–1960), cereal breeding was very successful in developing high-yield crops varieties; however, these cultivars were maximized for highest yield under optimal conditions, and did not present suitable traits for tolerance under unfavorable conditions. The improvement of crop abiotic stress tolerance requires a deep knowledge of the phenomena underlying tolerance, to devise novel approaches and decipher the key components of agricultural production systems. Approaches to improve food production combining both enhanced water use efficiency (WUE) and acceptable yields are critical to create a sustainable agriculture in the future. This paper analyzes the latest results on abiotic stress tolerance in Poaceae. In particular, the focus will be directed toward various aspects of water deprivation and salinity response efficiency in Poaceae. Aspects related to cell wall metabolism will be covered, given the importance of the plant cell wall in sensing environmental constraints and in mediating a response; the role of silicon (Si), an important element for monocots' normal growth and development, will also be discussed, since it activates a broad-spectrum response to different exogenous stresses. Perspectives valorizing studies on landraces conclude the survey, as they help identify key traits for breeding purposes. PMID:28744298

Identification of abiotic and biotic reductive dechlorination in a chlorinated ethene plume after thermal source remediation by means of isotopic and molecular biology tools

NASA Astrophysics Data System (ADS)

Badin, Alice; Broholm, Mette M.; Jacobsen, Carsten S.; Palau, Jordi; Dennis, Philip; Hunkeler, Daniel

2016-09-01

Thermal tetrachloroethene (PCE) remediation by steam injection in a sandy aquifer led to the release of dissolved organic carbon (DOC) from aquifer sediments resulting in more reduced redox conditions, accelerated PCE biodegradation, and changes in microbial populations. These changes were documented by comparing data collected prior to the remediation event and eight years later. Based on the premise that dual C-Cl isotope slopes reflect ongoing degradation pathways, the slopes associated with PCE and TCE suggest the predominance of biotic reductive dechlorination near the source area. PCE was the predominant chlorinated ethene near the source area prior to thermal treatment. After thermal treatment, cDCE became predominant. The biotic contribution to these changes was supported by the presence of Dehalococcoides sp. DNA (Dhc) and Dhc targeted rRNA close to the source area. In contrast, dual C-Cl isotope analysis together with the almost absent VC 13C depletion in comparison to cDCE 13C depletion suggested that cDCE was subject to abiotic degradation due to the presence of pyrite, possible surface-bound iron (II) or reduced iron sulphides in the downgradient part of the plume. This interpretation is supported by the relative lack of Dhc in the downgradient part of the plume. The results of this study show that thermal remediation can enhance the biodegradation of chlorinated ethenes, and that this effect can be traced to the mobilisation of DOC due to steam injection. This, in turn, results in more reduced redox conditions which favor active reductive dechlorination and/or may lead to a series of redox reactions which may consecutively trigger biotically induced abiotic degradation. Finally, this study illustrates the valuable complementary application of compound-specific isotopic analysis combined with molecular biology tools to evaluate which biogeochemical processes are taking place in an aquifer contaminated with chlorinated ethenes.

Fate of Engineered Nanoparticles: Implications in the ...

EPA Pesticide Factsheets

The increased flux of the engineered nanoparticles (ENPs) in consumer and commercial products has become a viable threat, particularly if their release affects the environment. The aim of this paper is to review the recent literature results pertaining to the underlying mechanisms initiating the transformations of ENPs for both, the biotic and abiotic processes. The transformation of ENPs is necessarily interrelated to multiple environmental aspects and many concepts overlap. Physicochemical, macromolecular, and biological pathways contribute to assessing the impact of the altered activities of ENPs on the surrounding environmental matrices. Transformations involving both organic and inorganic ligands are vital in soil and water systems. Energy-efficient biocatalytic pathways can easily facilitate biotransformation involving enzymatic reactions and biomolecules. The relationship between physicochemical and biological parameters triggers transformation, greatly affecting the bioavailability and aging of ENPs to various extents. Therefore, the interaction of ENPs in environmental matrices is significant in understanding the risk of potential exposure and/or uptake by biota. Submitted to Elsevier journal, Coordination Chemistry Reviews

Catalase and ascorbate peroxidase-representative H2O2-detoxifying heme enzymes in plants.

PubMed

Anjum, Naser A; Sharma, Pallavi; Gill, Sarvajeet S; Hasanuzzaman, Mirza; Khan, Ekhlaque A; Kachhap, Kiran; Mohamed, Amal A; Thangavel, Palaniswamy; Devi, Gurumayum Devmanjuri; Vasudhevan, Palanisamy; Sofo, Adriano; Khan, Nafees A; Misra, Amarendra Narayan; Lukatkin, Alexander S; Singh, Harminder Pal; Pereira, Eduarda; Tuteja, Narendra

2016-10-01

Plants have to counteract unavoidable stress-caused anomalies such as oxidative stress to sustain their lives and serve heterotrophic organisms including humans. Among major enzymatic antioxidants, catalase (CAT; EC 1.11.1.6) and ascorbate peroxidase (APX; EC 1.11.1.11) are representative heme enzymes meant for metabolizing stress-provoked reactive oxygen species (ROS; such as H2O2) and controlling their potential impacts on cellular metabolism and functions. CAT mainly occurs in peroxisomes and catalyzes the dismutation reaction without requiring any reductant; whereas, APX has a higher affinity for H2O2 and utilizes ascorbate (AsA) as specific electron donor for the reduction of H2O2 into H2O in organelles including chloroplasts, cytosol, mitochondria, and peroxisomes. Literature is extensive on the glutathione-associated H2O2-metabolizing systems in plants. However, discussion is meager or scattered in the literature available on the biochemical and genomic characterization as well as techniques for the assays of CAT and APX and their modulation in plants under abiotic stresses. This paper aims (a) to introduce oxidative stress-causative factors and highlights their relationship with abiotic stresses in plants; (b) to overview structure, occurrence, and significance of CAT and APX in plants; (c) to summarize the principles of current technologies used to assay CAT and APX in plants; (d) to appraise available literature on the modulation of CAT and APX in plants under major abiotic stresses; and finally, (e) to consider a brief cross-talk on the CAT and APX, and this also highlights the aspects unexplored so far.

Introduction of Pea DNA Helicase 45 Into Sugarcane (Saccharum spp. Hybrid) Enhances Cell Membrane Thermostability And Upregulation Of Stress-responsive Genes Leads To Abiotic Stress Tolerance.

PubMed

Augustine, Sruthy Maria; Ashwin Narayan, J; Syamaladevi, Divya P; Appunu, C; Chakravarthi, M; Ravichandran, V; Tuteja, Narendra; Subramonian, N

2015-05-01

DNA helicases are motor proteins that play an essential role in nucleic acid metabolism, by providing a duplex-unwinding function. To improve the drought and salinity tolerance of sugarcane, a DEAD-box helicase gene isolated from pea with a constitutive promoter, Port Ubi 2.3 was transformed into the commercial sugarcane variety Co 86032 through Agrobacterium-mediated transformation, and the transgenics were screened for tolerance to soil moisture stress and salinity. The transgene integration was confirmed through polymerase chain reaction, and the V 0 transgenic events showed significantly higher cell membrane thermostability under normal irrigated conditions. The V 1 transgenic events were screened for tolerance to soil moisture stress and exhibited significantly higher cell membrane thermostability, transgene expression, relative water content, gas exchange parameters, chlorophyll content, and photosynthetic efficiency under soil moisture stress compared to wild-type (WT). The overexpression of PDH45 transgenic sugarcane also led to the upregulation of DREB2-induced downstream stress-related genes. The transgenic events demonstrated higher germination ability and better chlorophyll retention than WT under salinity stress. Our results suggest the possibility for development of increased abiotic stress tolerant sugarcane cultivars through overexpression of PDH45 gene. Perhaps this is the first report, which provides evidence for increased drought and salinity tolerance in sugarcane through overexpression of PDH45.

A 2D tank test on remediation of nitrobenzene-contaminated aquifer using in-situ reactive zone with emulsified nanoscale zero-valent iron.

PubMed

Dong, Jun; Dong, Yang; Wen, Chunyu; Gao, Song; Ren, Liming; Bao, Qiburi

2018-05-15

Nitrobenzene (NB) is one of the most challenging pollutants for groundwater remediation due to its great harm and recalcitrance. Emulsified nanoscale zero-valent iron (EZVI) is considered as a promising agent for in-situ remediation of contaminated groundwater for its high reactivity, good durability and low cost. In this paper, 2D tank experiment was conducted to evaluate the effectiveness of enhanced remediation of NB-contaminated groundwater with EZVI. 9 L of EZVI solution was injected into aquifer to establish in-situ reactive zone (IRZ) before 40 d of NB contamination. Results indicate that injection of EZVI leads to 90% reduction of total NB, which is mainly converted to aniline (AN). NB concentration decreases along the flow path in the tank. Fe 2+ is generated from Fe 0 oxidation. Significant acetate and bicarbonate are released due to emulsified oil decomposition during the whole operation time. Groundwater pH maintains in neutral value (6.6-8.2) owing to the balance between organic acids and OH - released after iron oxidation. Drastic decrease of ORP and DO indicates the transformation from oxidizing to reducing condition, leading to the reduction of oxidative species (e.g. sulfate, nitrate) in subsurface. Calculation of reducing equivalents suggests that microbial breakdown of emulsified oil provides more electrons than Fe 0 oxidation does to the system. Both biotic and abiotic processes are involved in the enhanced degradation of NB. Copyright © 2018 Elsevier Ltd. All rights reserved.

Methods for genetic transformation in Dendrobium.

PubMed

da Silva, Jaime A Teixeira; Dobránszki, Judit; Cardoso, Jean Carlos; Chandler, Stephen F; Zeng, Songjun

2016-03-01

The genetic transformation of Dendrobium orchids will allow for the introduction of novel colours, altered architecture and valuable traits such as abiotic and biotic stress tolerance. The orchid genus Dendrobium contains species that have both ornamental value and medicinal importance. There is thus interest in producing cultivars that have increased resistance to pests, novel horticultural characteristics such as novel flower colours, improved productivity, longer flower spikes, or longer post-harvest shelf-life. Tissue culture is used to establish clonal plants while in vitro flowering allows for the production of flowers or floral parts within a sterile environment, expanding the selection of explants that can be used for tissue culture or genetic transformation. The latter is potentially the most effective, rapid and practical way to introduce new agronomic traits into Dendrobium. Most (69.4 %) Dendrobium genetic transformation studies have used particle bombardment (biolistics) while 64 % have employed some form of Agrobacterium-mediated transformation. A singe study has explored ovary injection, but no studies exist on floral dip transformation. While most of these studies have involved the use of selector or reporter genes, there are now a handful of studies that have introduced genes for horticulturally important traits.

Bioconcentration, bioaccumulation, and metabolism of pesticides in aquatic organisms.

PubMed

Katagi, Toshiyuki

2010-01-01

The ecotoxicological assessment of pesticide effects in the aquatic environment should normally be based on a deep knowledge of not only the concentration of pesticides and metabolites found but also on the influence of key abiotic and biotic processes that effect rates of dissipation. Although the bioconcentration and bioaccumulation potentials of pesticides in aquatic organisms are conveniently estimated from their hydrophobicity (represented by log K(ow), it is still indispensable to factor in the effects of key abiotic and biotic processes on such pesticides to gain a more precise understanding of how they may have in the natural environment. Relying only on pesticide hydrophobicity may produce an erroneous environmental impact assessment. Several factors affect rates of pesticide dissipation and accumulation in the aquatic environment. Such factors include the amount and type of sediment present in the water and type of diet available to water-dwelling organisms. The particular physiological behavior profiles of aquatic organisms in water, such as capacity for uptake, metabolism, and elimination, are also compelling factors, as is the chemistry of the water. When evaluating pesticide uptake and bioconcentration processes, it is important to know the amount and nature of bottom sediments present and the propensity that the stuffed aquatic organisms have to absorb and process xenobiotics. Extremely hydrophobic pesticides such as the organochlorines and pyrethroids are susceptible to adsorb strongly to dissolved organic matter associated with bottom sediment. Such absorption reduces the bioavailable fraction of pesticide dissolved in the water column and reduces the probable ecotoxicological impact on aquatic organisms living the water. In contrast, sediment dweller may suffer from higher levels of direct exposure to a pesticide, unless it is rapidly degraded in sediment. Metabolism is important to bioconcentration and bioaccumulation processes, as is detoxification and bioactivation. Hydrophobic pesticides that are expected to be highly stored in tissues would not be bioconcentrated if susceptible to biotic transformation by aquatic organisms to more rapidly metabolized to hydrophilic entities are generally less toxic. By analogy, pesticides that are metabolized to similar entities by aquatic species surely are les ecotoxicologically significant. One feature of fish and other aquatic species that makes them more relevant as targets of environmental studies and of regulation is that they may not only become contaminated by pesticides or other chemicals, but that they constitute and important part of the human diet. In this chapter, we provide an overview of the enzymes that are capable of metabolizing or otherwise assisting in the removal of xenobiotics from aquatic species. Many studies have been performed on the enzymes that are responsible for metabolizing xenobiotics. In addition to the use of conventional biochemical methods, such studies on enzymes are increasingly being conducted using immunochemical methods and amino acid or gene sequences analysis. Such studies have been performed in algae, in some aquatic macrophytes, and in bivalva, but less information is available for other aquatic species such as crustacea, annelids, aquatic insecta, and other species. Although their catabolizing activity is often lower than in mammals, oxidases, especially cytochrome P450 enzymes, play a central role in transforming pesticides in aquatic organisms. Primary metabolites, formed from such initial enzymatic action, are further conjugated with natural components such as carbohydrates, and this aids removal form the organisms. The pesticides that are susceptible to abiotic hydrolysis are generally also biotically degraded by various esterases to from hydrophilic conjugates. Reductive transformation is the main metabolic pathway for organochlorine pesticides, but less information on reductive enzymology processes is available. The information on aquatic species, other than fish, that pertains to bioconcentration factors, metabolism, and elimination is rather limited in the literature. The kinds of basic information that is unavailable but is needed on important aquatic species includes biochemistry, physiology, position in food web, habitat, life cycle, etc. such information is very important to obtaining improved ecotoxicology risk assessments for many pesticides and other chemicals. More research attention on the behavior of pesticides in, and affect on many standard aquatic test species (e.g., daphnids, chironomids, oligochaetes and some bivalves) would particularly be welcome. In addition to improving ecotoxicology risk assessments on target species, such information would also assist in better delineating affects on species at higher trophic levels that are predaceous on the target species. There is also need for designing and employing more realistic approaches to measure bioconcentration and bioaccumulation, and ecotoxicology effects of pesticides in natural environment. The currently employed steady-state laboratory exposure studies are insufficient to deal with the complexity of parameters that control the contrasts to the abiotic processes of pesticide investigated under the strictly controlled conditions, each process is significantly affected in the natural environment not only by the site-specific chemistry of water and sediment but also by climate. From this viewpoint, ecotoxicological assessment should be conducted, together with the detailed analyses of abiotic processes, when higher-tier mesocosm studies are performed. Moreover, in-depth investigation is needed to better understand the relationship between pesticide residues in organisms and associated ecotoxicological endpoints. The usual exposure assessment is based on apparent (nominal) concentrations fo pesticides, and the residues of pesticides or their metabolites in the organisms are not considered in to the context of ecotoxicological endpoints. Therefore, more metabolic and tissue distribution information for terminal pesticide residues is needed for aquatic species both in laboratory settings and in higher-tier (microcosm, mesocosm) studies.

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

Vermeul, Vince R.; Szecsody, Jim E.; Truex, Michael J.

This treatability study was conducted by Pacific Northwest National Laboratory (PNNL), at the request of the U. S. Environmental Protection Agency (EPA) Region 2, to evaluate the feasibility of using in situ treatment technologies for chromate reduction and immobilization at the Puchack Well Field Superfund Site in Pennsauken Township, New Jersey. In addition to in situ reductive treatments, which included the evaluation of both abiotic and biotic reduction of Puchack aquifer sediments, natural attenuation mechanisms were evaluated (i.e., chromate adsorption and reduction). Chromate exhibited typical anionic adsorption behavior, with greater adsorption at lower pH, at lower chromate concentration, and atmore » lower concentrations of other competing anions. In particular, sulfate (at 50 mg/L) suppressed chromate adsorption by up to 50%. Chromate adsorption was not influenced by inorganic colloids.« less

Environmental microbes can speciate and cycle arsenic.

PubMed

Rhine, E Danielle; Garcia-Dominguez, Elizabeth; Phelps, Craig D; Young, L Y

2005-12-15

Naturally occurring arsenic is found predominantly as arsenate [As(V)] or arsenite [As(III)], and can be readily oxidized or reduced by microorganisms. Given the health risks associated with arsenic in groundwater and the interest in arsenic-active microorganisms, we hypothesized that environmental microorganisms could mediate a redox cycling of arsenic that is linked to their metabolism. This hypothesis was tested using an As(V) respiring reducer (strain Y5) and an aerobic chemoautotrophic As(II) oxidizer (strain OL1 ) both isolated from a Superfund site, Onondaga Lake, in Syracuse, NY. Strains were grown separately and together in sealed serum bottles, and the oxic/anoxic condition was the only parameter changed. Initially, under anoxic conditions when both isolates were grown together, 2 mM As(V) was stoichiometrically reduced to As(III) within 14 days. Following complete reduction, sterile ambient air was added and within 24 h As(III) was completely oxidized to As(V). The anoxic-oxic cycle was repeated, and sterile controls showed no abiotic transformation within the 28-day incubation period. These results demonstrate that microorganisms can cycle arsenic in response to dynamic environmental conditions, thereby affecting the speciation, and hence mobility and toxicity of arsenic in the environment.

Overexpression of a glyoxalase gene, OsGly I, improves abiotic stress tolerance and grain yield in rice (Oryza sativa L.).

PubMed

Zeng, Zhengming; Xiong, Fangjie; Yu, Xiaohong; Gong, Xiaoping; Luo, Juntao; Jiang, Yudong; Kuang, Haochi; Gao, Bijun; Niu, Xiangli; Liu, Yongsheng

2016-12-01

Glyoxalase I (Gly I) is a component of the glyoxalase system which is involved in the detoxification of methylglyoxal, a byproduct of glycolysis. In the present study, a gene of rice (Oryza sativa L., cv. Nipponbare) encoding Gly I was cloned and characterized. The quantitative real-time PCR analysis indicated that rice Gly I (OsGly I) was ubiquitously expressed in root, stem, leaf, leaf sheath and spikelet with varying abundance. OsGly I was markedly upregulated in response to NaCl, ZnCl 2 and mannitol in rice seedlings. For further functional investigation, OsGly I was overexpressed in rice using Agrobacterium-mediated transformation. Transgenic rice lines exhibited increased glyoxalase enzyme activity, decreased methylglyoxal level and improved tolerance to NaCl, ZnCl 2 and mannitol compared to wild-type plants. Enhancement of stress tolerance in transgenic lines was associated with reduction of malondialdehyde content which was derived from cellular lipid peroxidation. In addition, the OsGly I-overexpression transgenic plants performed higher seed setting rate and yield. Collectively, these results indicate the potential of bioengineering the Gly I gene in crops. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Fourier transform mid infrared spectroscopy applications for monitoring the structural plasticity of plant cell walls

PubMed Central

Largo-Gosens, Asier; Hernández-Altamirano, Mabel; García-Calvo, Laura; Alonso-Simón, Ana; Álvarez, Jesús; Acebes, José L.

2014-01-01

Fourier transform mid-infrared (FT-MIR) spectroscopy has been extensively used as a potent, fast and non-destructive procedure for analyzing cell wall architectures, with the capacity to provide abundant information about their polymers, functional groups, and in muro entanglement. In conjunction with multivariate analyses, this method has proved to be a valuable tool for tracking alterations in cell walls. The present review examines recent progress in the use of FT-MIR spectroscopy to monitor cell wall changes occurring in muro as a result of various factors, such as growth and development processes, genetic modifications, exposition or habituation to cellulose biosynthesis inhibitors and responses to other abiotic or biotic stresses, as well as its biotechnological applications. PMID:25071791

Does natural variation in diversity affect biotic resistance?

USGS Publications Warehouse

Harrison, Susan; Cornell, Howard; Grace, James B.

2015-01-01

Theories linking diversity to ecosystem function have been challenged by the widespread observation of more exotic species in more diverse native communities. Few studies have addressed the key underlying process by dissecting how community diversity is shaped by the same environmental gradients that determine biotic and abiotic resistance to new invaders. In grasslands on highly heterogeneous soils, we used addition of a recent invader, competitor removal and structural equation modelling (SEM) to analyse soil influences on community diversity, biotic and abiotic resistance and invader success. Biotic resistance, measured by reduction in invader success in the presence of the resident community, was negatively correlated with species richness and functional diversity. However, in the multivariate SEM framework, biotic resistance was independent of all forms of diversity and was positively affected by soil fertility via community biomass. Abiotic resistance, measured by invader success in the absence of the resident community, peaked on infertile soils with low biomass and high community diversity. Net invader success was determined by biotic resistance, consistent with this invader's better performance on infertile soils in unmanipulated conditions. Seed predation added slightly to biotic resistance without qualitatively changing the results. Soil-related genotypic variation in the invader also did not affect the results. Synthesis. In natural systems, diversity may be correlated with invasibility and yet have no effect on either biotic or abiotic resistance to invasion. More generally, the environmental causes of variation in diversity should not be overlooked when considering the potential functional consequences of diversity.

Pre-mRNA splicing repression triggers abiotic stress signaling in plants.

PubMed

Ling, Yu; Alshareef, Sahar; Butt, Haroon; Lozano-Juste, Jorge; Li, Lixin; Galal, Aya A; Moustafa, Ahmed; Momin, Afaque A; Tashkandi, Manal; Richardson, Dale N; Fujii, Hiroaki; Arold, Stefan; Rodriguez, Pedro L; Duque, Paula; Mahfouz, Magdy M

2017-01-01

Alternative splicing (AS) of precursor RNAs enhances transcriptome plasticity and proteome diversity in response to diverse growth and stress cues. Recent work has shown that AS is pervasive across plant species, with more than 60% of intron-containing genes producing different isoforms. Mammalian cell-based assays have discovered various inhibitors of AS. Here, we show that the macrolide pladienolide B (PB) inhibits constitutive splicing and AS in plants. Also, our RNA sequencing (RNA-seq) data revealed that PB mimics abiotic stress signals including salt, drought and abscisic acid (ABA). PB activates the abiotic stress- and ABA-responsive reporters RD29A::LUC and MAPKKK18::uidA in Arabidopsis thaliana and mimics the effects of ABA on stomatal aperture. Genome-wide analysis of AS by RNA-seq revealed that PB perturbs the splicing machinery and leads to a striking increase in intron retention and a reduction in other forms of AS. Interestingly, PB treatment activates the ABA signaling pathway by inhibiting the splicing of clade A PP2C phosphatases while still maintaining to some extent the splicing of ABA-activated SnRK2 kinases. Taken together, our data establish PB as an inhibitor and modulator of splicing and a mimic of abiotic stress signals in plants. Thus, PB reveals the molecular underpinnings of the interplay between stress responses, ABA signaling and post-transcriptional regulation in plants. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Maize, tropical (Zea mays L.).

PubMed

Assem, Shireen K

2015-01-01

Maize (Zea mays L.) is the third most important food crop globally after wheat and rice. In sub-Saharan Africa, tropical maize has traditionally been the main staple of the diet; 95 % of the maize grown is consumed directly as human food and as an important source of income for the resource-poor rural population. The biotechnological approach to engineer biotic and abiotic traits implies the availability of an efficient plant transformation method. The production of genetically transformed plants depends both on the ability to integrate foreign genes into target cells and the efficiency with which plants are regenerated. Maize transformation and regeneration through immature embryo culture is the most efficient system to regenerate normal transgenic plants. However, this system is highly genotype dependent. Genotypes adapted to tropic areas are difficult to regenerate. Therefore, transformation methods used with model genotypes adapted to temperate areas are not necessarily efficient with tropical lines. Agrobacterium-mediated transformation is the method of choice since it has been first achieved in 1996. In this report, we describe a transformation method used successfully with several tropical maize lines. All the steps of transformation and regeneration are described in details. This protocol can be used with a wide variety of tropical lines. However, some modifications may be needed with recalcitrant lines.

Abiotic and bioaugmented granular activated carbon for the treatment of 1,4-dioxane-contaminated water.

PubMed

Myers, Michelle A; Johnson, Nicholas W; Marin, Erick Zerecero; Pornwongthong, Peerapong; Liu, Yun; Gedalanga, Phillip B; Mahendra, Shaily

2018-06-04

1,4-Dioxane is a probable human carcinogen and an emerging contaminant that has been detected in surface water and groundwater resources. Many conventional water treatment technologies are not effective for the removal of 1,4-dioxane due to its high water solubility and chemical stability. Biological degradation is a potentially low-cost, energy-efficient approach to treat 1,4-dioxane-contaminated waters. Two bacterial strains, Pseudonocardia dioxanivorans CB1190 (CB1190) and Mycobacterium austroafricanum JOB5 (JOB5), have been previously demonstrated to break down 1,4-dioxane through metabolic and co-metabolic pathways, respectively. However, both CB1190 and JOB5 have been primarily studied in laboratory planktonic cultures, while most environmental microbes grow in biofilms on surfaces. Another treatment technology, adsorption, has not historically been considered an effective means of removing 1,4-dioxane due to the contaminant's low K oc and K ow values. We report that the granular activated carbon (GAC), Norit 1240, is an adsorbent with high affinity for 1,4-dioxane as well as physical dimensions conducive to attached bacterial growth. In abiotic batch reactor studies, 1,4-dioxane adsorption was reversible to a large extent. By bioaugmenting GAC with 1,4-dioxane-degrading microbes, the adsorption reversibility was minimized while achieving greater 1,4-dioxane removal when compared with abiotic GAC (95-98% reduction of initial 1,4-dioxane as compared to an 85-89% reduction of initial 1,4-dioxane, respectively). Bacterial attachment and viability was visualized using fluorescence microscopy and confirmed by amplification of taxonomic genes by quantitative polymerase chain reaction (qPCR) and an ATP assay. Filtered samples of industrial wastewater and contaminated groundwater were also tested in the bioaugmented GAC reactors. Both CB1190 and JOB5 demonstrated 1,4-dioxane removal greater than that of the abiotic adsorbent controls. This study suggests that bioaugmented adsorbents could be an effective technology for 1,4-dioxane removal from contaminated water resources. Copyright © 2018 Elsevier Ltd. All rights reserved.

Microbiological and abiotic processes in modelling longer-term marine corrosion of steel.

PubMed

Melchers, Robert E

2014-06-01

Longer term exposure of mild steel in natural (biotic) waters progresses as a bimodal function of time, both for corrosion mass loss and for pit depth. Recent test results, however, found this also for immersion in clean fresh, almost pure and triply distilled waters. This shows chlorides or microbiological activity is not essential for the electrochemical processes producing bimodal behaviour. It is proposed that the first mode is aerobic corrosion that eventually produces a non-homogeneous corroded surface and rust coverage sufficient to allow formation of anoxic niches. Within these, aggressive autocatalytic reduction then occurs under anoxic abiotic conditions, caused by sulfide species originating from the MnS inclusions typical in steels. This is consistent with Wranglen's model for abiotic anoxic crevice and pitting corrosion without external aggressive ions. In biotic conditions, metabolites from anaerobic bacterial activity within and near the anoxic niches provides additional (sulfide) species to contribute to the severity of corrosion. Limited observational evidence that supports this hypothesis is given but further investigation is required to determine all contributor(s) to the cathodic current for the electrochemical reaction. The results are important for estimating the contribution of microbiological corrosion in infrastructure applications. © 2013.

Rainfall limit of the N cycle on Earth

USGS Publications Warehouse

Ewing, S.A.; Michalski, G.; Thiemens, M.; Quinn, R.C.; Macalady, J.L.; Kohl, S.; Wankel, Scott D.; Kendall, C.; McKay, C.P.; Amundson, Ronald

2007-01-01

In most climates on Earth, biological processes control soil N. In the Atacama Desert of Chile, aridity severely limits biology, and soils accumulate atmospheric NO3-. We examined this apparent transformation of the soil N cycle using a series of ancient Atacama Desert soils (>2 My) that vary in rainfall (21 to <2 mm yr-1). With decreasing rainfall, soil organic C decreases to 0.3 kg C m-2 and biological activity becomes minimal, while soil NO3- and organic N increase to 4 kg N m-2 and 1.4 kg N m-2, respectively. Atmospheric NO3- (??17O = 23.0???) increases from 39% to 80% of total soil NO3- as rainfall decreases. These soils capture the transition from a steady state, biologically mediated soil N cycle to a dominantly abiotic, transient state of slowly accumulating atmospheric N. This transition suggests that oxidized soil N may be present in an even more and and abiotic environment: Mars. Copyright 2007 by the American Geophysical Union.

ABI-like transcription factor gene TaABL1 from wheat improves multiple abiotic stress tolerances in transgenic plants.

PubMed

Xu, Dong-Bei; Gao, Shi-Qing; Ma, You-Zhi; Xu, Zhao-Shi; Zhao, Chang-Ping; Tang, Yi-Miao; Li, Xue-Yin; Li, Lian-Cheng; Chen, Yao-Feng; Chen, Ming

2014-12-01

The phytohormone abscisic acid (ABA) plays crucial roles in adaptive responses of plants to abiotic stresses. ABA-responsive element binding proteins (AREBs) are basic leucine zipper transcription factors that regulate the expression of downstream genes containing ABA-responsive elements (ABREs) in promoter regions. A novel ABI-like (ABA-insensitive) transcription factor gene, named TaABL1, containing a conserved basic leucine zipper (bZIP) domain was cloned from wheat. Southern blotting showed that three copies were present in the wheat genome. Phylogenetic analyses indicated that TaABL1 belonged to the AREB subfamily of the bZIP transcription factor family and was most closely related to ZmABI5 in maize and OsAREB2 in rice. Expression of TaABL1 was highly induced in wheat roots, stems, and leaves by ABA, drought, high salt, and low temperature stresses. TaABL1 was localized inside the nuclei of transformed wheat mesophyll protoplast. Overexpression of TaABL1 enhanced responses of transgenic plants to ABA and hastened stomatal closure under stress, thereby improving tolerance to multiple abiotic stresses. Furthermore, overexpression of TaABL1 upregulated or downregulated the expression of some stress-related genes controlling stomatal closure in transgenic plants under ABA and drought stress conditions, suggesting that TaABL1 might be a valuable genetic resource for transgenic molecular breeding.

Molecular responses of genetically modified maize to abiotic stresses as determined through proteomic and metabolomic analyses

PubMed Central

Benevenuto, Rafael Fonseca; Agapito-Tenfen, Sarah Zanon; Vilperte, Vinicius; Wikmark, Odd-Gunnar; van Rensburg, Peet Jansen; Nodari, Rubens Onofre

2017-01-01

Some genetically modified (GM) plants have transgenes that confer tolerance to abiotic stressors. Meanwhile, other transgenes may interact with abiotic stressors, causing pleiotropic effects that will affect the plant physiology. Thus, physiological alteration might have an impact on the product safety. However, routine risk assessment (RA) analyses do not evaluate the response of GM plants exposed to different environmental conditions. Therefore, we here present a proteome profile of herbicide-tolerant maize, including the levels of phytohormones and related compounds, compared to its near-isogenic non-GM variety under drought and herbicide stresses. Twenty differentially abundant proteins were detected between GM and non-GM hybrids under different water deficiency conditions and herbicide sprays. Pathway enrichment analysis showed that most of these proteins are assigned to energetic/carbohydrate metabolic processes. Among phytohormones and related compounds, different levels of ABA, CA, JA, MeJA and SA were detected in the maize varieties and stress conditions analysed. In pathway and proteome analyses, environment was found to be the major source of variation followed by the genetic transformation factor. Nonetheless, differences were detected in the levels of JA, MeJA and CA and in the abundance of 11 proteins when comparing the GM plant and its non-GM near-isogenic variety under the same environmental conditions. Thus, these findings do support molecular studies in GM plants Risk Assessment analyses. PMID:28245233

Interaction of Microbial and Abiotic Processes in Soil Leading to the (Bio)Conversion and Ultimate Attenuation of New Insensitive Munitions Compounds

DTIC Science & Technology

2016-12-30

Toxicity is expressed as percentage of toxicant- free activity 125 Figure 4.12-1. Panel A: (Bio)transformation pathways of DNAN in anaerobic incubations...O-demethylation of the methoxy group was confirmed by formation of formaldehye. Cell free extracts of the Bacillus culture yielded formation of 2...periodically until the production of methane became constant in the toxicant- free controls. The maximum specific methanogenic activity of the

Thermal Studies of Ammonium Cyanide Reactions: A Model for Thermal Alteration of Prebiotic Compounds in Meteorite Parent Bodies

NASA Technical Reports Server (NTRS)

Hammer, P. G.; Locke, D. R.; Burton, A. S.; Callahan, M. P.

2017-01-01

Organic compounds in carbonaceous chondrites were likely transformed by a variety of parent body processes including thermal and aqueous processing. Here, we analyzed ammonium cyanide reactions that were heated at different temperatures and times by multiple analytical techniques. The goal of this study is to better understand the effect of hydrothermal alteration on cyanide chemistry, which is believed to be responsible for the abiotic synthesis of purine nucleobases and their structural analogs detected in carbonaceous chondrites.

Reduction in the cumulative effect of stress-induced inbreeding depression due to intragenerational purging in Drosophila melanogaster.

PubMed

Enders, L S; Nunney, L

2016-03-01

Environmental stress generally exacerbates the harmful effects of inbreeding and it has been proposed that this could be exploited in purging deleterious alleles from threatened inbred populations. However, understanding what factors contribute to variability in the strength of inbreeding depression (ID) observed across adverse environmental conditions remains a challenge. Here, we examined how the nature and timing of stress affects ID and the potential for purging using inbred and outbred Drosophila melanogaster larvae exposed to biotic (larval competition, bacteria infection) and abiotic (ethanol, heat) stressors compared with unstressed controls. ID was measured during (larval survival) and after (male mating success) stress exposure. The level of stress imposed by each stressor was approximately equal, averaging a 42% reduction in outbred larval survival relative to controls. All stressors induced on average the same ID, causing a threefold increase in lethal equivalents for larval survival relative to controls. However, stress-induced ID in larval success was followed by a 30% reduction in ID in mating success of surviving males. We propose that this fitness recovery is due to 'intragenerational purging' whereby fitness correlations facilitate stress-induced purging that increases the average fitness of survivors in later life history stages. For biotic stressors, post-stress reductions in ID are consistent with intragenerational purging, whereas for abiotic stressors, there appeared to be an interaction between purging and stress-induced physiological damage. For all stressors, there was no net effect of stress on lifetime ID compared with unstressed controls, undermining the prediction that stress enhances the effectiveness of population-level purging across generations.

Reduction in the cumulative effect of stress-induced inbreeding depression due to intragenerational purging in Drosophila melanogaster

PubMed Central

Enders, L S; Nunney, L

2016-01-01

Environmental stress generally exacerbates the harmful effects of inbreeding and it has been proposed that this could be exploited in purging deleterious alleles from threatened inbred populations. However, understanding what factors contribute to variability in the strength of inbreeding depression (ID) observed across adverse environmental conditions remains a challenge. Here, we examined how the nature and timing of stress affects ID and the potential for purging using inbred and outbred Drosophila melanogaster larvae exposed to biotic (larval competition, bacteria infection) and abiotic (ethanol, heat) stressors compared with unstressed controls. ID was measured during (larval survival) and after (male mating success) stress exposure. The level of stress imposed by each stressor was approximately equal, averaging a 42% reduction in outbred larval survival relative to controls. All stressors induced on average the same ID, causing a threefold increase in lethal equivalents for larval survival relative to controls. However, stress-induced ID in larval success was followed by a 30% reduction in ID in mating success of surviving males. We propose that this fitness recovery is due to ‘intragenerational purging' whereby fitness correlations facilitate stress-induced purging that increases the average fitness of survivors in later life history stages. For biotic stressors, post-stress reductions in ID are consistent with intragenerational purging, whereas for abiotic stressors, there appeared to be an interaction between purging and stress-induced physiological damage. For all stressors, there was no net effect of stress on lifetime ID compared with unstressed controls, undermining the prediction that stress enhances the effectiveness of population-level purging across generations. PMID:26604190

Review of literature on climate change and forest diseases of western North America

Treesearch

John T. Kliejunas; Brian W. Geils; Jessie Micales Glaeser; Ellen Michaels Goheen; Paul Hennon; Mee-Sook Kim; Harry Kope; Jeff Stone; Rona Sturrock; Susan J. Frankel

2009-01-01

A summary of the literature on relationships between climate and various types of tree diseases, and the potential effects of climate change on pathogens in western North American forests is provided. Climate change generally will lead to reductions in tree health and will improve conditions for some highly damaging pathogens. Sections on abiotic diseases, declines,...

REMOVAL OF ADDED NITRATE IN THE SINGLE, BINARY, AND TERNARY SYSTEMS OF COTTON BURR COMPOST, ZEROVALENT IRON, AND SEDIMENT: IMPLICATIONS FOR GROUNDWATER NITRATE REMEDIATION USING PERMEABLE REACTIVE BARRIERS

EPA Science Inventory

Recent research has shown that carbonaceous solid materials and zerovalent iron (Fe0) may potentially be used as media in permeable reactive barriers (PRBs) to degrade groundwater nitrate via heterotrophic denitrification in the solid carbon system, and via abiotic reduction and ...

Combining Low-Energy Electrical Resistance Heating with Biotic and Abiotic Reactions for Treatment of Chlorinated Solvent DNAPL Source Areas

DTIC Science & Technology

2015-01-01

5 2.1.2 In Situ Bioremediation ...Technology Certification Program gpm gallons per minute ISB in situ bioremediation JBLM Joint Base Lewis-McChord mmol millimole MROD Mount...EXECUTIVE SUMMARY BACKGROUND The applicability of in situ groundwater remedies such as in situ bioremediation (ISB) or zero valent iron (ZVI) reduction

The Stable Isotope Fractionation of Abiotic Reactions: A Benchmark in the Detection of Life

NASA Technical Reports Server (NTRS)

Summers, David P.

2003-01-01

One very important tool in the analysis of biogenic, and potentially biogenic, samples is the study of their stable isotope distributions. The isotope distribution of a sample depends on the process(es) that created it. One important application of the analysis of C & N stable isotope ratios has been in the determination of whether organic matter in a sample is of biological origin or was produced abiotically. For example, the delta C-13 of organic material found embedded in phosphate grains was cited as a critical part of the evidence for life in 3.8 billion year old samples. The importance of such analysis in establishing biogenicity was highlighted again by the role this issue played in the recent debate over the validity of what had been accepted as the Earth s earliest microfossils. These kinds of analysis imply a comparison with the fractionation that one would have seen if the organic material had been produced by alternative, abiotic, pathways. Could abiotic reactions account for the same level of fractionation? Additionally, since the fractionation can vary between different abiotic reactions, understanding their fractionations can be important in distinguishing what reactions may have been significant in the formation of different abiological samples (such as extraterrestrial samples). There is however, a scarcity of data on the fractionation of carbon and nitrogen by abiotic reactions. In order to interpret properly what the stable isotope ratios of samples tell us about their biotic or abiotic nature, more needs to be known about how abiotic reactions fractionate C and N. Carbon isotope fractionations have been studied for a few abiotic processes. These studies presumed the presence of a reducing atmosphere, focusing on reactions involving spark discharge, W photolysis of reducing gas mixtures, and cyanide polymerization in the presence of ammonia. They did find that the initial products showed a depletion in I3C with values in the range of a few per mil to as low as -60 % (potentially comparable to that which accompanies the biosynthesis of organic matter). We need to understand what kind of fractionations are observed with reactions under the non-reducing or mildly reducing conditions now thought to be present on the early Earth. While nitrogen is receiving increased attention as a tool for these kinds of analyses, almost nothing is known about the isotope fractionation that one would expect for abiotic sources of fixed/reduced nitrogen. This project will measure the fixation from a series of abiotic reactions that may have been present on the early Earth (and other terrestrial planets) and produced organic material that could have ended up in the rock record. The work will look at a number of reactions, under a non- reducing, or mildly reducing, atmosphere, covering sources of prebiotic organic C & N from shock heating, to photochemistry, to hydrothermal reactions. Some reactions that we plan to study are; Shock heating of a non-reducing atmosphere to produce CO and NO (in collaboration with Chris McKay), formation of formaldehyde (and related compounds) from COY the formation of ammonia from nitrogen oxides (ultimately from NO) by ferrous iron reduction, and the hydrothermal synthesis of compounds including the hydrocarboxylation/hydrocarbonylation reaction (in collaboration with George Cody), reactions of oxalate to form hydrocarbons and other oxygenated compounds and the formation of lipids from oxalic/formic acid (in collaboration with Tom McCollom), and reactions of carbon monoxide & carbon dioxide with N2, ammonia or nitritehitrate to form hydrogen cyanide, nitriles, ammonia/amines and nitrous

The freshwater cyanobacterium Anabaena doliolum transformed with ApGSMT-DMT exhibited enhanced salt tolerance and protection to nitrogenase activity, but became halophilic.

PubMed

Singh, Meenakshi; Sharma, Naveen K; Prasad, Shyam Babu; Yadav, Suresh Singh; Narayan, Gopeshwar; Rai, Ashwani K

2013-03-01

Glycine betaine (GB) is an important osmolyte synthesized in response to different abiotic stresses, including salinity. The two known pathways of GB synthesis involve: 1) two step oxidation of choline (choline → betaine aldehyde → GB), generally found in plants, microbes and animals; and 2) three step methylation of glycine (glycine → sarcosine → dimethylglycine → GB), mainly found in halophilic archaea, sulphur bacteria and the cyanobacterium Aphanothece (Ap.) halophytica. Here, we transformed a salt-sensitive freshwater diazotrophic filamentous cyanobacterium Anabaena (An.) doliolum with N-methyltransferase genes (ApGSMT-DMT) from Ap. halophytica using the triparental conjugation method. The transformed An. doliolum synthesized and accumulated GB in cells, and showed increased salt tolerance and protection to nitrogenase activity. The salt responsiveness of the transformant was also apparent as GB synthesis increased with increasing concentrations of NaCl in the nutrient solution, and maximal [12.92 µmol (g dry weight)(-1)] in cells growing at 0.5 M NaCl. Therefore, the transformed cyanobacterium has changed its behaviour from preferring freshwater to halophily. This study may have important biotechnological implications for the development of stress tolerant nitrogen-fixing cyanobacteria as biofertilizers for sustainable agriculture.

Successful recovery of transgenic cowpea (Vigna unguiculata) using the 6-phosphomannose isomerase gene as the selectable marker.

PubMed

Bakshi, Souvika; Saha, Bedabrata; Roy, Nand Kishor; Mishra, Sagarika; Panda, Sanjib Kumar; Sahoo, Lingaraj

2012-06-01

A new method for obtaining transgenic cowpea was developed using positive selection based on the Escherichia coli 6-phosphomannose isomerase gene as the selectable marker and mannose as the selective agent. Only transformed cells were capable of utilizing mannose as a carbon source. Cotyledonary node explants from 4-day-old in vitro-germinated seedlings of cultivar Pusa Komal were inoculated with Agrobacterium tumefaciens strain EHA105 carrying the vector pNOV2819. Regenerating transformed shoots were selected on medium supplemented with a combination of 20 g/l mannose and 5 g/l sucrose as carbon source. The transformed shoots were rooted on medium devoid of mannose. Transformation efficiency based on PCR analysis of individual putative transformed shoots was 3.6%. Southern blot analysis on five randomly chosen PCR-positive plants confirmed the integration of the pmi transgene. Qualitative reverse transcription (qRT-PCR) analysis demonstrated the expression of pmi in T₀ transgenic plants. Chlorophenol red (CPR) assays confirmed the activity of PMI in transgenic plants, and the gene was transmitted to progeny in a Mendelian fashion. The transformation method presented here for cowpea using mannose selection is efficient and reproducible, and could be used to introduce a desirable gene(s) into cowpea for biotic and abiotic stress tolerance.

Abiotic Stress Resistance, a Novel Moonlighting Function of Ribosomal Protein RPL44 in the Halophilic Fungus Aspergillus glaucus

PubMed Central

Liu, Xiao-Dan; Xie, Lixia; Wei, Yi; Zhou, Xiaoyang; Jia, Baolei; Liu, Jinliang

2014-01-01

Ribosomal proteins are highly conserved components of basal cellular organelles, primarily involved in the translation of mRNA leading to protein synthesis. However, certain ribosomal proteins moonlight in the development and differentiation of organisms. In this study, the ribosomal protein L44 (RPL44), associated with salt resistance, was screened from the halophilic fungus Aspergillus glaucus (AgRPL44), and its activity was investigated in Saccharomyces cerevisiae and Nicotiana tabacum. Sequence alignment revealed that AgRPL44 is one of the proteins of the large ribosomal subunit 60S. Expression of AgRPL44 was upregulated via treatment with salt, sorbitol, or heavy metals to demonstrate its response to osmotic stress. A homologous sequence from the model fungus Magnaporthe oryzae, MoRPL44, was cloned and compared with AgRPL44 in a yeast expression system. The results indicated that yeast cells with overexpressed AgRPL44 were more resistant to salt, drought, and heavy metals than were yeast cells expressing MoRPL44 at a similar level of stress. When AgRPL44 was introduced into M. oryzae, the transformants displayed obviously enhanced tolerance to salt and drought, indicating the potential value of AgRPL44 for genetic applications. To verify the value of its application in plants, tobacco was transformed with AgRPL44, and the results were similar. Taken together, we conclude that AgRPL44 supports abiotic stress resistance and may have value for genetic application. PMID:24814782

Microbial- and thiosulfate-mediated dissolution of mercury sulfide minerals and transformation to gaseous mercury

DOE PAGES

Vázquez-Rodríguez, Adiari I.; Hansel, Colleen M.; Zhang, Tong; ...

2015-06-23

Mercury (Hg) is a toxic heavy metal that poses significant environmental and human health risks. Soils and sediments, where Hg can exist as the Hg sulfide mineral metacinnabar (β-HgS), represent major Hg reservoirs in aquatic environments. Metacinnabar has historically been considered a sink for Hg in all but severely acidic environments, and thus disregarded as a potential source of Hg back to aqueous or gaseous pools. In this study, we conducted a combination of field and laboratory incubations to identify the potential for metacinnabar as a source of dissolved Hg within near neutral pH environments and the underpinning (a)biotic mechanismsmore » at play. We show that the abundant and widespread sulfur-oxidizing bacteria of the genus Thiobacillus extensively colonized metacinnabar chips incubated within aerobic, near neutral pH creek sediments. Laboratory incubations of axenic Thiobacillus thioparus cultures led to the release of metacinnabar-hosted Hg(II) and subsequent volatilization to Hg(0). This dissolution and volatilization was greatly enhanced in the presence of thiosulfate, which served a dual role by enhancing HgS dissolution through Hg complexation and providing an additional metabolic substrate for Thiobacillus. These findings reveal a new coupled abiotic-biotic pathway for the transformation of metacinnabar-bound Hg(II) to Hg(0), while expanding the sulfide substrates available for neutrophilic chemosynthetic bacteria to Hg-laden sulfides. Lastly, they also point to mineral-hosted Hg as an underappreciated source of gaseous elemental Hg to the environment.« less

Microbial- and thiosulfate-mediated dissolution of mercury sulfide minerals and transformation to gaseous mercury

PubMed Central

Vázquez-Rodríguez, Adiari I.; Hansel, Colleen M.; Zhang, Tong; Lamborg, Carl H.; Santelli, Cara M.; Webb, Samuel M.; Brooks, Scott C.

2015-01-01

Mercury (Hg) is a toxic heavy metal that poses significant environmental and human health risks. Soils and sediments, where Hg can exist as the Hg sulfide mineral metacinnabar (β-HgS), represent major Hg reservoirs in aquatic environments. Metacinnabar has historically been considered a sink for Hg in all but severely acidic environments, and thus disregarded as a potential source of Hg back to aqueous or gaseous pools. Here, we conducted a combination of field and laboratory incubations to identify the potential for metacinnabar as a source of dissolved Hg within near neutral pH environments and the underpinning (a)biotic mechanisms at play. We show that the abundant and widespread sulfur-oxidizing bacteria of the genus Thiobacillus extensively colonized metacinnabar chips incubated within aerobic, near neutral pH creek sediments. Laboratory incubations of axenic Thiobacillus thioparus cultures led to the release of metacinnabar-hosted Hg(II) and subsequent volatilization to Hg(0). This dissolution and volatilization was greatly enhanced in the presence of thiosulfate, which served a dual role by enhancing HgS dissolution through Hg complexation and providing an additional metabolic substrate for Thiobacillus. These findings reveal a new coupled abiotic-biotic pathway for the transformation of metacinnabar-bound Hg(II) to Hg(0), while expanding the sulfide substrates available for neutrophilic chemosynthetic bacteria to Hg-laden sulfides. They also point to mineral-hosted Hg as an underappreciated source of gaseous elemental Hg to the environment. PMID:26157421

Combining Low-Energy Electrical Resistance Heating with Biotic and Abiotic Reactions for Treatment of Chlorinated Solvent DNAPL Source Area

DTIC Science & Technology

2012-12-01

DEPTH DRILLED INTO ROCK NIA 18. TOTAL CORE RECOVERY FOR BORING 9. TOTAL DEPTH OF HOLE 3o.o I 19. SIGNATURE OF INSPECT/’fi1’ ~V.U.. ELEVATION...EPA/540/-93/ 505 , U.S. Environmental Protection Agency Risk Reduction Engineering Laboratory, Cincinnati, OH. Farrell, J., Kason, M., Melitas, N., Li

Biological treatment of TNT-contaminated soil. 1: Anaerobic cometabolic reduction and interaction of TNT and metabolites with soil components

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

Daun, G.; Lenke, H.; Knackmuss, H.J.

1998-07-01

The explosive 2,4,6-trinitrotoluene (TNT), found as a major contaminant at armament plants from the two world wars, is reduced by a variety of microorganisms when electron donors such as glucose are added. This study shows that the cometabolic reduction of TNT to 2,4,6-triaminotoluene by an undefined anaerobic consortium increased considerably with increasing TNT concentrations and decreased with decreasing concentrations and feeding rates of glucose. The interactions of TNT and its reduction products with montmorillonitic clay and humic acids were investigated in abiotic adsorption experiments and during the microbial reduction of TNT. The results indicate that reduction products of TNT particularlymore » hydroxylaminodinitrotoluenes and 2,4,6-triaminotoluene bind irreversibly to soil components, which would prevent or prolong mineralization of the contaminants. Irreversible binding also hinders a further spread of the contaminants through soil or leaching into the groundwater.« less

Transformation of chlorpyrifos and chlorpyrifos-methyl in prairie pothole pore waters.

PubMed

Adams, Rachel M; McAdams, Brandon C; Arnold, William A; Chin, Yu-Ping

2016-11-09

Non-point source pesticide pollution is a concern for wetlands in the prairie pothole region (PPR). Recent studies have demonstrated that reduced sulfur species (e.g., bisulfide and polysulfides) in PPR wetland pore waters directly undergo reactions with chloroacetanilide and dinitroaniline compounds. In this paper, the abiotic transformation of two organophosphate compounds, chlorpyrifos and chlorpyrifos-methyl, was studied in PPR wetland pore waters. Chlorpyrifos-methyl reacted significantly faster (up to 4 times) in pore water with reduced sulfur species relative to hydrolysis. No rate enhancement was observed in the transformation of chlorpyrifos in pore water with reduced sulfur species. The lack of reactivity was most likely caused by steric hindrance from the ethyl groups and partitioning to dissolved organic matter (DOM), thereby shielding chlorpyrifos from nucleophilic attack. Significant decreases in reaction rates were observed for chlorpyrifos in pore water with high concentrations of DOM. Rate enhancement due to other reactive species (e.g., organo-sulfur compounds) in pore water was minor for both compounds relative to the influence of bisulfide and DOM.

CHROTRAN, 1.0

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

Hansen, Scott K.; Pandey, Sachin; Karra, Satish

2017-04-13

CHROTRAN is a fork of the widely-used PFLOTRAN flow and reactive transport numerical simulation code. It implements custom physics and chemistry appropriate to the design of in-situ reduction of heavy metals such as Cr(VI) in groundwater. CHROTRAN includes full dynamics for five species: the metal to be remediated, an electron donor, biofilm, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, and biofilm inactivation. The software implementation handles heterogeneous flow fields, arbitrarily many chemical species and amendment injectionmore » points, and features full coupling between flow and reactive transport, allowing for assessment of the effect of bio-fouling.« less

Biodegradability of degradable plastic waste.

PubMed

Agamuthu, P; Faizura, Putri Nadzrul

2005-04-01

Plastic waste constitutes the third largest waste volume in Malaysian municipal solid waste (MSW), next to putrescible waste and paper. The plastic component in MSW from Kuala Lumpur averages 24% (by weight), whereas the national mean is about 15%. The 144 waste dumps in the country receive about 95% of the MSW, including plastic waste. The useful life of the landfills is fast diminishing as the plastic waste stays un-degraded for more than 50 years. In this study the compostability of polyethylene and pro-oxidant additive-based environmentally degradable plastics (EDP) was investigated. Linear low-density polyethylene (LLDPE) samples exposed hydrolytically or oxidatively at 60 degrees C showed that the abiotic degradation path was oxidative rather than hydrolytic. There was a weight loss of 8% and the plastic has been oxidized as shown by the additional carbonyl group exhibited in the Fourier transform infra red (FTIR) Spectrum. Oxidation rate seemed to be influenced by the amount of pro-oxidant additive, the chemical structure and morphology of the plastic samples, and the surface area. Composting studies during a 45-day experiment showed that the percentage elongation (reduction) was 20% for McD samples [high-density polyethylene, (HDPE) with 3% additive] and LL samples (LLDPE with 7% additive) and 18% reduction for totally degradable plastic (TDP) samples (HDPE with 3% additive). Lastly, microbial experiments using Pseudomonas aeroginosa on carbon-free media with degradable plastic samples as the sole carbon source, showed confirmatory results. A positive bacterial growth and a weight loss of 2.2% for degraded polyethylene samples were evident to show that the degradable plastic is biodegradable.

Chromium (VI) reduction in acetate- and molasses-amended natural media: empirical model development

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

Hansen, Scott; Boukhalfa, Hakim; Karra, Satish

Stimulating indigenous microbes to reduce heavy metals from highly toxic oxidized species to more benign reduced species is a promising groundwater remediation technique that has already seen successful field applications. Designing such a bio-remediation scheme requires a model incorporating the kinetics of nonlinear bio-geochemical interactions between multiple species. With this motivation, we performed a set of microcosm experiments in natural sediments and their indigenous pore water and microbes, generating simultaneous time series for concentrations of Cr(VI), an electron donor (both molasses and acetate were considered), and biomass. Molasses was found to undergo a rapid direct abiotic reaction which eliminated allmore » Cr(VI) before any biomass had time to grow. This was not found in the acetate microcosms, and a distinct zero-order bio-reduction process was observed. Existing models were found inappropriate and a new set of three coupled governing equations representing these process dynamics were developed and their parameters calibrated against the time series from the acetate-amended microcosms. Cell suspension batch experiments were also performed to calibrate bio-reduction rates in the absence of electron donor and sediment. The donor used to initially grow the cells (molasses or acetate) was found not to impact the reduction rate constants in suspension, which were orders of magnitude larger than those explaining the natural media microcosm experiments. This suggests the limited utility of kinetics determined in suspension for remedial design. Scoping studies on the natural media microcosms were also performed, suggesting limited impact of foreign abiotic material and minimal effect of diffusion limitation in the vertical dimension. These analyses may be of independent value to future researchers.« less

Plant abiotic stress diagnostic by laser induced chlorophyll fluorescence spectral analysis of in vivo leaf tissue of biofuel species

NASA Astrophysics Data System (ADS)

Gouveia-Neto, Artur S.; Silva, Elias A., Jr.; Costa, Ernande B.; Bueno, Luciano A.; Silva, Luciana M. H.; Granja, Manuela M. C.; Medeiros, Maria J. L.; Câmara, Terezinha J. R.; Willadino, Lilia G.

2010-02-01

Laser induced fluorescence is exploited to evaluate the effect of abiotic stresses upon the evolution and characteristics of in vivo chlorophyll emission spectra of leaves tissues of brazilian biofuel plants species(Saccharum officinarum and Jatropha curcas). The chlorophyll fluorescence spectra of 20 min predarkened intact leaves were studied employing several excitation wavelengths in the UV-VIS spectral region. Red(Fr) and far-red (FFr) chlorophyll fluorescence emission signals around 685 nm and 735 nm, respectively, were analyzed as a function of the stress intensity and the time of illumination(Kautsky effect). The Chl fluorescence ratio Fr/FFr which is a valuable nondestructive indicator of the chlorophyll content of leaves was investigated during a period of time of 30 days. The dependence of the Chl fluorescence ratio Fr/FFr upon the intensity of the abiotic stress(salinity) was examined. The results indicated that the salinity plays a major hole in the chlorophyll concentration of leaves in both plants spieces, with a significant reduction in the chlorophyll content for NaCl concentrations in the 25 - 200 mM range. The laser induced chlorophyll fluorescence analysis allowed detection of damage caused by salinity in the early stages of the plants growing process, and can be used as an early-warning indicator of salinity stress

African Orphan Crops under Abiotic Stresses: Challenges and Opportunities.

PubMed

Tadele, Zerihun

2018-01-01

A changing climate, a growing world population, and a reduction in arable land devoted to food production are all problems facing the world food security. The development of crops that can yield under uncertain and extreme climatic and soil growing conditions can play a key role in mitigating these problems. Major crops such as maize, rice, and wheat are responsible for a large proportion of global food production but many understudied crops (commonly known as "orphan crops") including millets, cassava, and cowpea feed millions of people in Asia, Africa, and South America and are already adapted to the local environments in which they are grown. The application of modern genetic and genomic tools to the breeding of these crops can provide enormous opportunities for ensuring world food security but is only in its infancy. In this review, the diversity and types of understudied crops will be introduced, and the beneficial traits of these crops as well as their role in the socioeconomics of Africa will be discussed. In addition, the response of orphan crops to diverse types of abiotic stresses is investigated. A review of the current tools and their application to the breeding of enhanced orphan crops will also be described. Finally, few examples of global efforts on tackling major abiotic constraints in Africa are presented.

African Orphan Crops under Abiotic Stresses: Challenges and Opportunities

PubMed Central

2018-01-01

A changing climate, a growing world population, and a reduction in arable land devoted to food production are all problems facing the world food security. The development of crops that can yield under uncertain and extreme climatic and soil growing conditions can play a key role in mitigating these problems. Major crops such as maize, rice, and wheat are responsible for a large proportion of global food production but many understudied crops (commonly known as “orphan crops”) including millets, cassava, and cowpea feed millions of people in Asia, Africa, and South America and are already adapted to the local environments in which they are grown. The application of modern genetic and genomic tools to the breeding of these crops can provide enormous opportunities for ensuring world food security but is only in its infancy. In this review, the diversity and types of understudied crops will be introduced, and the beneficial traits of these crops as well as their role in the socioeconomics of Africa will be discussed. In addition, the response of orphan crops to diverse types of abiotic stresses is investigated. A review of the current tools and their application to the breeding of enhanced orphan crops will also be described. Finally, few examples of global efforts on tackling major abiotic constraints in Africa are presented. PMID:29623231

ENVIRONMENTAL CHARACTERISTICS AFFECTING REDUCTIVE TRANSFORMATION OF ORGANIC POLLUTANTS IN ANOXIC SEDIMENTS

EPA Science Inventory

Reductive transformations are important processes for determining the fate of organic pollutants in anoxic environments. These processes are most often microbially mediated by both direct and indirect means. For example, specific bacteria transform organic pollutants directly as ...

Bioreactor production of secondary metabolites from cell cultures of periwinkle and sandalwood.

PubMed

Valluri, Jagan V

2009-01-01

A bench-top bioreactor allowing continuous extraction of secondary metabolites is designed for Catharanthus roseus L. (G.) Don (periwinkle) and Santalum album L. (sandalwood) plant cell suspensions. Periwinkle cell cultures are exposed to biotic elicitors (Aspergillus niger, crude chitin) and abiotic elicitors (mannitol, methyl jasmonate) to induce alkaloid production. Whereas most of the biotic elicitors are effective when added on day 15 of culture, the abiotic elicitors are effective when added on day 20. The use of trans-cinnamic acid, an inhibitor of phenylalanine ammonia lyase (PAL) activity, results in significant increase in the alkaloid production of periwinkle cell cultures. Exposure of the cells to mannitol-induced osmotic stress produced marked increment in the total alkaloid production. When biotic and abiotic stress treatments are applied sequentially, an additive effect in alkaloid accumulation is observed. Although no essential oils are detected, secondary metabolites in the form of phenolics are produced by the sandalwood cell cultures in the bioreactor environment. The use of morphologic modification such as organ cultures and transformed cultures is believed to be required for both production and storage of essential oil constituents in sandalwood. The present chapter demonstrates that periwinkle and sandalwood cell suspensions could be developed and successfully cultured in a modified air-lift bioreactor. The exploitation of variant cell strains and biotransformation of added precursors can certainly improve the use of periwinkle and sandalwood cell cultures for the bioproduction of desired compounds.

Expression Patterns and Identified Protein-Protein Interactions Suggest That Cassava CBL-CIPK Signal Networks Function in Responses to Abiotic Stresses.

PubMed

Mo, Chunyan; Wan, Shumin; Xia, Youquan; Ren, Ning; Zhou, Yang; Jiang, Xingyu

2018-01-01

Cassava is an energy crop that is tolerant of multiple abiotic stresses. It has been reported that the interaction between Calcineurin B-like (CBL) protein and CBL-interacting protein kinase (CIPK) is implicated in plant development and responses to various stresses. However, little is known about their functions in cassava. Herein, 8 CBL ( MeCBL ) and 26 CIPK ( MeCIPK ) genes were isolated from cassava by genome searching and cloning of cDNA sequences of Arabidopsis CBL s and CIPK s. Reverse-transcriptase polymerase chain reaction (RT-PCR) analysis showed that the expression levels of MeCBL and MeCIPK genes were different in different tissues throughout the life cycle. The expression patterns of 7 CBL and 26 CIPK genes in response to NaCl, PEG, heat and cold stresses were analyzed by quantitative real-time PCR (qRT-PCR), and it was found that the expression of each was induced by multiple stimuli. Furthermore, we found that many pairs of CBLs and CIPKs could interact with each other via investigating the interactions between 8 CBL and 25 CIPK proteins using a yeast two-hybrid system. Yeast cells co-transformed with cassava MeCIPK24, MeCBL10 , and Na + /H + antiporter MeSOS1 genes exhibited higher salt tolerance compared to those with one or two genes. These results suggest that the cassava CBL-CIPK signal network might play key roles in response to abiotic stresses.

Expression Patterns and Identified Protein-Protein Interactions Suggest That Cassava CBL-CIPK Signal Networks Function in Responses to Abiotic Stresses

PubMed Central

Mo, Chunyan; Wan, Shumin; Xia, Youquan; Ren, Ning; Zhou, Yang; Jiang, Xingyu

2018-01-01

Cassava is an energy crop that is tolerant of multiple abiotic stresses. It has been reported that the interaction between Calcineurin B-like (CBL) protein and CBL-interacting protein kinase (CIPK) is implicated in plant development and responses to various stresses. However, little is known about their functions in cassava. Herein, 8 CBL (MeCBL) and 26 CIPK (MeCIPK) genes were isolated from cassava by genome searching and cloning of cDNA sequences of Arabidopsis CBLs and CIPKs. Reverse-transcriptase polymerase chain reaction (RT-PCR) analysis showed that the expression levels of MeCBL and MeCIPK genes were different in different tissues throughout the life cycle. The expression patterns of 7 CBL and 26 CIPK genes in response to NaCl, PEG, heat and cold stresses were analyzed by quantitative real-time PCR (qRT-PCR), and it was found that the expression of each was induced by multiple stimuli. Furthermore, we found that many pairs of CBLs and CIPKs could interact with each other via investigating the interactions between 8 CBL and 25 CIPK proteins using a yeast two-hybrid system. Yeast cells co-transformed with cassava MeCIPK24, MeCBL10, and Na+/H+ antiporter MeSOS1 genes exhibited higher salt tolerance compared to those with one or two genes. These results suggest that the cassava CBL-CIPK signal network might play key roles in response to abiotic stresses. PMID:29552024

Using the Model Perennial Grass Brachypodium sylvaticum to Engineer Resistance to Multiple Abiotic Stresses

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

Gordon, Sean; Reguera, Maria; Sade, Nir

2015-03-20

We are using the perennial model grass Brachypodium sylvaticum to identify combinations of transgenes that enhance tolerance to multiple, simultaneous abiotic stresses. The most successful transgene combinations will ultimately be used to create improved switchgrass (Panicum virgatum L.) cultivars. To further develop B. sylvaticum as a perennial model grass, and facilitate our planned transcriptional profiling, we are sequencing and annotating the genome. We have generated ~40x genome coverage using PacBio sequencing of the largest possible size selected libraries (18, 22, 25 kb). Our initial assembly using only long-read sequence contained 320 Mb of sequence with an N50 contig length ofmore » 315 kb and an N95 contig length of 40 kb. This assembly consists of 2,430 contigs, the largest of which was 1.6 Mb. The estimated genome size based on c-values is 340 Mb indicating that about 20 Mb of presumably repetitive DNA remains yet unassembled. Significantly, this assembly is far superior to an assembly created from paired-end short-read sequence, ~100x genome coverage. The short-read-only assembly contained only 226 Mb of sequence in 19k contigs. To aid the assembly of the scaffolds into chromosome-scale assemblies we produced an F2 mapping population and have genotyped 480 individuals using a genotype by sequence approach. One of the reasons for using B. sylvaticum as a model system is to determine if the transgenes adversely affect perenniality and winter hardiness. Toward this goal, we examined the freezing tolerance of wild type B. sylvaticum lines to determine the optimal conditions for testing the freezing tolerance of the transgenics. A survey of seven accessions noted significant natural variation in freezing tolerance. Seedling or adult Ain-1 plants, the line used for transformation, survived an 8 hour challenge down to -6 oC and 50% survived a challenge down to -9 oC. Thus, we will be able to easily determine if the transgenes compromise freezing tolerance. In the effort to develop biotechnological tools for perennial grass improvement, we have completed the transformation of B. sylvaticum with constructs containing 20 genes shown to be associated with enhanced abiotic stress tolerance in monocots. In addition, we have transformed plants with constructs containing a combination of genes (i.e. SARK::IPT- Ubi::HSR1::Ubi::NHX1) in order to simultaneously overexpress genes associated with drought + heat tolerance + salt tolerance. We generated single copy insert T1 lines for all constructs and the generation and bulking of homozygous T2 lines is well underway. In addition to our B. sylvaticum transgenics, we transformed B. distachyon with many of the same genes. Some of the transgenic B. distachyon plants subjected to a combined stress of both drought and salinity were able to produced higher yields than wild type plants. Our results indicate a great potential for the development of grasses with improved performance and yield in water-limited areas.« less

[Key microbial processes in nitrous oxide emissions of agricultural soil and mitigation strategies].

PubMed

Zhu, Yong-Guan; Wang, Xiao-Hui; Yang, Xiao-Ru; Xu, Hui-Juan; Jia, Yan

2014-02-01

Nitrous oxide (N2O) is a powerful atmospheric greenhouse gas, which does not only have a strong influence on the global climate change but also depletes the ozone layer and induces the enhancement of ultraviolet radiation to ground surface, so numerous researches have been focused on global climate change and ecological environmental change. Soil is the foremost source of N2O emissions to the atmosphere, and approximately two-thirds of these emissions are generally attributed to microbiological processes including bacterial and fungal denitrification and nitrification processes, largely as a result of the application of nitrogenous fertilizers. Here the available knowledge concerning the research progress in N2O production in agricultural soils was reviewed, including denitrification, nitrification, nitrifier denitrification and dissimilatory nitrate reduction to ammonium, and the abiotic (including soil pH, organic and inorganic nitrogen, organic matter, soil humidity and temperature) and biotic factors that have direct and indirect effects on N2O fluxes from agricultural soils were also summarized. In addition, the strategies for mitigating N2O emissions and the future research direction were proposed. Therefore, these studies are expected to provide valuable and scientific evidence for the study on mitigation strategies for the emission of greenhouse gases, adjustment of nitrogen transformation processes and enhancement of nitrogen use efficiency.

Prospects for Remediation of 1,2,3-Trichloropropane by Natural and Engineered Abiotic Degradation Reactions

DTIC Science & Technology

2010-06-01

represent predicted values calculated from QSARs described in (8). Blue symbols represent experimental data from (10...C) and FeBH (theor/C) refer to values estimated from QSARs for granular mm sized nano-iron (8) and borohydride reduced nano-iron (14), respectively...Both papers report QSARs for reduction of chlorinated aliphatics using energies of the lowest unoccupied molecular orbital (ELUMO) as the

Microbiologically Influenced Corrosion: Global Phenomena, Local Mechanisms

DTIC Science & Technology

2011-02-17

Chandrasekaran and Dexter 1993) who suggested that Epl, for a stainless steel covered by a biofilm might be different from that measured in an abiotic...1985) observed that the presence of a biofilm dramatically increased the current density required to polarize stainless steel to a potential of... biofilms on corrosion potential and oxygen reduction of stainless steel . Corrosion 44 (10) 717-723. Dexter, SC and Maruthamuthu. S (2001). Reponse of

Enhancement of In Situ Bioremediation of Energetic Compounds by Coupled Abiotic/Biotic Processes

DTIC Science & Technology

2007-08-01

reduced in the laboratory and successfully treat energetics (RDX, TNT, CL-20, NDMA ), chlorinated solvents (PCE, TCE, TCA, 1,1-DCE, cis-DCE), and...Fruchter, M Williams, V Vermeul, H Fredrickson, and K Thompson. 2006. In situ chemical reduction of sediments for TCE, energetics, and NDMA remediation...sediments for TCE, energetics, and NDMA remediation, Remediation of Chlorinated and Recalcitrant Compounds, Monterey, California, May 2006. Szecsody J

Aluminium Toxicity to Plants as Influenced by the Properties of the Root Growth Environment Affected by Other Co-Stressors: A Review.

PubMed

Siecińska, Joanna; Nosalewicz, Artur

Aluminium toxicity to crops depends on the acidity of the soil and specific plant resistance. However, it is also strongly affected by other environmental factors that have to be considered to properly evaluate the resultant effects on plants. Observed weather perturbations and predicted climate changes will increase the probability of co-occurrence of aluminium toxicity and other abiotic stresses.In this review the mechanisms of plant-aluminium interactions are shown to be influenced by soil mineral nutrients, heavy metals, organic matter, oxidative stress and drought. Described effects of aluminium toxicity include: root growth inhibition, reduction in the uptake of mineral nutrients resulting from the inhibition of transport processes through ion channels; epigenetic changes to DNA resulting in gene silencing. Complex processes occurring in the rhizosphere are highlighted, including the role of soil organic matter and aluminium detoxification by mucilage.There is a considerable research gap in the understanding of root growth in the soil environment in the presence of toxic aluminium concentrations as affected by interactions with abiotic stressors. This knowledge is important for the selection of feasible methods aimed at the reduction of negative consequences of crop production in acidic soils affected by adverse growth environment.

Effect of phosphorus addition on the reductive transformation of pentachlorophenol (PCP) and iron reduction with microorganism involvement.

PubMed

Wang, Yongkui; Liu, Xianli; Huang, Jiexun; Xiao, Wensheng; Zhang, Jiaquan; Yin, Chunqin

2017-10-01

The transformation of phosphorus added to the soil environment has been proven to be influenced by the Fe biochemical process, which thereby may affect the transformation of organic chlorinated contaminants. However, the amount of related literatures regarding this topic is limited. This study aimed to determine the effects of phosphorus addition on pentachlorophenol (PCP) anaerobic transformation, iron reduction, and paddy soil microbial community structure. Results showed that the transformation of phosphorus, iron, and PCP were closely related to the microorganisms. Moreover, phosphorus addition significantly influenced PCP transformation and iron reduction, which promoted and inhibited these processes at low and high concentrations, respectively. Both the maximum reaction rate of PCP transformation and the maximum Fe(II) amount produced were obtained at 1 mmol/L phosphorus concentration. Among the various phosphorus species, dissolved P and NaOH-P considerably changed, whereas only slight changes were observed for the remaining phosphorus species. Microbial community structure analysis demonstrated that adding low concentration of phosphorus promoted the growth of Clostridium bowmanii, Clostridium hungatei, and Clostridium intestinale and Pseudomonas veronii. By contrast, high-concentration phosphorus inhibited growth of these microorganisms, similar to the curves of PCP transformation and iron reduction. These observations indicated that Clostridium and P. veronii, especially Clostridium, played a vital role in the transformation of related substances in the system. All these findings may serve as a reference for the complicated reactions among the multiple components of soils.

Recovery of palladium(II) by methanogenic granular sludge.

PubMed

Pat-Espadas, Aurora M; Field, James A; Otero-Gonzalez, Lila; Razo-Flores, Elías; Cervantes, Francisco J; Sierra-Alvarez, Reyes

2016-02-01

This is the first report that demonstrates the ability of anaerobic methanogenic granular sludge to reduce Pd(II) to Pd(0). Different electron donors were evaluated for their effectiveness in promoting Pd reduction. Formate and H2 fostered both chemically and biologically mediated Pd reduction. Ethanol only promoted the reduction of Pd(II) under biotic conditions and the reduction was likely mediated by H2 released from ethanol fermentation. No reduction was observed in biotic or abiotic assays with all other substrates tested (acetate, lactate and pyruvate) although a large fraction of the total Pd was removed from the liquid medium likely due to biosorption. Pd(II) displayed severe inhibition towards acetoclastic and hydrogenotrophic methanogens, as indicated by 50% inhibiting concentrations as low as 0.96 and 2.7 mg/L, respectively. The results obtained indicate the potential of utilizing anaerobic granular sludge bioreactor technology as a practical and promising option for Pd(II) reduction and recovery offering advantages over pure cultures. Copyright © 2015 Elsevier Ltd. All rights reserved.

Directed evolution of artificial metalloenzymes for in vivo metathesis

NASA Astrophysics Data System (ADS)

Jeschek, Markus; Reuter, Raphael; Heinisch, Tillmann; Trindler, Christian; Klehr, Juliane; Panke, Sven; Ward, Thomas R.

2016-09-01

The field of biocatalysis has advanced from harnessing natural enzymes to using directed evolution to obtain new biocatalysts with tailor-made functions. Several tools have recently been developed to expand the natural enzymatic repertoire with abiotic reactions. For example, artificial metalloenzymes, which combine the versatile reaction scope of transition metals with the beneficial catalytic features of enzymes, offer an attractive means to engineer new reactions. Three complementary strategies exist: repurposing natural metalloenzymes for abiotic transformations; in silico metalloenzyme (re-)design; and incorporation of abiotic cofactors into proteins. The third strategy offers the opportunity to design a wide variety of artificial metalloenzymes for non-natural reactions. However, many metal cofactors are inhibited by cellular components and therefore require purification of the scaffold protein. This limits the throughput of genetic optimization schemes applied to artificial metalloenzymes and their applicability in vivo to expand natural metabolism. Here we report the compartmentalization and in vivo evolution of an artificial metalloenzyme for olefin metathesis, which represents an archetypal organometallic reaction without equivalent in nature. Building on previous work on an artificial metallohydrolase, we exploit the periplasm of Escherichia coli as a reaction compartment for the ‘metathase’ because it offers an auspicious environment for artificial metalloenzymes, mainly owing to low concentrations of inhibitors such as glutathione, which has recently been identified as a major inhibitor. This strategy facilitated the assembly of a functional metathase in vivo and its directed evolution with substantially increased throughput compared to conventional approaches that rely on purified protein variants. The evolved metathase compares favourably with commercial catalysts, shows activity for different metathesis substrates and can be further evolved in different directions by adjusting the workflow. Our results represent the systematic implementation and evolution of an artificial metalloenzyme that catalyses an abiotic reaction in vivo, with potential applications in, for example, non-natural metabolism.

Comparative study of biogenic and abiotic iron-containing materials

NASA Astrophysics Data System (ADS)

Cherkezova-Zheleva, Z.; Shopska, M.; Paneva, D.; Kovacheva, D.; Kadinov, G.; Mitov, I.

2016-12-01

Series of iron-based biogenic materials prepared by cultivation of Leptothrix group of bacteria in different feeding media ( Sphaerotilus-Leptothrix group of bacteria isolation medium, Adler, Lieske and silicon-iron-glucose-peptone) were studied. Control samples were obtained in the same conditions and procedures but the nutrition media were not infected with bacteria, i.e. they were sterile. Room and low temperature Mössbauer spectroscopy, powder X-ray diffraction (XRD), and infrared spectroscopy (IRS) were used to reveal the composition and physicochemical properties of biomass and respective control samples. Comparative analysis showed differences in their composition and dispersity of present phases. Sample composition included different ratio of nanodimensional iron oxyhydroxide and oxide phases. Relaxation phenomena such as superparamagnetism or collective magnetic excitation behaviour were registered for some of them. The experimental data showed that the biogenic materials were enriched in oxyhydroxides of high dispersion. Catalytic behaviour of a selected biomass and abiotic material were studied in the reaction of CO oxidation. In situ diffuse-reflectance (DR) IRS was used to monitor the phase transformations in the biomass and CO conversion.

Abiotic Protein Fragmentation by Manganese Oxide: Implications for a Mechanism to Supply Soil Biota with Oligopeptides.

PubMed

Reardon, Patrick N; Chacon, Stephany S; Walter, Eric D; Bowden, Mark E; Washton, Nancy M; Kleber, Markus

2016-04-05

The ability of plants and microorganisms to take up organic nitrogen in the form of free amino acids and oligopeptides has received increasing attention over the last two decades, yet the mechanisms for the formation of such compounds in soil environments remain poorly understood. We used Nuclear Magnetic Resonance (NMR) and Electron Paramagnetic Resonance (EPR) spectroscopies to distinguish the reaction of a model protein with a pedogenic oxide (Birnessite, MnO2) from its response to a phyllosilicate (Kaolinite). Our data demonstrate that birnessite fragments the model protein while kaolinite does not, resulting in soluble peptides that would be available to soil biota and confirming the existence of an abiotic pathway for the formation of organic nitrogen compounds for direct uptake by plants and microorganisms. The absence of reduced Mn(II) in the solution suggests that birnessite acts as a catalyst rather than an oxidant in this reaction. NMR and EPR spectroscopies are shown to be valuable tools to observe these reactions and capture the extent of protein transformation together with the extent of mineral response.

Elevating vitamin C content via overexpression of myo-inositol oxygenase and l-gulono-1,4-lactone oxidase in Arabidopsis leads to enhanced biomass and tolerance to abiotic stresses.

PubMed

Lisko, Katherine A; Torres, Raquel; Harris, Rodney S; Belisle, Melinda; Vaughan, Martha M; Jullian, Berangère; Chevone, Boris I; Mendes, Pedro; Nessler, Craig L; Lorence, Argelia

2013-12-01

l-Ascorbic acid (vitamin C) is an abundant metabolite in plant cells and tissues. Ascorbate functions as an antioxidant, as an enzyme cofactor, and plays essential roles in multiple physiological processes including photosynthesis, photoprotection, control of cell cycle and cell elongation, and modulation of flowering time, gene regulation, and senescence. The importance of this key molecule in regulating whole plant morphology, cell structure, and plant development has been clearly established via characterization of low vitamin C mutants of Arabidopsis , potato, tobacco, tomato, and rice. However, the consequences of elevating ascorbate content in plant growth and development are poorly understood. Here we demonstrate that Arabidopsis lines over-expressing a myo -inositol oxygenase or an l-gulono-1,4-lactone oxidase, containing elevated ascorbate, display enhanced growth and biomass accumulation of both aerial and root tissues. To our knowledge this is the first study demonstrating such a marked positive effect in plant growth in lines engineered to contain elevated vitamin C content. In addition, we present evidence showing that these lines are tolerant to a wide range of abiotic stresses including salt, cold, and heat. Total ascorbate content of the transgenic lines remained higher than those of controls under the abiotic stresses tested. Interestingly, exposure to pyrene, a polycyclic aromatic hydrocarbon and known inducer of oxidative stress in plants, leads to stunted growth of the aerial tissue, reduction in the number of root hairs, and inhibition of leaf expansion in wild type plants, while these symptoms are less severe in the over-expressers. Our results indicate the potential of this metabolic engineering strategy to develop crops with enhanced biomass, abiotic stress tolerance, and phytoremediation capabilities.

Transgenic mimicry of pathogen attack stimulates growth and secondary metabolite accumulation.

PubMed

Chaudhuri, Kuntal; Das, Sudripta; Bandyopadhyay, Moumita; Zalar, Andreja; Kollmann, Albert; Jha, Sumita; Tepfer, David

2009-02-01

Plant secondary metabolites, including pharmaceuticals, flavorings and aromas, are often produced in response to stress. We used chemical inducers of the pathogen defense response (jasmonic acid, salicylate, killed fungi, oligosaccharides and the fungal elicitor protein, cryptogein) to increase metabolite and biomass production in transformed root cultures of the medicinal plant, Withania somnifera, and the weed, Convolvulus sepium. In an effort to genetically mimic the observed effects of cryptogein, we employed Agrobacterium rhizogenes to insert a synthetic gene encoding cryptogein into the roots of C. sepium, W. somnifera and Tylophora tanakae. This genetic transformation was associated with stimulation in both secondary metabolite production and growth in the first two species, and in growth in the third. In whole plants of Convolvulus arvensis and Arabidopsis thaliana, transformation with the cryptogein gene led, respectively, to increases in the calystegines and certain flavonoids. A similar transgenic mimicry of pathogen attack was previously employed to stimulate resistance to the pathogen and abiotic stress. In the present study of biochemical phenotype, we show that transgenic mimicry is correlated with increased secondary metabolite production in transformed root cultures and whole plants. We propose that natural transformation with genes encoding the production of microbial elicitors could influence interactions between plants and other organisms.

Prediction of Hydrolysis Products of Organic Chemicals under Environmental pH Conditions.

PubMed

Tebes-Stevens, Caroline; Patel, Jay M; Jones, W Jack; Weber, Eric J

2017-05-02

Cheminformatics-based software tools can predict the molecular structure of transformation products using a library of transformation reaction schemes. This paper presents the development of such a library for abiotic hydrolysis of organic chemicals under environmentally relevant conditions. The hydrolysis reaction schemes in the library encode the process science gathered from peer-reviewed literature and regulatory reports. Each scheme has been ranked on a scale of one to six based on the median half-life in a data set compiled from literature-reported hydrolysis rates. These ranks are used to predict the most likely transformation route when more than one structural fragment susceptible to hydrolysis is present in a molecule of interest. Separate rank assignments are established for pH 5, 7, and 9 to represent standard conditions in hydrolysis studies required for registration of pesticides in Organisation for Economic Co-operation and Development (OECD) member countries. The library is applied to predict the likely hydrolytic transformation products for two lists of chemicals, one representative of chemicals used in commerce and the other specific to pesticides, to evaluate which hydrolysis reaction pathways are most likely to be relevant for organic chemicals found in the natural environment.

Speciation of organic phosphorus in a sediment profile of Lake Taihu. I: Chemical forms and their transformation.

PubMed

Xu, Di; Ding, Shiming; Li, Bin; Bai, Xiuling; Fan, Chengxin; Zhang, Chaosheng

2013-04-01

Organic phosphorus (nonreactive P, NRP) is a major component of P in sediments, but information about its chemical forms and dynamic transformation is limited. The chemical forms and dynamic behaviors of NRP in a sediment profile from Lake Taihu, a freshwater and eutrophic lake in China, were investigated. Five forms of NRP in the sediments were extracted based on a chemical fractionation technique, including easily labile NRP (NaHCO3-NRP), reactive metal oxide-bound NRP (HCl-NRP), humic acid-associated NRP (NaOH-NRP(HA)), fulvic acid-associated NRP (NaOH-NRP(FA)) and residual NRP (Res-TP). There were notable transformations with increasing sediment depth from the labile NaHCO3-NRP and NaOH-NRP pools to the recalcitrant HCl-NRP and Res-TP pools, which caused the NRP to become increasingly recalcitrant as the early diagenetic processes proceeded. Further analyses showed that the relative changes in contents of organic matter and reactive Fe oxides in the sediment profile triggered a competition for binding NRP fractions and led to the transformation of NRP. The results highlighted the importance of abiotic processes in regulating the diagenesis of organic P and its stability in sediments.

Chemical Disequilibria and Sources of Gibbs Free Energy Inside Enceladus

NASA Astrophysics Data System (ADS)

Zolotov, M. Y.

2010-12-01

Non-photosynthetic organisms use chemical disequilibria in the environment to gain metabolic energy from enzyme catalyzed oxidation-reduction (redox) reactions. The presence of carbon dioxide, ammonia, formaldehyde, methanol, methane and other hydrocarbons in the eruptive plume of Enceladus [1] implies diverse redox disequilibria in the interior. In the history of the moon, redox disequilibria could have been activated through melting of a volatile-rich ice and following water-rock-organic interactions. Previous and/or present aqueous processes are consistent with the detection of NaCl and Na2CO3/NaHCO3-bearing grains emitted from Enceladus [2]. A low K/Na ratio in the grains [2] and a low upper limit for N2 in the plume [3] indicate low temperature (possibly < 273 K) of aqueous processes. Although many of the energetically favorable redox reactions are sluggish at low temperature, they could be catalyzed by enzymes if organisms were (are) present. The redox conditions in aqueous systems and amounts of available Gibbs free energy should have been affected by the production, consumption and escape of hydrogen. Aqueous oxidation of minerals (Fe-Ni metal, Fe-Ni phosphides, etc.) accreted on Enceladus should have led to H2 production, which is consistent with H2 detection in the plume [1]. Numerical evaluations based on concentrations of plume gases [1] reveal sufficient energy sources available to support metabolically diverse life at a wide range of activities (a) of dissolved H2 (log aH2 from 0 to -10). Formaldehyde, carbon dioxide [c.f. 4], HCN (if it is present), methanol, acetylene and other hydrocarbons have the potential to react with H2 to form methane. Aqueous hydrogenations of acetylene, HCN and formaldehyde to produce methanol are energetically favorable as well. Both favorable hydrogenation and hydration of HCN lead to formation of ammonia. Condensed organic species could also participate in redox reactions. Methane and ammonia are the final products of these putative redox transformations. Sulfates may have not formed in cold and/or short-term aqueous environments with a limited H2 escape. In contrast to Earth, Mars and Europa, the moon may have no (or very limited [4]) potential for sulfate reduction. Despite nutrient (C, N, P and S) and metal (e.g. Fe, Ni) rich environments and multiple sources of Gibbs free energy during aqueous episode(s), putative life on Enceladus [4] would have adapted to survive in low water activity alkaline brines rich in ammonia, methanol and organic liquids at temperature >150-170 K. The comet-like abundances of major plume gases and apparent redox disequilibria in aquatic systems are consistent with a minimal influence of aqueous processes on endogenic chemical reactions and may indicate abiotic interior. Alternatively, plume gases may represent never melted primordial parcels of the icy shell, while the deeper interior could contain altered species transformed in abiotic and/or biological processes. Refs: [1] Waite J. et al. (2009) Nature 460, 487-490. [2] Postberg F. et al. (2009) Nature 459, 1098-1101. [3] Hansen C. et al. (2010) 38th COSPAR Sci. Assembly. [4] McKay C. et al. (2008) Astrobiology 8, 909-919.

Overexpression of wheat ferritin gene TaFER-5B enhances tolerance to heat stress and other abiotic stresses associated with the ROS scavenging.

PubMed

Zang, Xinshan; Geng, Xiaoli; Wang, Fei; Liu, Zhenshan; Zhang, Liyuan; Zhao, Yue; Tian, Xuejun; Ni, Zhongfu; Yao, Yingyin; Xin, Mingming; Hu, Zhaorong; Sun, Qixin; Peng, Huiru

2017-01-14

The yield of wheat (Triticum aestivum L.), an important crop, is adversely affected by heat stress in many regions of the world. However, the molecular mechanisms underlying thermotolerance are largely unknown. A novel ferritin gene, TaFER, was identified from our previous heat stress-responsive transcriptome analysis of a heat-tolerant wheat cultivar (TAM107). TaFER was mapped to chromosome 5B and named TaFER-5B. Expression pattern analysis revealed that TaFER-5B was induced by heat, polyethylene glycol (PEG), H 2 O 2 and Fe-ethylenediaminedi(o-hydroxyphenylacetic) acid (Fe-EDDHA). To confirm the function of TaFER-5B in wheat, TaFER-5B was transformed into the wheat cultivar Jimai5265 (JM5265), and the transgenic plants exhibited enhanced thermotolerance. To examine whether the function of ferritin from mono- and dico-species is conserved, TaFER-5B was transformed into Arabidopsis, and overexpression of TaFER-5B functionally complemented the heat stress-sensitive phenotype of a ferritin-lacking mutant of Arabidopsis. Moreover, TaFER-5B is essential for protecting cells against heat stress associated with protecting cells against ROS. In addition, TaFER-5B overexpression also enhanced drought, oxidative and excess iron stress tolerance associated with the ROS scavenging. Finally, TaFER-5B transgenic Arabidopsis and wheat plants exhibited improved leaf iron content. Our results suggest that TaFER-5B plays an important role in enhancing tolerance to heat stress and other abiotic stresses associated with the ROS scavenging.

Stressed out symbiotes: hypotheses for the influence of abiotic stress on arbuscular mycorrhizal fungi.

PubMed

Millar, Niall S; Bennett, Alison E

2016-11-01

Abiotic stress is a widespread threat to both plant and soil communities. Arbuscular mycorrhizal (AM) fungi can alleviate effects of abiotic stress by improving host plant stress tolerance, but the direct effects of abiotic stress on AM fungi are less well understood. We propose two hypotheses predicting how AM fungi will respond to abiotic stress. The stress exclusion hypothesis predicts that AM fungal abundance and diversity will decrease with persistent abiotic stress. The mycorrhizal stress adaptation hypothesis predicts that AM fungi will evolve in response to abiotic stress to maintain their fitness. We conclude that abiotic stress can have effects on AM fungi independent of the effects on the host plant. AM fungal communities will change in composition in response to abiotic stress, which may mean the loss of important individual species. This could alter feedbacks to the plant community and beyond. AM fungi will adapt to abiotic stress independent of their host plant. The adaptation of AM fungi to abiotic stress should allow the maintenance of the plant-AM fungal mutualism in the face of changing climates.

Barrier island community change: What controls it?

NASA Astrophysics Data System (ADS)

Dows, B.; Young, D.; Zinnert, J.

2014-12-01

Conversion from grassland to woody dominated communities has been observed globally. In recent decades, this pattern has been observed in coastal communities along the mid-Atlantic U.S. In coastal environments, a suite of biotic and abiotic factors interact as filters to determine plant community structure and distribution. Microclimatic conditions: soil and air temperature, soil moisture and salinity, and light attenuation under grass cover were measured across a grassland-woody encroachment gradient on a Virginia barrier island; to identify the primary factors that mediate this change. Woody establishment was associated with moderately dense (2200 shoots/m2) grass cover, but reduced at high (> 6200 shoots/ m2) and low (< 1250 shoots/ m2) densities. Moderately dense grass cover reduced light attenuation (82.50 % reduction) to sufficiently reduce soil temperature thereby limiting soil moisture evaporation. However, high grass density reduced light attenuation (98.7 % reduction) enough to inhibit establishment of woody species; whereas low grass density attenuated much less light (48.7 % reduction) which allowed for greater soil moisture evaporation. Soil salinity was dynamic as rainfall, tidal inundation, and sea spray produce spatiotemporal variation throughout the barrier island landscape. The importance of light and temperature were compounded as they also indirectly affect soil salinity via their affects on soil moisture. Determining how these biotic and abiotic factors relate to sea level rise and climate change will improve understanding coastal community response as global changes proceed. Understanding how community shifts affect ecosystem function and their potential to affect adjacent systems will also improve predictive ability of coastal ecosystem responses.

Chloroethene dechlorination in acidic groundwater: Implications for combining fenton's treatment with natural attenuation

USGS Publications Warehouse

Bradley, Paul M.; Singletary , Michael A.; Chapelle, Francis H.

2007-01-01

A sulfuric acid leak in 1988 at a chloroethene-contaminated groundwater site at the Naval Air Station Pensacola has resulted in a long-term record of the behavior of chloroethene contaminants at low pH and a unique opportunity to assess the potential impact of source area treatment technologies, which involve acidification of the groundwater environment (e.g., Fenton's-based in situ chemical oxidation), on downgradient natural attenuation processes. The greater than 75 percent decrease in trichloroethene (TCE) concentrations and the shift in contaminant composition toward predominantly reduced daughter products (dichloroethene [DCE] and vinyl chloride [VC]) that were observed along a 30-m groundwater flow path characterized by highly acidic conditions (pH = 3.5 ± 0.4) demonstrated that chloroethene reductive dechlorination can continue to be efficient under persistent acidic conditions. The detection of Dehalococcoides-type bacteria within the sulfuric acid/chloroethene co-contaminant plume was consistent with biotic chloroethene reductive dechlorination. Microcosm studies conducted with 14C-TCE and 14C-VC confirmed biotic reductive dechlorination in sediment collected from within the sulfuric acid/chloroethene co-contaminant plume. Microcosms prepared with sediment from two other locations within the acid plume, however, demonstrated only a limited mineralization to 14CO2 and 14CO, which was attributed to abiotic degradation because no significant differences were observed between experimental and autoclaved control treatments. These results indicated that biotic and abiotic mechanisms contributed to chloroethene attenuation in the acid plume at NAS Pensacola and that remediation techniques involving acidification of the groundwater environment (e.g., Fenton's-based source area treatment) do not necessarily preclude efficient chloroethene degradation.

Deformation, Fluid Flow and Mantle Serpentinization at Oceanic Transform Faults

NASA Astrophysics Data System (ADS)

Rupke, L.; Hasenclever, J.

2017-12-01

Oceanic transform faults (OTF) and fracture zones have long been hypothesized to be sites of enhanced fluid flow and biogeochemical exchange. In this context, the serpentine forming interaction between seawater and cold lithospheric mantle rocks is particularly interesting. The transformation of peridotite to serpentinite not only leads to hydration of oceanic plates and is thereby an important agent of the geological water cycle, it is also a mechanism of abiotic hydrogen and methane formation, which can support archeal and bacterial communities at the seafloor. Inferring the likely amount of mantle undergoing serpentinization reactions therefore allows estimating the amount of biomass that may be autotrophically produced at and around oceanic transform faults and mid-ocean ridges Here we present results of 3-D geodynamic model simulations that explore the interrelations between deformation, fluid flow, and mantle serpentinization at oceanic transform faults. We investigate how slip rate and fault offset affect the predicted patterns of mantle serpentinization around oceanic transform faults. Global rates of mantle serpentinization and associated H2 production are calculated by integrating the modeling results with plate boundary data. The global additional OTF-related production of H2 is found to be between 6.1 and 10.7 x 1011 mol per year, which is comparable to the predicted background mid-ocean ridge rate of 4.1 - 15.0 x 1011 mol H2/yr. This points to oceanic transform faults as potential sites of intense fluid-rock interaction, where chemosynthetic life could be sustained by serpentinization reactions.

Transformation products and human metabolites of triclocarban and tricllosan in sewage sludge across the United States

USGS Publications Warehouse

Pycke, Benny F.G.; Roll, Isaac B.; Brownawell, Bruce J.; Kinney, Chad A.; Furlong, Edward T.; Kolpin, Dana W.; Halden, Rolf U.

2014-01-01

Removal of triclocarban (TCC) and triclosan (TCS) from wastewater is a function of adsorption, abiotic degradation, and microbial mineralization or transformation, reactions that are not currently controlled or optimized in the pollution control infrastructure of standard wastewater treatment. Here, we report on the levels of eight transformation products, human metabolites, and manufacturing byproducts of TCC and TCS in raw and treated sewage sludge. Two sample sets were studied: samples collected once from 14 wastewater treatment plants (WWTPs) representing nine states, and multiple samples collected from one WWTP monitored for 12 months. Time-course analysis of significant mass fluxes (α = 0.01) indicate that transformation of TCC (dechlorination) and TCS (methylation) occurred during sewage conveyance and treatment. Strong linear correlations were found between TCC and the human metabolite 2′-hydroxy-TCC (r = 0.84), and between the TCC-dechlorination products dichlorocarbanilide (DCC) and monochlorocarbanilide (r = 0.99). Mass ratios of DCC-to-TCC and of methyl-triclosan (MeTCS)-to-TCS, serving as indicators of transformation activity, revealed that transformation was widespread under different treatment regimes across the WWTPs sampled, though the degree of transformation varied significantly among study sites (α = 0.01). The analysis of sludge sampled before and after different unit operation steps (i.e., anaerobic digestion, sludge heat treatment, and sludge drying) yielded insights into the extent and location of TCC and TCS transformation. Results showed anaerobic digestion to be important for MeTCS transformation (37–74%), whereas its contribution to partial TCC dechlorination was limited (0.4–2.1%). This longitudinal and nationwide survey is the first to report the occurrence of transformation products, human metabolites, and manufacturing byproducts of TCC and TCS in sewage sludge.

Transformation products and human metabolites of triclocarban and triclosan in sewage sludge across the United States.

PubMed

Pycke, Benny F G; Roll, Isaac B; Brownawell, Bruce J; Kinney, Chad A; Furlong, Edward T; Kolpin, Dana W; Halden, Rolf U

2014-07-15

Removal of triclocarban (TCC) and triclosan (TCS) from wastewater is a function of adsorption, abiotic degradation, and microbial mineralization or transformation, reactions that are not currently controlled or optimized in the pollution control infrastructure of standard wastewater treatment. Here, we report on the levels of eight transformation products, human metabolites, and manufacturing byproducts of TCC and TCS in raw and treated sewage sludge. Two sample sets were studied: samples collected once from 14 wastewater treatment plants (WWTPs) representing nine states, and multiple samples collected from one WWTP monitored for 12 months. Time-course analysis of significant mass fluxes (α=0.01) indicate that transformation of TCC (dechlorination) and TCS (methylation) occurred during sewage conveyance and treatment. Strong linear correlations were found between TCC and the human metabolite 2'-hydroxy-TCC (r=0.84), and between the TCC-dechlorination products dichlorocarbanilide (DCC) and monochlorocarbanilide (r=0.99). Mass ratios of DCC-to-TCC and of methyl-triclosan (MeTCS)-to-TCS, serving as indicators of transformation activity, revealed that transformation was widespread under different treatment regimes across the WWTPs sampled, though the degree of transformation varied significantly among study sites (α=0.01). The analysis of sludge sampled before and after different unit operation steps (i.e., anaerobic digestion, sludge heat treatment, and sludge drying) yielded insights into the extent and location of TCC and TCS transformation. Results showed anaerobic digestion to be important for MeTCS transformation (37-74%), whereas its contribution to partial TCC dechlorination was limited (0.4-2.1%). This longitudinal and nationwide survey is the first to report the occurrence of transformation products, human metabolites, and manufacturing byproducts of TCC and TCS in sewage sludge.

Transformation Products and Human Metabolites of Triclocarban and Triclosan in Sewage Sludge Across the United States

PubMed Central

2015-01-01

Removal of triclocarban (TCC) and triclosan (TCS) from wastewater is a function of adsorption, abiotic degradation, and microbial mineralization or transformation, reactions that are not currently controlled or optimized in the pollution control infrastructure of standard wastewater treatment. Here, we report on the levels of eight transformation products, human metabolites, and manufacturing byproducts of TCC and TCS in raw and treated sewage sludge. Two sample sets were studied: samples collected once from 14 wastewater treatment plants (WWTPs) representing nine states, and multiple samples collected from one WWTP monitored for 12 months. Time-course analysis of significant mass fluxes (α = 0.01) indicate that transformation of TCC (dechlorination) and TCS (methylation) occurred during sewage conveyance and treatment. Strong linear correlations were found between TCC and the human metabolite 2′-hydroxy-TCC (r = 0.84), and between the TCC-dechlorination products dichlorocarbanilide (DCC) and monochlorocarbanilide (r = 0.99). Mass ratios of DCC-to-TCC and of methyl-triclosan (MeTCS)-to-TCS, serving as indicators of transformation activity, revealed that transformation was widespread under different treatment regimes across the WWTPs sampled, though the degree of transformation varied significantly among study sites (α = 0.01). The analysis of sludge sampled before and after different unit operation steps (i.e., anaerobic digestion, sludge heat treatment, and sludge drying) yielded insights into the extent and location of TCC and TCS transformation. Results showed anaerobic digestion to be important for MeTCS transformation (37–74%), whereas its contribution to partial TCC dechlorination was limited (0.4–2.1%). This longitudinal and nationwide survey is the first to report the occurrence of transformation products, human metabolites, and manufacturing byproducts of TCC and TCS in sewage sludge. PMID:24932693

Biogeochemistry of manganese in ferruginous Lake Matano, Indonesia

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

Jones, C.; Crowe, S.A.; Sturm, A.

2012-12-13

This study explores Mn biogeochemistry in a stratified, ferruginous lake, a modern analogue to ferruginous oceans. Intense Mn cycling occurs in the chemocline where Mn is recycled at least 15 times before sedimentation. The product of biologically catalyzed Mn oxidation in Lake Matano is birnessite. Although there is evidence for abiotic Mn reduction with Fe(II), Mn reduction likely occurs through a variety of pathways. The flux of Fe(II) is insufficient to balance the reduction of Mn at 125m depth in the water column, and Mn reduction could be a significant contributor to CH{sub 4} oxidation. By combining results from synchrotron-basedmore » X-ray fluorescence and X-ray spectroscopy, extractions of sinking particles, and reaction transport modeling, we find the kinetics of Mn reduction in the lake's reducing waters are sufficiently rapid to preclude the deposition of Mn oxides from the water column to the sediments underlying ferruginous water. This has strong implications for the interpretation of the sedimentary Mn record.« less

Réduction des nitrates et de l'uranium par les bactéries indigènes

NASA Astrophysics Data System (ADS)

Abdelouas, Abdesselam; Lutze, Werner; Nuttall, Eric

1998-07-01

A bioremediation concept has been developed to clean up ground water contaminated with nitrate (1200 mg·L -1) and uranium (0.25 mg·L -1). We studied the Tuba City mill tailings site, Arizona, USA. Indigenous bacteria capable of catalyzing the reduction of NO 3- and U(VI) were identified in the ground water and in the host rock, the Navajo sandstone. After complete reduction of O 2 and NO 3- within one week, U(VI) was reduced and precipitated as uraninite. Final uranium concentrations < 15 μg·L -1 were reached after a few weeks at 24 °C. Iron sulfide also precipitated as a result of reduction of Fe(III) on the sand surface and sulfate in the ground water. U(VI) was not reduced by sulfide. It was found that enzymatic reduction of U(VI) is faster than abiotic reduction under the conditions given by the composition of the ground water.

Age-related Decline of Abiotic Stress Tolerance in Young Drosophila melanogaster Adults.

PubMed

Colinet, Hervé; Chertemps, Thomas; Boulogne, Isabelle; Siaussat, David

2016-12-01

Stress tolerance generally declines with age as a result of functional senescence. Age-dependent alteration of stress tolerance can also occur in early adult life. In Drosophila melanogaster, evidence of such a decline in young adults has only been reported for thermotolerance. It is not known whether early adult life entails a general stress tolerance reduction and whether the response is peculiar to thermal traits. The present work was designed to investigate whether newly eclosed D melanogaster adults present a high tolerance to a range of biotic and abiotic insults. We found that tolerance to most of the abiotic stressors tested (desiccation, paraquat, hydrogen peroxide, deltamethrin, and malathion) was high in newly eclosed adults before dramatically declining over the next days of adult life. No clear age-related pattern was found for resistance to biotic stress (septic or fungal infection) and starvation. These results suggest that newly eclosed adults present a culminating level of tolerance to extrinsic stress which is likely unrelated to immune process. We argue that stress tolerance variation at very young age is likely a residual attribute from the previous life stage (ontogenetic carryover) or a feature related to the posteclosion development. © The Author 2015. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Abiotic and biotic factors responsible for antimonite oxidation in Agrobacterium tumefaciens GW4

PubMed Central

Li, Jingxin; Yang, Birong; Shi, Manman; Yuan, Kai; Guo, Wei; Wang, Qian; Wang, Gejiao

2017-01-01

Antimonite [Sb(III)]-oxidizing bacteria can transform the toxic Sb(III) into the less toxic antimonate [Sb(V)]. Recently, the cytoplasmic Sb(III)-oxidase AnoA and the periplasmic arsenite [As(III)] oxidase AioAB were shown to responsible for bacterial Sb(III) oxidation, however, disruption of each gene only partially decreased Sb(III) oxidation efficiency. This study showed that in Agrobacterium tumefaciens GW4, Sb(III) induced cellular H2O2 content and H2O2 degradation gene katA. Gene knock-out/complementation of katA, anoA, aioA and anoA/aioA and Sb(III) oxidation and growth experiments showed that katA, anoA and aioA were essential for Sb(III) oxidation and resistance and katA was also essential for H2O2 resistance. Furthermore, linear correlations were observed between cellular H2O2 and Sb(V) content in vivo and chemical H2O2 and Sb(V) content in vitro (R2 = 0.93 and 0.94, respectively). These results indicate that besides the biotic factors, the cellular H2O2 induced by Sb(III) also catalyzes bacterial Sb(III) oxidation as an abiotic oxidant. The data reveal a novel mechanism that bacterial Sb(III) oxidation is associated with abiotic (cellular H2O2) and biotic (AnoA and AioAB) factors and Sb(III) oxidation process consumes cellular H2O2 which contributes to microbial detoxification of both Sb(III) and cellular H2O2. PMID:28252030

Evidence for abiotic sulfurization of marine dissolved organic matter in sulfidic environments

NASA Astrophysics Data System (ADS)

Pohlabeln, A. M.; Niggemann, J.; Dittmar, T.

2016-02-01

Sedimentary organic matter abiotically sulfurizes in sulfidic marine environments. Here we hypothesize that sulfurization also affects dissolved organic matter (DOM), and that sulfidic marine environments are sources of dissolved organic sulfur (DOS) to the ocean. To test these hypotheses we studied solid-phase extractable (SPE) DOS in the Black Sea at various water column depths (oxic and anoxic) and in sediment porewaters from the German Wadden Sea. The concentration and molecular composition of SPE-DOS from these sites and from the oxic water columns of the North Sea (Germany) and of the North Pacific were compared. In support of our hypotheses, SPE-DOS concentrations were elevated in sulfidic waters compared to oxic waters. For a detailed molecular characterization of SPE-DOS, selective wet-chemical alteration experiments targeting different sulfur-containing functional groups were applied prior to Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). These experiments included harsh hydrolysis, selective derivatization of thiols, oxidation, and deoxygenation to test for thioesters, sulfonic acid esters, alkylsulfates, thiols, non-aromatic thioethers, and sulfoxides. Additionally, collision-induced fragmentation experiments were applied to test for sulfonic acids. The tests revealed that the sulfonic acid group was the main structural feature in SPE-DOS, independent of the environmental conditions of the sampling site. Only in Wadden Sea anoxic porewater also non-aromatic thioethers were found which are presumably not stable in oxic waters. The findings from our field studies were confirmed in laboratory experiments, where we abiotically sulfurized marine and algal-derived DOM under conditions similar to that in anoxic marine sediments.

Abiotic and biotic factors responsible for antimonite oxidation in Agrobacterium tumefaciens GW4

NASA Astrophysics Data System (ADS)

Li, Jingxin; Yang, Birong; Shi, Manman; Yuan, Kai; Guo, Wei; Wang, Qian; Wang, Gejiao

2017-03-01

Antimonite [Sb(III)]-oxidizing bacteria can transform the toxic Sb(III) into the less toxic antimonate [Sb(V)]. Recently, the cytoplasmic Sb(III)-oxidase AnoA and the periplasmic arsenite [As(III)] oxidase AioAB were shown to responsible for bacterial Sb(III) oxidation, however, disruption of each gene only partially decreased Sb(III) oxidation efficiency. This study showed that in Agrobacterium tumefaciens GW4, Sb(III) induced cellular H2O2 content and H2O2 degradation gene katA. Gene knock-out/complementation of katA, anoA, aioA and anoA/aioA and Sb(III) oxidation and growth experiments showed that katA, anoA and aioA were essential for Sb(III) oxidation and resistance and katA was also essential for H2O2 resistance. Furthermore, linear correlations were observed between cellular H2O2 and Sb(V) content in vivo and chemical H2O2 and Sb(V) content in vitro (R2 = 0.93 and 0.94, respectively). These results indicate that besides the biotic factors, the cellular H2O2 induced by Sb(III) also catalyzes bacterial Sb(III) oxidation as an abiotic oxidant. The data reveal a novel mechanism that bacterial Sb(III) oxidation is associated with abiotic (cellular H2O2) and biotic (AnoA and AioAB) factors and Sb(III) oxidation process consumes cellular H2O2 which contributes to microbial detoxification of both Sb(III) and cellular H2O2.

Assessing the Role of Iron Sulfides in the Long Term Sequestration of Uranium by Sulfate-Reducing Bacteria

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

Hayes, Kim F.; Bi, Yuqiang; Carpenter, Julian

2013-12-31

This overarching aim of this project was to identify the role of biogenic and synthetic iron-sulfide minerals in the long-term sequestration of reduced U(IV) formed under sulfate-reducing conditions when subjected to re-oxidizing conditions. The work reported herein was achieved through the collaborative research effort conducted at Arizona State University (ASU) and the University of Michigan (UM). Research at ASU, focused on the biogenesis aspects, examined the biogeochemical bases for iron-sulfide production by Desulfovibrio vulgaris, a Gram-negative bacterium that is one of the most-studied strains of sulfate-reducing bacteria. A series of experimental studies were performed to investigate comprehensively important metabolic andmore » environmental factors that affect the rates of sulfate reduction and iron-sulfide precipitation, the mineralogical characteristics of the iron sulfides, and how uranium is reduced or co-reduced by D. vulagaris. FeS production studies revealed that controlling the pH affected the growth of D. vulgaris and strongly influenced the formation and growth of FeS solids. In particular, lower pH produced larger-sized mackinawite (Fe 1+xS). Greater accumulation of free sulfide, from more sulfate reduction by D. vulgaris, also led to larger-sized mackinawite and stimulated mackinawite transformation to greigite (Fe 3S 4) when the free sulfide concentration was 29.3 mM. On the other hand, using solid Fe(III) (hydr)oxides as the iron source led to less productivity of FeS due to their slow and incomplete dissolution and scavenging of sulfide. Furthermore, sufficient free Fe 2+, particularly during Fe(III) (hydr)oxide reductions, led to the additional formation of vivianite [Fe 3(PO 4) 2•8(H 2O)]. The U(VI) reduction studies revealed that D. vulgaris reduced U(VI) fastest when accumulating sulfide from concomitant sulfate reduction, since direct enzymatic and sulfide-based reductions of U(VI) occurred in parallel. The UO 2 produced in presence of ferrous iron was poorly crystalline. At UM, laboratory-scale reactor studies were performed to assess the potential for the predominant abiotic reductants formed under sulfate reducing conditions (SRCs) to: (1) reduce U(VI) in contaminated groundwater sediments), and (2) inhibit the re-oxidation of U(IV) species, and in particular, uraninite (UO 2(s)). Under SRCs, mackinawite and aqueous sulfide are the key reductants expected to form. To assess their potential for abiotic reduction of U(VI) species, a series of experiments were performed in which either FeS or S(-II) was added to solutions of U(VI), with the rates of conversion to U(IV) solids monitored as a function of pH, and carbonate and calcium concentration. In the presence of FeS and absence of oxygen or carbonate, U(IV) was completely reduced uraninite. S(-II) was also found to be an effective reductant of aqueous phase U(VI) species and produced uraninite, with the kinetics and extent of reduction depending on geochemical conditions. U(VI) reduction to uraninite was faster under higher S(-II) concentrations but was slowed by an increase in the dissolved Ca or carbonate concentration. Rapid reduction of U(VI) occurred at circumneutral pH but virtually no reduction occurred at pH 10.7. In general, dissolved Ca and carbonate slowed abiotic U(VI) reduction by forming stable Ca-U(VI)-carbonate soluble complexes that are resistant to reaction with aqueous sulfide. To investigate the stability of U(IV) against re-oxidation in the presence of iron sulfides by oxidants in simulated groundwater environments, and to develop a mechanistic understanding the controlling redox processes, continuously-mixed batch reactor (CMBR) and flow-through reactor (CMFR) studies were performed at UM. In these studies a series of experiments were conducted under various oxic groundwater conditions to examine the effectiveness of FeS as an oxygen scavenger to retard UO 2 dissolution. The results indicate that FeS is an effective oxygen scavenger, and can lower the rate of oxidative dissolution of UO 2 by over an order of magnitude compared to the absence of FeS, depending on pH, FeS content, and DO concentrations. Column reactor studies were performed at UM to assess the impact of mackinawite on uraninite oxidation under hydrodynamic flow conditions more representative of packed porous media at contaminated groundwater sites. In these studies, Rifle sediments were packed in the two columns which were subjected to different bioreduction steps and then run in parallel. The first column was bioreduced under SRCs (i.e., with sulfate in the influent) to generate mackinawite, mixed with uraninite, gamma-sterilized to inhibit subsequent microbiological activity, and then subjected to groundwater influent containing first nitrite and then oxygen. The second column was bioreduced (but in absence of sulfate in the influent) so that no iron sulfides would form, and then subjected to identical steps and influent as the first column. When nitrite was introduced in the influent of both columns, no significant release of U(VI) relative to the anoxic flow prior to nitrite addition occurred. However, when oxygen was introduced, the column which had undergone sulfate reduction (and had produced mackinawite as later verified by XAS) significantly lowered the peak U(VI) effluent concentrations, and in general, slowed U(VI) release considerably compared to the column with no FeS. Overall, these studies demonstrated that the presence of mackinawite can be a significant scavenger of oxygen and inhibit the oxidation of uraninite by oxygen, whereas nitrite had little impact on uraninite oxidation either in the presence or absence of FeS.« less

Selenium isotope fractionation during reduction by Fe(II)-Fe(III) hydroxide-sulfate (green rust)

USGS Publications Warehouse

Johnson, T.M.; Bullen, T.D.

2003-01-01

We have determined the extent of Se isotope fractionation induced by reduction of selenate by sulfate interlayered green rust (GRSO4), a Fe(II)-Fe(III) hydroxide-sulfate. This compound is known to reduce selenate to Se(0), and it is the only naturally relevant abiotic selenate reduction pathway documented to date. Se reduction reactions, when they occur in nature, greatly reduce Se mobility and bioavailability. Se stable isotope analysis shows promise as an indicator of Se reduction, and Se isotope fractionation by various Se reactions must be known in order to refine this tool. We measured the increase in the 80Se/76Se ratio of dissolved selenate as lighter isotopes were preferentially consumed during reduction by GRSO4. Six different experiments that used GRSO4 made by two methods, with varying solution compositions and pH, yielded identical isotopic fractionations. Regression of all the data yielded an instantaneous isotope fractionation of 7.36 ?? 0.24???. Selenate reduction by GRSO4 induces much greater isotopic fractionation than does bacterial selenate reduction. If selenate reduction by GRSO4 occurs in nature, it may be identifiable on the basis of its relatively large isotopic fractionation. ?? 2003 Elsevier Science Ltd.

The response of transgenic Brassica species to salt stress: a review.

PubMed

Shah, Nadil; Anwar, Sumera; Xu, Jingjing; Hou, Zhaoke; Salah, Akram; Khan, Shahbaz; Gong, Jianfang; Shang, Zhengwei; Qian, Li; Zhang, Chunyu

2018-06-01

Salt stress is considered one of the main abiotic factors to limit crop growth and productivity by affecting morpho-physiological and biochemical processes. Genetically, a number of salt tolerant Brassica varieties have been developed and introduced, but breeding of such varieties is time consuming. Therefore, current focus is on transgenic technology, which plays an important role in the development of salt tolerant varieties. Various salt tolerant genes have been characterized and incorporated into Brassica. Therefore, such genetic transformation of Brassica species is a significant step for improvement of crops, as well as conferring salt stress resistance qualities to Brassica species. Complete genome sequencing has made the task of genetically transforming Brassica species easier, by identifying desired candidate genes. The present review discusses relevant information about the principles which should be employed to develop transgenic Brassica species, and also will recommend tools for improved tolerance to salinity.

Biotic and Abiotic Reduction and Solubilization of Pu(IV)O2•xH2O(am) as Affected by Anthraquinone-2,6-disulfonate (AQDS) and Ethylenediaminetetraacetate (EDTA)

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

Plymale, Andrew E.; Bailey, Vanessa L.; Fredrickson, Jim K.

2012-01-24

In the presence of hydrogen (H{sub 2}), the synthetic chelating agent ethylenediaminetetraacetate (EDTA), and the electron shuttle anthraquinone-2,6-disulfonate (AQDS), the dissimilatory metal-reducing bacteria (DMRB) Shewanella oneidensis and Geobacter sulfurreducens both reductively solubilized 100% of added 0.5 mM plutonium (IV) hydrous oxide (Pu(IV)O{sub 2} {lg_bullet} xH{sub 2}O{sub (am)}) in {approx}24 h at pH 7 in a non-complexing buffer. In the absence of AQDS, bioreduction was much slower ({approx}22 days) and less extensive ({approx}83-94%). In the absence of DMRB but under comparable conditions, 89% (without AQDS) to 98% (with AQDS) of added 0.5 mM PuO{sub 2} {lg_bullet} xH{sub 2}O{sub (am)} was reductivelymore » solubilized over 418 days. Under comparable conditions but in the absence of EDTA, <0.001% of the 0.5 mM PuO{sub 2} {lg_bullet} xH{sub 2}O{sub (am)} was solubilized, with or without bacteria. However, Pu(aq) increased by as much as an order of magnitude in some EDTA-free treatments, both biotic and abiotic, and increases in solubility were associated with the production of both Pu(OH)3(am) and Pu(III)(aq). Incubation with DMRB in the absence of EDTA increased the polymeric and crystalline content of the PuO{sub 2} {lg_bullet} xH{sub 2}O{sub (am)} and also decreased Pu solubility in 6-N HCl. Results from an in vitro assay demonstrated electron transfer to PuO{sub 2} {lg_bullet} xH{sub 2}O{sub (am)} from the S. oneidensis outer-membrane c-type cytochrome MtrC, and EDTA increased the oxidation of MtrC by PuO{sub 2} {lg_bullet} xH{sub 2}O{sub (am)}. Our results suggest that PuO{sub 2} {lg_bullet} xH{sub 2}O{sub (am)} biotic and abiotic reduction and solubilization may be important in anoxic, reducing environments, especially where complexing ligands and electron shuttling compounds are present.« less

Reductive Sequestration Of Pertechnetate (99TcO4–) By Nano Zerovalent Iron (nZVI) Transformed By Abiotic Sulfide

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

Fan, Dimin; Anitori, Roberto; Tebo, Bradley M.

2013-04-24

Under anoxic conditions, soluble 99TcO4– can be reduced to less soluble TcO2•nH2O, but the oxide is highly susceptible to reoxidation. Here we investigate an alternative strategy for remediation of Tc-contaminated groundwater whereby sequestration as Tc sulfide is favored by sulfidic conditions stimulated by nano zero-valent iron (nZVI). nZVI was pre-exposed to increasing concentrations of sulfide in simulated Hanford groundwater for 24 hrs to mimic the stages of aquifer sulfate reduction and onset of biotic sulfidogenesis. Solid-phase characterizations of the sulfidated nZVI confirmed the formation of nanocrystalline FeS phases, but higher S/Fe ratios (>0.112) did not result in the formation ofmore » significantly more FeS. The kinetics of Tc sequestration by these materials showed faster Tc removal rates with increasing S/Fe between S/Fe = 0–0.056, but decreasing Tc removal rates with S/Fe > 0.224. The more favorable Tc removal kinetics at low S/Fe could be due to a higher affinity of TcO4– for FeS (over iron oxides), and electron microscopy confirmed that the majority of the Tc was associated with FeS phases. The inhibition of Tc removal at high S/Fe appears to have been caused by excess HS–. X-ray absorption spectroscopy revealed that as S/Fe increased, Tc speciation shifted from TcO2•nH2O to TcS2. The most substantial change of Tc speciation occurred at low S/Fe, coinciding with the rapid increase of Tc removal rate. This agreement further confirms the importance of FeS in Tc sequestration.« less

Photoassisted carbon dioxide reduction and formation of twoand three-carbon compounds. [prebiological photosynthesis

NASA Technical Reports Server (NTRS)

Halmann, M.; Aurian-Blajeni, B.; Bloch, S.

1981-01-01

The photoassisted reduction of aqueous carbon dioxide in the presence of naturally occurring minerals is investigated as a possible abiotic precursor of photosynthesis. Aqueous carbon dioxide saturated suspensions or surfaces of the minerals nontronite, bentonite, anatase, wolframite, molybdenite, minium, cinnabar and hematite were irradiated with high-pressure mercury lamps or sunlight. Chemical analyses reveal the production of formic acid, formaldehyde, methanol and methane, and the two and three-carbon compounds glyoxal (CHOCHO) and malonaldehyde (CH2(CHO)2). It is suggested that such photosynthetic reactions with visible light in the presence of semiconducting minerals may provide models for prebiological carbon and nitrogen fixation in both oxidized and reduced atmospheres.

Control of Sulfidogenesis Through Bio-oxidation of H 2S Coupled to (per)chlorate Reduction

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

Gregoire, Patrick; Engelbrektson, Anna; Hubbard, Christopher G.

2014-04-04

Here, we investigate H 2S attenuation by dissimilatory perchlorate-reducing bacteria (DPRB). All DPRB tested oxidized H 2S coupled to (per)chlorate reduction without sustaining growth. H 2S was preferentially utilized over organic electron donors resulting in an enriched (34S)-elemental sulfur product. Electron microscopy revealed elemental sulfur production in the cytoplasm and on the cell surface of the DPRB Azospira suillum. We also propose a novel hybrid enzymatic-abiotic mechanism for H 2S oxidation similar to that recently proposed for nitrate-dependent Fe(II) oxidation. The results of this study have implications for the control of biosouring and biocorrosion in a range of industrial environments.

Performance evaluation of low cost microbial fuel cell fabricated using earthen pot with biotic and abiotic cathode.

PubMed

Behera, Manaswini; Jana, Partha S; Ghangrekar, M M

2010-02-01

An attempt has been made to produce low cost MFC from the commercially available earthen pots in India, without involving any costly membrane. This MFC gave a maximum power output of 16.8 W/m(3) at a Coulombic efficiency (CE) of 31.3% with graphite plate cathode. With stainless steel mesh cathode and KMnO(4) as cathodic electrolyte the power production and CE of 70.48 W/m(3) and 64.5%, respectively, was obtained. The performance of this earthen pot MFC was evaluated with biotic and abiotic cathode. Although, biofilm formation on the cathode is observed to be helpful in enhancing power out put, the thicker biofilm on the cathode showed reduction in power. This MFC demonstrated competitive performance as compared to MFC incorporated with membrane. This low cost MFC, with total production cost of less than 1.0$, as per Indian market, demonstrated its utility as a wastewater treatment and onsite power generation device.

Abiotic transformation of high explosives by freshly precipitated iron minerals in aqueous Fe¹¹ solutions

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

Boparai, Hardiljeet K.; Comfort, Steve; Satapanajaru, Tunlawit

Zerovalent iron barriers have become a viable treatment for field-scale cleanup of various ground water contaminants. While contact with the iron surface is important for contaminant destruction, the interstitial pore water within and near the iron barrier will be laden with aqueous, adsorbed and precipitated FeII phases. These freshly precipitated iron minerals could play an important role in transforming high explosives (HE). Our objective was to determine the transformation of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine), HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine), and TNT (2,4,6-trinitrotoluene) by freshly precipitated iron FeII/FeIII minerals. This was accomplished by quantifying the effects of initial FeII concentration, pH, and the presence of aquifermore » solids (FeIII phases) on HE transformation rates. Results showed that at pH 8.2, freshly precipitated iron minerals transformed RDX, HMX, and TNT with reaction rates increasing with increasing FeII concentrations. RDX and HMX transformations in these solutions also increased with increasing pH (5.8-8.55). By contrast, TNT transformation was not influenced by pH (6.85-8.55) except at pH values <6.35. Transformations observed via LC/MS included a variety of nitroso products (RDX, HMX) and amino degradation products (TNT). XRD analysis identified green rust and magnetite as the dominant iron solid phases that precipitated from the aqueous FeII during HE treatment under anaerobic conditions. Geochemical modeling also predicted FeII activity would likely be controlled by green rust and magnetite. These results illustrate the important role freshly precipitated FeII/FeIII minerals in aqueous FeII solutions play in the transformation of high explosives.« less

Photochemical transformation of the insensitive munitions compound 2,4-dinitroanisole.

PubMed

Rao, Balaji; Wang, Wei; Cai, Qingsong; Anderson, Todd; Gu, Baohua

2013-01-15

The insensitive munitions compound 2,4-dinitroanisole (DNAN) is increasingly being used as a replacement for traditional, sensitive munitions compounds (e.g., trinitrotoluene [TNT]), but the environmental fate and photo-transformation of DNAN in natural water systems are currently unknown. In this study, we investigated the photo-transformation rates of DNAN with both ultraviolet (UV) and sunlight irradiation under different environmentally relevant conditions. Sunlight photo-transformation of DNAN in water was found to follow predominantly pseudo-first-order decay kinetics with an average half-life (t(1/2)) of approximately 0.70 d and activation energy (E(a)) of 53 kJ mol(-1). Photo-transformation rates of DNAN were dependent on the wavelength of the light source: irradiation with UV-B light (280-315 nm) resulted in a greater quantum yield of transformation (φ(UV-B)=3.7×10(-4)) than rates obtained with UV-A light (φ(UV-A)=2.9×10(-4) at 316-400 nm) and sunlight (φ(sun)=1.1×10(-4)). Photo-oxidation was the dominant mechanism for DNAN photo-transformation, based on the formation of nitrite (NO(2)(-)) and nitrate (NO(3)(-)) as major N species and 2,4-dinitrophenol as the minor species. Environmental factors (e.g., temperature, pH, and the presence or absence of naturally dissolved organic matter) displayed modest to little effects on the rate of DNAN photo-transformation. These observations indicate that sunlight-induced photo-transformation of DNAN may represent a significant abiotic degradation pathway in surface water, which may have important implications in evaluating the potential impacts and risks of DNAN in the environment. Published by Elsevier B.V.

Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation.

PubMed

Payne, Karl Ap; Quezada, Carolina P; Fisher, Karl; Dunstan, Mark S; Collins, Fraser A; Sjuts, Hanno; Levy, Colin; Hay, Sam; Rigby, Stephen Ej; Leys, David

2015-01-22

Organohalide chemistry underpins many industrial and agricultural processes, and a large proportion of environmental pollutants are organohalides. Nevertheless, organohalide chemistry is not exclusively of anthropogenic origin, with natural abiotic and biological processes contributing to the global halide cycle. Reductive dehalogenases are responsible for biological dehalogenation in organohalide respiring bacteria, with substrates including polychlorinated biphenyls or dioxins. Reductive dehalogenases form a distinct subfamily of cobalamin (B12)-dependent enzymes that are usually membrane associated and oxygen sensitive, hindering detailed studies. Here we report the characterization of a soluble, oxygen-tolerant reductive dehalogenase and, by combining structure determination with EPR (electron paramagnetic resonance) spectroscopy and simulation, show that a direct interaction between the cobalamin cobalt and the substrate halogen underpins catalysis. In contrast to the carbon-cobalt bond chemistry catalysed by the other cobalamin-dependent subfamilies, we propose that reductive dehalogenases achieve reduction of the organohalide substrate via halogen-cobalt bond formation. This presents a new model in both organohalide and cobalamin (bio)chemistry that will guide future exploitation of these enzymes in bioremediation or biocatalysis.

Enhanced Indirect Photochemical Transformation of Histidine and Histamine through Association with Chromophoric Dissolved Organic Matter.

PubMed

Chu, Chiheng; Lundeen, Rachel A; Remucal, Christina K; Sander, Michael; McNeill, Kristopher

2015-05-05

Photochemical transformations greatly affect the stability and fate of amino acids (AAs) in sunlit aquatic ecosystems. Whereas the direct phototransformation of dissolved AAs is well investigated, their indirect photolysis in the presence of chromophoric dissolved organic matter (CDOM) is poorly understood. In aquatic systems, CDOM may act both as sorbent for AAs and as photosensitizer, creating microenvironments with high concentrations of photochemically produced reactive intermediates, such as singlet oxygen (1O2). This study provides a systematic investigation of the indirect photochemical transformation of histidine (His) and histamine by 1O2 in solutions containing CDOM as a function of solution pH. Both His and histamine showed pH-dependent enhanced phototransformation in the CDOM systems as compared to systems in which model, low-molecular-weight 1O2 sensitizers were used. Enhanced reactivity resulted from sorption of His and histamine to CDOM and thus exposure to elevated 1O2 concentrations in the CDOM microenvironment. The extent of reactivity enhancement depended on solution pH via its effects on the protonation state of His, histamine, and CDOM. Sorption-enhanced reactivity was independently supported by depressed rate enhancements in the presence of a cosorbate that competitively displaced His and histamine from CDOM. Incorporating sorption and photochemical transformation processes into a reaction rate prediction model improved the description of the abiotic photochemical transformation rates of His in the presence of CDOM.

Isolation and functional characterization of CE1 binding proteins.

PubMed

Lee, Sun-ji; Park, Ji Hye; Lee, Mi Hun; Yu, Ji-hyun; Kim, Soo Young

2010-12-16

Abscisic acid (ABA) is a plant hormone that controls seed germination, protective responses to various abiotic stresses and seed maturation. The ABA-dependent processes entail changes in gene expression. Numerous genes are regulated by ABA, and promoter analyses of the genes revealed that cis-elements sharing the ACGTGGC consensus sequence are ubiquitous among ABA-regulated gene promoters. The importance of the core sequence, which is generally known as ABA response element (ABRE), has been demonstrated by various experiments, and its cognate transcription factors known as ABFs/AREBs have been identified. Although necessary, ABRE alone is not sufficient, and another cis-element known as "coupling element (CE)" is required for full range ABA-regulation of gene expression. Several CEs are known. However, despite their importance, the cognate transcription factors mediating ABA response via CEs have not been reported to date. Here, we report the isolation of transcription factors that bind one of the coupling elements, CE1. To isolate CE1 binding proteins, we carried out yeast one-hybrid screens. Reporter genes containing a trimer of the CE1 element were prepared and introduced into a yeast strain. The yeast was transformed with library DNA that represents RNA isolated from ABA-treated Arabidopsis seedlings. From the screen of 3.6 million yeast transformants, we isolated 78 positive clones. Analysis of the clones revealed that a group of AP2/ERF domain proteins binds the CE1 element. We investigated their expression patterns and analyzed their overexpression lines to investigate the in vivo functions of the CE element binding factors (CEBFs). Here, we show that one of the CEBFs, AtERF13, confers ABA hypersensitivity in Arabidopsis, whereas two other CEBFs enhance sugar sensitivity. Our results indicate that a group of AP2/ERF superfamily proteins interacts with CE1. Several CEBFs are known to mediate defense or abiotic stress response, but the physiological functions of other CEBFs remain to be determined. Our in vivo functional analysis of several CEBFs suggests that they are likely to be involved in ABA and/or sugar response. Together with previous results reported by others, our current data raise an interesting possibility that the coupling element CE1 may function not only as an ABRE but also as an element mediating biotic and abiotic stress responses.

An XRPD and EPR spectroscopy study of microcrystalline calcite bioprecipitated by Bacillus subtilis

NASA Astrophysics Data System (ADS)

Perito, B.; Romanelli, M.; Buccianti, A.; Passaponti, M.; Montegrossi, G.; Di Benedetto, F.

2018-05-01

We report in this study the first XRPD and EPR spectroscopy characterisation of a biogenic calcite, obtained from the activity of the bacterium Bacillus subtilis. Microcrystalline calcite powders obtained from bacterial culture in a suitable precipitation liquid medium were analysed without further manipulation. Both techniques reveal unusual parameters, closely related to the biological source of the mineral, i.e., to the bioprecipitation process and in particular to the organic matrix observed inside calcite. In detail, XRPD analysis revealed that bacterial calcite has slightly higher c/a lattice parameters ratio than abiotic calcite. This correlation was already noticed in microcrystalline calcite samples grown by bio-mineralisation processes, but it had never been previously verified for bacterial biocalcites. EPR spectroscopy evidenced an anomalously large value of W 6, a parameter that can be linked to occupation by different chemical species in the next nearest neighbouring sites. This parameter allows to clearly distinguish bacterial and abiotic calcite. This latter achievement was obtained after having reduced the parameters space into an unbiased Euclidean one, through an isometric log-ratio transformation. We conclude that this approach enables the coupled use of XRPD and EPR for identifying the traces of bacterial activity in fossil carbonate deposits.

Biotechnological applications in in vitro plant regeneration studies of broccoli (Brassica oleracea L. var. italica), an important vegetable crop.

PubMed

Kumar, Pankaj; Srivastava, Dinesh Kumar

2016-04-01

Biotechnology holds promise for genetic improvement of important vegetable crops. Broccoli (Brassica oleracea L. var. italica) is an important vegetable crop of the family Brassicaceae. However, various biotic and abiotic stresses cause enormous crop yield losses during commercial cultivation of broccoli. Establishment of a reliable, reproducible and efficient in vitro plant regeneration system with cell and tissue culture is a vital prerequisite for biotechnological application of crop improvement programme. An in vitro plant regeneration technique refers to culturing, cell division, cell multiplication, de-differentiation and differentiation of cells, protoplasts, tissues and organs on defined liquid/solid medium under aseptic and controlled environment. Recent progress in the field of plant tissue culture has made this area one of the most dynamic and promising in experimental biology. There are many published reports on in vitro plant regeneration studies in broccoli including direct organogenesis, indirect organogenesis and somatic embryogenesis. This review summarizes those plant regeneration studies in broccoli that could be helpful in drawing the attention of the researchers and scientists to work on it to produce healthy, biotic and abiotic stress resistant plant material and to carry out genetic transformation studies for the production of transgenic plants.

Dissolved inorganic nitrogen composition, transformation, retention, and transport in naturally phosphate-rich and phosphate-poor tropical streams

USGS Publications Warehouse

Triska, F.J.; Pringle, C.M.; Zellweger, G.W.; Duff, J.H.; Avanzino, R.J.

1993-01-01

In Costa Rica, the Salto River is enriched by geothermal-based soluble reactive phosphorus (SRP), which raises the concentration up to 200 ??g/L whereas Pantano Creek, an unimpacted tributary, has an SRP concentration <10 ??g/L. Ammonium concentration in springs adjacent to the Salto and Pantano was typically greater than channel water (13 of 22 locations) whereas nitrate concentration was less (20 of 22 locations). Ground waters were typically high in ammonium relative to nitrate whereas channel waters were high in nitrate relative to ammonium. Sediment slurry studies indicated nitrification potential in two sediment types, firm clay (3.34 ??g N.cm-3.d-1) and uncompacted organic-rich sediment (1.76 ??g N.cm-3.d-1). Ammonium and nitrate amendments to each stream separately resulted in nitrate concentrations in excess of that expected after correlation for dilution using a conservative tracer. SRP concentration was not affected by DIN amendment to either stream. SRP concentration in the Pantano appeared to be regulated by abiotic sediment exchange reactions. DIN composition and concentration were regulated by a combination of biotic and abiotic processes. -from Authors

FINAL REPORT: Adopting Biophysics Methods in Pursuit of Biogeophysical Research: Advancing the Measurement and Modeling of Electrical Signatures of Microbe-Mineral Transformations Impacting Contaminant Transport

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

PRODAN, CAMELIA; SLATER, LEE; NTARLAGIANNIS, DIMITRIOS

2012-09-01

This exploratory project involved laboratory experiments to investigate three hypotheses: (H1) Physics-based modeling of low-frequency dispersions (henceforth referred to as alpha) measured in broadband dielectric spectroscopy (DS) data can quantify pore-scale geometric changes impacting contaminant transport resulting from biomineralization; (H2) Physics-based modeling of high-frequency dispersions (henceforth referred to as beta) measured in broadband dielectric spectroscopy data can quantify rates of mineral growth in/on the cell wall; (H3) Application of this measurement and modeling approach can enhance geophysical interpretation of bioremediation experiments conducted at the RIFLE IFC by providing constraints on bioremediation efficiency (biomass concentration, mineral uptake within the cell wall,more » biomineralization rate). We tested H1 by performing DS measurements (alpha and beta range) on iron (Fe) particles of dimensions similar to microbial cells, dispersed within agar gels over a range of Fe concentrations. We have tested the ability of the physics-based modeling to predict volume concentrations of the Fe particles by assuming that the Fe particles are polarizable inclusions within an otherwise nonpolarizable medium. We evaluated the smallest volume concentration that can be detected with the DS method. Similar experiments and modeling have been performed on the sulfate-reducing bacteria D. vulgaris. Synchrotron x-ray absorption measurements were conducted to determine the local structure of biominerals coatings on D. vulgaris which were grown in the presence of different Fe concentrations. We imaged the mineral growth on cell wall using SEM. We used dielectric spectroscopy to differentiate between iron sulfide precipitates of biotic and abiotic nature. Biotic measurements were made on D. vulgaris bacteria grown in the presence of different concentrations of iron to form different thicknesses of iron sulfide precipitates around themselves and abiotic measurements were made on different concentrations of pyrrhotite particles suspended in agar. Results show a decrease in dielectric permittivity as a function of frequency for biotic minerals and an opposite trend is observed for abiotic minerals. Our results suggest that dielectric spectroscopy offers a noninvasive and fast approach for distinguishing between abiotic and biotic mineral precipitates.« less

Adopting Biophysics Methods in Pursuit of Biogeophysical Research: Advancing the measurement and modeling of electrical signatures of microbe-mineral transformations impacting contaminant transport

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

Prodan, Camelia

2013-06-14

This exploratory project involved laboratory experiments to investigate three hypotheses: (H1) Physics-based modeling of low-frequency dispersions (henceforth referred to as alpha) measured in broadband dielectric spectroscopy (DS) data can quantify pore-scale geometric changes impacting contaminant transport resulting from biomineralization; (H2) Physics-based modeling of high-frequency dispersions (henceforth referred to as beta) measured in broadband dielectric spectroscopy data can quantify rates of mineral growth in/on the cell wall; (H3) Application of this measurement and modeling approach can enhance geophysical interpretation of bioremediation experiments conducted at the RIFLE IFC by providing constraints on bioremediation efficiency (biomass concentration, mineral uptake within the cell wall,more » biomineralization rate). We tested H1 by performing DS measurements (alpha and beta range) on iron (Fe) particles of dimensions similar to microbial cells, dispersed within agar gels over a range of Fe concentrations. We have tested the ability of the physics-based modeling to predict volume concentrations of the Fe particles by assuming that the Fe particles are polarizable inclusions within an otherwise nonpolarizable medium. We evaluated the smallest volume concentration that can be detected with the DS method. Similar experiments and modeling have been performed on the sulfate-reducing bacteria D. vulgaris. Synchrotron x-ray absorption measurements were conducted to determine the local structure of biominerals coatings on D. vulgaris which were grown in the presence of different Fe concentrations. We imaged the mineral growth on cell wall using SEM. We used dielectric spectroscopy to differentiate between iron sulfide precipitates of biotic and abiotic nature. Biotic measurements were made on D. vulgaris bacteria grown in the presence of different concentrations of iron to form different thicknesses of iron sulfide precipitates around themselves and abiotic measurements were made on different concentrations of pyrrhotite particles suspended in agar. Results show a decrease in dielectric permittivity as a function of frequency for biotic minerals and an opposite trend is observed for abiotic minerals. Our results suggest that dielectric spectroscopy offers a noninvasive and fast approach for distinguishing between abiotic and biotic mineral precipitates.« less

Enhanced Oxidative Bioremediation of cis-dichloroethene (cis-DCE) and Vinyl Chloride (VC) using Electron Shuttles

DTIC Science & Technology

2009-07-01

1989) Abiotic Reduction of Nitro Aromatic Pesticides in Anaerobic Laboratory Systems. J, Agric, Food Chem, 37: 248. 13 Doménech-Carbó A., Doménech-Carbó...in general. Agricultural Use Humic acids have been used for decades as soil amendments and adjuvants for pesticide formulations for various food...necessary" to support an exception tolerance for pesticide formulations (EPA 2000, Federal Register, July 18, Vol 65, Number 138). Further, materials

Cr(VI) remediation by enriched sediment with anthraquinone-2,6-disulfonate as electron shuttles

NASA Astrophysics Data System (ADS)

Chen, Hong; Li, Xiaojuan; Xu, Zhiwei

Hexavalent chromium (Cr(VI)) is a priority pollutant in the USA and many other countries. This study investigated the simultaneous remediation of Cr(VI) in sediment enriched with quinone-reducing microorganisms via a closely coupled, biotic-abiotic pathway. The results showed that Cr(VI) remediation was achieved by sediment adsorption and reduction of quinone-reducing microorganism. Moreover, microorganism reduction of Cr(VI) could be continued when sediment adsorption was saturated after long-term Cr(VI) remediation. The acetate and anthraquinone-2,6-disulfonate (AQDS), which acted as exogenous carbon and electron shuttle, respectively, were two crucial factors. The optimum concentrations of acetate and AQDS were 5 mM and 1 mM when the initial Cr(VI) concentration was 10 mg/L. AQDS was recycled, and it acted in a catalytic-type manner for the bacterial reduction of Cr(VI). Thus, biological humus reduction might provide an extensive pathway for the sequestration and detoxification of Cr(VI) in anaerobic soils, water, and industrial effluents.

Improvement of Arabidopsis Biomass and Cold, Drought and Salinity Stress Tolerance by Modified Circadian Clock-Associated PSEUDO-RESPONSE REGULATORs.

PubMed

Nakamichi, Norihito; Takao, Saori; Kudo, Toru; Kiba, Takatoshi; Wang, Yin; Kinoshita, Toshinori; Sakakibara, Hitoshi

2016-05-01

Plant circadian clocks control the timing of a variety of genetic, metabolic and physiological processes. Recent studies revealed a possible molecular mechanism for circadian clock regulation. Arabidopsis thaliana (Arabidopsis) PSEUDO-RESPONSE REGULATOR (PRR) genes, including TIMING OF CAB EXPRESSION 1 (TOC1), encode clock-associated transcriptional repressors that act redundantly. Disruption of multiple PRR genes results in drastic phenotypes, including increased biomass and abiotic stress tolerance, whereas PRR single mutants show subtle phenotypic differences due to genetic redundancy. In this study, we demonstrate that constitutive expression of engineered PRR5 (PRR5-VP), which functions as a transcriptional activator, can increase biomass and abiotic stress tolerance, similar to prr multiple mutants. Concomitant analyses of relative growth rate, flowering time and photosynthetic activity suggested that increased biomass of PRR5-VP plants is mostly due to late flowering, rather than to alterations in photosynthetic activity or growth rate. In addition, genome-wide gene expression profiling revealed that genes related to cold stress and water deprivation responses were up-regulated in PRR5-VP plants. PRR5-VP plants were more resistant to cold, drought and salinity stress than the wild type, whereas ft tsf and gi, well-known late flowering and increased biomass mutants, were not. These findings suggest that attenuation of PRR function by a single transformation of PRR-VP is a valuable method for increasing biomass as well as abiotic stress tolerance in Arabidopsis. Because the PRR gene family is conserved in vascular plants, PRR-VP may regulate biomass and stress responses in many plants, but especially in long-day annual plants. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Use of 13C Labeled Carbon Tetrachloride to Demonstrate the Transformation to Carbon Dioxide under Anaerobic Conditions in a Continuous Flow Column

NASA Astrophysics Data System (ADS)

Semprini, L.; Azizian, M.

2012-12-01

The demonstration of transformation of chlorinated aliphatic compounds (CAHs) in the subsurface is a challenge, especially when the products are carbon dioxide (CO2) and chloride ion. The groundwater contaminant carbon tetrachloride (CT) is of particular interest since a broad range of transformation products can be potentially formed under anaerobic conditions. The ability to demonstrate the transformation of CT to CO2 as a non toxic endproduct, is also of great interest. Results will be presented from a continuous flow column study where 13C labeled CT was used to demonstrate its transformation to CO2. The column was packed with a quartz sand and bioaugmented the Evanite Culture (EV) that is capable of transforming tetrachloroethene (PCE) to ethene. The column was continously fed a synthetic groundwater that was amended with PCE (0.10 mM) and either formate (1.5 mM) or lactate (1.1 mM), which ferments to produce hydrogen (H2) as the ultimate electron donor. Earlier CT transformation studies with the column, in the absence of sulfate reduction, and with formate added as a donor found CT (0.015 mM) was over 98% transformed with about 20% converted to chloroform (CF) (0.003 mM) and with a transient detection of chloromethane (CM). Methane and carbon disulfide, as potential products, were not detected. Neither CT nor CF inhibited the reductive dehalogenation of PCE to ethene. A series of transient studies conducted after these initial CT transformation tests, but in the absence of CT, showed formate remained an effective substrate for maintaining sulfate reduction and PCE transformation. Lactate, which was effectively fermented prior to CT addition, was not effectively fermented, with propionate accumulating as a fermentation product. When lactate was added, PCE was mainly transformed to cis-dichloroethene (cis-DCE) and VC, and sulfate reduction did not occur. In order to restore effective lactate fermentation the column was then bioaugmented with an EV culture that was capable of lactate fermentation. After bioaugmentation, effective lactate fermentation, sulfate reduction and PCE transformation to ethene was achieved. Unlabeled CT (0.015 mM) addition was then started and complete transformation was achieved with a transient build-up of CF and chloromethane, which were subsequently removed below their detection limits. CT continued to be completely transformed after the influent concentration was increased to 0.03 mM. 13C labeled CT (0.03 mM) was then added to the column. GC-MS analysis showed that 13C labeled CO2 was formed at near stoichiometric levels to the CT that was transformed. The results clearly demonstrate that CT can being transformed to CO2 at high CT concentrations, while maintaining effective PCE dehalogenation, sulfate reduction and lactate fermentation. The results also illustrate the great potential of using 13C labeled compounds in subsurface investigations.

Evaluating reaction pathways of hydrothermal abiotic organic synthesis at elevated temperatures and pressures using carbon isotopes

NASA Astrophysics Data System (ADS)

Fu, Qi; Socki, Richard A.; Niles, Paul B.

2015-04-01

Experiments were performed to better understand the role of environmental factors on reaction pathways and corresponding carbon isotope fractionations during abiotic hydrothermal synthesis of organic compounds using piston cylinder apparatus at 750 °C and 5.5 kbars. Chemical compositions of experimental products and corresponding carbon isotopic values were obtained by a Pyrolysis-GC-MS-IRMS system. Alkanes (methane and ethane), straight-chain saturated alcohols (ethanol and n-butanol) and monocarboxylic acids (formic and acetic acids) were generated with ethanol being the only organic compound with higher δ13C than CO2. CO was not detected in experimental products owing to the favorable water-gas shift reaction under high water pressure conditions. The pattern of δ13C values of CO2, carboxylic acids and alkanes are consistent with their equilibrium isotope relationships: CO2 > carboxylic acids > alkanes, but the magnitude of the fractionation among them is higher than predicted isotope equilibrium values. In particular, the isotopic fractionation between CO2 and CH4 remained constant at ∼31‰, indicating a kinetic effect during CO2 reduction processes. No "isotope reversal" of δ13C values for alkanes or carboxylic acids was observed, which indicates a different reaction pathway than what is typically observed during Fischer-Tropsch synthesis under gas phase conditions. Under constraints imposed in experiments, the anomalous 13C isotope enrichment in ethanol suggests that hydroxymethylene is the organic intermediate, and that the generation of other organic compounds enriched in 12C were facilitated by subsequent Rayleigh fractionation of hydroxymethylene reacting with H2 and/or H2O. Carbon isotope fractionation data obtained in this study are instrumental in assessing the controlling factors on abiotic formation of organic compounds in hydrothermal systems. Knowledge on how environmental conditions affect reaction pathways of abiotic synthesis of organic compounds is critical for understanding deep subsurface ecosystems and the origin of organic compounds on Mars and other planets.

Disturbance-mediated facilitation by an intertidal ecosystem engineer.

PubMed

Wright, Jeffrey T; Gribben, Paul E

2017-09-01

Ecosystem engineers facilitate communities by providing a structural habitat that reduces abiotic stress or predation pressure for associated species. However, disturbance may damage or move the engineer to a more stressful environment, possibly increasing the importance of facilitation for associated communities. In this study, we determined how disturbance to intertidal boulders (i.e., flipping) and the subsequent movement of a structural ecosystem engineer, the tube-forming serpulid worm Galeolaria caespitosa, from the bottom (natural state, low abiotic stress) to the top (disturbed state, high abiotic stress) surface of boulders influenced the importance of facilitation for intertidal communities across two intertidal zones. Theory predicts stronger relative facilitation should occur in the harsher environments of the top of boulders and the high intertidal zone. To test this prediction, we experimentally positioned boulders with the serpulids either face up or face down for 12 months in low and high zones in an intertidal boulder field. There were very different communities associated with the different boulders and serpulids had the strongest facilitative effects on the more stressful top surface of boulders with approximately double the species richness compared to boulders lacking serpulids. Moreover, within the serpulid matrix itself there was also approximately double the species richness (both zones) and abundance (high zone only) of small invertebrates on the top of boulders compared to the bottom. The high relative facilitation on the top of boulders reflected a large reduction in temperature by the serpulid matrix on that surface (up to 10°C) highlighting a key role for modification of the abiotic environment in determining the community-wide facilitation. This study has demonstrated that disturbance and subsequent movement of an ecosystem engineer to a more stressful environment increased the importance of facilitation and allowed species to persist that would otherwise be unable to survive in that environment. © 2017 by the Ecological Society of America.

A proposed abiotic reaction scheme for hydroxylamine and monochloramine under chloramination relevant drinking water conditions.

PubMed

Wahman, David G; Speitel, Gerald E; Machavaram, Madhav V

2014-09-01

Drinking water monochloramine (NH2Cl) use may promote ammonia-oxidizing bacteria (AOB). AOB use (i) ammonia monooxygenase for biological ammonia (NH3) oxidation to hydroxylamine (NH2OH) and (ii) hydroxylamine oxidoreductase for NH2OH oxidation to nitrite. NH2Cl and NH2OH may react, providing AOB potential benefits and detriments. The NH2Cl/NH2OH reaction would benefit AOB by removing the disinfectant (NH2Cl) and releasing their growth substrate (NH3), but the NH2Cl/NH2OH reaction would also provide a possible additional inactivation mechanism besides direct NH2Cl reaction with cells. Because biological NH2OH oxidation supplies the electrons required for biological NH3 oxidation, the NH2Cl/NH2OH reaction provides a direct mechanism for NH2Cl to inhibit NH3 oxidation, starving the cell of reductant by preventing biological NH2OH oxidation. To investigate possible NH2Cl/NH2OH reaction implications on AOB, an understanding of the underlying abiotic reaction is first required. The present study conducted a detailed literature review and proposed an abiotic NH2Cl/NH2OH reaction scheme (RS) for chloramination relevant drinking water conditions (μM concentrations, air saturation, and pH 7-9). Next, RS literature based kinetics and end-products were evaluated experimentally between pHs 7.7 and 8.3, representing (i) the pH range for future experiments with AOB and (ii) mid-range pHs typically found in chloraminated drinking water. In addition, a (15)N stable isotope experiment was conducted to verify nitrous oxide and nitrogen gas production and their nitrogen source. Finally, the RS was slightly refined using the experimental data and an AQUASIM implemented kinetic model. A chloraminated drinking water relevant RS is proposed and provides the abiotic reaction foundation for future AOB biotic experiments. Published by Elsevier Ltd.

One-dimensional model for biogeochemical interactions and permeability reduction in soils during leachate permeation.

PubMed

Singhal, Naresh; Islam, Jahangir

2008-02-19

This paper uses the findings from a column study to develop a reactive model for exploring the interactions occurring in leachate-contaminated soils. The changes occurring in the concentrations of acetic acid, sulphate, suspended and attached biomass, Fe(II), Mn(II), calcium, carbonate ions, and pH in the column are assessed. The mathematical model considers geochemical equilibrium, kinetic biodegradation, precipitation-dissolution reactions, bacterial and substrate transport, and permeability reduction arising from bacterial growth and gas production. A two-step sequential operator splitting method is used to solve the coupled transport and biogeochemical reaction equations. The model gives satisfactory fits to experimental data and the simulations show that the transport of metals in soil is controlled by multiple competing biotic and abiotic reactions. These findings suggest that bioaccumulation and gas formation, compared to chemical precipitation, have a larger influence on hydraulic conductivity reduction.

NP1EC Degradation Pathways Under Oxic and Microxic Conditions

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

Montgomery-Brown, John; Li, Yongmei; Ding, Wang-Hsien

2008-03-22

The degradation pathway of nonylphenol ethoxyacetic acid (NP1EC) and the conditions favoring CAP1EC formation were studied in aerobic microcosms constructed with soil from the Mesa soil aquifer treatment (SAT) facility (Arizona, USA) and pristine sediments from Coyote Creek (California, USA). In the Mesa microcosms, para-NP1EC was transformed to para-NP, before being rapidly transformed to nonyl alcohols via ipso-hydroxylation. While the formation of NP from APEMs has been observed by several researchers under anaerobic conditions, this is the first time the transient formation of NP from APEMs has been observed under aerobic conditions. Unlike the Mesa microcosms, large quantities of CAP1ECsmore » were observed in the Coyote Creek microcosms. Initially, CA8P1ECs were the dominant metabolites, but as biodegradation continued, CA6P1ECs became the dominant metabolites. Compared to the CA8P1ECs, the number of CA6P1ECs peaks observed was small (<6) even though their concentrations were high. This suggests that several CA8P1ECs are degraded to only a few CA6P1EC isomers (i.e., the degradation pathway converges) or that some CA6P1EC metabolites are significantly more recalcitrant than others. The different biodegradation pathways observed in the Mesa and Coyote Creek microcosms result from the limited availability of dissolved oxygen in the Coyote Creek microcosms. In both sets of microcosms, the ortho isomers were transformed more slowly than the para isomers and in the Coyote Creek microcosms several ortho-CAP1ECs were observed. In addition, several unknown metabolites were observed in the Coyote Creek microcosms that were not seen in the abiotic or Mesa microcosms; these metabolites appear to be CAP1EC metabolites, have a -CH2-C6H4- fragment, and contain one carboxylic acid. Nitro-nonylphenol was observed in the Mesa microcosms, however, further experimentation illustrated that it was the product of an abiotic reaction between nitrite and nonylphenol under acidic conditions.« less

Evaluating bioremediation: distinguishing fact from fiction.

PubMed

Shannon, M J; Unterman, R

1993-01-01

Bioremediation options encompass diverse types of biochemical mechanisms that may lead to a target's mineralization, partial transformation, humification, or altered redox state (e.g. for metallic elements). Because these various mechanisms produce alternative fates of the targeted pollutants, it is often necessary to use diverse evaluation criteria to qualify a successful bioremediation. Too often target depletion from a treated matrix can be mistakenly ascribed to biological activity when in fact the depletion is caused by abiotic losses (e.g. volatilization, leaching, and stripping). Thus, effective, and therefore convincing, evaluation requires that experimental and engineering designs anticipate all possible routes of target depletion and that these routes be carefully monitored.

Fukunaga-Koontz transform based dimensionality reduction for hyperspectral imagery

NASA Astrophysics Data System (ADS)

Ochilov, S.; Alam, M. S.; Bal, A.

2006-05-01

Fukunaga-Koontz Transform based technique offers some attractive properties for desired class oriented dimensionality reduction in hyperspectral imagery. In FKT, feature selection is performed by transforming into a new space where feature classes have complimentary eigenvectors. Dimensionality reduction technique based on these complimentary eigenvector analysis can be described under two classes, desired class and background clutter, such that each basis function best represent one class while carrying the least amount of information from the second class. By selecting a few eigenvectors which are most relevant to desired class, one can reduce the dimension of hyperspectral cube. Since the FKT based technique reduces data size, it provides significant advantages for near real time detection applications in hyperspectral imagery. Furthermore, the eigenvector selection approach significantly reduces computation burden via the dimensionality reduction processes. The performance of the proposed dimensionality reduction algorithm has been tested using real-world hyperspectral dataset.

Abiotic stresses affect Trichoderma harzianum T39-induced resistance to downy mildew in grapevine.

PubMed

Roatti, Benedetta; Perazzolli, Michele; Gessler, Cesare; Pertot, Ilaria

2013-12-01

Enhancement of plant defense through the application of resistance inducers seems a promising alternative to chemical fungicides for controlling crop diseases but the efficacy can be affected by abiotic factors in the field. Plants respond to abiotic stresses with hormonal signals that may interfere with the mechanisms of induced systemic resistance (ISR) to pathogens. In this study, we exposed grapevines to heat, drought, or both to investigate the effects of abiotic stresses on grapevine resistance induced by Trichoderma harzianum T39 (T39) to downy mildew. Whereas the efficacy of T39-induced resistance was not affected by exposure to heat or drought, it was significantly reduced by combined abiotic stresses. Decrease of leaf water potential and upregulation of heat-stress markers confirmed that plants reacted to abiotic stresses. Basal expression of defense-related genes and their upregulation during T39-induced resistance were attenuated by abiotic stresses, in agreement with the reduced efficacy of T39. The evidence reported here suggests that exposure of crops to abiotic stress should be carefully considered to optimize the use of resistance inducers, especially in view of future global climate changes. Expression analysis of ISR marker genes could be helpful to identify when plants are responding to abiotic stresses, in order to optimize treatments with resistance inducers in field.

The theory behind, and the challenges of, conserving nature's stage in a time of rapid change.

PubMed

Lawler, Joshua J; Ackerly, David D; Albano, Christine M; Anderson, Mark G; Dobrowski, Solomon Z; Gill, Jacquelyn L; Heller, Nicole E; Pressey, Robert L; Sanderson, Eric W; Weiss, Stuart B

2015-06-01

Most conservation planning to date has focused on protecting today's biodiversity with the assumption that it will be tomorrow's biodiversity. However, modern climate change has already resulted in distributional shifts of some species and is projected to result in many more shifts in the coming decades. As species redistribute and biotic communities reorganize, conservation plans based on current patterns of biodiversity may fail to adequately protect species in the future. One approach for addressing this issue is to focus on conserving a range of abiotic conditions in the conservation-planning process. By doing so, it may be possible to conserve an abiotically diverse "stage" upon which evolution will play out and support many actors (biodiversity). We reviewed the fundamental underpinnings of the concept of conserving the abiotic stage, starting with the early observations of von Humboldt, who mapped the concordance of abiotic conditions and vegetation, and progressing to the concept of the ecological niche. We discuss challenges posed by issues of spatial and temporal scale, the role of biotic drivers of species distributions, and latitudinal and topographic variation in relationships between climate and landform. For example, abiotic conditions are not static, but change through time-albeit at different and often relatively slow rates. In some places, biotic interactions play a substantial role in structuring patterns of biodiversity, meaning that patterns of biodiversity may be less tightly linked to the abiotic stage. Furthermore, abiotic drivers of biodiversity can change with latitude and topographic position, meaning that the abiotic stage may need to be defined differently in different places. We conclude that protecting a diversity of abiotic conditions will likely best conserve biodiversity into the future in places where abiotic drivers of species distributions are strong relative to biotic drivers, where the diversity of abiotic settings will be conserved through time, and where connectivity allows for movement among areas providing different abiotic conditions. © 2015 Society for Conservation Biology.

Biodegradability and ecotoxicitiy of tramadol, ranitidine, and their photoderivatives in the aquatic environment.

PubMed

Bergheim, Marlies; Gieré, Reto; Kümmerer, Klaus

2012-01-01

This study was designed to assess the fate and the overall potential impacts of the widely prescribed drugs ranitidine and tramadol after their introduction into the aquatic environment. The probability to detect these two drugs in the aquatic environment was studied by analyzing their abiotic and biotic degradation properties. For this purpose, samples were irradiated with different light sources, and three widely used biodegradability tests from the OECD series, the closed bottle test (OECD 301 D), the manometric respirometry test (OECD 301 F) and the Zahn-Wellens test (OECD 302 B), were conducted. The ecotoxicity of the photolytically formed transformation products was assessed by performing the bacterial growth inhibition test (EN ISO 10712). Furthermore, quantitative structure-activity relationship analysis and a risk analysis based on the calculation of the predicted environmental concentrations have also been conducted to assess the environmental risk potential of the transformation products. The possible formation of stable products by microbial or photolytical transformation has been investigated with DOC and LC-MS analytics. In the present study, neither ranitidine, nor tramadol, nor their photoderivatives were found to be readily or inherently biodegradable according to test guidelines. The photolytic transformation was faster under a UV lamp compared to the reaction under an Xe lamp with a spectrum that mimics sunlight. No chronic toxicity against bacteria was found for ranitidine or its photolytic decomposition products, but a low toxicity was detected for the resulting mixture of the photolytic transformation products of tramadol. The study demonstrates that transformation products may have a higher environmental risk potential than the respective parent compounds.

Two ABREs, two redundant root-specific and one W-box cis-acting elements are functional in the sunflower HAHB4 promoter.

PubMed

Manavella, Pablo A; Dezar, Carlos A; Ariel, Federico D; Chan, Raquel L

2008-10-01

HAHB4 is a sunflower gene encoding a homeodomain-leucine zipper (HD-Zip) transcription factor. It was previously demonstrated that this gene is regulated at the transcriptional level by several abiotic factors and hormones. A previous analysis in the PLACE database revealed the presence of four putative ABREs. In this work these four elements and also one W-box and two root-specific expression elements were characterized as functional. Site-directed mutagenesis on the promoter, stable transformation of Arabidopis plants as well as transient transformation of sunflower leaves, were performed. The analysis of the transformants was carried out by histochemistry and real time RT-PCR. The results indicate that just one ABRE out of the four is responsible for ABA, NaCl and drought regulation. However, NaCl induction occurs also by an additional ABA-independent way involving another two overlapped ABREs. On the other hand, it was determined that the W-box located 5' upstream is responsive to ethylene and only two root-specific expression elements, among the several detected, are functional but redundant. Conservation of molecular mechanisms between sunflower and Arabidopsis is strongly supported by this experimental work.

Genetic transformation of fruit trees: current status and remaining challenges.

PubMed

Gambino, Giorgio; Gribaudo, Ivana

2012-12-01

Genetic transformation has emerged as a powerful tool for genetic improvement of fruit trees hindered by their reproductive biology and their high levels of heterozygosity. For years, genetic engineering of fruit trees has focussed principally on enhancing disease resistance (against viruses, fungi, and bacteria), although there are few examples of field cultivation and commercial application of these transgenic plants. In addition, over the years much work has been performed to enhance abiotic stress tolerance, to induce modifications of plant growth and habit, to produce marker-free transgenic plants and to improve fruit quality by modification of genes that are crucially important in the production of specific plant components. Recently, with the release of several genome sequences, studies of functional genomics are becoming increasingly important: by modification (overexpression or silencing) of genes involved in the production of specific plant components is possible to uncover regulatory mechanisms associated with the biosynthesis and catabolism of metabolites in plants. This review focuses on the main advances, in recent years, in genetic transformation of the most important species of fruit trees, devoting particular attention to functional genomics approaches and possible future challenges of genetic engineering for these species in the post-genomic era.

Synergistic degradation of chlorinated hydrocarbons with microorganisms and zero valent iron

NASA Astrophysics Data System (ADS)

Schöftner, Philipp; Summer, Dorothea; Leitner, Simon; Watzinger, Andrea; Wimmer, Bernhard; Reichenauer, Thomas

2016-04-01

Sites contaminated with chlorinated hydrocarbons (CHC) are located mainly within build-up regions. Therefore in most cases only in-situ technologies without excavation of soil material can be used for remediation. This project examines a novel in-situ remediation method, in which the biotic degradation via bacteria is combined with abiotic degradation via zero-valent iron particles (ZVI). ZVI particles are injected into the aquifer where CHC-molecules are reductively dechlorinated. However Fe0 is also oxidized by reaction with water leading to generation of H2 without any CHC degradation. To achieve biotic degradation often strictly anaerobic strains of the bacteria Dehalococcoides are used. These bacteria can dechlorinate CHC by utilizing H2. By combining these processes the H2, produced during the anaerobic corrosion of Fe0, could be used by bacteria for further CHC degradation. Therefore the amount of used Fe0 and as a consequence also remediation costs could be reduced. Additionally the continuous supply of H2 could make the bacterial degradation more controllable. Different Fe0 particles (nano- and micro-scale) were tested for their perchloroethene (PCE) degradation rate and H2 production rate in microcosms. PCE-degradation rate by different bacterial cultures was investigated in the same microcosm system. In course of these experiments the 13C enrichment factors of the PCE degradation of the different particles and cultures were determined to enable the differentiation of biotic and abiotic degradation. Preliminary results showed, that the nano-scale particles reacted faster with PCE and water than their micro-scaled counterparts. The PCE degradation via micro-scaled particles lead to 13C enrichment factors in the range of -3,6 ‰ ± 0,6 to -9,5 ‰ ± 0,2. With one of the examined bacterial cultures a fast reduction of PCE to ethene was observed. Although PCE and TCE were completely degraded by this culture the metabolites DCE and VC could still be detected. Further microcosm experiments will be implemented by the time of the EGU General Assembly 2016. In the framework of these experiments other bacterial cultures and ZVI particles as well as the combination of biotic and abiotic dehalogenation will be investigated.

The shifting influence of abiotic drivers during landslide succession in Puerto Rico

Treesearch

L. R. Walker; A. B. Shiels; P. J. Bellingham; A. D. Sparrow; N. Fetcher; F. H. Landau; D. J. Lodge

2013-01-01

Summary 1. Abiotic variables are critical drivers of succession in most primary seres, but how their influence on biota changes over time is rarely examined. Landslides provide good model systems for examining abiotic influences because they are spatially and temporally heterogeneous habitats with distinct abiotic and biotic gradients and post-landslide erosion. 2. In...

Abiotic degradation of plastic films

NASA Astrophysics Data System (ADS)

Ángeles-López, Y. G.; Gutiérrez-Mayen, A. M.; Velasco-Pérez, M.; Beltrán-Villavicencio, M.; Vázquez-Morillas, A.; Cano-Blanco, M.

2017-01-01

Degradable plastics have been promoted as an option to mitigate the environmental impacts of plastic waste. However, there is no certainty about its degradability under different environmental conditions. The effect of accelerated weathering (AW), natural weathering (NW) and thermal oxidation (TO) on different plastics (high density polyethylene, HDPE; oxodegradable high density polyethylene, HDPE-oxo; compostable plastic, Ecovio ® metalized polypropylene, PP; and oxodegradable metalized polypropylene, PP-oxo) was studied. Plastics films were exposed to AW per 110 hours; to NW per 90 days; and to TO per 30 days. Plastic films exposed to AW and NW showed a general loss on mechanical properties. The highest reduction in elongation at break on AW occurred to HDPE-oxo (from 400.4% to 20.9%) and was higher than 90% for HDPE, HDPE-oxo, Ecovio ® and PP-oxo in NW. No substantial evidence of degradation was found on plastics exposed to TO. Oxo-plastics showed higher degradation rates than their conventional counterparts, and the compostable plastic was resistant to degradation in the studied abiotic conditions. This study shows that degradation of plastics in real life conditions will vary depending in both, their composition and the environment.

Transformation products of submicron-sized aluminum-substituted magnetite: Color and reductant solubility

NASA Technical Reports Server (NTRS)

Golden, D. C.; Ming, D. W.; Lauer, H. V., Jr.

1991-01-01

Magnetite, when present as fine particles, is soluble in acid ammonium oxalate (pH equals 3). However, the commonly used extractant for free iron oxides (i.e., citrate dithionite-bicarbonate (CDB) is not very effective in dissolving magnetite in soils and geologic materials. Upon oxidation, magnetite transforms to maghemite; at elevated temperatures, maghemite inverts to hematite. This transformation causes a change in color from black to red and may affect the reductant solubility as well. The objectives here were to examine the color and reflectance spectral characteristics of products during the transformation of magnetite to maghemite to hematite and to study the effect of Al-substitution in magnetite on the above process. Reductant solubility of Al-substituted magnetite, maghemite, and hematite was also studied. In summary, the transformation of magnetite to maghemite was accompanied by a change in color from black to red because of the oxidation of Fe2(+) to Fe3(+). The phase change maghemite to hematite had a relatively minor effect on the color and the reflectance spectra.

[Effects of seasonal snow cover on soil nitrogen transformation in alpine ecosystem: a review].

PubMed

Liu, Lin; Wu, Yan; He, Yi-xin; Wu, Ning; Sun, Geng; Zhang, Lin; Xu, Jun-jun

2011-08-01

Seasonal snow cover has pronounced effects on the soil nitrogen concentration and transformation in alpine ecosystem. Snowfall is an important form of nitrogen deposition, which directly affects the content of soil available nitrogen. Different depths and different duration of snow cover caused by snowfall may lead the heterogeneity of abiotic factors (soil temperature and moisture) and biotic factors (soil microbes, alpine plants, and alpine animals), and further, produce complicated effects on the mineralization and immobilization of soil nitrogen. This paper introduced in emphasis the inherent mechanisms of soil nitrogen mineralization and leaching under the effects of frequent freeze-thaw events during the durative melting of snow cover, and summarized the main research results of field in situ experiments about the effects of seasonal snow cover on soil nitrogen in alpine ecosystem based on the possible changes in snow cover in the future. Some suggestions with regard to the effects of seasonal snow cover on soil nitrogen were put forward.

Enhancement of microalgal growth and biocomponent-based transformations for improved biofuel recovery: A review.

PubMed

Salama, El-Sayed; Hwang, Jae-Hoon; El-Dalatony, Marwa M; Kurade, Mayur B; Kabra, Akhil N; Abou-Shanab, Reda A I; Kim, Ki-Hyun; Yang, Il-Seung; Govindwar, Sanjay P; Kim, Sunjoon; Jeon, Byong-Hun

2018-06-01

Microalgal biomass has received much attention as feedstock for biofuel production due to its capacity to accumulate a substantial amount of biocomponents (including lipid, carbohydrate, and protein), high growth rate, and environmental benefit. However, commercial realization of microalgal biofuel is a challenge due to its low biomass production and insufficient technology for complete utilization of biomass. Recently, advanced strategies have been explored to overcome the challenges of conventional approaches and to achieve maximum possible outcomes in terms of growth. These strategies include a combination of stress factors; co-culturing with other microorganisms; and addition of salts, flue gases, and phytohormones. This review summarizes the recent progress in the application of single and combined abiotic stress conditions to stimulate microalgal growth and its biocomponents. An innovative schematic model is presented of the biomass-energy conversion pathway that proposes the transformation of all potential biocomponents of microalgae into biofuels. Copyright © 2018 Elsevier Ltd. All rights reserved.

EFFECT OF REDOX ZONATION ON THE REDUCTIVE TRANSFORMATION OF P-CYANONITROBENZENE IN A LABORATORY SEDIMENT COLUMN

EPA Science Inventory

The reductive transformation of a model compound, p-cyanonitrobenzene (pCNB), was investigated in a laboratory sediment column that had been characterized with respect to redox zonation. Characterization of the redox zones was assessed by measurement of the solution phase concent...

Review of recent transgenic studies on abiotic stress tolerance and future molecular breeding in potato.

PubMed

Kikuchi, Akira; Huynh, Huu Duc; Endo, Tsukasa; Watanabe, Kazuo

2015-03-01

Global warming has become a major issue within the last decade. Traditional breeding programs for potato have focused on increasing productivity and quality and disease resistance, thus, modern cultivars have limited tolerance of abiotic stresses. The introgression of abiotic stress tolerance into modern cultivars is essential work for the future. Recently, many studies have investigated abiotic stress using transgenic techniques. This manuscript focuses on the study of abiotic stress, in particular drought, salinity and low temperature, during this century. Dividing studies into these three stress categories for this review was difficult. Thus, based on the study title and the transgene property, transgenic studies were classified into five categories in this review; oxidative scavengers, transcriptional factors, and above three abiotic categories. The review focuses on studies that investigate confer of stress tolerance and the identification of responsible factors, including wild relatives. From a practical application perspective, further evaluation of transgenic potato with abiotic stress tolerance is required. Although potato plants, including wild species, have a large potential for abiotic stress tolerance, exploration of the factors responsible for conferring this tolerance is still developing. Molecular breeding, including genetic engineering and conventional breeding using DNA markers, is expected to develop in the future.

Over-expression of a NAC 67 transcription factor from finger millet (Eleusine coracana L.) confers tolerance against salinity and drought stress in rice.

PubMed

Rahman, Hifzur; Ramanathan, Valarmathi; Nallathambi, Jagedeeshselvam; Duraialagaraja, Sudhakar; Muthurajan, Raveendran

2016-05-11

NAC proteins (NAM (No apical meristem), ATAF (Arabidopsis transcription activation factor) and CUC (cup-shaped cotyledon)) are plant-specific transcription factors reported to be involved in regulating growth, development and stress responses. Salinity responsive transcriptome profiling in a set of contrasting finger millet genotypes through RNA-sequencing resulted in the identification of a NAC homolog (EcNAC 67) exhibiting differential salinity responsive expression pattern. Full length cDNA of EcNAC67 was isolated, characterized and validated for its role in abiotic stress tolerance through agrobacterium mediated genetic transformation in a rice cultivar ASD16. Bioinformatics analysis of putative NAC transcription factor (TF) isolated from a salinity tolerant finger millet showed its genetic relatedness to NAC67 family TFs in related cereals. Putative transgenic lines of rice over-expressing EcNAC67 were generated through Agrobacterium mediated transformation and presence/integration of transgene was confirmed through PCR and southern hybridization analysis. Transgenic rice plants harboring EcNAC67 showed enhanced tolerance against drought and salinity under greenhouse conditions. Transgenic rice plants were found to possess higher root and shoot biomass during stress and showed better revival ability upon relief from salinity stress. Upon drought stress, transgenic lines were found to maintain higher relative water content and lesser reduction in grain yield when compared to non-transgenic ASD16 plants. Drought induced spikelet sterility was found to be much lower in the transgenic lines than the non-transgenic ASD16. Results revealed the significant role of EcNAC67 in modulating responses against dehydration stress in rice. No detectable abnormalities in the phenotypic traits were observed in the transgenic plants under normal growth conditions. Results indicate that EcNAC67 can be used as a novel source for engineering tolerance against drought and salinity stress in rice and other crop plants.

Revisiting the Role of Plant Transcription Factors in the Battle against Abiotic Stress.

PubMed

Khan, Sardar-Ali; Li, Meng-Zhan; Wang, Suo-Min; Yin, Hong-Ju

2018-05-31

Owing to diverse abiotic stresses and global climate deterioration, the agricultural production worldwide is suffering serious losses. Breeding stress-resilient crops with higher quality and yield against multiple environmental stresses via application of transgenic technologies is currently the most promising approach. Deciphering molecular principles and mining stress-associate genes that govern plant responses against abiotic stresses is one of the prerequisites to develop stress-resistant crop varieties. As molecular switches in controlling stress-responsive genes expression, transcription factors (TFs) play crucial roles in regulating various abiotic stress responses. Hence, functional analysis of TFs and their interaction partners during abiotic stresses is crucial to perceive their role in diverse signaling cascades that many researchers have continued to undertake. Here, we review current developments in understanding TFs, with particular emphasis on their functions in orchestrating plant abiotic stress responses. Further, we discuss novel molecular mechanisms of their action under abiotic stress conditions. This will provide valuable information for understanding regulatory mechanisms to engineer stress-tolerant crops.

Enantiomer signature and carbon isotope evidence for the migration and transformation of DDTs in arable soils across China

NASA Astrophysics Data System (ADS)

Niu, Lili; Xu, Chao; Zhu, Siyu; Bao, Huiming; Xu, Yang; Li, Hongyi; Zhang, Zhijian; Zhang, Xichang; Qiu, Jiguo; Liu, Weiping

2016-12-01

Due to the adverse impact of DDTs on ecosystems and humans, a full fate assessment deems a comprehensive study on their occurrence in soils over a large region. Through a sampling campaign across China, we measured the concentrations, enantiomeric fractions (EFs), compound-specific carbon isotope composition of DDT and its metabolites, and the microbial community in related arable soils. The geographically total DDT concentrations are higher in eastern than western China. The EFs and δ13C of o,p’-DDT in soils from western China show smaller deviations from those of racemic/standard compound, indicating the DDT residues there mainly result from atmospheric transport. However, the sources of DDT in eastern China are mainly from historic application of technical DDTs and dicofol. The inverse dependence of o,p’-DDT and p,p’-DDE on temperature evidences the transformation of parent DDT to its metabolites. Initial usage, abiotic parameters and microbial communities are found to be the main factors influencing the migration and transformation of DDT isomers and their metabolites in soils. In addition, a prediction equation of DDT concentrations in soils based on stepwise multiple regression analysis is developed. Results from this study offer insights into the migration and transformation pathways of DDTs in Chinese arable soils, which will allow data-based risk assessment on their use.

Authentic Research Experience and “Big Data” Analysis in the Classroom: Maize Response to Abiotic Stress

PubMed Central

Makarevitch, Irina; Frechette, Cameo; Wiatros, Natalia

2015-01-01

Integration of inquiry-based approaches into curriculum is transforming the way science is taught and studied in undergraduate classrooms. Incorporating quantitative reasoning and mathematical skills into authentic biology undergraduate research projects has been shown to benefit students in developing various skills necessary for future scientists and to attract students to science, technology, engineering, and mathematics disciplines. While large-scale data analysis became an essential part of modern biological research, students have few opportunities to engage in analysis of large biological data sets. RNA-seq analysis, a tool that allows precise measurement of the level of gene expression for all genes in a genome, revolutionized molecular biology and provides ample opportunities for engaging students in authentic research. We developed, implemented, and assessed a series of authentic research laboratory exercises incorporating a large data RNA-seq analysis into an introductory undergraduate classroom. Our laboratory series is focused on analyzing gene expression changes in response to abiotic stress in maize seedlings; however, it could be easily adapted to the analysis of any other biological system with available RNA-seq data. Objective and subjective assessment of student learning demonstrated gains in understanding important biological concepts and in skills related to the process of science. PMID:26163561

Changes in abiotic influences on seed plants and ferns during 18 years of primary succession on Puerto Rican landslides

Treesearch

Lawrence R. Walker; Aaron B. Shiels; Peter J. Bellingham; Ashley D. Sparrow; Ned Fetcher; Fred H. Landau; Deborah J. Lodge

2013-01-01

Abiotic variables are critical drivers of succession in most primary seres, but how their influence on biota changes over time is rarely examined. Landslides provide good model systems for examining abiotic influences because they are spatially and temporally heterogeneous habitats with distinct abiotic and biotic gradients and post-landslide erosion. In an 18-year...

Kinetics and Products of Chromium(VI) Reduction by Iron(II/III)-Bearing Clay Minerals.

PubMed

Joe-Wong, Claresta; Brown, Gordon E; Maher, Kate

2017-09-05

Hexavalent chromium is a water-soluble pollutant, the mobility of which can be controlled by reduction of Cr(VI) to less soluble, environmentally benign Cr(III). Iron(II/III)-bearing clay minerals are widespread potential reductants of Cr(VI), but the kinetics and pathways of Cr(VI) reduction by such clay minerals are poorly understood. We reacted aqueous Cr(VI) with two abiotically reduced clay minerals: an Fe-poor montmorillonite and an Fe-rich nontronite. The effects of ionic strength, pH, total Fe content, and the fraction of reduced structural Fe(II) [Fe(II)/Fe(total)] were examined. The last variable had the largest effect on Cr(VI) reduction kinetics: for both clay minerals, the rate constant of Cr(VI) reduction varies by more than 3 orders of magnitude with Fe(II)/Fe(total) and is described by a linear free energy relationship. Under all conditions examined, Cr and Fe K-edge X-ray absorption near-edge structure spectra show that the main Cr-bearing product is a Cr(III)-hydroxide and that Fe remains in the clay structure after reacting with Cr(VI). This study helps to quantify our understanding of the kinetics of Cr(VI) reduction by Fe(II/III)-bearing clay minerals and may improve predictions of Cr(VI) behavior in subsurface environments.

Functional and transcriptome analysis reveals an acclimatization strategy for abiotic stress tolerance mediated by Arabidopsis NF-YA family members.

PubMed

Leyva-González, Marco Antonio; Ibarra-Laclette, Enrique; Cruz-Ramírez, Alfredo; Herrera-Estrella, Luis

2012-01-01

Nuclear Factor Y (NF-Y) is a heterotrimeric complex formed by NF-YA/NF-YB/NF-YC subunits that binds to the CCAAT-box in eukaryotic promoters. In contrast to other organisms, in which a single gene encodes each subunit, in plants gene families of over 10 members encode each of the subunits. Here we report that five members of the Arabidopsis thaliana NF-YA family are strongly induced by several stress conditions via transcriptional and miR169-related post-transcriptional mechanisms. Overexpression of NF-YA2, 7 and 10 resulted in dwarf late-senescent plants with enhanced tolerance to several types of abiotic stress. These phenotypes are related to alterations in sucrose/starch balance and cell elongation observed in NF-YA overexpressing plants. The use of transcriptomic analysis of transgenic plants that express miR169-resistant versions of NF-YA2, 3, 7, and 10 under an estradiol inducible system, as well as a dominant-repressor version of NF-YA2 revealed a set of genes, whose promoters are enriched in NF-Y binding sites (CCAAT-box) and that may be directly regulated by the NF-Y complex. This analysis also suggests that NF-YAs could participate in modulating gene regulation through positive and negative mechanisms. We propose a model in which the increase in NF-YA transcript levels in response to abiotic stress is part of an adaptive response to adverse environmental conditions in which a reduction in plant growth rate plays a key role.

Chicken Juice Enhances Surface Attachment and Biofilm Formation of Campylobacter jejuni

PubMed Central

Brown, Helen L.; Reuter, Mark; Salt, Louise J.; Cross, Kathryn L.; Betts, Roy P.

2014-01-01

The bacterial pathogen Campylobacter jejuni is primarily transmitted via the consumption of contaminated foodstuffs, especially poultry meat. In food processing environments, C. jejuni is required to survive a multitude of stresses and requires the use of specific survival mechanisms, such as biofilms. An initial step in biofilm formation is bacterial attachment to a surface. Here, we investigated the effects of a chicken meat exudate (chicken juice) on C. jejuni surface attachment and biofilm formation. Supplementation of brucella broth with ≥5% chicken juice resulted in increased biofilm formation on glass, polystyrene, and stainless steel surfaces with four C. jejuni isolates and one C. coli isolate in both microaerobic and aerobic conditions. When incubated with chicken juice, C. jejuni was both able to grow and form biofilms in static cultures in aerobic conditions. Electron microscopy showed that C. jejuni cells were associated with chicken juice particulates attached to the abiotic surface rather than the surface itself. This suggests that chicken juice contributes to C. jejuni biofilm formation by covering and conditioning the abiotic surface and is a source of nutrients. Chicken juice was able to complement the reduction in biofilm formation of an aflagellated mutant of C. jejuni, indicating that chicken juice may support food chain transmission of isolates with lowered motility. We provide here a useful model for studying the interaction of C. jejuni biofilms in food chain-relevant conditions and also show a possible mechanism for C. jejuni cell attachment and biofilm initiation on abiotic surfaces within the food chain. PMID:25192991

Abiotic Organic Chemistry in Hydrothermal Systems.

NASA Astrophysics Data System (ADS)

Simoneit, B. R.; Rushdi, A. I.

2004-12-01

Abiotic organic chemistry in hydrothermal systems is of interest to biologists, geochemists and oceanographers. This chemistry consists of thermal alteration of organic matter and minor prebiotic synthesis of organic compounds. Thermal alteration has been extensively documented to yield petroleum and heavy bitumen products from contemporary organic detritus. Carbon dioxide, carbon monoxide, ammonia and sulfur species have been used as precursors in prebiotic synthesis experiments to organic compounds. These inorganic species are common components of hot spring gases and marine hydrothermal systems. It is of interest to further test their reactivities in reductive aqueous thermolysis. We have synthesized organic compounds (lipids) in aqueous solutions of oxalic acid, and with carbon disulfide or ammonium bicarbonate at temperatures from 175-400° C. The synthetic lipids from oxalic acid solutions consisted of n-alkanols, n-alkanoic acids, n-alkyl formates, n-alkanones, n-alkenes and n-alkanes, typically to C30 with no carbon number preferences. The products from CS2 in acidic aqueous solutions yielded cyclic thioalkanes, alkyl polysulfides, and thioesters with other numerous minor compounds. The synthesis products from oxalic acid and ammonium bicarbonate solutions were homologous series of n-alkyl amides, n-alkyl amines, n-alkanes and n-alkanoic acids, also to C30 with no carbon number predominance. Condensation (dehydration) reactions also occur under elevated temperatures in aqueous medium as tested by model reactions to form amide, ester and nitrile bonds. It is concluded that the abiotic formation of aliphatic lipids, condensation products (amides, esters, nitriles, and CS2 derivatives (alkyl polysulfides, cyclic polysulfides) is possible under hydrothermal conditions and warrants further studies.

Functional and Transcriptome Analysis Reveals an Acclimatization Strategy for Abiotic Stress Tolerance Mediated by Arabidopsis NF-YA Family Members

PubMed Central

Leyva-González, Marco Antonio; Ibarra-Laclette, Enrique; Cruz-Ramírez, Alfredo; Herrera-Estrella, Luis

2012-01-01

Nuclear Factor Y (NF-Y) is a heterotrimeric complex formed by NF-YA/NF-YB/NF-YC subunits that binds to the CCAAT-box in eukaryotic promoters. In contrast to other organisms, in which a single gene encodes each subunit, in plants gene families of over 10 members encode each of the subunits. Here we report that five members of the Arabidopsis thaliana NF-YA family are strongly induced by several stress conditions via transcriptional and miR169-related post-transcriptional mechanisms. Overexpression of NF-YA2, 7 and 10 resulted in dwarf late-senescent plants with enhanced tolerance to several types of abiotic stress. These phenotypes are related to alterations in sucrose/starch balance and cell elongation observed in NF-YA overexpressing plants. The use of transcriptomic analysis of transgenic plants that express miR169-resistant versions of NF-YA2, 3, 7, and 10 under an estradiol inducible system, as well as a dominant-repressor version of NF-YA2 revealed a set of genes, whose promoters are enriched in NF-Y binding sites (CCAAT-box) and that may be directly regulated by the NF-Y complex. This analysis also suggests that NF-YAs could participate in modulating gene regulation through positive and negative mechanisms. We propose a model in which the increase in NF-YA transcript levels in response to abiotic stress is part of an adaptive response to adverse environmental conditions in which a reduction in plant growth rate plays a key role. PMID:23118940

Summary of transformation equations and equations of motion used in free flight and wind tunnel data reduction and analysis

NASA Technical Reports Server (NTRS)

Gainer, T. G.; Hoffman, S.

1972-01-01

Basic formulations for developing coordinate transformations and motion equations used with free-flight and wind-tunnel data reduction are presented. The general forms presented include axes transformations that enable transfer back and forth between any of the five axes systems that are encountered in aerodynamic analysis. Equations of motion are presented that enable calculation of motions anywhere in the vicinity of the earth. A bibliography of publications on methods of analyzing flight data is included.

Speckle noise reduction in quantitative optical metrology techniques by application of the discrete wavelet transformation

NASA Astrophysics Data System (ADS)

Furlong, Cosme; Pryputniewicz, Ryszard J.

2002-06-01

Effective suppression of speckle noise content in interferometric data images can help in improving accuracy and resolution of the results obtained with interferometric optical metrology techniques. In this paper, novel speckle noise reduction algorithms based on the discrete wavelet transformation are presented. The algorithms proceed by: (a) estimating the noise level contained in the interferograms of interest, (b) selecting wavelet families, (c) applying the wavelet transformation using the selected families, (d) wavelet thresholding, and (e) applying the inverse wavelet transformation, producing denoised interferograms. The algorithms are applied to the different stages of the processing procedures utilized for generation of quantitative speckle correlation interferometry data of fiber-optic based opto-electronic holography (FOBOEH) techniques, allowing identification of optimal processing conditions. It is shown that wavelet algorithms are effective for speckle noise reduction while preserving image features otherwise faded with other algorithms.

Effect of migration and transformation of iron on the endogenous reduction of H2S in anaerobic landfill.

PubMed

Long, Yu-Yang; Du, Yao; Fang, Yuan; Xu, Jing; He, Yan-Ni; Shen, Dong-Sheng

2016-07-01

Hydrogen sulfide (H2S) is a major odor in landfill gas and needs urgent treatment. In this study, the effect of migration and transformation of iron on the endogenous reduction of H2S was investigated in two simulated landfills. The results showed that the H2S emission concentration from the landfill cover of conventional anaerobic landfill (CL) and anaerobic landfill with leachate recirculation (RL) could reach 19.4mgm(-3) and 24.1mgm(-3), respectively. However, the migration and transformation of iron in anaerobic landfill with different operational modes results in different endogenous reduction mechanism for H2S. The proportion of precipitation-reduction mechanism and oxidation-reduction mechanism in CL was 73.3% and 26.3%, respectively. But for RL, the function of oxidation was enhanced, and the sulfide content was reduced 23.1% compared with CL. The iron in landfill with leachate recirculation revealed good endogenous reduction effect on H2S control after a period of time landfilling. Copyright © 2015 Elsevier Ltd. All rights reserved.

Numerical Modeling of Arsenic Mobility during Reductive Iron-Mineral Transformations.

PubMed

Rawson, Joey; Prommer, Henning; Siade, Adam; Carr, Jackson; Berg, Michael; Davis, James A; Fendorf, Scott

2016-03-01

Millions of individuals worldwide are chronically exposed to hazardous concentrations of arsenic from contaminated drinking water. Despite massive efforts toward understanding the extent and underlying geochemical processes of the problem, numerical modeling and reliable predictions of future arsenic behavior remain a significant challenge. One of the key knowledge gaps concerns a refined understanding of the mechanisms that underlie arsenic mobilization, particularly under the onset of anaerobic conditions, and the quantification of the factors that affect this process. In this study, we focus on the development and testing of appropriate conceptual and numerical model approaches to represent and quantify the reductive dissolution of iron oxides, the concomitant release of sorbed arsenic, and the role of iron-mineral transformations. The initial model development in this study was guided by data and hypothesized processes from a previously reported,1 well-controlled column experiment in which arsenic desorption from ferrihydrite coated sands by variable loads of organic carbon was investigated. Using the measured data as constraints, we provide a quantitative interpretation of the processes controlling arsenic mobility during the microbial reductive transformation of iron oxides. Our analysis suggests that the observed arsenic behavior is primarily controlled by a combination of reductive dissolution of ferrihydrite, arsenic incorporation into or co-precipitation with freshly transformed iron minerals, and partial arsenic redox transformations.

Missing texture reconstruction method based on error reduction algorithm using Fourier transform magnitude estimation scheme.

PubMed

Ogawa, Takahiro; Haseyama, Miki

2013-03-01

A missing texture reconstruction method based on an error reduction (ER) algorithm, including a novel estimation scheme of Fourier transform magnitudes is presented in this brief. In our method, Fourier transform magnitude is estimated for a target patch including missing areas, and the missing intensities are estimated by retrieving its phase based on the ER algorithm. Specifically, by monitoring errors converged in the ER algorithm, known patches whose Fourier transform magnitudes are similar to that of the target patch are selected from the target image. In the second approach, the Fourier transform magnitude of the target patch is estimated from those of the selected known patches and their corresponding errors. Consequently, by using the ER algorithm, we can estimate both the Fourier transform magnitudes and phases to reconstruct the missing areas.

Automatic variance reduction for Monte Carlo simulations via the local importance function transform

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

Turner, S.A.

1996-02-01

The author derives a transformed transport problem that can be solved theoretically by analog Monte Carlo with zero variance. However, the Monte Carlo simulation of this transformed problem cannot be implemented in practice, so he develops a method for approximating it. The approximation to the zero variance method consists of replacing the continuous adjoint transport solution in the transformed transport problem by a piecewise continuous approximation containing local biasing parameters obtained from a deterministic calculation. He uses the transport and collision processes of the transformed problem to bias distance-to-collision and selection of post-collision energy groups and trajectories in a traditionalmore » Monte Carlo simulation of ``real`` particles. He refers to the resulting variance reduction method as the Local Importance Function Transform (LIFI) method. He demonstrates the efficiency of the LIFT method for several 3-D, linearly anisotropic scattering, one-group, and multigroup problems. In these problems the LIFT method is shown to be more efficient than the AVATAR scheme, which is one of the best variance reduction techniques currently available in a state-of-the-art Monte Carlo code. For most of the problems considered, the LIFT method produces higher figures of merit than AVATAR, even when the LIFT method is used as a ``black box``. There are some problems that cause trouble for most variance reduction techniques, and the LIFT method is no exception. For example, the author demonstrates that problems with voids, or low density regions, can cause a reduction in the efficiency of the LIFT method. However, the LIFT method still performs better than survival biasing and AVATAR in these difficult cases.« less

Geomicrobiological cycling of antimony

NASA Astrophysics Data System (ADS)

Kulp, T. R.; Terry, L.; Dovick, M. A.; Braiotta, F.

2013-12-01

Microbiologically catalyzed oxidation and reduction of toxic metalloids (e.g., As, Se, and Te) generally proceeds much faster than corresponding abiotic reactions. These microbial transformations constitute biogeochemical cycles that control chemical speciation and environmental behavior of metalloids in aqueous environments. Particular progress has been made over the past two decades in documenting microbiological biotransformations of As, which include anaerobic respiratory reduction of As(V) to As(III), oxidation of As(III) to As(V) linked to chemoautotrophy or photoautotrophy, and cellular detoxification pathways. By contrast, microbial interactions with Sb, As's group 15 neighbor and a toxic element of emerging global concern, are poorly understood. Our work with sediment microcosms, enrichment cultures, and bacterial isolates suggests that prokaryotic metabolisms may be similarly important to environmental Sb cycling. Enrichment cultures and isolates from a Sb-contaminated mine site in Idaho exhibited Sb(V)-dependent heterotrophic respiration under anaerobic conditions and Sb(III)-dependent autotrophic growth in the presence of air. Live, anoxic cultures reduced 2 mM Sb(V) to Sb(III) within 5 d, while no activity occurred in killed controls. Sb(V) reduction was stimulated by lactate or acetate and was quantitatively coupled to the oxidation of lactate. The oxidation of radiolabeled 14C-acetate (monitored by GC-GPC) demonstrated Sb(V)-dependent oxidation to 14CO2, suggesting a dissimilatory process. Sb(V) dependent growth in cultures was demonstrated by direct counting. Microbiological reduction of Sb(V) also occurred in anerobic sediment microcosms from an uncontaminated suburban lake, but did not appear to be linked to growth and is interpreted as a mechanism of biological detoxification. Aerobic microcosms and cultures from the Idaho mine oxidized 2 mM Sb(III) to Sb(V) within 7 d and coupled this reaction to cell growth quantified by direct counting. An anoxygenic photosynthetic community of purple sulfur bacteria from Pyramid Lake, NV, however, that was capable of growth via anoxygenic photosynthesis using As(III) as an electron donor was not capable of similar growth using Sb(III). These results suggest that geomicrobiological Sb cycling is an important influence on the environmental speciation and behavior of Sb, and portend the presence of a global biogeochemical Sb cycle that is analogous to but distinct from that for As.

Abiotic and Biotic Mechanisms Controlling In Situ Remediation of NDMA

DTIC Science & Technology

2009-05-01

FINAL REPORT Abiotic and Biotic Mechanisms Controlling In Situ Remediation of NDMA SERDP Project ER-1421 MAY 2009 James E. Szecsody...00-2009 4. TITLE AND SUBTITLE Abiotic and Biotic Mechanisms Controlling In Situ Remediation of NDMA 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c...investigate whether in situ coupled abiotic/biotic degradation of N-nitrosodimethylamine ( NDMA , an emerging contaminant) could be used as a permeable

A Continuous Flow Column Study of Anaerobic PCE Transformation With the Evanite Culture and Hanford Aquifer Solids

NASA Astrophysics Data System (ADS)

Semprini, L.; Behrens, S.; Azizian, M.; Sabalowsky, A.; Dolan, M.; Ruiz-Hass, P.; Ingle, J.; Spormann, A.

2005-12-01

Anaerobic reductive dehalogenation of tetrachloroethene (PCE) and trichoroethene (TCE) is a promising technology for the in situ treatment of high concentration source zones in contaminated aquifers. Continuous flow column studies were performed where a mixed dehalogenating culture (Evanite culture) that contains Dehalococcides-like microorganisms was bioaugmented into aquifer solids from the Hanford DOE site. Studies conducted prior to bioaugmentation showed PCE transport was retarded due to sorption onto the aquifer solids. Upon bioaugmentation and with continuous lactate addition, PCE (10 mg/L) was transformed to cis-dichloroethene ( cis-DCE), and enhanced transformation of sorbed PCE was observed. Prolonged production of cis-DCE was associated with iron reducing conditions, while eventual vinyl chloride (VC) reduction to ethene was associated with sulfate reducing conditions. Microbial processes included lactate fermentation to acetate and propionate, iron reduction, sulfate reduction, and reductive dehalogenation, with reductive dehalogenation utilizing 2 to 3% of the electron donor addition. PCE was completely transformed to ethene within a hydraulic residence time of one day. Upon competition of the column tests spatial samples of aquifer solids were analyzed using molecular methods and solids were used in batch microcosm activity tests. Dehalococcoides sp. 16S rRNA gene copy numbers dropped from ~ 74% of total Eubacterial 16S rRNA genes in the original inoculum, to about 0.5 to 4% through out the column, consistent with the estimates of electron donor utilization for dehalogenation reactions. Microcosm tests showed most of PCE transformation activity at the entrance of the column, consistent with the Dehalococcoides sp. 16S rRNA gene copy numbers being highest in that area. Roughly 20% of the Dehalococcoides sp. population in the column possessed a vcrA gene for the respiration of VC to ethene. The vcrA-positive subpopulation decreases to about 5% towards the column outflow, while VC microcosm activity tests show fairly constant rates of VC transformation across the column. The column studies demonstrated that complete transformation of PCE to ethene can be obtained over short spatial and temporal scales.

Biotic and abiotic reduction and solubilization of Pu(IV)O₂•xH₂O(am) as affected by anthraquinone-2,6-disulfonate (AQDS) and ethylenediaminetetraacetate (EDTA).

PubMed

Plymale, Andrew E; Bailey, Vanessa L; Fredrickson, James K; Heald, Steve M; Buck, Edgar C; Shi, Liang; Wang, Zheming; Resch, Charles T; Moore, Dean A; Bolton, Harvey

2012-02-21

This study measured reductive solubilization of plutonium(IV) hydrous oxide (Pu(IV)O(2)·xH(2)O((am))) with hydrogen (H(2)) as electron donor, in the presence or absence of dissimilatory metal-reducing bacteria (DMRB), anthraquinone-2,6-disulfonate (AQDS), and ethylenediaminetetraacetate (EDTA). In PIPES buffer at pH 7 with excess H(2), Shewanella oneidensis and Geobacter sulfurreducens both solubilized <0.001% of 0.5 mM Pu(IV)O(2)·xH(2)O((am)) over 8 days, with or without AQDS. However, Pu((aq)) increased by an order of magnitude in some treatments, and increases in solubility were associated with production of Pu(III)((aq)). The solid phase of these treatments contained Pu(III)(OH)(3(am)), with more in the DMRB treatments compared with abiotic controls. In the presence of EDTA and AQDS, PuO(2)·xH(2)O((am)) was completely solubilized by S. oneidensis and G. sulfurreducens in ∼24 h. Without AQDS, bioreductive solubilization was slower (∼22 days) and less extensive (∼83-94%). In the absence of DMRB, EDTA facilitated reductive solubilization of 89% (without AQDS) to 98% (with AQDS) of the added PuO(2)·xH(2)O((am)) over 418 days. An in vitro assay demonstrated electron transfer to PuO(2)·xH(2)O((am)) from the S. oneidensis outer-membrane c-type cytochrome MtrC. Our results (1) suggest that PuO(2)·xH(2)O((am)) reductive solubilization may be important in reducing environments, especially in the presence of complexing ligands and electron shuttles, (2) highlight the environmental importance of polynuclear, colloidal Pu, (3) provide additional evidence that Pu(III)-EDTA is a more likely mobile form of Pu than Pu(IV)-EDTA, and (4) provide another example of outer-membrane cytochromes and electron-shuttling compounds facilitating bioreduction of insoluble electron acceptors in geologic environments.

Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation

PubMed Central

Fisher, Karl; Dunstan, Mark S; Collins, Fraser A; Sjuts, Hanno; Levy, Colin; Hay, Sam; Rigby, Stephen EJ; Leys, David

2015-01-01

Organohalide chemistry underpins many industrial and agricultural processes, and a large proportion of environmental pollutants are organohalides1. Nevertheless, organohalide chemistry is not exclusively of anthropogenic origin, with natural abiotic and biological processes contributing to the global halide cycle2–3. Reductive dehalogenases are responsible for biological dehalogenation in organohalide respiring bacteria4–5, with substrates including the notorious polychlorinated biphenyls (PCBs) or dioxins6–7. These proteins form a distinct subfamily of cobalamin (B12) dependent enzymes that are usually membrane-associated and oxygen-sensitive, hindering detailed studies8–12. We report the characterisation of a soluble, oxygen-tolerant reductive dehalogenase and, by combining structure determination with EPR spectroscopy and simulation, show that a direct interaction between the cobalamin cobalt and the substrate halogen underpins catalysis. In contrast to the carbon-Co bond chemistry catalyzed by the other cobalamin-dependent subfamilies13 we propose that reductive dehalogenases achieve reduction of the organohalide substrate via halogen-Co bond formation. This presents a new paradigm in both organohalide and cobalamin (bio)chemistry that will guide future exploitation of these enzymes in bioremediation or biocatalysis. PMID:25327251

Relationships between biotic and abiotic factors and regeneration of chestnut oak, white oak, and northern red oak

Treesearch

Songlin Fei; Kim C. Steiner; James C. Finley; Marc E. McDill

2003-01-01

A series of substantial field surveys of 38 mixed-oak stands in central Pennsylvania were carried out during 1996-2000. All the stands were surveyed 1 year prior to harvest, and 16 stands have been surveyed 1 year after harvest. Three abiotic factors at stand scale, four abiotic factors at plot scale, and two biotic factors and one abiotic factor at subplot scale was...

[Transgenic rice breeding for abiotic stress tolerance--present and future].

PubMed

Zhao, Feng-Yun; Zhang, Hui

2007-01-01

Environmental stresses and the continuing deterioration of arable land, along with an explosive increase in world population, pose serious threats to global agricultural production and food security. Improving the tolerance of the major crop plants to abiotic stresses has been a main goal in agriculture for a long time. As rice is considered one of the major crops, the development of new cultivars with enhanced abiotic stress-tolerance will undoubtedly have an important effect on global food production. The transgenic approach offers an attractive alternative to conventional techniques for the genetic improvement of rice cultivars. In recent years, an array of stress-related genes has already been transferred to rice to improve its resistance against abiotic stresses. Many transgenic rice plants with enhanced abiotic stress-tolerance have been obtained. This article focuses on the progress in the study of abiotic stress tolerance in transgenic rice breeding.

Sulfate-reducing bacteria influence the nucleation and growth of mackinawite and greigite

NASA Astrophysics Data System (ADS)

Picard, Aude; Gartman, Amy; Clarke, David R.; Girguis, Peter R.

2018-01-01

Sedimentary iron sulfide minerals play a key role in maintaining the oxygenation of Earth's atmosphere over geological timescales; they also record critical geochemical information that can be used to reconstruct paleo-environments. On modern Earth, sedimentary iron sulfide mineral formation takes places in low-temperature environments and requires the production of free sulfide by sulfate-reducing microorganisms (SRM) under anoxic conditions. Yet, most of our knowledge on the properties and formation pathways of iron sulfide minerals, including pyrite, derives from experimental studies performed in abiotic conditions, and as such the role of biotic processes in the formation of sedimentary iron sulfide minerals is poorly understood. Here we investigate the role of SRM in the nucleation and growth of iron sulfide minerals in laboratory experiments. We set out to test the hypothesis that SRM can influence Fe-S mineralization in ways other than providing sulfide through the comparison of the physical properties of iron sulfide minerals precipitated in the presence and in the absence of the sulfate-reducing bacterium Desulfovibrio hydrothermalis AM13 under well-controlled conditions. X-ray diffraction and microscopy analyses reveal that iron sulfide minerals produced in the presence of SRM exhibit unique morphology and aggregate differently than abiotic minerals formed in media without cells. Specifically, mackinawite growth is favored in the presence of both live and dead SRM, when compared to the abiotic treatments tested. The cell surface of live and dead SRM, and the extracellular polymers produced by live cells, provide templates for the nucleation of mackinawite and favor mineral growth. The morphology of minerals is however different when live and dead cells are provided. The transformation of greigite from mackinawite occurred after several months of incubation only in the presence of live SRM, suggesting that SRM might accelerate the kinetics of greigite formation under strict anoxic conditions. Pyrite formation was not observed in any experiments. While SRM provide nearly all the sulfide to the Fe-S system at low temperatures, we also posit that SRM play an additional formative role in the size, morphology and potentially the mineralogy of iron sulfide minerals in sedimentary environments, therefore potentially influencing their reactivity. Attempting to reconstruct modern and ancient biogeochemical cycles based on the geochemistry of iron sulfide minerals formed under purely abiotic conditions should be therefore done with caution.

Reactive Minerals and Dechlorinating Communities: Mechanisms Governing the Degradation of Chlorinated Ethenes during Back Diffusion from Low Permeability Zones in Aerobic and Anaerobic Environments

NASA Astrophysics Data System (ADS)

Berns, E. C.; Zeng, R.; Singh, H.; Valocchi, A. J.; Sanford, R. A.; Strathmann, T. J.; Schaefer, C. E.; Werth, C. J.

2017-12-01

Low permeability zones (LPZs) comprised of silts and clays, and contaminated with chlorinated ethenes, can act as a long term source of contaminated groundwater by diffusion into adjacent high permeability zones (HPZs). Following initial remediation efforts, chlorinated ethenes that have diffused into LPZs will back diffuse and recontaminate HPZs. Because chlorinated ethenes are known to cause cancer and damage the liver, kidneys, and central nervous system, it is important to understand how they degrade in natural systems and how to model their fate and transport. Previous work has shown that anaerobic hydrogenolysis reactions are facilitated by both dechlorinating microorganisms and reactive minerals. Abiotic dichloro-elimination reactions with reactive minerals can also degrade chlorinated ethenes to acetylene, albeit at slower rates than biotic processes. More recently, studies have explored aerobic abiotic degradation of chlorinated ethenes to formate, glycolate, and carbon dioxide. This study focuses on these biotic and abiotic reactions and their contributions to chlorinated ethene degradation under aerobic and anaerobic conditions at the LPZ/HPZ interface. A two-dimensional flow cell was constructed to model this interface using clay and sand from Pease Air Force Base. The clay was inoculated with a dechlorinating enrichment culture. Tenax adsorbent beads equilibrated with trichloroethylene (TCE) were used as a chlorinated ethene source zone at the base of the clay. TCE and its degradation products diffused from the clay into the sand, where they were removed from the flow cell by groundwater at a rate of 50 mL/day. Volatile compounds were trapped in a sample loop and removed every 48 hours for analysis by GC-FID. Organic and inorganic ions in the effluent were analyzed on the HPLC and IC. The experiment was terminated by freezing the flow cell, and chemical profiles through the flow cell material were created to show the spatial distribution of degradation products. Chemical profiles through the clay were modeled using a 1D diffusion-reaction model, and the contributions of abiotic and biotic processes to TCE degradation were determined. The model and experimental data lend insights into transformation processes that control the fate and transport of chlorinated ethenes at contaminated sites.

Reduction of Cr(VI) under acidic conditions by the facultative Fe(III)-reducing bacterium Acidiphilium cryptum

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

David E. Cummings; Scott Fendorf; Rajesh K. Sani

2007-01-01

The potential for biological reduction of Cr(VI) under acidic conditions was evaluated with the acidophilic, facultatively metal-reducing bacterium Acidiphilium cryptum strain JF-5 to explore the role of acidophilic microorganisms in the Cr cycle in low-pH environments. An anaerobic suspension of washed A. cryptum cells rapidly reduced 50 M Cr(VI) at pH 3.2; biological reduction was detected from pH 1.7-4.7. The reduction product, confirmed by XANES analysis, was entirely Cr(III) that was associated predominantly with the cell biomass (70-80%) with the residual residing in the aqueous phase. Reduction of Cr(VI) showed a pH optimum similar to that for growth and wasmore » inhibited by 5 mM HgCl2, suggesting that the reaction was enzyme-mediated. Introduction of O2 into the reaction medium slowed the reduction rate only slightly, whereas soluble Fe(III) (as ferric sulfate) increased the rate dramatically, presumably by the shuttling of electrons from bioreduced Fe(II) to Cr(VI) in a coupled biotic-abiotic cycle. Starved cells could not reduce Cr(VI) when provided as sole electron acceptor, indicating that Cr(VI) reduction is not an energy-conserving process in A. cryptum. We speculate, rather, that Cr(VI) reduction is used here as a detoxification mechanism.« less

Diurnal and Seasonal Responses of High Frequency Chlorophyll Fluorescence and PRI Measurements to Abiotic Stress in Almonds

NASA Astrophysics Data System (ADS)

Bambach-Ortiz, N. E.; Paw U, K. T.

2016-12-01

Plants have evolved to efficiently utilize light to synthesize energy-rich carbon compounds, and at the same time, dissipate absorbed but excessive photon that would otherwise transfer excitation energy to potentially toxic reactive oxygen species (ROS). Nevertheless, even the most rapidly growing plants with the highest rates of photosynthesis only utilize about half of the light their leaves absorb during the hours of peak irradiance in sun-exposed habitats. Usually, that daily peak of irradiance coincides with high temperature and a high vapor pressure deficit, which are conditions related to plant stomata closure. Consequently, specially in water stressed environments, plants need to have mechanisms to dissipate most of absorbed photons. Plants avoid photo-oxidative damage of the photosynthetic apparatus due to the formation of ROS under excess light using different mechanisms in order to either lower the amount of ROS formation or detoxify already formed ROS. Photoinhibition is defined as a reduction in photosynthetic activity due largely to a sustained reduction in the photochemical efficiency of Photosystem II (PSII), which can be assessed by monitoring Chlorophyll a fluorescence (ChlF). Alternatively, monitoring abiotic stress effects upon photosynthetic activity and photoinhibition may be possible using high frequency spectral reflectance sensors. We aim to find the potential relationships between high frequency PRI and ChlF as indicators of photoinhibition and permanent photodamage at a seasonal scale. Preliminary results show that PRI responses are sensitive to photoinhibition, but provide a poor representation of permanent photodamage observed at a seasonal scale.

VIP1 and Its Homologs Are Not Required for Agrobacterium-Mediated Transformation, but Play a Role in Botrytis and Salt Stress Responses

PubMed Central

Lapham, Rachelle; Lee, Lan-Ying; Tsugama, Daisuke; Lee, Sanghun; Mengiste, Tesfaye; Gelvin, Stanton B.

2018-01-01

The bZIP transcription factor VIP1 interacts with the Agrobacterium virulence protein VirE2, but the role of VIP1 in Agrobacterium-mediated transformation remains controversial. Previously tested vip1-1 mutant plants produce a truncated protein containing the crucial bZIP DNA-binding domain. We generated the CRISPR/Cas mutant vip1-2 that lacks this domain. The transformation susceptibility of vip1-2 and wild-type plants is similar. Because of potential functional redundancy among VIP1 homologs, we tested transgenic lines expressing VIP1 fused to a SRDX repression domain. All VIP1-SRDX transgenic lines showed wild-type levels of transformation, indicating that neither VIP1 nor its homologs are required for Agrobacterium-mediated transformation. Because VIP1 is involved in innate immune response signaling, we tested the susceptibility of vip1 mutant and VIP1-SRDX plants to Pseudomonas syringae and Botrytis cinerea. vip1 mutant and VIP1-SRDX plants show increased susceptibility to B. cinerea but not to P. syringae infection, suggesting a role for VIP1 in B. cinerea, but not in P. syringae, defense signaling. B. cinerea susceptibility is dependent on abscisic acid (ABA) which is also important for abiotic stress responses. The germination of vip1 mutant and VIP1-SRDX seeds is sensitive to exogenous ABA, suggesting a role for VIP1 in response to ABA. vip1 mutant and VIP1-SRDX plants show increased tolerance to growth in salt, indicating a role for VIP1 in response to salt stress. PMID:29946325

Disentangling synergistic climate drivers on the evolution of two species of planktonic foraminifera on regional and global scales

NASA Astrophysics Data System (ADS)

Brombacher, A.; Wilson, P. A.; Bailey, I.; Ezard, T. H. G.

2016-02-01

Evolution is driven by a combination of biotic and abiotic factors. When quantifying the effects of abiotic drivers, evolutionary change is generally described as a response to a single environmental parameter assumed to represent global climate. However, climate is a complex system of many interacting factors and characterized by high regional variability. Therefore, to understand the role of climate in evolutionary change, we need to consider multiple environmental parameters, across local, regional and global scales, as well as their interactions. The deep-sea microfossil record is sufficiently complete that sufficiently continuous multivariate climatic and multivariate trait data can be obtained from the same samples. Here we present morphological records of the planktonic foraminifera species Globoconella puncticulata and Truncorotalia crassaformis over a 500,000-year interval directly preceding the extinction of G. puncticulata (2.41 Ma). Material was collected from five North Atlantic sites (ODP Sites 659 [18° N], 925 [3° N] and 981 [55° N], IODP Site U1313 [41° N] and DSDP Site 606 [37° N]). Test size and shape of over 35,000 individuals were measured and compared to site-specific records of sea surface temperature, primary productivity and marine aeolian dust deposition, as well as to global records of ice volume, ocean circulation and atmospheric CO2, and all two-way interactions. Morphological parameters respond weakly to individual climate parameters. Once interactions among all studied climate parameters were incorporated, abiotic change explained around 35% of the evolutionary variance. Observed covariances between environmental parameters vary strongly with glacial-interglacial cyclicity, implying that the relationships among climate variables and their relative influences on evolutionary change varied through time. This time dependence cautions against unfettered use of dimension reduction techniques, such as principal components analysis, to extract a single, supposedly dominant, proxy. Furthermore species' responses differed between geographic locations, impressing the need to test how interactions among multiple climate variables at different regional settings shape the biotic microevolutionary response to local and global abiotic change.

Abiotic vs biological sources and fates of organic compounds in a low temperature continental serpentinizing system

NASA Astrophysics Data System (ADS)

Robinson, K.; Noble, S. M.; Shock, E.

2016-12-01

Serpentinization is likely the most common water-rock reaction in our solar system. During this process ultramafic silicates are hydrated, a calcium hydroxide solution is formed, and H2O is reduced to H2 coupled to the oxidation of Fe2+ to Fe3+. The resulting hyper-alkaline, reduced conditions generate thermodynamic drives for numerous carbon compound reactions, including the precipitation of various carbonate minerals and the reduction of inorganic carbonate to organic carbon. Testing the extent to which these thermodynamic drives lead to observable results led to the present study of the flow and transformations of carbon through the active continental serpentinizing system at the Samail Ophiolite in the Sultanate of Oman. Water samples were collected from shallow groundwater (representing system input), hyper-alkaline seeps (system output), boreholes (system intermediate), and surface fluid mixing zones, and analyzed for concentrations of dissolved inorganic carbon (DIC + δ13C), organic carbon (+ δ13C), formate, acetate, H2, methane (+ δ13C), ethane, and an accompanying suite of other geochemical solutes. These analyses indicate that the vast majority of DIC in these serpentinizing fluids precipitates in the subsurface as carbonate minerals; however, a significant amount of DIC is converted into organic acids and light hydrocarbons and expelled at the surface in hyper-alkaline seeps. Based on thermodynamic calculations, it seems most likely that formate last equilibrated with dolomite (CaMg[CO3]2) in the subsurface, acetate last equilibrated with calcite (CaCO3) near the surface, and methane and ethane last equilibrated in a distinct carbon-limited region of the subsurface. As for the fates of these compounds, energetic calculations reveal that a combination of oxidative, reductive, and fermentative metabolisms are thermodynamically favorable. Indeed, δ13C trends record microbial methane oxidation at the surface and cannot rule out methane as biologically sourced from the subsurface.

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

Authors, Various

Planning a rational energy future requires anticipating the environmental consequences of various technologies. This is difficult to do with precision as the effects of pollutants are often determined by interactions between and among complex physical (abiotic) and biological (biotic) systems. A given pollutant may affect human beings through direct exposure or indirectly through inducing changes to biological systems which humans need to utilize. The concentration of a toxin in the food chain or the destruction of organisms necessary for the maintenance of high quality water are examples of indirect effects. Pollutants can be transformed and/or degraded as they establish residencemore » in various components of an ecosystem. Anticipation and amelioration of pollutant effects involves the integration of a vast range of data. This data includes: (1) physical and chemical characterization cf the pollutant as it enters the environment; (2) determining effects on the various components (biotic and abiotic) within the context of the functioning ecosystem of interest; (3) transformation in movements and/or degradation of the pollutant within that ecosystem and within specific organisms and physical components; and (4) determining a detailed biochemical and biological picture of the interactions of pollutants with particular organisms and/or their cellular components judged salient for various processes. The major programs described below are designed to answer parts of the above fundamental questions relevant to pollutants generated by energy related technologies. Their emphasis is on anticipating consequences to the biological components of various ecosystems. The work ranges from studies involving parts of a single cell (the membranes) to studies involving the whole ecosystem (in the pelagic zone of a lake). The programs take advantage of expertise and technical abilities present at LBL. Two small exploratory projects which were of brief duration and not related to anticipating biological effects of pollutants are included in this section. They concern geothermal technology and its improvement using techniques based on organic and physical properties of certain materials.« less

Arsenic repartitioning during biogenic sulfidization and transformation of ferrihydrite

NASA Astrophysics Data System (ADS)

Kocar, Benjamin D.; Borch, Thomas; Fendorf, Scott

2010-02-01

Iron (hydr)oxides are strong sorbents of arsenic (As) that undergo reductive dissolution and transformation upon reaction with dissolved sulfide. Here we examine the transformation and dissolution of As-bearing ferrihydrite and subsequent As repartitioning amongst secondary phases during biotic sulfate reduction. Columns initially containing As(V)-ferrihydrite coated sand, inoculated with the sulfate reducing bacteria Desulfovibrio vulgaris (Hildenborough), were eluted with artificial groundwater containing sulfate and lactate. Rapid and consistent sulfate reduction coupled with lactate oxidation is observed at low As(V) loading (10% of the adsorption maximum). The dominant Fe solid phase transformation products at low As loading include amorphous FeS within the zone of sulfate reduction (near the inlet of the column) and magnetite downstream where Fe(II) (aq) concentrations increase; As is displaced from the zone of sulfidogenesis and Fe(III) (s) depletion. At high As(V) loading (50% of the adsorption maximum), sulfate reduction and lactate oxidation are initially slow but gradually increase over time, and all As(V) is reduced to As(III) by the end of experimentation. With the higher As loading, green rust(s), as opposed to magnetite, is a dominant Fe solid phase product. Independent of loading, As is strongly associated with magnetite and residual ferrihydrite, while being excluded from green rust and iron sulfide. Our observations illustrate that sulfidogenesis occurring in proximity with Fe (hydr)oxides induce Fe solid phase transformation and changes in As partitioning; formation of As sulfide minerals, in particular, is inhibited by reactive Fe(III) or Fe(II) either through sulfide oxidation or complexation.

Arsenic Repartitioning during Biogenic Sulfidization and Transformation of Ferrihydrite

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

Kocar, B.; Borch, T; Fendorf, S

Iron (hydr)oxides are strong sorbents of arsenic (As) that undergo reductive dissolution and transformation upon reaction with dissolved sulfide. Here we examine the transformation and dissolution of As-bearing ferrihydrite and subsequent As repartitioning amongst secondary phases during biotic sulfate reduction. Columns initially containing As(V)-ferrihydrite coated sand, inoculated with the sulfate reducing bacteria Desulfovibrio vulgaris (Hildenborough), were eluted with artificial groundwater containing sulfate and lactate. Rapid and consistent sulfate reduction coupled with lactate oxidation is observed at low As(V) loading (10% of the adsorption maximum). The dominant Fe solid phase transformation products at low As loading include amorphous FeS within themore » zone of sulfate reduction (near the inlet of the column) and magnetite downstream where Fe(II){sub (aq)} concentrations increase; As is displaced from the zone of sulfidogenesis and Fe(III){sub (s)} depletion. At high As(V) loading (50% of the adsorption maximum), sulfate reduction and lactate oxidation are initially slow but gradually increase over time, and all As(V) is reduced to As(III) by the end of experimentation. With the higher As loading, green rust(s), as opposed to magnetite, is a dominant Fe solid phase product. Independent of loading, As is strongly associated with magnetite and residual ferrihydrite, while being excluded from green rust and iron sulfide. Our observations illustrate that sulfidogenesis occurring in proximity with Fe (hydr)oxides induce Fe solid phase transformation and changes in As partitioning; formation of As sulfide minerals, in particular, is inhibited by reactive Fe(III) or Fe(II) either through sulfide oxidation or complexation.« less

Arsenic repartitioning during biogenic sulfidization and transformation of ferrihydrite

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

Kocar, Benjamin D.; Borch, Thomas; Fendorf, Scott

Iron (hydr)oxides are strong sorbents of arsenic (As) that undergo reductive dissolution and transformation upon reaction with dissolved sulfide. Here we examine the transformation and dissolution of As-bearing ferrihydrite and subsequent As repartitioning amongst secondary phases during biotic sulfate reduction. Columns initially containing As(V)-ferrihydrite coated sand, inoculated with the sulfate reducing bacteria Desulfovibrio vulgaris (Hildenborough), were eluted with artificial groundwater containing sulfate and lactate. Rapid and consistent sulfate reduction coupled with lactate oxidation is observed at low As(V) loading (10% of the adsorption maximum). The dominant Fe solid phase transformation products at low As loading include amorphous FeS within themore » zone of sulfate reduction (near the inlet of the column) and magnetite downstream where Fe(II)(aq) concentrations increase; As is displaced from the zone of sulfidogenesis and Fe(III)(s) depletion. At high As(V) loading (50% of the adsorption maximum), sulfate reduction and lactate oxidation are initially slow but gradually increase over time, and all As(V) is reduced to As(III) by the end of experimentation. With the higher As loading, green rust(s), as opposed to magnetite, is a dominant Fe solid phase product. Independent of loading, As is strongly associated with magnetite and residual ferrihydrite, while being excluded from green rust and iron sulfide. Our observations illustrate that sulfidogenesis occurring in proximity with Fe (hydr)oxides induce Fe solid phase transformation and changes in As partitioning; formation of As sulfide minerals, in particular, is inhibited by reactive Fe(III) or Fe(II) either through sulfide oxidation or complexation.« less

Evaluation of Potential Energy Loss Reduction and Savings for U. S. Army Electrical Distribution Systems

DTIC Science & Technology

1993-09-01

Different Size Transformers (Per Transformer ) 41 15 Additional Energy Losses for Mis-Sized Transformers (Per Transformer ) 42 16 Power System ...directly affects the amount of neutral line power loss in the system . Since most Army three-phase loads are distribution transformers spread out over a...61 Balancing Three-Phase Loads Balancing Feeder Circuit Loads Power Factor Correction Optimal Transformer Sizing Conductor Sizing Combined

CRISPR/Cas9-mediated efficient genome editing via blastospore-based transformation in entomopathogenic fungus Beauveria bassiana.

PubMed

Chen, Jingjing; Lai, Yiling; Wang, Lili; Zhai, Suzhen; Zou, Gen; Zhou, Zhihua; Cui, Chunlai; Wang, Sibao

2017-04-03

Beauveria bassiana is an environmentally friendly alternative to chemical insecticides against various agricultural insect pests and vectors of human diseases. However, its application has been limited due to slow kill and sensitivity to abiotic stresses. Understanding of the molecular pathogenesis and physiological characteristics would facilitate improvement of the fungal performance. Loss-of-function mutagenesis is the most powerful tool to characterize gene functions, but it is hampered by the low rate of homologous recombination and the limited availability of selectable markers. Here, by combining the use of uridine auxotrophy as recipient and donor DNAs harboring auxotrophic complementation gene ura5 as a selectable marker with the blastospore-based transformation system, we established a highly efficient, low false-positive background and cost-effective CRISPR/Cas9-mediated gene editing system in B. bassiana. This system has been demonstrated as a simple and powerful tool for targeted gene knock-out and/or knock-in in B. bassiana in a single gene disruption. We further demonstrated that our system allows simultaneous disruption of multiple genes via homology-directed repair in a single transformation. This technology will allow us to study functionally redundant genes and holds significant potential to greatly accelerate functional genomics studies of B. bassiana.

CRISPR/Cas9-mediated efficient genome editing via blastospore-based transformation in entomopathogenic fungus Beauveria bassiana

PubMed Central

Chen, Jingjing; Lai, Yiling; Wang, Lili; Zhai, Suzhen; Zou, Gen; Zhou, Zhihua; Cui, Chunlai; Wang, Sibao

2017-01-01

Beauveria bassiana is an environmentally friendly alternative to chemical insecticides against various agricultural insect pests and vectors of human diseases. However, its application has been limited due to slow kill and sensitivity to abiotic stresses. Understanding of the molecular pathogenesis and physiological characteristics would facilitate improvement of the fungal performance. Loss-of-function mutagenesis is the most powerful tool to characterize gene functions, but it is hampered by the low rate of homologous recombination and the limited availability of selectable markers. Here, by combining the use of uridine auxotrophy as recipient and donor DNAs harboring auxotrophic complementation gene ura5 as a selectable marker with the blastospore-based transformation system, we established a highly efficient, low false-positive background and cost-effective CRISPR/Cas9-mediated gene editing system in B. bassiana. This system has been demonstrated as a simple and powerful tool for targeted gene knock-out and/or knock-in in B. bassiana in a single gene disruption. We further demonstrated that our system allows simultaneous disruption of multiple genes via homology-directed repair in a single transformation. This technology will allow us to study functionally redundant genes and holds significant potential to greatly accelerate functional genomics studies of B. bassiana. PMID:28368054

Analysis, occurrence, fate and risks of proton pump inhibitors, their metabolites and transformation products in aquatic environment: A review.

PubMed

Kosma, Christina I; Lambropoulou, Dimitra A; Albanis, Triantafyllos A

2016-11-01

Proton pump inhibitors (PPIs) which include omeprazole, esomeprazole, lansoprazole, pantoprazole and rabeprazole, are extensively used for the relief of gastro-intestinal disorders. Despite their high worldwide consumption, PPIs are extensively metabolized in human bodies and therefore are not regularly detected in monitoring studies. Very recently, however, it has been shown that some omeprazole metabolites may enter and are likely to persist in aquatic environment. Hence, to fully assess the environmental exposures and risks associated with PPIs, it is important to better understand and evaluate the fate and behavior not only of the parent compound but also of their metabolites and their transformation products arising from biotic and abiotic processes (hydrolysis, photodegradation, biodegradation etc.) in the environment. In this light, the purpose of this review is to summarize the present state of knowledge on the introduction and behavior of these chemicals in natural and engineering systems and highlight research needs and gaps. It draws attention to their transformation, the increase contamination by their metabolites/TPs in different environmental matrices and their potential adverse effects in the environment. Furthermore, existing research on analytical developments with respect to sample treatment, separation and detection of PPIs and their metabolites/TPs is provided. Copyright © 2016 Elsevier B.V. All rights reserved.

Transgenic barley: a prospective tool for biotechnology and agriculture.

PubMed

Mrízová, Katarína; Holasková, Edita; Öz, M Tufan; Jiskrová, Eva; Frébort, Ivo; Galuszka, Petr

2014-01-01

Barley (Hordeum vulgare L.) is one of the founder crops of agriculture, and today it is the fourth most important cereal grain worldwide. Barley is used as malt in brewing and distilling industry, as an additive for animal feed, and as a component of various food and bread for human consumption. Progress in stable genetic transformation of barley ensures a potential for improvement of its agronomic performance or use of barley in various biotechnological and industrial applications. Recently, barley grain has been successfully used in molecular farming as a promising bioreactor adapted for production of human therapeutic proteins or animal vaccines. In addition to development of reliable transformation technologies, an extensive amount of various barley genetic resources and tools such as sequence data, microarrays, genetic maps, and databases has been generated. Current status on barley transformation technologies including gene transfer techniques, targets, and progeny stabilization, recent trials for improvement of agricultural traits and performance of barley, especially in relation to increased biotic and abiotic stress tolerance, and potential use of barley grain as a protein production platform have been reviewed in this study. Overall, barley represents a promising tool for both agricultural and biotechnological transgenic approaches, and is considered an ancient but rediscovered crop as a model industrial platform for molecular farming. © 2013 Elsevier Inc. All rights reserved.

Organic functional group transformations in water at elevated temperature and pressure: Reversibility, reactivity, and mechanisms

NASA Astrophysics Data System (ADS)

Shipp, Jessie; Gould, Ian R.; Herckes, Pierre; Shock, Everett L.; Williams, Lynda B.; Hartnett, Hilairy E.

2013-03-01

Many transformation reactions involving hydrocarbons occur in the presence of H2O in hydrothermal systems and deep sedimentary systems. We investigate these reactions using laboratory-based organic chemistry experiments at high temperature and pressure (300 °C and 100 MPa). Organic functional group transformation reactions using model organic compounds based on cyclohexane with one or two methyl groups provided regio- and stereochemical markers that yield information about reversibility and reaction mechanisms. We found rapidly reversible interconversion between alkanes, alkenes, dienes, alcohols, ketones, and enones. The alkane-to-ketone reactions were not only completely reversible, but also exhibited such extensive reversibility that any of the functional groups along the reaction path (alcohol, ketone, and even the diene) could be used as the reactant and form all the other groups as products. There was also a propensity for these ring-based structures to dehydrogenate; presumably from the alkene, through a diene, to an aromatic ring. The product suites provide strong evidence that water behaved as a reactant and the various functional groups showed differing degrees of reactivity. Mechanistically-revealing products indicated reaction mechanisms that involve carbon-centered cation intermediates. This work therefore demonstrates that a wide range of organic compound types can be generated by abiotic reactions at hydrothermal conditions.

A review of selection-based tests of abiotic surrogates for species representation.

PubMed

Beier, Paul; Sutcliffe, Patricia; Hjort, Jan; Faith, Daniel P; Pressey, Robert L; Albuquerque, Fabio

2015-06-01

Because conservation planners typically lack data on where species occur, environmental surrogates--including geophysical settings and climate types--have been used to prioritize sites within a planning area. We reviewed 622 evaluations of the effectiveness of abiotic surrogates in representing species in 19 study areas. Sites selected using abiotic surrogates represented more species than an equal number of randomly selected sites in 43% of tests (55% for plants) and on average improved on random selection of sites by about 8% (21% for plants). Environmental diversity (ED) (42% median improvement on random selection) and biotically informed clusters showed promising results and merit additional testing. We suggest 4 ways to improve performance of abiotic surrogates. First, analysts should consider a broad spectrum of candidate variables to define surrogates, including rarely used variables related to geographic separation, distance from coast, hydrology, and within-site abiotic diversity. Second, abiotic surrogates should be defined at fine thematic resolution. Third, sites (the landscape units prioritized within a planning area) should be small enough to ensure that surrogates reflect species' environments and to produce prioritizations that match the spatial resolution of conservation decisions. Fourth, if species inventories are available for some planning units, planners should define surrogates based on the abiotic variables that most influence species turnover in the planning area. Although species inventories increase the cost of using abiotic surrogates, a modest number of inventories could provide the data needed to select variables and evaluate surrogates. Additional tests of nonclimate abiotic surrogates are needed to evaluate the utility of conserving nature's stage as a strategy for conservation planning in the face of climate change. © 2015 Society for Conservation Biology.

Abiotic controls on N2O emissions from soils and wetlands

NASA Astrophysics Data System (ADS)

Horwath, W. R.

2016-12-01

The increase in atmospheric nitrous oxide (N2O) is a critical climate change issue contributing to global warming. Most studies on N2O production attribute microbial processes and their associated enzymatic reactions to be the main driver affecting emissions. The role of redox capable iron, manganese and organic compounds that can react with intermediates in the nitrogen cycle has also been shown to produce N2O abiotically. The importance of the abiotic pathways, however, is highly debated. The abiotic production of N2O is related to biophysiochemical controls and unique isotopic signatures of nitrogen cycle intermediates (hydroxylamine, nitric oxide, and nitrite), redox-active metals (iron and manganese) and organic matter (humic and fulvic acids). In a range of soils, we find that the iron directly associated with organic compounds is the strongest variable relating to N2O emissions. In addition to these factors, management is also assumed to affect abiotic N2O production through its impact on nitrogen cycle intermediates, but the environmental and physiochemical conditions that are changed by management are rarely considered in the abiotic production of N2O. We find that the amount and quality of organic compounds in soils directly determines the fate of soil N2O production (i.e. be emitted or consumed). Water depth in rice paddies and wetlands also plays a significant role in partitioning production and consumption of N2O. What is evident from studies on N2O emission is that abiotic reactions are coupled to biotic processes and they cannot be easily separated. The biotic/abiotic interactions have important ecological outcomes that influence abiotic production mechanisms and should be recognized as important controllers of N2O production and consumption processes in soils and sediments.

The Combined Role Of Manganese Oxides And Microbes In The yAbiotic Uptake Of Amino Acid Nitrogen Into Litter And Soil Organic yMatter

NASA Astrophysics Data System (ADS)

Filley, T. R.; Dria, K.

2004-12-01

Soil organic matter (SOM) is the largest terrestrial C and N store. Microbial yand abiotic processes that control the transformation of protein nitrogen in litter and ysoils into macromolecular humic materials play an important role in organic matter ystorage and soil productivity. There are major gaps, however, in our understanding of ythese processes and behaviors. Abiotic reactions of amines, phenols and sugars derived yfrom forest leachates or present in detrital and litter organic matter are known to be ykey processes in the formation of complex organic nitrogen. We present here the yresults from a study designed to investigate how the inherent chemistry of lignin, leaf ylitter, and progressively advanced brown-rot wood decay impact the chemical reaction yof amino acids with this organic matter. Additionally, experiments in the presence of ybirnessite (MnO2) were also conducted to investigate the role of mineral induced phenol yoxidation on specific amino acid chemical humifcation processes. Solid and liquid state yNMR, 13C-labelled tetramethyl ammonium hydroxide thermochemolysis and stable ycarbon and nitrogen isotope ratio mass spectrometry were used to track the alteration yof litter material and document uptake of 13C and 15N labeled amino acids. yPreliminary results from birnessite-containing experiments suggest that the metal-ypromoted oxidation of the lignin, leaf litter, and, in particular, demethylated brown rot ywood residues, is necessary to convert the phenols to quinones of some type permitting yamine addition. This relationship is particularly true for the production of soluble yfractions after two and six weeks of reaction in the presence of the manganese oxides. yAdditionally, the production of leachable organic matter with incorporated N was ypromoted in the soluble fractions. Ongoing NMR studies will elucidate the nature of ythe chemical binding in these experiments. y

Simultaneous anaerobic transformation of tetrachloroethene and carbon tetrachloride in a continuous flow column

NASA Astrophysics Data System (ADS)

Azizian, Mohammad F.; Semprini, Lewis

2016-07-01

Tetrachloroethene (PCE) and carbon tetrachloride (CT) were simultaneously transformed in a packed column that was bioaugmented with the Evanite culture (EV). The data presented here have been obtained over a period of 1930 days. Initially the column was continuously fed synthetic groundwater with PCE (0.1 mM), sulfate (SO42 -) (0.2 mM) and formate (2.1 mM) or lactate (1.1 mM), but not CT. In these early stages of the study the effluent H2 concentrations ranged from 7 to 19 nM, and PCE was transformed to ethene (ETH) (81 to 85%) and vinyl chloride (VC) (11 to 17%), and SO42 - was completely reduced when using either lactate or formate as electron donors. SO42 - reduction occurred concurrently with cis-DCE and VC dehalogenation. Formate was a more effective substrate for promoting dehalogenation based on electron donor utilization efficiency. Simultaneous PCE and CT tests found CT (0.015 mM) was completely transformed with 20% observed as chloroform (CF) and trace amounts of chloromethane (CM) and dichloromethane (DCM), but no methane (CH4) or carbon disulfide (CS2). PCE transformation to ETH improved with CT addition in response to increases in H2 concentrations to 160 nM that resulted from acetate formation being inhibited by either CT or CF. Lactate fermentation was negatively impacted after CT transformation tests, with propionate accumulating, and H2 concentrations being reduced to below 1 nM. Under these conditions both SO42 - reduction and dehalogenation were negatively impacted, with sulfate reduction not occurring and PCE being transformed to cis-dichloroethene (c-DCE) (52%) and VC (41%). Upon switching to formate, H2 concentrations increased to 40 nM, and complete SO42 - reduction was achieved, while PCE was transformed to ETH (98%) and VC (1%), with no acetate detected. Throughout the study PCE dehalogenation to ethene was positively correlated with the effluent H2 concentrations.

Abiotic regulation: a common way for proteins to modulate their functions.

PubMed

Zou, Zhi; Fu, Xinmiao

2015-01-01

Modulation of protein intrinsic activity in cells is generally carried out via a combination of four common ways, i.e., allosteric regulation, covalent modification, proteolytic cleavage and association of other regulatory proteins. Accumulated evidence indicate that changes of certain abiotic factors (e.g., temperature, pH, light and mechanical force) within or outside the cells directly influence protein structure and thus profoundly modulate the functions of a wide range of proteins, termed as abiotic regulatory proteins (e.g., heat shock factor, small heat shock protein, hemoglobin, zymogen, integrin, rhodopsin). Such abiotic regulation apparently differs from the four classic ways in perceiving and response to the signals. Importantly, it enables cells to directly and also immediately response to extracellular stimuli, thus facilitating the ability of organisms to resist against and adapt to the abiotic stress and thereby playing crucial roles in life evolution. Altogether, abiotic regulation may be considered as a common way for proteins to modulate their functions.

Carbon Isotope Systematics in Mineral-Catalyzed Hydrothermal Organic Synthesis Processes at High Temperature and Pressures

NASA Technical Reports Server (NTRS)

Fu, Qi; Socki, R. A.; Niles, Paul B.

2011-01-01

Observation of methane in the Martian atmosphere has been reported by different detection techniques. Reduction of CO2 and/or CO during serpentization by mineral surface catalyzed Fischer-Tropsch Type (FTT) synthesis may be one possible process responsible for methane generation on Mars. With the evidence a recent study has discovered for serpentinization in deeply buried carbon rich sediments, and more showing extensive water-rock interaction in Martian history, it seems likely that abiotic methane generation via serpentinization reactions may have been common on Mars. Experiments involving mineral-catalyzed hydrothermal organic synthesis processes were conducted at 750 C and 5.5 Kbars. Alkanes, alcohols and carboxylic acids were identified as organic compounds. No "isotopic reversal" of delta C-13 values was observed for alkanes or carboxylic acids, suggesting a different reaction pathway than polymerization. Alcohols were proposed as intermediaries formed on mineral surfaces at experimental conditions. Carbon isotope data were used in this study to unravel the reaction pathways of abiotic formation of organic compounds in hydrothermal systems at high temperatures and pressures. They are instrumental in constraining the origin and evolution history of organic compounds on Mars and other planets.

The multiple stressor ecological risk assessment for the mercury-contaminated South River and upper Shenandoah River using the Bayesian network-relative risk model.

PubMed

Landis, Wayne G; Ayre, Kimberley K; Johns, Annie F; Summers, Heather M; Stinson, Jonah; Harris, Meagan J; Herring, Carlie E; Markiewicz, April J

2017-01-01

We have conducted a regional scale risk assessment using the Bayesian Network Relative Risk Model (BN-RRM) to calculate the ecological risks to the South River and upper Shenandoah River study area. Four biological endpoints (smallmouth bass, white sucker, Belted Kingfisher, and Carolina Wren) and 4 abiotic endpoints (Fishing River Use, Swimming River Use, Boating River Use, and Water Quality Standards) were included in this risk assessment, based on stakeholder input. Although mercury (Hg) contamination was the original impetus for the site being remediated, other chemical and physical stressors were evaluated. There were 3 primary conclusions from the BN-RRM results. First, risk varies according to location, type and quality of habitat, and exposure to stressors within the landscape. The patterns of risk can be evaluated with reasonable certitude. Second, overall risk to abiotic endpoints was greater than overall risk to biotic endpoints. By including both biotic and abiotic endpoints, we are able to compare risk to endpoints that represent a wide range of stakeholder values. Third, whereas Hg reduction is the regulatory priority for the South River, Hg is not the only stressor driving risk to the endpoints. Ecological and habitat stressors contribute risk to the endpoints and should be considered when managing this site. This research provides the foundation for evaluating the risks of multiple stressors of the South River to a variety of endpoints. From this foundation, tools for the evaluation of management options and an adaptive management tools have been forged. Integr Environ Assess Manag 2017;13:85-99. © 2016 SETAC. © 2016 SETAC.

Determinism in fish assemblages of floodplain lakes of the vastly disturbed Mississippi Alluvial Valley

USGS Publications Warehouse

Miranda, L.E.; Lucas, G.M.

2004-01-01

The Mississippi Alluvial Valley between southern Illinois and southern Louisiana contains hundreds of floodplain lakes, most of which have been adversely affected by landscape modifications used to control flooding and support agriculture. We examined fish assemblages in lakes of this region to determine whether deterministic patterns developed in relation to prominent abiotic lake characteristics and to explore whether relevant abiotic factors could be linked to specific assemblage structuring mechanisms. The distributions of 14 taxa in 29 lakes were governed primarily by two gradients that contrasted assemblages in terms of lake area, lake elongation, and water clarity. The knowledge of whether a lake was clear or turbid, large or small, and long or short helped determine fish assemblage characteristics. Abiotic factors influenced fish assemblage structures, plausibly through limitations on foraging and physiological tolerances. Determinism in assemblage organization of floodplain lakes relative to recurrence in physicochemical features has been documented for unaltered rivers. Whereas the Mississippi Alluvial Valley has been subjected to vast anthropogenic disturbances and is not a fully functional floodplain river, fish assemblages in its floodplain lakes remain deterministic and organized by the underlying factors that also dictate assemblages in unaltered rivers. In advanced stages of lake aging, fish assemblages in these lakes are expected to largely include species that thrive in turbid, shallow systems with few predators and low oxygen concentrations. The observed patterns related to physical characteristics of these lakes suggest three general conservation foci, including (1) watershed management to control erosion, (2) removal of sediments or increases in water level to alleviate depth reductions and derived detriments to water physicochemistry, and (3) management of fish populations through stockings, removals, and harvest regulations.

Exogenous Trehalose Treatment Enhances the Activities of Defense-Related Enzymes and Triggers Resistance against Downy Mildew Disease of Pearl Millet.

PubMed

Govind, Sharathchandra R; Jogaiah, Sudisha; Abdelrahman, Mostafa; Shetty, Hunthrike S; Tran, Lam Son P

2016-01-01

In recent years, diverse physiological functions of various sugars are the subject of investigations. Their roles in signal transduction in plant responses to adverse biotic and abiotic stress conditions have become apparent, and growing scientific evidence has indicated that disaccharides like sucrose and trehalose mediate plant defense responses in similar way as those induced by elicitors against the pathogens. Trehalose is a well-known metabolic osmoregulator, stress-protectant and non-reducing disaccharide existing in a variety of organisms, including fungi, bacteria, and plants. Commercially procured trehalose was applied to seeds of susceptible pearl millet ( Pennisetum glaucum ) cultivar "HB3," and tested for its ability to reduce downy mildew disease incidence by induction of resistance. Seed treatment with trehalose at 200 mM for 9 h recorded 70.25% downy mildew disease protection, followed by those with 100 and 50 mM trehalose which offered 64.35 and 52.55% defense, respectively, under greenhouse conditions. Furthermore, under field conditions treatment with 200 mM trehalose for 9 h recorded 67.25% downy mildew disease protection, and reduced the disease severity to 32.75% when compared with untreated control which displayed 90% of disease severity. Trehalose did not affect either sporangial formation or zoospore release from sporangia, indicating that the reduction in disease incidence was not due to direct inhibition but rather through induction of resistance responses in the host. Additionally, trehalose was shown to enhance the levels of polyphenol oxidase, phenylalanine ammonia lyase, and peroxidase, which are known as markers of both biotic and abiotic stress responses. Our study shows that osmoregulators like trehalose could be used to protect plants against pathogen attacks by seed treatment, thus offering dual benefits of biotic and abiotic stress tolerance.

Exogenous Trehalose Treatment Enhances the Activities of Defense-Related Enzymes and Triggers Resistance against Downy Mildew Disease of Pearl Millet

PubMed Central

Govind, Sharathchandra R.; Jogaiah, Sudisha; Abdelrahman, Mostafa; Shetty, Hunthrike S.; Tran, Lam-Son P.

2016-01-01

In recent years, diverse physiological functions of various sugars are the subject of investigations. Their roles in signal transduction in plant responses to adverse biotic and abiotic stress conditions have become apparent, and growing scientific evidence has indicated that disaccharides like sucrose and trehalose mediate plant defense responses in similar way as those induced by elicitors against the pathogens. Trehalose is a well-known metabolic osmoregulator, stress-protectant and non-reducing disaccharide existing in a variety of organisms, including fungi, bacteria, and plants. Commercially procured trehalose was applied to seeds of susceptible pearl millet (Pennisetum glaucum) cultivar “HB3,” and tested for its ability to reduce downy mildew disease incidence by induction of resistance. Seed treatment with trehalose at 200 mM for 9 h recorded 70.25% downy mildew disease protection, followed by those with 100 and 50 mM trehalose which offered 64.35 and 52.55% defense, respectively, under greenhouse conditions. Furthermore, under field conditions treatment with 200 mM trehalose for 9 h recorded 67.25% downy mildew disease protection, and reduced the disease severity to 32.75% when compared with untreated control which displayed 90% of disease severity. Trehalose did not affect either sporangial formation or zoospore release from sporangia, indicating that the reduction in disease incidence was not due to direct inhibition but rather through induction of resistance responses in the host. Additionally, trehalose was shown to enhance the levels of polyphenol oxidase, phenylalanine ammonia lyase, and peroxidase, which are known as markers of both biotic and abiotic stress responses. Our study shows that osmoregulators like trehalose could be used to protect plants against pathogen attacks by seed treatment, thus offering dual benefits of biotic and abiotic stress tolerance. PMID:27895647

RNAi-directed downregulation of betaine aldehyde dehydrogenase 1 (OsBADH1) results in decreased stress tolerance and increased oxidative markers without affecting glycine betaine biosynthesis in rice (Oryza sativa).

PubMed

Tang, Wei; Sun, Jiaqi; Liu, Jia; Liu, Fangfang; Yan, Jun; Gou, Xiaojun; Lu, Bao-Rong; Liu, Yongsheng

2014-11-01

As an important osmoprotectant, glycine betaine (GB) plays an essential role in resistance to abiotic stress in a variety of organisms, including rice (Oryza sativa L.). However, GB content is too low to be detectable in rice, although rice genome possesses several orthologs coding for betaine aldehyde dehydrogenase (BADH) involved in plant GB biosynthesis. Rice BADH1 (OsBADH1) has been shown to be targeted to peroxisome and its overexpression resulted in increased GB biosynthesis and tolerance to abiotic stress. In this study, we demonstrated a pivotal role of OsBADH1 in stress tolerance without altering GB biosynthesis capacity, using the RNA interference (RNAi) technique. OsBADH1 was ubiquitously expressed in different organs, including roots, stems, leaves and flowers. Transgenic rice lines downregulating OsBADH1 exhibited remarkably reduced tolerance to NaCl, drought and cold stresses. The decrease of stress tolerance occurring in the OsBADH1-RNAi repression lines was associated with an elevated level of malondialdehyde content and hydrogen peroxidation. No GB accumulation was detected in transgene-positive and transgene-negative lines derived from heterozygous transgenic T0 plants. Moreover, transgenic OsBADH1-RNAi repression lines showed significantly reduced seed set and yield. In conclusion, the downregulation of OsBADH1, even though not causing any change of GB content, was accounted for the reduction of ability to dehydrogenate the accumulating metabolism-derived aldehydes and subsequently resulted in decreased stress tolerance and crop productivity. These results suggest that OsBADH1 possesses an enzyme activity to catalyze other aldehydes in addition to betaine aldehyde (the precursor of GB) and thus alleviate their toxic effects under abiotic stresses.

Co-transforming bar and CsLEA enhanced tolerance to drought and salt stress in transgenic alfalfa (Medicago sativa L.).

PubMed

Zhang, Jiyu; Duan, Zhen; Zhang, Daiyu; Zhang, Jianquan; Di, Hongyan; Wu, Fan; Wang, Yanrong

2016-03-25

Drought and high salinity are two major abiotic factors that restrict alfalfa productivity. A dehydrin protein, CsLEA, from the desert grass Cleistogenes songorica was transformed into alfalfa (Medicago sativa L.) via Agrobacterium-mediated transformation using the bar gene as a selectable marker, and the drought and salt stress tolerances of the transgenic plants were assessed. Thirty-nine of 119 transformants were positive, as screened by Basta, and further molecularly authenticated using PCR and RT-PCR. Phenotype observations revealed that the transgenic plants grew better than the wild-type (WT) plants after 15d of drought stress and 10d of salt stress: the leaves of WT alfalfa turned yellow, whereas the transgenic alfalfa leaves only wilted; after rewatering, the transgenic plants returned to a normal state, though the WT plants could not be restored. Evaluation of physiologic and biochemical indices during drought and salt stresses showed a relatively lower Na(+) content in the leaves of the transgenic plants, which would reduce toxic ion effects. In addition, the transgenic plants were able to maintain a higher relative water content (RWC), higher shoot biomass, fewer photosystem changes, decreased membrane injury, and a lower level of osmotic stress injury. These results demonstrate that overexpression of the CsLEA gene can enhance the drought and salt tolerance of transgenic alfalfa; in addition, carrying the bar gene in the genome may increase herbicide resistance. Copyright © 2016 Elsevier Inc. All rights reserved.

Natural remediation in the Great Lakes

USGS Publications Warehouse

Passino-Reader, Dora R.; Kamrin, Michael A.; Hickey, James P.; Swindoll, C. Michael; Stahl, Ralph G.; Ells, Stephen J.

2000-01-01

Overall, the existence of stricter environmental laws during the last 30 years and a reduction in the manufacturing base in the Great Lakes has resulted in improvement in conditions in harbors, rivers, and nearshore waters. Problems remain, such as the inability to dredge certain harbors and remove sediments because of lack of disposal facilities for contaminated sediments. Because of the wide extent of of contaminated sediments in the Great Lakes, much work remains to be done to document the condition of contaminated areas and the degree to which remediation of these areas is occurring from biotic and abiotic natural processes.

Biotic and abiotic studies on the biological fate, transport and ecotoxicity of toxic and hazardous waste in the Mississippi River basin

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

Abdelghani, A.; Pramar, Y.; Mandal, T.

1996-05-02

This project assesses the levels of xenobiotics in Devils Swamp and studies their biological fate, transport, ecotoxicity, and potential toxicity to man. This article reports on the following studies: assessment of the acute toxicity of individual xenobiotics and toxicity of organic compounds hexachlorobutadience (HCB) and hexachlorobenzene (HCBD) on juvenile crayfish; determination of the biotic influence of temperature, salinity, pH, oxidation-reduction potential, and sediment composition on the migration of xenobiotics; development of a pharmacokinetics model for xenobiotic absorption and storage, distribution and excretion by fish and crayfish.

Computation of transform domain covariance matrices

NASA Technical Reports Server (NTRS)

Fino, B. J.; Algazi, V. R.

1975-01-01

It is often of interest in applications to compute the covariance matrix of a random process transformed by a fast unitary transform. Here, the recursive definition of fast unitary transforms is used to derive recursive relations for the covariance matrices of the transformed process. These relations lead to fast methods of computation of covariance matrices and to substantial reductions of the number of arithmetic operations required.

ABIOTIC IN SITU TECHNOLOGIES FOR GROUNDWATER REMEDIATION CONFERENCE: PROCEEDINGS

EPA Science Inventory

The USEPA conference on Abiotic In Situ Technologies for Groundwater Remediation was held in Dallas, TX, 8/31-9/2/99. The goal of the meeting was to disseminate current information on abiotic in situ groundwater treatment echnologies. Although much information is being provided a...

A noniterative improvement of Guyan reduction

NASA Technical Reports Server (NTRS)

Ganesan, N.

1993-01-01

In determining the natural modes and frequencies of a linear elastic structure, Guyan reduction is often used to reduce the size of the mass and stiffness matrices and the solution of the reduced system is obtained first. The reduced system modes are then expanded to the size of the original system by using a static transformation linking the retained degrees of freedom to the omitted degrees of freedom. In the present paper, the transformation matrix of Guyan reduction is modified to include additional terms from a series accounting for the inertial effects. However, the inertial terms are dependent on the unknown frequencies. A practical approximation is employed to compute the inertial terms without any iteration. This new transformation is implemented in NASTRAN using a DMAP sequence alter. Numerical examples using a cantilever beam illustrate the necessary condition for allowing a large number of additional terms in the proposed series correction of Guyan reduction. A practical example of a large model of the Plasma Motor Generator module to be flown on a Delta launch vehicle is also presented.

REACTIVITY OF CHEMICAL REDUCTANTS AS A FUNCTION OF REDOX ZONATION

EPA Science Inventory

The incorporation of reductive transformations into fate models continues to be a challenging problem. The occurrence of chemical reductants in anaerobic sediments and aquifers is a result of the reduction of inorganic, electron acceptors coupled to the microbial oxidation of org...

Recent Molecular Advances on Downstream Plant Responses to Abiotic Stress

PubMed Central

dos Reis, Sávio Pinho; Lima, Aline Medeiros; de Souza, Cláudia Regina Batista

2012-01-01

Abiotic stresses such as extremes of temperature and pH, high salinity and drought, comprise some of the major factors causing extensive losses to crop production worldwide. Understanding how plants respond and adapt at cellular and molecular levels to continuous environmental changes is a pre-requisite for the generation of resistant or tolerant plants to abiotic stresses. In this review we aimed to present the recent advances on mechanisms of downstream plant responses to abiotic stresses and the use of stress-related genes in the development of genetically engineered crops. PMID:22942725

A chemodynamic approach for estimating losses of target organic chemicals from water during sample holding time

USGS Publications Warehouse

Capel, P.D.; Larson, S.J.

1995-01-01

Minimizing the loss of target organic chemicals from environmental water samples between the time of sample collection and isolation is important to the integrity of an investigation. During this sample holding time, there is a potential for analyte loss through volatilization from the water to the headspace, sorption to the walls and cap of the sample bottle; and transformation through biotic and/or abiotic reactions. This paper presents a chemodynamic-based, generalized approach to estimate the most probable loss processes for individual target organic chemicals. The basic premise is that the investigator must know which loss process(es) are important for a particular analyte, based on its chemodynamic properties, when choosing the appropriate method(s) to prevent loss.

Exploration for the Salinity Tolerance-Related Genes from Xero-Halophyte Atriplex canescens Exploiting Yeast Functional Screening System

PubMed Central

Li, Jingtao; Sun, Xinhua; Liu, Yanzhi; Wang, Xueliang; Zhang, Hao; Pan, Hongyu

2017-01-01

Plant productivity is limited by salinity stress, both in natural and agricultural systems. Identification of salt stress-related genes from halophyte can provide insights into mechanisms of salt stress tolerance in plants. Atriplex canescens is a xero-halophyte that exhibits optimum growth in the presence of 400 mM NaCl. A cDNA library derived from highly salt-treated A. canescens plants was constructed based on a yeast expression system. A total of 53 transgenic yeast clones expressing enhanced salt tolerance were selected from 105 transformants. Their plasmids were sequenced and the gene characteristics were annotated using a BLASTX search. Retransformation of yeast cells with the selected plasmids conferred salt tolerance to the resulting transformants. The expression patterns of 28 of these stress-related genes were further investigated in A. canescens leaves by quantitative reverse transcription-PCR. In this study, we provided a rapid and robust assay system for large-scale screening of genes for varied abiotic stress tolerance with high efficiency in A. canescens. PMID:29149055

Abiotic protein fragmentation by manganese oxide: Implications for a mechanism to supply soil biota with oligopeptides

DOE PAGES

Reardon, Patrick N.; Chacon, Stephany S.; Walter, Eric D.; ...

2016-03-14

Proteins facilitate a wide range of chemical transformations important in soil as well as being a major reservoir of soil nitrogen themselves. The interactions and reactions of proteins with soils and minerals are of key importance to our understanding of their functional persistence in the environment. We combined NMR and EPR spectroscopies to distinguish the reaction of a model protein with a redox active mineral surface (Birnessite, MnO 2) from its response to a redox neutral phyllosilicate (Kaolinite). Our data demonstrate that birnessite fragments the model protein while kaolinite has little impact on the protein structure. NMR and EPR spectroscopiesmore » are shown to be valuable tools to observe these reactions and capture the extent of protein transformation together with the extent of mineral response. These data suggest that mineral surfaces can have both promoting and retarding roles in terrestrial nitrogen cycling, with redox active minerals acting as accelerators by catalyzing the breakdown of proteins and proteinaceous materials while phyllosilicates are more likely to act as preservative media.« less

Identification and Characterization of the Diverse Stress-Responsive R2R3-RMYB Transcription Factor from Hibiscus sabdariffa L.

PubMed Central

Mohamed, Bahaeldeen Babikar; Aftab, Beenish; Sarwar, Muhammad Bilal; Ahmad, Zarnab; Hassan, Sameera; Husnain, Tayyab

2017-01-01

Various regulatory proteins play a fundamental role to manage the healthy plant growth under stress conditions. Differential display reverse transcriptase PCR and random amplification of cDNA ends (RACE) was used to explore the osmotic stress-responsive transcripts. We identified and characterized the salt stress-responsive R2R3 type RMYB transcription factor from Hibiscus sabdariffa which has an open reading frame of 690 bp, encoding 229 long chain amino acids. In silico analysis confirmed the conserved R2 and R3 domain as well as an NLS-1 localization site. The deduced amino acids of RMYB shared 83, 81, 80, 79, 72, 71, and 66% homology with Arabidopsis thaliana, Glycine max, Oryza sativa, Zea maize, Malus domestica, Populus tremula × Populus alba, and Medicago sativa specific MYB family, respectively. We observed the gene upregulation in stem, leaf, and root tissue in response to abiotic stress. Furthermore, RMYB gene was cloned into plant expression vector under CaMV35S promoter and transformed to Gossypium hirsutum: a local cotton cultivar. Overexpression of RMYB was observed in transgenic plants under abiotic stresses which further suggests its regulatory role in response to stressful conditions. The RMYB transcription factor-overexpressing in transgenic cotton plants may be used as potential agent for the development of stress tolerant crop cultivars. PMID:29181384

75 FR 72818 - Proposed Collection; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-26

...; Comment Request AGENCY: Business Transformation Agency, DoD. ACTION: Notice. SUMMARY: In compliance with Section 3506(c)(2)(A) of the Paperwork Reduction Act of 1995, the Business Transformation Agency announces..., please write to the Business Transformation Agency, Attn: Wide Area Workflow Program Management Office...

Kinetic Behavior and Microstructure of Pearlite Isothermal Transformation Under High Undercooling

NASA Astrophysics Data System (ADS)

Liang, Yu; Xu, Pingwei; Xiang, Song; Liang, Yilong; Xiong, Hu; Li, Jing

2018-06-01

The kinetic behavior of highly undercooled austenite and its effects on the microstructural evolution and mechanical properties of high-carbon steel are studied. The undercooling degree is increased through a temporary undercooling treatment at the bainite transformation temperature of 380 °C to 450 °C before the pearlite isothermal transformation at 500 °C to 620 °C. The transformation kinetics reveals an increased nose temperature and a rightward shift of the transformation curve under high undercooling conditions. In addition, the undercooling treatment leads to an increased driving force during pearlite transformation, which is responsible for the refined hierarchical structures of pearlite. As a result, a 20 to 40 pct size reduction is achieved for pearlite colonies and lamellae. Such refinement is in turn attributed to an 26 pct increase in reduction in area. This work provides both a new understanding of high-performance fully pearlitic steels for practical applications and new perspectives for potential technological applications in drawing processes for hypoeutectoid steels.

Divergent Synthesis of Solanidine and 22-epi-Solanidine.

PubMed

Hou, Ling-Li; Shi, Yong; Zhang, Zhi-Dan; Wu, Jing-Jing; Yang, Qing-Xiong; Tian, Wei-Sheng

2017-07-21

A divergent synthesis of solanidine and 22-epi-solanidine, two 25S natural steroidal alkaloids, from 25R-configured diosgenin acetate, is described. Initially, solanidine was synthesized through a series of transformations including a cascade ring-switching process of furostan-26-acid, an epimerization of C25 controlled by the conformation of six-membered lactone ring, an intramolecular Schmidt reaction, and an imine reduction/intramolecular aminolysis process. To address the epimerization issue during Schmidt reaction, an improved synthesis was developed, which also led to a synthesis of 22-epi-solanidine. In this synthesis, selective transformation of azido lactone to azido diol and amino diol was realized through a reduction relay tactic. The azido diol was transformed to solanidine via an intramolecular Schmidt reaction/N-alkylation/reduction process and to 22-epi-solanidine via an intramolecular double N-alkylation process.

Effect of temperature in the selective reduction process of limonite nickel ore

NASA Astrophysics Data System (ADS)

Mayangsari, W.; Febriana, Eni; Prasetyo, A. B.

2018-05-01

Temperature is the main factor for the reduction process that influence to reduction degree, phase and morphology transformation. In order to determine these effects which is caused by reduction temperature, this study was conducted. Limoniticnickel ore was prepared by drying and size reduction. A part of prepared limonitewas characterized with XRF to determine the chemical composition. The other part was mixed with reducing agent and CaSO4 to produce pellet. A series of selective reduction processes were conducted to the pellet by using graphite crucible in the muffle furnace carbolite at 800° - 1100°C for 60 minutes. Reduced ore characterized by using XRD and SEM analysis. Based on the result study, weight loss and reduction degree increase as temperature raised along with CaSO4 addition. Moreover, it caused decomposition and transformation to the metallic phase of kamacite and iron up to 7.51% and 41.44% respectively in the reduction process at 1100°C for 60 minutes. Furthermore, particle size growth as metallic phase content increased.

Advanced concepts for transformers pressboard dielectric constant and mechanical strength

NASA Astrophysics Data System (ADS)

1982-03-01

Of the numerous electrical considerations in a material, the value of the dielectric constant serves as an important criterion in designing proper insulation systems. Ways to reduce the dielectric constant of solid (fibrous) insulating materials were investigated. A literature search was made on cellulosic and synthetic fibers and also additives which offered the potential for dielectric constant reduction of the solid insulation. Sample board structures were produced in the laboratory and tested for electrical, mechanical and chemical characteristics. Electrical tests determined the suitability of the material at transformer test and operating conditions. The mechanical tests established the physical characteristics of the modified board structures. Chemical tests checked the conductivity of the aqueous extract, acidity, and ash content. Further, compatibility with transformer oil and some aging tests were performed. An actual computer transformer design was made based on one of the modified board structures and the reduction in core steel and transformer losses were shown.

Symbolic computation of equivalence transformations and parameter reduction for nonlinear physical models

NASA Astrophysics Data System (ADS)

Cheviakov, Alexei F.

2017-11-01

An efficient systematic procedure is provided for symbolic computation of Lie groups of equivalence transformations and generalized equivalence transformations of systems of differential equations that contain arbitrary elements (arbitrary functions and/or arbitrary constant parameters), using the software package GeM for Maple. Application of equivalence transformations to the reduction of the number of arbitrary elements in a given system of equations is discussed, and several examples are considered. The first computational example of generalized equivalence transformations where the transformation of the dependent variable involves an arbitrary constitutive function is presented. As a detailed physical example, a three-parameter family of nonlinear wave equations describing finite anti-plane shear displacements of an incompressible hyperelastic fiber-reinforced medium is considered. Equivalence transformations are computed and employed to radically simplify the model for an arbitrary fiber direction, invertibly reducing the model to a simple form that corresponds to a special fiber direction, and involves no arbitrary elements. The presented computation algorithm is applicable to wide classes of systems of differential equations containing arbitrary elements.

Research advances in major cereal crops for adaptation to abiotic stresses

PubMed Central

Maiti, RK; Satya, Pratik

2014-01-01

With devastating increase in population there is a great necessity to increase crop productivity of staple crops but the productivity is greatly affected by various abiotic stress factors such as drought, salinity. An attempt has been made a brief account on abiotic stress resistance of major cereal crops viz. In spite of good successes obtained on physiological and use molecular biology, the benefits of this high cost technology are beyond the reach of developing countries. This review discusses several morphological, anatomical, physiological, biochemical and molecular mechanisms of major cereal crops related to the adaptation of these crop to abiotic stress factors. It discusses the effect of abiotic stresses on physiological processes such as flowering, grain filling and maturation and plant metabolisms viz. photosynthesis, enzyme activity, mineral nutrition, and respiration. Though significant progress has been attained on the physiological, biochemical basis of resistance to abiotic stress factors, very little progress has been achieved to increase productivity under sustainable agriculture. Therefore, there is a great necessity of inter-disciplinary research to address this issue and to evolve efficient technology and its transfer to the farmers’ fields. PMID:25523172

Research advances in major cereal crops for adaptation to abiotic stresses.

PubMed

Maiti, R K; Satya, Pratik

2014-01-01

With devastating increase in population there is a great necessity to increase crop productivity of staple crops but the productivity is greatly affected by various abiotic stress factors such as drought, salinity. An attempt has been made a brief account on abiotic stress resistance of major cereal crops viz. In spite of good successes obtained on physiological and use molecular biology, the benefits of this high cost technology are beyond the reach of developing countries. This review discusses several morphological, anatomical, physiological, biochemical and molecular mechanisms of major cereal crops related to the adaptation of these crop to abiotic stress factors. It discusses the effect of abiotic stresses on physiological processes such as flowering, grain filling and maturation and plant metabolisms viz. photosynthesis, enzyme activity, mineral nutrition, and respiration. Though significant progress has been attained on the physiological, biochemical basis of resistance to abiotic stress factors, very little progress has been achieved to increase productivity under sustainable agriculture. Therefore, there is a great necessity of inter-disciplinary research to address this issue and to evolve efficient technology and its transfer to the farmers' fields.

Mass dependent stable isotope fractionation of mercury during mer mediated microbial degradation of monomethylmercury

NASA Astrophysics Data System (ADS)

Kritee, K.; Barkay, Tamar; Blum, Joel D.

2009-03-01

Controlling bioaccumulation of toxic monomethylmercury (MMHg) in aquatic food chains requires differentiation between biotic and abiotic pathways that lead to its production and degradation. Recent mercury (Hg) stable isotope measurements of natural samples suggest that Hg isotope ratios can be a powerful proxy for tracing dominant Hg transforming pathways in aquatic ecosystems. Specifically, it has been shown that photo-degradation of MMHg causes both mass dependent (MDF) and mass independent fractionation (MIF) of Hg isotopes. Because the extent of MDF and MIF observed in natural samples (e.g., fish, soil and sediments) can potentially be used to determine the relative importance of pathways leading to MMHg accumulation, it is important to determine the potential role of microbial pathways in contributing to the fractionation, especially MIF, observed in these samples. This study reports the extent of fractionation of Hg stable isotopes during degradation of MMHg to volatile elemental Hg and methane via the microbial Hg resistance ( mer) pathway in Escherichia coli carrying a mercury resistance ( mer) genetic system on a multi-copy plasmid. During experimental microbial degradation of MMHg, MMHg remaining in reactors became progressively heavier (increasing δ202Hg) with time and underwent mass dependent Rayleigh fractionation with a fractionation factor α202/198 = 1.0004 ± 0.0002 (2SD). However, MIF was not observed in any of the microbial MMHg degradation experiments indicating that the isotopic signature left by mer mediated MMHg degradation is significantly different from fractionation observed during DOC mediated photo-degradation of MMHg. Additionally, a clear suppression of Hg isotope fractionation, both during reduction of Hg(II) and degradation of MMHg, was observed when the cell densities increased, possibly due to a reduction in substrate bioavailability. We propose a multi-step framework for understanding the extent of fractionation seen in our MMHg degradation experiments and, based on estimates of the rates of the various steps involved in this mer mediated pathway, suggest which steps in the process could contribute towards the observed extent of fractionation. This framework suggests that at lower cell densities catalysis by MerB was the rate limiting step while at higher cell densities transport into the cell, which does not cause fractionation, became the rate limiting step. In addition to presenting evidence for absence of MIF during mer mediated Hg transformations, based on the nature of Hg compounds and microbe-Hg interactions, we suggest that the nuclear spin dependent MIF (i.e., the magnetic isotope effect) is also unlikely to occur during other non mer mediated 'dark' microbial Hg transformations (e.g., formation of MMHg and oxidative degradation of MMHg). Because of the important implications of the absence of MIF during biological processes on Hg isotope systematics, we discuss theoretical considerations and experimental strategies that could be used to confirm this suggestion.

Polarity inversion of bioanode for biocathodic reduction of aromatic pollutants.

PubMed

Yun, Hui; Liang, Bin; Kong, De-Yong; Cheng, Hao-Yi; Li, Zhi-Ling; Gu, Ya-Bing; Yin, Hua-Qun; Wang, Ai-Jie

2017-06-05

The enrichment of specific pollutant-reducing consortium is usually required prior to the startup of biocathode bioelectrochemical system (BES) and the whole process is time consuming. To rapidly establish a non-specific functional biocathode, direct polar inversion from bioanode to biocathode is proposed in this study. Based on the diverse reductases and electron transfer related proteins of anode-respiring bacteria (ARB), the acclimated electrochemically active biofilm (EAB) may catalyze reduction of different aromatic pollutants. Within approximately 12 d, the acclimated bioanodes were directly employed as biocathodes for nitroaromatic nitrobenzene (NB) and azo dye acid orange 7 (AO7) reduction. Our results indicated that the established biocathode significantly accelerated the reduction of NB to aniline (AN) and AO7 to discolored products compared with the abiotic cathode and open circuit controls. Several microbes possessing capabilities of nitroaromatic/azo dye reduction and bidirectional electron transfer were maintained or enriched in the biocathode communities. Cyclic voltammetry highlighted the decreased over-potentials and enhanced electron transfer of biocathode as well as demonstrated the ARB Geobacter containing cytochrome c involved in the backward electron transfer from electrode to NB. This study offers new insights into the rapid establishment and modularization of functional biocathodes for the potential treatment of complicated electron acceptors-coexisting wastewaters. Copyright © 2017 Elsevier B.V. All rights reserved.

Regulation of MIR Genes in Response to Abiotic Stress in Hevea brasiliensis

PubMed Central

Gébelin, Virginie; Leclercq, Julie; Hu, Songnian; Tang, Chaorong; Montoro, Pascal

2013-01-01

Increasing demand for natural rubber (NR) calls for an increase in latex yield and also an extension of rubber plantations in marginal zones. Both harvesting and abiotic stresses lead to tapping panel dryness through the production of reactive oxygen species. Many microRNAs regulated during abiotic stress modulate growth and development. The objective of this paper was to study the regulation of microRNAs in response to different types of abiotic stress and hormone treatments in Hevea. Regulation of MIR genes differs depending on the tissue and abiotic stress applied. A negative co-regulation between HbMIR398b with its chloroplastic HbCuZnSOD target messenger is observed in response to salinity. The involvement of MIR gene regulation during latex harvesting and tapping panel dryness (TPD) occurrence is further discussed. PMID:24084713

Overexpression of EaDREB2 and pyramiding of EaDREB2 with the pea DNA helicase gene (PDH45) enhance drought and salinity tolerance in sugarcane (Saccharum spp. hybrid).

PubMed

Augustine, Sruthy Maria; Ashwin Narayan, J; Syamaladevi, Divya P; Appunu, C; Chakravarthi, M; Ravichandran, V; Tuteja, Narendra; Subramonian, N

2015-02-01

EaDREB2 overexpressed in sugarcane enhanced tolerance to drought and salinity. When co-transformed with plant DNA helicase gene, DREB2 showed greater level of salinity tolerance than in single-gene transgenics. Drought is one of the most challenging agricultural issues limiting sustainable sugarcane production and can potentially cause up to 50 % yield loss. DREB proteins play a vital regulatory role in abiotic stress tolerance in plants. We previously reported that expression of EaDREB2 is enhanced by drought stress in Erianthus arundinaceus. In this study, we have isolated the DREB2 gene from E. arundinaceus, transformed one of the most popular sugarcane variety Co 86032 in tropical India with EaDREB2 through Agrobacterium-mediated transformation, pyramided the EaDREB2 gene with the gene coding for PDH45 driven by Port Ubi 2.3 promoter through particle bombardment and evaluated the V1 transgenics for soil deficit moisture and salinity stresses. Soil moisture stress was imposed at the tillering phase by withholding irrigation. Physiological, molecular and morphological parameters were used to assess drought tolerance. Salinity tolerance was assessed through leaf disc senescence and bud sprout assays under salinity stress. Our results indicate that overexpression of EaDREB2 in sugarcane enhances drought and salinity tolerance to a greater extent than the untransformed control plants. This is the first report of the co-transformation of EaDREB2 and PDH45 which shows higher salinity tolerance but lower drought tolerance than EaDREB2 alone. The present study seems to suggest that, for combining drought and salinity tolerance together, co-transformation is a better approach.

The Real Difference between Biotic and Abiotic Methane

NASA Astrophysics Data System (ADS)

Cao, X.; Bao, H.; Peng, Y.

2017-12-01

Methane has both biotic and abiotic origins, and the identification of these two origins has important implications not only in understanding terrestrial processes but also in searching for extraterrestrial life. Carbon and hydrogen isotopes in methane have been used to identify certain biosignatures, but such efforts often suffer from ambiguity. Recent advancement in our capability in measuring multiply substituted isotopologues of methane (i.e. 13CDH3 and 12CD2H2) has found large 12CD2H2 depletion in abiotic methane. Quantum tunneling has been proposed to account for the apparent abiotic signature. However, quantum tunneling is neither unique to abiotic processes nor consistent with the observed not-so-depleted hydrogen isotope composition. Here we constructed a general kinetic model for methane formation from CO2, and validated it by fitting its parameters to observed 13CDH3, 12CD2H2, and 12CDH3. Our model revealed that the fundamental difference between biotic and abiotic methane isotopic signatures is in the source of hydrogens during methane formation. Hydrogens in biotic methane originate from the stronger carbon-hydrogen and sulfur-hydrogen bonds, while hydrogens in abiotic methane originate from the much weaker metal-hydrogen adsorption bond. This hydrogen source difference results in abiotic methane being more depleted in 12CD2H2 than the biotic one. Our model also shows that the primary kinetic hydrogen isotope effect is at approximately 0.6 for both abiotic and biotic pathways, a normal value further nullifying the role of quantum tunneling. The active and exclusive shuttling of reduced hydrogen via strong chemical bonds like carbon-hydrogen and sulfur-hydrogen in coenzymes is proposed here to be a unique signature of life. In an ironic sense, it is the equilibrated hydrogen isotope composition in the hydrogen donors that distinguishes the living from the non-living.

Identification and Expression Analysis of Cytokinin Metabolic Genes in Soybean under Normal and Drought Conditions in Relation to Cytokinin Levels

PubMed Central

Le, Dung Tien; Nishiyama, Rie; Watanabe, Yasuko; Vankova, Radomira; Tanaka, Maho; Seki, Motoaki; Ham, Le Huy; Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo; Tran, Lam-Son Phan

2012-01-01

Cytokinins (CKs) mediate cellular responses to drought stress and targeted control of CK metabolism can be used to develop drought-tolerant plants. Aiming to manipulate CK levels to improve drought tolerance of soybean cultivars through genetic engineering of CK metabolic genes, we surveyed the soybean genome and identified 14 CK biosynthetic (isopentenyltransferase, GmIPT) and 17 CK degradative (CK dehydrogenase, GmCKX) genes. Comparative analyses of GmIPTs and GmCKXs with Arabidopsis counterparts revealed their similar architecture. The average numbers of abiotic stress-inducible cis-elements per promoter were 0.4 and 1.2 for GmIPT and GmCKX genes, respectively, suggesting that upregulation of GmCKXs, thereby reduction of CK levels, maybe the major events under abiotic stresses. Indeed, the expression of 12 GmCKX genes was upregulated by dehydration in R2 roots. Overall, the expressions of soybean CK metabolic genes in various tissues at various stages were highly responsive to drought. CK contents in various organs at the reproductive (R2) stage were also determined under well-watered and drought stress conditions. Although tRNA-type GmIPT genes were highly expressed in soybean, cis-zeatin and its derivatives were found at low concentrations. Moreover, reduction of total CK content in R2 leaves under drought was attributable to the decrease in dihydrozeatin levels, suggesting a role of this molecule in regulating soybean's responses to drought stress. Our systematic analysis of the GmIPT and GmCKX families has provided an insight into CK metabolism in soybean under drought stress and a solid foundation for in-depth characterization and future development of improved drought-tolerant soybean cultivars by manipulation of CK levels via biotechnological approach. PMID:22900018

Interactive effects of grapevine leafroll-associated virus 3 (GLRaV-3) and water stress on the physiology of Vitis vinifera L. cv. Malvasia de Banyalbufar and Giro-Ros.

PubMed

El Aou-Ouad, Hanan; Montero, Rafael; Medrano, Hipólito; Bota, Josefina

2016-06-01

Among several biotic and abiotic stress combinations, interaction between drought and pathogen is one of the most studied combinations in some crops but still not in grapevine. In the present work, we focused on the interaction effects of biotic (GLRaV-3) and abiotic (drought) stresses on grapevine photosynthetic metabolism on two cultivars (cvs. 'Malvasia de Banyalbufar and Giro-Ros'). Non-infected and GLRaV-3 infected potted plants were compared under water stress conditions (WS) and well-watered (WW) conditions. Under WW condition, the results showed that photosynthesis (AN) in both cultivars was decreased by the presence of GLRaV-3. The stomatal conductance (gs) was the main factor for decreasing AN in Malvasia, meanwhile reductions in Giro-Ros were closely related to decreases in gm. The observed differences in gm between both cultivars might result from variation in their leaf anatomical, Giro-Ros having higher values of gm and leaf porosity (in all treatments). Moderate water deficit resulted in a closure of stomata and a decrease in gm accompanied by a decrease in AN in both cultivars. The maximum velocity of carboxylation (Vcmax) and electron transport rate (Jmax) were also reduced under water stress. Moreover, the combined stress resulted in a reduction of most physiological parameters compared to healthy irrigated plants. However, no considerable differences were found between non-infected and virus infected (GLRaV-3) plants under water stress. Most of the results could be explained by the difference of virus concentration between cultivars and treatments. Copyright © 2016 Elsevier GmbH. All rights reserved.

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

Betterton, E.A.; Arnold, R.G.; Liu, Zhijie

Three abiotic systems are described that catalyze the reductive dehalogenation of heavily halogenated environmental pollutants, including carbon tetrachloride, trichloroethene, and perchloroethene. These systems include (a) an electrolytic reactor in which the potential on the working electrode (cathode) is fixed by using a potentiostat, (b) a light-driven system consisting of a semiconductor and (covalently attached) macrocycle that can accept light transmitted via an optical fiber, and a light-driven, two-solvent (isopropanol/acetone) system that promotes dehalogenation reactions via an unknown mechanism. Each is capable of accelerating reductive dehalogenation reactions to very high rates under laboratory conditions. Typically, millimolar concentrations of aqueous-phase targets canmore » be dehalogenated in minutes to hours. The description of each system includes the elements of reaction mechanism (to the extent known), typical kinetic data, and a discussion of the feasibility of applying this technology for the in situ destruction of hazardous compounds. 14 refs., 11 figs., 2 tabs.« less

Hydrogen peroxide and the evolution of oxygenic photosynthesis

NASA Technical Reports Server (NTRS)

Mckay, C. P.; Hartman, H.

1991-01-01

Possible pathways for the evolution of oxygenic photosynthesis in the early reducing atmosphere of the earth are discussed. It is suggested that the abiotic production of atmospheric oxidants could have provided a mechanism by which locally oxidizing conditions were sustained within spatially confined habitats thus removing the available reductants and forcing photosynthetic organisms to utilize water (rather than ferrous or sulfide ions) as the electron donor. It is argued that atmospheric H2O2 played the key role in inducing oxygenic photosynthesis, because, as peroxide concentrations local environments increased, primitive organisms would not only be faced with a loss of a reductant, but would be also forced to develop a biochemical apparatus (such as catalase) that would protect them against the products of oxygenic photosynthesis. This scenario allows for the early evolution of oxygenic photosynthesis at the time when global conditions were still anaerobic.

Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism

NASA Astrophysics Data System (ADS)

Patel, Bhavesh H.; Percivalle, Claudia; Ritson, Dougal J.; Duffy, Colm D.; Sutherland, John D.

2015-04-01

A minimal cell can be thought of as comprising informational, compartment-forming and metabolic subsystems. To imagine the abiotic assembly of such an overall system, however, places great demands on hypothetical prebiotic chemistry. The perceived differences and incompatibilities between these subsystems have led to the widely held assumption that one or other subsystem must have preceded the others. Here we experimentally investigate the validity of this assumption by examining the assembly of various biomolecular building blocks from prebiotically plausible intermediates and one-carbon feedstock molecules. We show that precursors of ribonucleotides, amino acids and lipids can all be derived by the reductive homologation of hydrogen cyanide and some of its derivatives, and thus that all the cellular subsystems could have arisen simultaneously through common chemistry. The key reaction steps are driven by ultraviolet light, use hydrogen sulfide as the reductant and can be accelerated by Cu(I)-Cu(II) photoredox cycling.

A new method for stable carbon isotope analysis of chlorofluorocarbons in contaminated groundwater

NASA Astrophysics Data System (ADS)

Horst, Axel; Lacrampe-Couloume, Georges; Sherwood Lollar, Barbara

2015-04-01

Chlorofluorocarbons (CFCs) and hydrochlorofluorocarbons (HCFCs) have been widely used as refrigerants, propellants, solvents, foaming agents and are important intermediates in the production of anesthetics and other fluorinated compounds. Due to their ozone depletion potential, production was banned for most uses under the Montreal Protocol (1987) and its amendments and atmospheric mixing ratios have started to decrease. In addition to the atmosphere, CFCs and HCFCs have been detected in groundwater, and emissions from various sources such as landfill sites are still ongoing. Previous studies have shown that both abiotic and biotic transformation of CFCs may occur under certain conditions. To investigate degradation that may take place in soils and groundwaters, a purge and trap method (P&T) has been developed to measure the stable carbon isotopic composition of CFCs and HCFCs extracted from waters. A set of pure phase working standards (HCFC-22, CFC-11, CFC-113) has been prepared offline and characterized by sealed tube combustion dual inlet mass spectrometry. Comparison between isotopic standards and CFCs extracted by our method demonstrates the sample P&T extraction steps do not induce significant δ13C fractionation (lt;0.5 per mill). Standards characterized by continuous flow CSIA (compound specific isotope analysis) after extraction agree with offline characterized values. Evaporation experiments were carried out to investigate any isotope effects due to volatile loss that might occur either due to sampling methods or sample handling in the lab. Monitoring δ13C values during progressive evaporation showed small isotopic fractionation associated with evaporation. Enrichment factors, obtained from Rayleigh plots, showed inverse isotope fractionation i.e depletion in 13C in the remaining compound. Notably, this effect is in the opposite direction to the fractionation (13C enrichment) that is likely to be associated with abiotic or biotic transformation effects. This bodes well for the use of CSIA to identify and monitor transformation in the field as any isotopic effects due to volatile loss would only result in a conservative estimate of transformation but not confuse the degradation signal. As a result, enrichment factors in field samples might be underestimated and lead to a more conservative estimate of degradation at contaminated sites. CFCs from several suppliers were characterized to investigate δ13C variation between sources and between different CFC compounds. Significant differences were observed between all measured compounds. However for each compound, δ13C values determined in this study were similar to ranges reported previously for other pure phase CFCs - suggesting a consistent range of source signatures may exist for each compound. As a last step of method evaluation, water samples from a contaminated industrial site were measured. This first preliminary field data will be discussed in comparison to pure phase compounds and with respect to potential degradation.

Isolation transformers for utility-interactive photovoltaic systems

NASA Astrophysics Data System (ADS)

Kern, E. C., Jr.

1982-12-01

Isolation transformers are used in some photovoltaic systems to isolate the photovoltaic system common mode voltage from the utility distribution system. In early system experiments with grid connected photovoltaics, such transformers were the source of significant power losses. A project at the Lincoln Laboratory and at Allied Chemical Corporation developed an improved isolation transformer to minimize such power losses. Experimental results and an analytical model of conventional and improved transformers are presented, showing considerable reductions of losses associated with the improved transformer.

Phytoplankton responses to temperature increases are constrained by abiotic conditions and community composition.

PubMed

Striebel, Maren; Schabhüttl, Stefanie; Hodapp, Dorothee; Hingsamer, Peter; Hillebrand, Helmut

2016-11-01

Effects of temperature changes on phytoplankton communities seem to be highly context-specific, but few studies have analyzed whether this context specificity depends on differences in the abiotic conditions or in species composition between studies. We present an experiment that allows disentangling the contribution of abiotic and biotic differences in shaping the response to two aspects of temperature change: permanent increase of mean temperature versus pulse disturbance in form of a heat wave. We used natural communities from six different sites of a floodplain system as well as artificially mixed communities from laboratory cultures and grew both, artificial and natural communities, in water from the six different floodplain lakes (sites). All 12 contexts (2 communities × 6 sites) were first exposed to three different temperature levels (12, 18, 24 °C, respectively) and afterward to temperature pulses (4 °C increase for 7 h day(-1)). Temperature-dependent changes in biomass and community composition depended on the initial composition of phytoplankton communities. Abiotic conditions had a major effect on biomass of phytoplankton communities exposed to different temperature conditions, however, the effect of biotic and abiotic conditions together was even more pronounced. Additionally, phytoplankton community responses to pulse temperature effects depended on the warming history. By disentangling abiotic and biotic effects, our study shows that temperature-dependent effects on phytoplankton communities depend on both, biotic and abiotic constraints.

Novel NAC Transcription Factor TaNAC67 Confers Enhanced Multi-Abiotic Stress Tolerances in Arabidopsis

PubMed Central

Mao, Xinguo; Chen, Shuangshuang; Li, Ang; Zhai, Chaochao; Jing, Ruilian

2014-01-01

Abiotic stresses are major environmental factors that affect agricultural productivity worldwide. NAC transcription factors play pivotal roles in abiotic stress signaling in plants. As a staple crop, wheat production is severely constrained by abiotic stresses whereas only a few NAC transcription factors have been characterized functionally. To promote the application of NAC genes in wheat improvement by biotechnology, a novel NAC gene designated TaNAC67 was characterized in common wheat. To determine its role, transgenic Arabidopsis overexpressing TaNAC67-GFP controlled by the CaMV-35S promoter was generated and subjected to various abiotic stresses for morphological and physiological assays. Gene expression showed that TaNAC67 was involved in response to drought, salt, cold and ABA treatments. Localization assays revealed that TaNAC67 localized in the nucleus. Morphological analysis indicated the transgenics had enhanced tolerances to drought, salt and freezing stresses, simultaneously supported by enhanced expression of multiple abiotic stress responsive genes and improved physiological traits, including strengthened cell membrane stability, retention of higher chlorophyll contents and Na+ efflux rates, improved photosynthetic potential, and enhanced water retention capability. Overexpression of TaNAC67 resulted in pronounced enhanced tolerances to drought, salt and freezing stresses, therefore it has potential for utilization in transgenic breeding to improve abiotic stress tolerance in crops. PMID:24427285

Transcriptomic Profiling of the Maize (Zea mays L.) Leaf Response to Abiotic Stresses at the Seedling Stage.

PubMed

Li, Pengcheng; Cao, Wei; Fang, Huimin; Xu, Shuhui; Yin, Shuangyi; Zhang, Yingying; Lin, Dezhou; Wang, Jianan; Chen, Yufei; Xu, Chenwu; Yang, Zefeng

2017-01-01

Abiotic stresses, including drought, salinity, heat, and cold, negatively affect maize ( Zea mays L.) development and productivity. To elucidate the molecular mechanisms of resistance to abiotic stresses in maize, RNA-seq was used for global transcriptome profiling of B73 seedling leaves exposed to drought, salinity, heat, and cold stress. A total of 5,330 differentially expressed genes (DEGs) were detected in differential comparisons between the control and each stressed sample, with 1,661, 2,019, 2,346, and 1,841 DEGs being identified in comparisons of the control with salinity, drought, heat, and cold stress, respectively. Functional annotations of DEGs suggested that the stress response was mediated by pathways involving hormone metabolism and signaling, transcription factors (TFs), very-long-chain fatty acid biosynthesis and lipid signaling, among others. Of the obtained DEGs (5,330), 167 genes are common to these four abiotic stresses, including 10 up-regulated TFs (five ERFs, two NACs, one ARF, one MYB, and one HD-ZIP) and two down-regulated TFs (one b-ZIP and one MYB-related), which suggested that common mechanisms may be initiated in response to different abiotic stresses in maize. This study contributes to a better understanding of the molecular mechanisms of maize leaf responses to abiotic stresses and could be useful for developing maize cultivars resistant to abiotic stresses.

Application of wavelet transformation and adaptive neighborhood based modified backpropagation (ANMBP) for classification of brain cancer

NASA Astrophysics Data System (ADS)

Werdiningsih, Indah; Zaman, Badrus; Nuqoba, Barry

2017-08-01

This paper presents classification of brain cancer using wavelet transformation and Adaptive Neighborhood Based Modified Backpropagation (ANMBP). Three stages of the processes, namely features extraction, features reduction, and classification process. Wavelet transformation is used for feature extraction and ANMBP is used for classification process. The result of features extraction is feature vectors. Features reduction used 100 energy values per feature and 10 energy values per feature. Classifications of brain cancer are normal, alzheimer, glioma, and carcinoma. Based on simulation results, 10 energy values per feature can be used to classify brain cancer correctly. The correct classification rate of proposed system is 95 %. This research demonstrated that wavelet transformation can be used for features extraction and ANMBP can be used for classification of brain cancer.

Hydrogen peroxide priming modulates abiotic oxidative stress tolerance: insights from ROS detoxification and scavenging

PubMed Central

Hossain, Mohammad A.; Bhattacharjee, Soumen; Armin, Saed-Moucheshi; Qian, Pingping; Xin, Wang; Li, Hong-Yu; Burritt, David J.; Fujita, Masayuki; Tran, Lam-Son P.

2015-01-01

Plants are constantly challenged by various abiotic stresses that negatively affect growth and productivity worldwide. During the course of their evolution, plants have developed sophisticated mechanisms to recognize external signals allowing them to respond appropriately to environmental conditions, although the degree of adjustability or tolerance to specific stresses differs from species to species. Overproduction of reactive oxygen species (ROS; hydrogen peroxide, H2O2; superoxide, O2⋅-; hydroxyl radical, OH⋅ and singlet oxygen, 1O2) is enhanced under abiotic and/or biotic stresses, which can cause oxidative damage to plant macromolecules and cell structures, leading to inhibition of plant growth and development, or to death. Among the various ROS, freely diffusible and relatively long-lived H2O2 acts as a central player in stress signal transduction pathways. These pathways can then activate multiple acclamatory responses that reinforce resistance to various abiotic and biotic stressors. To utilize H2O2 as a signaling molecule, non-toxic levels must be maintained in a delicate balancing act between H2O2 production and scavenging. Several recent studies have demonstrated that the H2O2-priming can enhance abiotic stress tolerance by modulating ROS detoxification and by regulating multiple stress-responsive pathways and gene expression. Despite the importance of the H2O2-priming, little is known about how this process improves the tolerance of plants to stress. Understanding the mechanisms of H2O2-priming-induced abiotic stress tolerance will be valuable for identifying biotechnological strategies to improve abiotic stress tolerance in crop plants. This review is an overview of our current knowledge of the possible mechanisms associated with H2O2-induced abiotic oxidative stress tolerance in plants, with special reference to antioxidant metabolism. PMID:26136756

Polyamines and abiotic stress in plants: a complex relationship1

PubMed Central

Minocha, Rakesh; Majumdar, Rajtilak; Minocha, Subhash C.

2014-01-01

The physiological relationship between abiotic stress in plants and polyamines was reported more than 40 years ago. Ever since there has been a debate as to whether increased polyamines protect plants against abiotic stress (e.g., due to their ability to deal with oxidative radicals) or cause damage to them (perhaps due to hydrogen peroxide produced by their catabolism). The observation that cellular polyamines are typically elevated in plants under both short-term as well as long-term abiotic stress conditions is consistent with the possibility of their dual effects, i.e., being protectors from as well as perpetrators of stress damage to the cells. The observed increase in tolerance of plants to abiotic stress when their cellular contents are elevated by either exogenous treatment with polyamines or through genetic engineering with genes encoding polyamine biosynthetic enzymes is indicative of a protective role for them. However, through their catabolic production of hydrogen peroxide and acrolein, both strong oxidizers, they can potentially be the cause of cellular harm during stress. In fact, somewhat enigmatic but strong positive relationship between abiotic stress and foliar polyamines has been proposed as a potential biochemical marker of persistent environmental stress in forest trees in which phenotypic symptoms of stress are not yet visible. Such markers may help forewarn forest managers to undertake amelioration strategies before the appearance of visual symptoms of stress and damage at which stage it is often too late for implementing strategies for stress remediation and reversal of damage. This review provides a comprehensive and critical evaluation of the published literature on interactions between abiotic stress and polyamines in plants, and examines the experimental strategies used to understand the functional significance of this relationship with the aim of improving plant productivity, especially under conditions of abiotic stress. PMID:24847338

DDE remediation and degradation.

PubMed

Thomas, John E; Ou, Li-Tse; All-Agely, Abid

2008-01-01

DDT and its metabolites, DDD and DDE, have been shown to be recalcitrant to degradation. The parent compound, DDT, was used extensively worldwide starting in 1939 and was banned in the United States in 1973. The daughter compound, DDE, may result from aerobic degradation, abiotic dehydrochlorination, or photochemical decomposition. DDE has also occurred as a contaminant in commercial-grade DDT. The p,p'-DDE isomer is more biologically active than the o,p-DDE, with a reported half-life of -5.7 years. However, when DDT was repeatedly applied to the soil, the DDE concentration may remain unchanged for more than 20 yr. Remediation of DDE-contaminated soil and water may be done by several techniques. Phytoremediation involves translocating DDT, DDD, and DDE from the soil into the plant, although some aquatic species (duckweed > elodea > parrot feather) can transform DDT into predominantly DDD with some DDE being formed. Of all the plants that can uptake DDE, Cucurbita pepo has been the most extensively studied, with translocation values approaching "hyperaccumulation" levels. Soil moisture, temperature, and plant density have all been documented as important factors in the uptake of DDE by Cucurbita pepo. Uptake may also be influenced positively by amendments such as biosurfactants, mycorrhizal inoculants, and low molecular weight organic acids (e.g., citric and oxalic acids). DDE microbial degradation by dehalogenases, dioxygenases, and hydrolases occurs under the proper conditions. Although several aerobic degradation pathways have been proposed, none has been fully verified. Very few aerobic pure cultures are capable of fully degrading DDE to CO2. Cometabolism of DDE by Pseudomonas sp., Alicaligens sp., and Terrabacter sp. grown on biphenyl has been reported; however, not all bacterial species that produce biphenyl dioxygenase degraded DDE. Arsenic and copper inhibit DDE degradation by aerobic microorganisms. Similarly, metal chelates such as EDTA inhibit the breakdown of DDE by the extracellular lignolytic enzymes produced by white rot fungi. The addition of adjutants such as sodium ion, surfactants, and cellulose increased the rate of DDT aerobic or anaerobic degradation but did little to enhance the rate of DDE disappearance under anaerobic conditions. Only in the past decade has it been demonstrated that DDE can undergo reductive dechlorination under methanogenic and sulfidogenic conditions to form the degradation product DDMU, 1-chloro-2,2'-bis-(4'-chlorophenyl)ethane. The only pure culture reported to degrade DDE under anaerobic conditions was the denitrifier Alcaligens denitrificans. The degradation of DDE by this bacterium was enhanced by glucose, whereas biphenyl fumes had no effect. Abiotic remediation by DDE volatilization was enhanced by flooding and irrigation and deepplowing inhibited the volatilization. The use of zero-valent iron and surfactants in flooded soils enhanced DDT degradation but did not significantly alter the rate of DDE removal. Other catalysts (palladized magnesium, palladium on carbon, and nickel/aluminum alloys) degraded DDT and its metabolites, including DDE. However, these systems are often biphasic or involve explosive gases or both. Safer abiotic alternatives use UV light with titanium oxide or visible light with methylene green to degrade DDT, DDD, and DDE in aqueous or mixed solvent systems. Remediation and degradation of DDE in soil and water by phytoextraction, aerobic and anaerobic microorganisms, or abiotic methods can be accomplished. However, success has been limited, and great care must be taken that the method does not transfer the contaminants to another locale (by volatilization, deep plowing, erosion, or runoff) or to another species (by ingestion of accumulating plants or contaminated water). Although the remediation of DDT-, DDD-, and DDE-contaminated soil and water is beset with myriad problems, there remain many open avenues of research.

The Role of Tomato WRKY Genes in Plant Responses to Combined Abiotic and Biotic Stresses

PubMed Central

Bai, Yuling; Sunarti, Sri; Kissoudis, Christos; Visser, Richard G. F.; van der Linden, C. G.

2018-01-01

In the field, plants constantly face a plethora of abiotic and biotic stresses that can impart detrimental effects on plants. In response to multiple stresses, plants can rapidly reprogram their transcriptome through a tightly regulated and highly dynamic regulatory network where WRKY transcription factors can act as activators or repressors. WRKY transcription factors have diverse biological functions in plants, but most notably are key players in plant responses to biotic and abiotic stresses. In tomato there are 83 WRKY genes identified. Here we review recent progress on functions of these tomato WRKY genes and their homologs in other plant species, such as Arabidopsis and rice, with a special focus on their involvement in responses to abiotic and biotic stresses. In particular, we highlight WRKY genes that play a role in plant responses to a combination of abiotic and biotic stresses.

Roles of melatonin in abiotic stress resistance in plants.

PubMed

Zhang, Na; Sun, Qianqian; Zhang, Haijun; Cao, Yunyun; Weeda, Sarah; Ren, Shuxin; Guo, Yang-Dong

2015-02-01

In recent years melatonin has emerged as a research highlight in plant studies. Melatonin has different functions in many aspects of plant growth and development. The most frequently mentioned functions of melatonin are related to abiotic stresses such as drought, radiation, extreme temperature, and chemical stresses. This review mainly focuses on the regulatory effects of melatonin when plants face harsh environmental conditions. Evidence indicates that environmental stress can increase the level of endogenous melatonin in plants. Overexpression of the melatonin biosynthetic genes elevates melatonin levels in transgenic plants. The transgenic plants show enhanced tolerance to abiotic stresses. Exogenously applied melatonin can also improve the ability of plants to tolerate abiotic stresses. The mechanisms by which melatonin alleviates abiotic stresses are discussed. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Designing cooperatively folded abiotic uni- and multimolecular helix bundles

NASA Astrophysics Data System (ADS)

de, Soumen; Chi, Bo; Granier, Thierry; Qi, Ting; Maurizot, Victor; Huc, Ivan

2018-01-01

Abiotic foldamers, that is foldamers that have backbones chemically remote from peptidic and nucleotidic skeletons, may give access to shapes and functions different to those of peptides and nucleotides. However, design methodologies towards abiotic tertiary and quaternary structures are yet to be developed. Here we report rationally designed interactional patterns to guide the folding and assembly of abiotic helix bundles. Computational design facilitated the introduction of hydrogen-bonding functionalities at defined locations on the aromatic amide backbones that promote cooperative folding into helix-turn-helix motifs in organic solvents. The hydrogen-bond-directed aggregation of helices not linked by a turn unit produced several thermodynamically and kinetically stable homochiral dimeric and trimeric bundles with structures that are distinct from the designed helix-turn-helix. Relative helix orientation within the bundles may be changed from parallel to tilted on subtle solvent variations. Altogether, these results prefigure the richness and uniqueness of abiotic tertiary structure behaviour.

Assessment of the Potential Role of Streptomyces in Cave Moonmilk Formation

PubMed Central

Maciejewska, Marta; Adam, Delphine; Naômé, Aymeric; Martinet, Loïc; Tenconi, Elodie; Całusińska, Magdalena; Delfosse, Philippe; Hanikenne, Marc; Baurain, Denis; Compère, Philippe; Carnol, Monique; Barton, Hazel A.; Rigali, Sébastien

2017-01-01

Moonmilk is a karstic speleothem mainly composed of fine calcium carbonate crystals (CaCO3) with different textures ranging from pasty to hard, in which the contribution of biotic rock-building processes is presumed to involve indigenous microorganisms. The real microbial input in the genesis of moonmilk is difficult to assess leading to controversial hypotheses explaining the origins and the mechanisms (biotic vs. abiotic) involved. In this work, we undertook a comprehensive approach in order to assess the potential role of filamentous bacteria, particularly a collection of moonmilk-originating Streptomyces, in the genesis of this speleothem. Scanning electron microscopy (SEM) confirmed that indigenous filamentous bacteria could indeed participate in moonmilk development by serving as nucleation sites for CaCO3 deposition. The metabolic activities involved in CaCO3 transformation were furthermore assessed in vitro among the collection of moonmilk Streptomyces, which revealed that peptides/amino acids ammonification, and to a lesser extend ureolysis, could be privileged metabolic pathways participating in carbonate precipitation by increasing the pH of the bacterial environment. Additionally, in silico search for the genes involved in biomineralization processes including ureolysis, dissimilatory nitrate reduction to ammonia, active calcium ion transport, and reversible hydration of CO2 allowed to identify genetic predispositions for carbonate precipitation in Streptomyces. Finally, their biomineralization abilities were confirmed by environmental SEM, which allowed to visualize the formation of abundant mineral deposits under laboratory conditions. Overall, our study provides novel evidences that filamentous Actinobacteria could be key protagonists in the genesis of moonmilk through a wide spectrum of biomineralization processes. PMID:28706508

Contrasting influence of NADPH and a NADPH-regenerating system on the metabolism of carbonyl-containing compounds in hepatic microsomes.

PubMed

Mazur, Christopher S; Kenneke, John F; Goldsmith, Michael-Rock; Brown, Cather

2009-09-01

Carbonyl containing xenobiotics may be susceptible to NADPH-dependent cytochrome P450 (P450) and carbonyl-reduction reactions. In vitro hepatic microsome assays are routinely supplied NADPH either by direct addition of NADPH or via an NADPH-regenerating system (NRS). In contrast to oxidative P450 transformations, which occur on the periphery of a microsome vesicle, intraluminal carbonyl reduction depends on transport of cofactors across the endoplasmic reticulum (ER) membrane into the lumen. Glucose 6-phosphate, a natural cofactor and component of the NRS matrix, is readily transported across the ER membrane and facilitates intraluminal NADPH production, whereas direct addition of NADPH has limited access to the lumen. In this study, we compared the effects of direct addition of NADPH and use of an NRS on the P450-mediated transformation of propiconazole and 11 beta-hydroxysteroid dehydrogenase type 1 (HSD1) carbonyl reduction of cortisone and the xenobiotic triadimefon in hepatic microsomes. Our results demonstrate that the use of NADPH rather than NRS can underestimate the kinetic rates of intraluminal carbonyl reduction, whereas P450-mediated transformations were unaffected. Therefore, in vitro depletion rates measured for a carbonyl-containing xenobiotic susceptible to both intraluminal carbonyl reduction and P450 processes may not be properly assessed with direct addition of NADPH. In addition, we used in silico predictions as follows: 1) to show that 11 beta-HSD1 carbonyl reduction was energetically more favorable than oxidative P450 transformation; and 2) to calculate chemical binding score and the distance between the carbonyl group and the hydride to be transferred by NADPH to identify other 11 beta-HSD1 substrates for which reaction kinetics may be underestimated by direct addition of NADPH.

Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits

NASA Astrophysics Data System (ADS)

Bhattacharyya, Amrita; Campbell, Kate M.; Kelly, Shelly D.; Roebbert, Yvonne; Weyer, Stefan; Bernier-Latmani, Rizlan; Borch, Thomas

2017-06-01

Historically, it is believed that crystalline uraninite, produced via the abiotic reduction of hexavalent uranium (U(VI)) is the dominant reduced U species formed in low-temperature uranium roll-front ore deposits. Here we show that non-crystalline U(IV) generated through biologically mediated U(VI) reduction is the predominant U(IV) species in an undisturbed U roll-front ore deposit in Wyoming, USA. Characterization of U species revealed that the majority (~58-89%) of U is bound as U(IV) to C-containing organic functional groups or inorganic carbonate, while uraninite and U(VI) represent only minor components. The uranium deposit exhibited mostly 238U-enriched isotope signatures, consistent with largely biotic reduction of U(VI) to U(IV). This finding implies that biogenic processes are more important to uranium ore genesis than previously understood. The predominance of a relatively labile form of U(IV) also provides an opportunity for a more economical and environmentally benign mining process, as well as the design of more effective post-mining restoration strategies and human health-risk assessment.

Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits

PubMed Central

Bhattacharyya, Amrita; Campbell, Kate M.; Kelly, Shelly D.; Roebbert, Yvonne; Weyer, Stefan; Bernier-Latmani, Rizlan; Borch, Thomas

2017-01-01

Historically, it is believed that crystalline uraninite, produced via the abiotic reduction of hexavalent uranium (U(VI)) is the dominant reduced U species formed in low-temperature uranium roll-front ore deposits. Here we show that non-crystalline U(IV) generated through biologically mediated U(VI) reduction is the predominant U(IV) species in an undisturbed U roll-front ore deposit in Wyoming, USA. Characterization of U species revealed that the majority (∼58-89%) of U is bound as U(IV) to C-containing organic functional groups or inorganic carbonate, while uraninite and U(VI) represent only minor components. The uranium deposit exhibited mostly 238U-enriched isotope signatures, consistent with largely biotic reduction of U(VI) to U(IV). This finding implies that biogenic processes are more important to uranium ore genesis than previously understood. The predominance of a relatively labile form of U(IV) also provides an opportunity for a more economical and environmentally benign mining process, as well as the design of more effective post-mining restoration strategies and human health-risk assessment. PMID:28569759

Biogenic non-crystalline U (IV) revealed as major component in uranium ore deposits

DOE PAGES

Bhattacharyya, Amrita; Campbell, Kate M.; Kelly, Shelly D.; ...

2017-06-01

Historically, it is believed that crystalline uraninite, produced via the abiotic reduction of hexavalent uranium (U (VI)) is the dominant reduced U species formed in low-temperature uranium roll-front ore deposits. Here we show that non-crystalline U (IV) generated through biologically mediated U (VI) reduction is the predominant U (IV) species in an undisturbed U roll-front ore deposit in Wyoming, USA. Characterization of U species revealed that the majority (~58-89%) of U is bound as U (IV) to C-containing organic functional groups or inorganic carbonate, while uraninite and U (VI) represent only minor components. The uranium deposit exhibited mostly 238U-enriched isotopemore » signatures, consistent with largely biotic reduction of U (VI) to U (IV). This finding implies that biogenic processes are more important to uranium ore genesis than previously understood. The predominance of a relatively labile form of U (IV) also provides an opportunity for a more economical and environmentally benign mining process, as well as the design of more effective post-mining restoration strategies and human health-risk assessment.« less

Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits.

PubMed

Bhattacharyya, Amrita; Campbell, Kate M; Kelly, Shelly D; Roebbert, Yvonne; Weyer, Stefan; Bernier-Latmani, Rizlan; Borch, Thomas

2017-06-01

Historically, it is believed that crystalline uraninite, produced via the abiotic reduction of hexavalent uranium (U (VI) ) is the dominant reduced U species formed in low-temperature uranium roll-front ore deposits. Here we show that non-crystalline U (IV)  generated through biologically mediated U (VI)  reduction is the predominant U (IV)  species in an undisturbed U roll-front ore deposit in Wyoming, USA. Characterization of U species revealed that the majority (∼58-89%) of U is bound as U (IV) to C-containing organic functional groups or inorganic carbonate, while uraninite and U (VI) represent only minor components. The uranium deposit exhibited mostly 238 U-enriched isotope signatures, consistent with largely biotic reduction of U (VI) to U (IV) . This finding implies that biogenic processes are more important to uranium ore genesis than previously understood. The predominance of a relatively labile form of U (IV) also provides an opportunity for a more economical and environmentally benign mining process, as well as the design of more effective post-mining restoration strategies and human health-risk assessment.

Biogenic non-crystalline U (IV) revealed as major component in uranium ore deposits

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

Bhattacharyya, Amrita; Campbell, Kate M.; Kelly, Shelly D.

Historically, it is believed that crystalline uraninite, produced via the abiotic reduction of hexavalent uranium (U (VI)) is the dominant reduced U species formed in low-temperature uranium roll-front ore deposits. Here we show that non-crystalline U (IV) generated through biologically mediated U (VI) reduction is the predominant U (IV) species in an undisturbed U roll-front ore deposit in Wyoming, USA. Characterization of U species revealed that the majority (~58-89%) of U is bound as U (IV) to C-containing organic functional groups or inorganic carbonate, while uraninite and U (VI) represent only minor components. The uranium deposit exhibited mostly 238U-enriched isotopemore » signatures, consistent with largely biotic reduction of U (VI) to U (IV). This finding implies that biogenic processes are more important to uranium ore genesis than previously understood. The predominance of a relatively labile form of U (IV) also provides an opportunity for a more economical and environmentally benign mining process, as well as the design of more effective post-mining restoration strategies and human health-risk assessment.« less

Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits

USGS Publications Warehouse

Bhattacharyya, Amrita; Campbell, Kate M.; Kelly, Shelly; Roebbert, Yvonne; Weyer, Stefan; Bernier-Latmani, Rizlan; Borch, Thomas

2017-01-01

Historically, it is believed that crystalline uraninite, produced via the abiotic reduction of hexavalent uranium (U(VI)) is the dominant reduced U species formed in low-temperature uranium roll-front ore deposits. Here we show that non-crystalline U(IV) generated through biologically mediated U(VI) reduction is the predominant U(IV) species in an undisturbed U roll-front ore deposit in Wyoming, USA. Characterization of U species revealed that the majority (∼58-89%) of U is bound as U(IV)to C-containing organic functional groups or inorganic carbonate, while uraninite and U(VI) represent only minor components. The uranium deposit exhibited mostly 238U-enriched isotope signatures, consistent with largely biotic reduction of U(VI) to U(IV). This finding implies that biogenic processes are more important to uranium ore genesis than previously understood. The predominance of a relatively labile form of U(IV) also provides an opportunity for a more economical and environmentally benign mining process, as well as the design of more effective post-mining restoration strategies and human health-risk assessment.

Suitability of non-lethal marker and marker-free systems for development of transgenic crop plants: present status and future prospects.

PubMed

Manimaran, P; Ramkumar, G; Sakthivel, K; Sundaram, R M; Madhav, M S; Balachandran, S M

2011-01-01

Genetically modified crops are one of the prudent options for enhancing the production and productivity of crop plants by safeguarding from the losses due to biotic and abiotic stresses. Agrobacterium-mediated and biolistic transformation methods are used to develop transgenic crop plants in which selectable marker genes (SMG) are generally deployed to identify 'true' transformants. The commonly used SMG obtained from prokaryotic sources when employed in transgenic plants pose risks due to their lethal nature during selection process. In the recent past, some non-lethal SMGs have been identified and used for selection of transformants with increased precision and high selection efficiency. Considering the concerns related to bio-safety of the environment, it is desirable to remove the SMG in order to maximize the commercial success through wide adoption and public acceptance of genetically modified (GM) food crops. In this review, we examine the availability, and the suitability of wide range of non-lethal selection markers and elimination of SMG methods to develop marker-free transgenics for achieving global food security. As the strategies for marker-free plants are still in proof-of-concept stage, adaptation of new genomics tools for identification of novel non-lethal marker systems and its application for developing marker-free transgenics would further strengthen the crop improvement program. Copyright © 2011 Elsevier Inc. All rights reserved.

Hydrologic, abiotic and biotic interactions: plant density, windspeed, leaf size and groundwater all affect oak water use efficiency

Treesearch

Darin J. Law; Deborah M. Finch

2011-01-01

Plant water use in drylands can be complex due to variation in hydrologic, abiotic and biotic factors, particularly near ephemeral or intermittent streams. Plant use of groundwater may be important but is usually uncertain. Disturbances like fire contribute to complex spatiotemporal heterogeneity. Improved understanding of how such hydrologic, abiotic, and biotic...

Area and percent of forest affected by abiotic agents beyond reference conditions

Treesearch

2012-01-01

Criterion 3, Indicator 16, of the Montréal Process Criteria and Indicators for the Conservation and Sustainable Management of Temperate and Boreal Forests was designed to assess the impact of abiotic agents upon forests (Montréal Process Working Group 2007). Various abiotic agents, both natural and human-induced, can change forest structure and species composition....

Photochemically assisted fast abiotic oxidation of manganese and formation of δ-MnO 2 nanosheets in nitrate solution

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

Jung, Haesung; Chadha, Tandeep S.; Kim, Doyoon

This study introduces a new and previously unconsidered fast abiotic formation of Mn(IV) oxides. We report photochemically assisted fast abiotic oxidation of Mn 2+ (aq) to Mn(IV) (s) by superoxide radicals generated from nitrate photolysis. This photochemical pathway generates randomly stacked layered birnessite (δ-MnO 2) nanosheets.

Can plant-natural enemy communication withstand disruption by biotic and abiotic factors?

PubMed

Clavijo McCormick, Andrea

2016-12-01

The attraction of natural enemies towards herbivore-induced plant volatiles is a well-documented phenomenon. However, the majority of published studies are carried under optimal water and nutrient regimes and with just one herbivore. But what happens when additional levels of ecological complexity are added? Does the presence of a second herbivore, microorganisms, and abiotic stress interfere with plant-natural enemy communication? or is communication stable enough to withstand disruption by additional biotic and abiotic factors?Investigating the effects of these additional levels of ecological complexity is key to understanding the stability of tritrophic interactions in natural ecosystems and may aid to forecast the impact of environmental disturbances on these, especially in climate change scenarios, which are often associated with modifications in plant and arthropod species distribution and increased levels of abiotic stress.This review explores the literature on natural enemy attraction to herbivore-induced volatiles when, besides herbivory, plants are challenged by additional biotic and abiotic factors.The aim of this review was to establish the impact of different biotic and abiotic factors on plant-natural enemy communication and to highlight critical aspects to guide future research efforts.

Analysis of Cell Wall-Related Genes in Organs of Medicago sativa L. under Different Abiotic Stresses.

PubMed

Behr, Marc; Legay, Sylvain; Hausman, Jean-Francois; Guerriero, Gea

2015-07-16

Abiotic constraints are a source of concern in agriculture, because they can have a strong impact on plant growth and development, thereby affecting crop yield. The response of plants to abiotic constraints varies depending on the type of stress, on the species and on the organs. Although many studies have addressed different aspects of the plant response to abiotic stresses, only a handful has focused on the role of the cell wall. A targeted approach has been used here to study the expression of cell wall-related genes in different organs of alfalfa plants subjected for four days to three different abiotic stress treatments, namely salt, cold and heat stress. Genes involved in different steps of cell wall formation (cellulose biosynthesis, monolignol biosynthesis and polymerization) have been analyzed in different organs of Medicago sativa L. Prior to this analysis, an in silico classification of dirigent/dirigent-like proteins and class III peroxidases has been performed in Medicago truncatula and M. sativa. The final goal of this study is to infer and compare the expression patterns of cell wall-related genes in response to different abiotic stressors in the organs of an important legume crop.

Analysis of Cell Wall-Related Genes in Organs of Medicago sativa L. under Different Abiotic Stresses

PubMed Central

Behr, Marc; Legay, Sylvain; Hausman, Jean-Francois; Guerriero, Gea

2015-01-01

Abiotic constraints are a source of concern in agriculture, because they can have a strong impact on plant growth and development, thereby affecting crop yield. The response of plants to abiotic constraints varies depending on the type of stress, on the species and on the organs. Although many studies have addressed different aspects of the plant response to abiotic stresses, only a handful has focused on the role of the cell wall. A targeted approach has been used here to study the expression of cell wall-related genes in different organs of alfalfa plants subjected for four days to three different abiotic stress treatments, namely salt, cold and heat stress. Genes involved in different steps of cell wall formation (cellulose biosynthesis, monolignol biosynthesis and polymerization) have been analyzed in different organs of Medicago sativa L. Prior to this analysis, an in silico classification of dirigent/dirigent-like proteins and class III peroxidases has been performed in Medicago truncatula and M. sativa. The final goal of this study is to infer and compare the expression patterns of cell wall-related genes in response to different abiotic stressors in the organs of an important legume crop. PMID:26193255

Interaction between Digestive Strategy and Niche Specialization Predicts Speciation Rates across Herbivorous Mammals.

PubMed

Tran, Lucy A P

2016-04-01

Biotic and abiotic factors often are treated as mutually exclusive drivers of diversification processes. In this framework, ecological specialists are expected to have higher speciation rates than generalists if abiotic factors are the primary controls on species diversity but lower rates if biotic interactions are more important. Speciation rate is therefore predicted to positively correlate with ecological specialization in the purely abiotic model but negatively correlate in the biotic model. In this study, I show that the positive relationship between ecological specialization and speciation expected from the purely abiotic model is recovered only when a species-specific trait, digestive strategy, is modeled in the terrestrial, herbivorous mammals (Mammalia). This result suggests a more nuanced model in which the response of specialized lineages to abiotic factors is dependent on a biological trait. I also demonstrate that the effect of digestive strategy on the ecological specialization-speciation rate relationship is not due to a difference in either the degree of ecological specialization or the speciation rate between foregut- and hindgut-fermenting mammals. Together, these findings suggest that a biological trait, alongside historical abiotic events, played an important role in shaping mammal speciation at long temporal and large geographic scales.

Managing and Transforming Waste Streams – A Tool for Communities

EPA Pesticide Factsheets

The Managing and Transforming Waste Streams Tool features 100 policy and program options communities can pursue to increase rates of recycling, composting, waste reduction, and materials reuse across waste stream generators.

Centrifugal distortion coefficients of asymmetric-top molecules: Reduction of the octic terms of the rotational Hamiltonian

NASA Astrophysics Data System (ADS)

Ramachandra Rao, Ch. V. S.

1983-11-01

The rotational Hamiltonian of an asymmetric-top molecule in its standard form, containing terms up to eighth degree in the components of the total angular momentum, is transformed by a unitary transformation with parameters Spqr to a reduced Hamiltonian so as to avoid the indeterminacies inherent in fitting the complete Hamiltonian to observed energy levels. Expressions are given for the nine determinable combinations of octic constants Θ' i ( i = 1 to 9) which are invariant under the unitary transformation. A method of reduction suitable for energy calculations by matrix diagonalization is considered. The relations between the coefficients of the transformed Hamiltonian, for suitable choice of the parameters Spqr, and those of the reduced Hamiltonian are given. This enables the determination of the nine octic constants Θ' i in terms of the experimental constants.

Landsat D Thematic Mapper image dimensionality reduction and geometric correction accuracy

NASA Technical Reports Server (NTRS)

Ford, G. E.

1986-01-01

To characterize and quantify the performance of the Landsat thematic mapper (TM), techniques for dimensionality reduction by linear transformation have been studied and evaluated and the accuracy of the correction of geometric errors in TM images analyzed. Theoretical evaluations and comparisons for existing methods for the design of linear transformation for dimensionality reduction are presented. These methods include the discrete Karhunen Loeve (KL) expansion, Multiple Discriminant Analysis (MDA), Thematic Mapper (TM)-Tasseled Cap Linear Transformation and Singular Value Decomposition (SVD). A unified approach to these design problems is presented in which each method involves optimizing an objective function with respect to the linear transformation matrix. From these studies, four modified methods are proposed. They are referred to as the Space Variant Linear Transformation, the KL Transform-MDA hybrid method, and the First and Second Version of the Weighted MDA method. The modifications involve the assignment of weights to classes to achieve improvements in the class conditional probability of error for classes with high weights. Experimental evaluations of the existing and proposed methods have been performed using the six reflective bands of the TM data. It is shown that in terms of probability of classification error and the percentage of the cumulative eigenvalues, the six reflective bands of the TM data require only a three dimensional feature space. It is shown experimentally as well that for the proposed methods, the classes with high weights have improvements in class conditional probability of error estimates as expected.

Radar cross-section reduction based on an iterative fast Fourier transform optimized metasurface

NASA Astrophysics Data System (ADS)

Song, Yi-Chuan; Ding, Jun; Guo, Chen-Jiang; Ren, Yu-Hui; Zhang, Jia-Kai

2016-07-01

A novel polarization insensitive metasurface with over 25 dB monostatic radar cross-section (RCS) reduction is introduced. The proposed metasurface is comprised of carefully arranged unit cells with spatially varied dimension, which enables approximate uniform diffusion of incoming electromagnetic (EM) energy and reduces the threat from bistatic radar system. An iterative fast Fourier transform (FFT) method for conventional antenna array pattern synthesis is innovatively applied to find the best unit cell geometry parameter arrangement. Finally, a metasurface sample is fabricated and tested to validate RCS reduction behavior predicted by full wave simulation software Ansys HFSSTM and marvelous agreement is observed.

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

Yung, M. M.; Cheah, S.; Magrini-Bair, K.

Sulfur K-edge XANES identified transformation of sulfides to sulfates during combined steam and air regeneration on a Ni/Mg/K/Al2O3 catalyst used to condition biomass-derived syngas. This catalyst was tested over multiple reaction/regeneration/reduction cycles. Postreaction catalysts showed the presence of sulfides on H2S-poisoned sites. Although H2S was observed to leave the catalyst bed during regeneration, sulfur remained on the catalyst, and a transformation from sulfides to sulfates was observed. Following the oxidative regeneration, the subsequent H2 reduction led to a partial reduction of sulfates back to sulfides, indicating the difficulty and sensitivity in achieving complete sulfur removal during regeneration for biomass-conditioning catalysts.

Induction of infectious petunia vein clearing (pararetro) virus from endogenous provirus in petunia

PubMed Central

Richert-Pöggeler, Katja R.; Noreen, Faiza; Schwarzacher, Trude; Harper, Glyn; Hohn, Thomas

2003-01-01

Infection by an endogenous pararetrovirus using forms of both episomal and chromosomal origin has been demonstrated and characterized, together with evidence that petunia vein clearing virus (PVCV) is a constituent of the Petunia hybrida genome. Our findings allow comparative and direct analysis of horizontally and vertically transmitted virus forms and demonstrate their infectivity using biolistic transformation of a provirus-free petunia species. Some integrants within the genome of P.hybrida are arranged in tandem, allowing direct release of virus by transcription. In addition to known inducers of endogenous pararetroviruses, such as genome hybridization, tissue culture and abiotic stresses, we observed activation of PVCV after wounding. Our data also support the hypothesis that the host plant uses DNA methylation to control the endogenous pararetrovirus. PMID:12970195

Analysis of Proportional Integral and Optimized Proportional Integral Controllers for Resistance Spot Welding System (RSWS) - A Performance Perspective

NASA Astrophysics Data System (ADS)

Rama Subbanna, S.; Suryakalavathi, M., Dr.

2017-08-01

This paper is an attempt to accomplish a performance analysis of the different control techniques on spikes reduction method applied on the medium frequency transformer based DC spot welding system. Spike reduction is an important factor to be considered while spot welding systems are concerned. During normal RSWS operation welding transformer’s magnetic core can become saturated due to the unbalanced resistances of both transformer secondary windings and different characteristics of output rectifier diodes, which causes current spikes and over-current protection switch-off of the entire system. The current control technique is a piecewise linear control technique that is inspired from the DC-DC converter control algorithms to register a novel spike reduction method in the MFDC spot welding applications. Two controllers that were used for the spike reduction portion of the overall applications involve the traditional PI controller and Optimized PI controller. Care is taken such that the current control technique would maintain a reduced spikes in the primary current of the transformer while it reduces the Total Harmonic Distortion. The performance parameter that is involved in the spikes reduction technique is the THD, Percentage of current spike reduction for both techniques. Matlab/SimulinkTM based simulation is carried out for the MFDC RSWS with KW and results are tabulated for the PI and Optimized PI controllers and a tradeoff analysis is carried out.

Target oriented dimensionality reduction of hyperspectral data by Kernel Fukunaga-Koontz Transform

NASA Astrophysics Data System (ADS)

Binol, Hamidullah; Ochilov, Shuhrat; Alam, Mohammad S.; Bal, Abdullah

2017-02-01

Principal component analysis (PCA) is a popular technique in remote sensing for dimensionality reduction. While PCA is suitable for data compression, it is not necessarily an optimal technique for feature extraction, particularly when the features are exploited in supervised learning applications (Cheriyadat and Bruce, 2003) [1]. Preserving features belonging to the target is very crucial to the performance of target detection/recognition techniques. Fukunaga-Koontz Transform (FKT) based supervised band reduction technique can be used to provide this requirement. FKT achieves feature selection by transforming into a new space in where feature classes have complimentary eigenvectors. Analysis of these eigenvectors under two classes, target and background clutter, can be utilized for target oriented band reduction since each basis functions best represent target class while carrying least information of the background class. By selecting few eigenvectors which are the most relevant to the target class, dimension of hyperspectral data can be reduced and thus, it presents significant advantages for near real time target detection applications. The nonlinear properties of the data can be extracted by kernel approach which provides better target features. Thus, we propose constructing kernel FKT (KFKT) to present target oriented band reduction. The performance of the proposed KFKT based target oriented dimensionality reduction algorithm has been tested employing two real-world hyperspectral data and results have been reported consequently.

Elucidating the Role of Electron Shuttles in Reductive Transformations in Anaerobic Sediments

EPA Science Inventory

Model studies have demonstrated that electron shuttles (ES) such as dissolved organic matter (DOM) can participate in the reduction of organic contaminants; however, much uncertainty exists concerning the significance of this solution phase pathway for contaminant reduction in na...

Continuous-flow column study of reductive dehalogenation of PCE upon bioaugmentation with the Evanite enrichment culture

NASA Astrophysics Data System (ADS)

Azizian, Mohammad F.; Behrens, Sebastian; Sabalowsky, Andrew; Dolan, Mark E.; Spormann, Alfred M.; Semprini, Lewis

2008-08-01

A continuous-flow anaerobic column experiment was conducted to evaluate the reductive dechlorination of tetrachloroethene (PCE) in Hanford aquifer material after bioaugmentation with the Evanite (EV) culture. An influent PCE concentration of 0.09 mM was transformed to vinyl chloride (VC) and ethene (ETH) within a hydraulic residence time of 1.3 days. The experimental breakthrough curves were described by the one-dimensional two-site-nonequilibrium transport model. PCE dechlorination was observed after bioaugmentation and after the lactate concentration was increased from 0.35 to 0.67 mM. At the onset of reductive dehalogenation, cis-dichloroethene (c-DCE) concentrations in the column effluent exceeded the influent PCE concentration indicating enhanced PCE desorption and transformation. When the lactate concentration was increased to 1.34 mM, c-DCE reduction to vinyl chloride (VC) and ethene (ETH) occurred. Spatial rates of PCE and VC transformation were determined in batch-incubated microcosms constructed with aquifer samples obtained from the column. PCE transformation rates were highest in the first 5 cm from the column inlet and decreased towards the column effluent. Dehalococcoides cell numbers dropped from ˜ 73.5% of the total Bacterial population in the original inocula, to about 0.5% to 4% throughout the column. The results were consistent with estimates of electron donor utilization, with 4% going towards dehalogenation reactions.

Polyamines and abiotic stress in plants: a complex relationship Frontiers in Plant Science

Treesearch

Rakesh Minocha; Rajtilak Majumdar; Subhash C. Minocha

2014-01-01

The physiological relationship between abiotic stress in plants and polyamines was reported more than 40 years ago. Ever since there has been a debate as to whether increased polyamines protect plants against abiotic stress (e.g., due to their ability to deal with oxidative radicals) or cause damage to them (perhaps due to hydrogen peroxide produced by their catabolism...

The importance of disturbance by fire and other abiotic and biotic factors in driving cheatgrass invasion varies based on invasion stage

Treesearch

Becky K. Kerns; Michelle A. Day

2017-01-01

Disturbances create fluctuations in resource availability that alter abiotic and biotic constraints. Exotic invader response may be due to multiple factors related to disturbance regimes and complex interactions between other small- and largescale abiotic and biotic processes that may vary across invasion stages. We explore how cheatgrass responds to both frequency and...

High potential of adhesion to biotic and abiotic surfaces by opportunistic Staphylococcus aureus strains isolated from orthodontic appliances.

PubMed

Merghni, Abderrahmen; Ben Nejma, Mouna; Dallel, Ines; Tobji, Samir; Ben Amor, Adel; Janel, Sébastien; Lafont, Frank; Aouni, Mahjoub; Mastouri, Maha

2016-02-01

Orthodontic and other oral appliances act as reservoir of opportunistic pathogens that can easily become resistant to antibiotics and cause systemic infections. The aim of this study was to investigate the ability of Staphylococcus aureus strains isolated from healthy patients with orthodontic appliances, to adhere to biotic (HeLa cells) and abiotic surfaces (polystyrene and dental alloy). Adhesive ability to polystyrene was tested by crystal violet staining and quantitative biofilm production on dental alloy surfaces was evaluated by MTT reduction assay. In addition, the presence of icaA and icaD genes was achieved by polymerase chain reaction (PCR). Qualitative biofilm production revealed that 70.6% of strains were slime producers. The metabolic activity of S. aureus biofilms on dental alloy surfaces was high and did not differ between tested strains. Moreover, all the isolates were adhesive to HeLa cells and 94% of them harbor icaA and icaD genes. Considerable adhesion and internalization capacity to the epithelial HeLa cells and strong biofilm production abilities together, with a high genotypic expression of icaA/icaD genes are an important equipment of S. aureus to colonize orthodontic appliances and eventually to disseminate towards other body areas. Copyright © 2015 Elsevier Ltd. All rights reserved.

The effect of consumer pressure and abiotic stress on positive plant interactions are mediated by extreme climatic events.

PubMed

Filazzola, Alessandro; Liczner, Amanda Rae; Westphal, Michael; Lortie, Christopher J

2018-01-01

Environmental extremes resulting from a changing climate can have profound implications for plant interactions in desert communities. Positive interactions can buffer plant communities from abiotic stress and consumer pressure caused by climatic extremes, but limited research has explored this empirically. We tested the hypothesis that the mechanism of shrub facilitation on an annual plant community can change with precipitation extremes in deserts. During years of extreme drought and above-average rainfall in a desert, we measured plant interactions and biomass while manipulating a soil moisture gradient and reducing consumer pressure. Shrubs facilitated the annual plant community at all levels of soil moisture through reductions in microclimatic stress in both years and herbivore protection in the wet year only. Shrub facilitation and the high rainfall year contributed to the dominance of a competitive annual species in the plant community. Precipitation patterns in deserts determine the magnitude and type of facilitation mechanisms. Moreover, shrub facilitation mediates the interspecific competition within the associated annual community between years with different rainfall amounts. Examining multiple drivers during extreme climate events is a challenging area of research, but it is a necessary consideration given forecasts predicting that these events will increase in frequency and magnitude. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

DEAR1, a transcriptional repressor of DREB protein that mediates plant defense and freezing stress responses in Arabidopsis.

PubMed

Tsutsui, Tomokazu; Kato, Wataru; Asada, Yutaka; Sako, Kaori; Sato, Takeo; Sonoda, Yutaka; Kidokoro, Satoshi; Yamaguchi-Shinozaki, Kazuko; Tamaoki, Masanori; Arakawa, Keita; Ichikawa, Takanari; Nakazawa, Miki; Seki, Motoaki; Shinozaki, Kazuo; Matsui, Minami; Ikeda, Akira; Yamaguchi, Junji

2009-11-01

Plants have evolved intricate mechanisms to respond and adapt to a wide variety of biotic and abiotic stresses in their environment. The Arabidopsis DEAR1 (DREB and EAR motif protein 1; At3g50260) gene encodes a protein containing significant homology to the DREB1/CBF (dehydration-responsive element binding protein 1/C-repeat binding factor) domain and the EAR (ethylene response factor-associated amphiphilic repression) motif. We show here that DEAR1 mRNA accumulates in response to both pathogen infection and cold treatment. Transgenic Arabidopsis overexpressing DEAR1 (DEAR1ox) showed a dwarf phenotype and lesion-like cell death, together with constitutive expression of PR genes and accumulation of salicylic acid. DEAR1ox also showed more limited P. syringae pathogen growth compared to wild-type, consistent with an activated defense phenotype. In addition, transient expression experiments revealed that the DEAR1 protein represses DRE/CRT (dehydration-responsive element/C-repeat)-dependent transcription, which is regulated by low temperature. Furthermore, the induction of DREB1/CBF family genes by cold treatment was suppressed in DEAR1ox, leading to a reduction in freezing tolerance. These results suggest that DEAR1 has an upstream regulatory role in mediating crosstalk between signaling pathways for biotic and abiotic stress responses.

A comparison of orthogonal transformations for digital speech processing.

NASA Technical Reports Server (NTRS)

Campanella, S. J.; Robinson, G. S.

1971-01-01

Discrete forms of the Fourier, Hadamard, and Karhunen-Loeve transforms are examined for their capacity to reduce the bit rate necessary to transmit speech signals. To rate their effectiveness in accomplishing this goal the quantizing error (or noise) resulting for each transformation method at various bit rates is computed and compared with that for conventional companded PCM processing. Based on this comparison, it is found that Karhunen-Loeve provides a reduction in bit rate of 13.5 kbits/s, Fourier 10 kbits/s, and Hadamard 7.5 kbits/s as compared with the bit rate required for companded PCM. These bit-rate reductions are shown to be somewhat independent of the transmission bit rate.

A novel approach to Hough Transform for implementation in fast triggers

NASA Astrophysics Data System (ADS)

Pozzobon, Nicola; Montecassiano, Fabio; Zotto, Pierluigi

2016-10-01

Telescopes of position sensitive detectors are common layouts in charged particles tracking, and programmable logic devices, such as FPGAs, represent a viable choice for the real-time reconstruction of track segments in such detector arrays. A compact implementation of the Hough Transform for fast triggers in High Energy Physics, exploiting a parameter reduction method, is proposed, targeting the reduction of the needed storage or computing resources in current, or next future, state-of-the-art FPGA devices, while retaining high resolution over a wide range of track parameters. The proposed approach is compared to a Standard Hough Transform with particular emphasis on their application to muon detectors. In both cases, an original readout implementation is modeled.

Oxygen and sulfur isotope systematics of sulfate produced by bacterial and abiotic oxidation of pyrite

USGS Publications Warehouse

Balci, N.; Shanks, Wayne C.; Mayer, B.; Mandernack, K.W.

2007-01-01

To better understand reaction pathways of pyrite oxidation and biogeochemical controls on ??18O and ??34S values of the generated sulfate in acid mine drainage (AMD) and other natural environments, we conducted a series of pyrite oxidation experiments in the laboratory. Our biological and abiotic experiments were conducted under aerobic conditions by using O2 as an oxidizing agent and under anaerobic conditions by using dissolved Fe(III)aq as an oxidant with varying ??18OH2O values in the presence and absence of Acidithiobacillus ferrooxidans. In addition, aerobic biological experiments were designed as short- and long-term experiments where the final pH was controlled at ???2.7 and 2.2, respectively. Due to the slower kinetics of abiotic sulfide oxidation, the aerobic abiotic experiments were only conducted as long term with a final pH of ???2.7. The ??34SSO4 values from both the biological and abiotic anaerobic experiments indicated a small but significant sulfur isotope fractionation (???-0.7???) in contrast to no significant fractionation observed from any of the aerobic experiments. Relative percentages of the incorporation of water-derived oxygen and dissolved oxygen (O2) to sulfate were estimated, in addition to the oxygen isotope fractionation between sulfate and water, and dissolved oxygen. As expected, during the biological and abiotic anaerobic experiments all of the sulfate oxygen was derived from water. The percentage incorporation of water-derived oxygen into sulfate during the oxidation experiments by O2 varied with longer incubation and lower pH, but not due to the presence or absence of bacteria. These percentages were estimated as 85%, 92% and 87% from the short-term biological, long-term biological and abiotic control experiments, respectively. An oxygen isotope fractionation effect between sulfate and water (??18 OSO4 s(-) H2 O) of ???3.5??? was determined for the anaerobic (biological and abiotic) experiments. This measured ??18 OSO42 - s(-) H2 O value was then used to estimate the oxygen isotope fractionation effects (??18 OSO42 - s(-) O2) between sulfate and dissolved oxygen in the aerobic experiments which were -10.0???, -10.8???, and -9.8??? for the short-term biological, long-term biological and abiotic control experiments, respectively. Based on the similarity between ??18OSO4 values in the biological and abiotic experiments, it is suggested that ??18OSO4 values cannot be used to distinguish biological and abiotic mechanisms of pyrite oxidation. The results presented here suggest that Fe(III)aq is the primary oxidant for pyrite at pH < 3, even in the presence of dissolved oxygen, and that the main oxygen source of sulfate is water-oxygen under both aerobic and anaerobic conditions. ?? 2007 Elsevier Ltd. All rights reserved.

Importance of Biotic vs Abiotic Controls on VOC Emissions from Ponderosa Pine

NASA Astrophysics Data System (ADS)

Eller, A. S.; Harley, P. C.; Monson, R. K.

2011-12-01

The emissions of VOCs, including monoterpenes (MTs) and 2-methyl-3-buten-2-ol (MBO), from ponderosa pine can be important contributors to the regional production of ozone and secondary organic aerosols in the Western United States. The goal of this study was to better characterize the influences of biotic and abiotic factors on the emissions of these compounds. Using PTR-MS coupled with measurements of photosynthesis and stomatal conductance (gs) we generated light and temperature curves from intact needles of mature ponderosa pine trees and used abscisic acid (ABA) to reduce gs and photosynthesis under constant light and temperature conditions. Stomatal conductance and photosynthesis were almost perfectly correlated during all our measurements, so we were unable to separate their influences. We found that increasing temperature by 10 oC increased emissions of both MTs and MBO by 80-120% even though gs and photosynthesis were reduced by ~50%. Light curves performed at 30 oC showed that gs and photosynthesis exhibited a strong control over MT and MBO emissions although the effect was more pronounced for MBO than MT emissions. In most cases a 60% reduction in gs and photosynthesis caused a ~50% reduction in MBO emissions and a 5-20% reduction in MT emissions. Using ABA we were able to induce stomatal closure while maintaining a constant light and temperature environment and we found that stomatal closure due to ABA caused declines in MT and MBO emissions that were similar in magnitude to those seen in the light curves. When compared at the same light and temperature conditions, individuals with lower gs and photosynthesis did not necessarily have lower emissions than those with higher gs and photosynthesis, indicating that gs and photosynthesis may not be good predictors of emissions between individuals, but within each individual the instantaneous changes in gs and photosynthesis did appear to exert control over the emissions of VOCs. These data show that plant physiology is an important constraint in regulating the instantaneous emissions of VOCs, but also that the relationships are modified by external temperature, probably through the increased volatility of the VOCs.

Low-Light Anoxygenic Photosynthesis and Fe-S-Biogeochemistry in a Microbial Mat

PubMed Central

Haas, Sebastian; de Beer, Dirk; Klatt, Judith M.; Fink, Artur; Rench, Rebecca McCauley; Hamilton, Trinity L.; Meyer, Volker; Kakuk, Brian; Macalady, Jennifer L.

2018-01-01

We report extremely low-light-adapted anoxygenic photosynthesis in a thick microbial mat in Magical Blue Hole, Abaco Island, The Bahamas. Sulfur cycling was reduced by iron oxides and organic carbon limitation. The mat grows below the halocline/oxycline at 30 m depth on the walls of the flooded sinkhole. In situ irradiance at the mat surface on a sunny December day was between 0.021 and 0.084 μmol photons m-2 s-1, and UV light (<400 nm) was the most abundant part of the spectrum followed by green wavelengths (475–530 nm). We measured a light-dependent carbon uptake rate of 14.5 nmol C cm-2 d-1. A 16S rRNA clone library of the green surface mat layer was dominated (74%) by a cluster (>97% sequence identity) of clones affiliated with Prosthecochloris, a genus within the green sulfur bacteria (GSB), which are obligate anoxygenic phototrophs. Typical photopigments of brown-colored GSB, bacteriochlorophyll e and (β-)isorenieratene, were abundant in mat samples and their absorption properties are well-adapted to harvest light in the available green and possibly even UV-A spectra. Sulfide from the water column (3–6 μmol L-1) was the main source of sulfide to the mat as sulfate reduction rates in the mats were very low (undetectable-99.2 nmol cm-3 d-1). The anoxic water column was oligotrophic and low in dissolved organic carbon (175–228 μmol L-1). High concentrations of pyrite (FeS2; 1–47 μmol cm-3) together with low microbial process rates (sulfate reduction, CO2 fixation) indicate that the mats function as net sulfide sinks mainly by abiotic processes. We suggest that abundant Fe(III) (4.3–22.2 μmol cm-3) is the major source of oxidizing power in the mat, and that abiotic Fe-S-reactions play the main role in pyrite formation. Limitation of sulfate reduction by low organic carbon availability along with the presence of abundant sulfide-scavenging iron oxides considerably slowed down sulfur cycling in these mats. PMID:29755448

Low-Light Anoxygenic Photosynthesis and Fe-S-Biogeochemistry in a Microbial Mat.

PubMed

Haas, Sebastian; de Beer, Dirk; Klatt, Judith M; Fink, Artur; Rench, Rebecca McCauley; Hamilton, Trinity L; Meyer, Volker; Kakuk, Brian; Macalady, Jennifer L

2018-01-01

We report extremely low-light-adapted anoxygenic photosynthesis in a thick microbial mat in Magical Blue Hole, Abaco Island, The Bahamas. Sulfur cycling was reduced by iron oxides and organic carbon limitation. The mat grows below the halocline/oxycline at 30 m depth on the walls of the flooded sinkhole. In situ irradiance at the mat surface on a sunny December day was between 0.021 and 0.084 μmol photons m -2 s -1 , and UV light (<400 nm) was the most abundant part of the spectrum followed by green wavelengths (475-530 nm). We measured a light-dependent carbon uptake rate of 14.5 nmol C cm -2 d -1 . A 16S rRNA clone library of the green surface mat layer was dominated (74%) by a cluster (>97% sequence identity) of clones affiliated with Prosthecochloris , a genus within the green sulfur bacteria (GSB), which are obligate anoxygenic phototrophs. Typical photopigments of brown-colored GSB, bacteriochlorophyll e and (β-)isorenieratene, were abundant in mat samples and their absorption properties are well-adapted to harvest light in the available green and possibly even UV-A spectra. Sulfide from the water column (3-6 μmol L -1 ) was the main source of sulfide to the mat as sulfate reduction rates in the mats were very low (undetectable-99.2 nmol cm -3 d -1 ). The anoxic water column was oligotrophic and low in dissolved organic carbon (175-228 μmol L -1 ). High concentrations of pyrite (FeS 2 ; 1-47 μmol cm -3 ) together with low microbial process rates (sulfate reduction, CO 2 fixation) indicate that the mats function as net sulfide sinks mainly by abiotic processes. We suggest that abundant Fe(III) (4.3-22.2 μmol cm -3 ) is the major source of oxidizing power in the mat, and that abiotic Fe-S-reactions play the main role in pyrite formation. Limitation of sulfate reduction by low organic carbon availability along with the presence of abundant sulfide-scavenging iron oxides considerably slowed down sulfur cycling in these mats.

Photosynthesis and yield reductions from wheat stem sawfly (Hymenoptera: Cephidae): interactions with wheat solidness, water stress, and phosphorus deficiency.

PubMed

Delaney, Kevin J; Weaver, David K; Peterson, Robert K D

2010-04-01

The impact of herbivory on plants is variable and influenced by several factors. The current study examined causes of variation in the impact of larval stem mining by the wheat stem sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae), on spring wheat, Triticum aestivum L. We performed greenhouse experiments over 2 yr to (1) study whether biotic (hollow versus solid stemmed host wheat) and abiotic (water, phosphorus stress) factors interact with C. cinctus stem mining to influence degree of mined stem physiological (photosynthesis) and yield (grain weight) reductions; and (2) determine whether whole plant yield compensatory responses occur to offset stem-mining reductions. Flag leaf photosynthetic reduction was not detected 16-20 d after infestation, but were detected at 40-42 d and doubled from water or phosphorus stresses. Main stem grain weight decreased from 10 to 25% from stem mining, largely due to reductions in grain size, with greater reductions under low phosphorus and/or water levels. Phosphorus-deficient plants without water stress were most susceptible to C. cinctus, more than doubling the grain weight reduction due to larval feeding relative to other water and phosphorus treatments. Two solid stemmed varieties with stem mining had less grain weight loss than a hollow stemmed variety, so greater internal mechanical resistance may reduce larval stem mining and plant yield reductions. Our results emphasize the importance of sufficient water and macronutrients for plants grown in regions impacted by C. cinctus. Also, solid stemmed varieties not only reduce wheat lodging from C. cinctus, they may reduce harvested grain losses from infested stems.

Microbial Transformations of Selenium Species of Relevance to Bioremediation

PubMed Central

Eswayah, Abdurrahman S.; Smith, Thomas J.

2016-01-01

Selenium species, particularly the oxyanions selenite (SeO32−) and selenate (SeO42−), are significant pollutants in the environment that leach from rocks and are released by anthropogenic activities. Selenium is also an essential micronutrient for organisms across the tree of life, including microorganisms and human beings, particularly because of its presence in the 21st genetically encoded amino acid, selenocysteine. Environmental microorganisms are known to be capable of a range of transformations of selenium species, including reduction, methylation, oxidation, and demethylation. Assimilatory reduction of selenium species is necessary for the synthesis of selenoproteins. Dissimilatory reduction of selenate is known to support the anaerobic respiration of a number of microorganisms, and the dissimilatory reduction of soluble selenate and selenite to nanoparticulate elemental selenium greatly reduces the toxicity and bioavailability of selenium and has a major role in bioremediation and potentially in the production of selenium nanospheres for technological applications. Also, microbial methylation after reduction of Se oxyanions is another potentially effective detoxification process if limitations with low reaction rates and capture of the volatile methylated selenium species can be overcome. This review discusses microbial transformations of different forms of Se in an environmental context, with special emphasis on bioremediation of Se pollution. PMID:27260359

Regio- and stereoselective reduction of 17-oxosteroids to 17β-hydroxysteroids by a yeast strain Zygowilliopsis sp. WY7905.

PubMed

Liu, Yuanyuan; Wang, Yu; Chen, Xi; Wu, Qiaqing; Wang, Min; Zhu, Dunming; Ma, Yanhe

2017-02-01

The reduction of 17-oxosteroids to 17β-hydroxysteroids is one of the important transformations for the preparation of many steroidal drugs and intermediates. The strain Zygowilliopsis sp. WY7905 was found to catalyze the reduction of C-17 carbonyl group of androst-4-ene-3,17-dione (AD) to give testosterone (TS) as the sole product by the constitutive 17β-hydroxysteroid dehydrogenase (17β-HSD). The optimal conditions for the reduction were pH 8.0 and 30°C with supplementing 10g/l glucose and 1% Tween 80 (w/v). Under the optimized transformation conditions, 0.75g/l AD was reduced to a single product TS with >90% yield and >99% diastereomeric excess (de) within 24h. This strain also reduced other 17-oxosteroids such as estrone, 3β-hydroxyandrost-5-en-17-one and norandrostenedione, to give the corresponding 17β-hydroxysteroids, while the C-3 and C-20 carbonyl groups were intact. The absence of by-products in this microbial 17β-reduction would facilitate the product purification. As such, the strain might serve as a useful biocatalyst for this important transformation. Copyright © 2016 Elsevier Inc. All rights reserved.

REDUCTIVE DEHALOGENATION OF HALOMETHANES IN IRON- AND SULFATE-REDUCING SEDIMENTS. 1. REACTIVITY PATTERN ANALYSIS

EPA Science Inventory

The incorporation of reductive transformations into environmental fate models requires the characterization of natural reductants in well-characterized sediments and aquifer materials. For this purpose, reactivity patterns (i.e., the range and relative order of reactivity) for a...

Do positive interactions increase with abiotic stress? A test from a semi-arid steppe.

PubMed Central

Maestre, Fernando T; Cortina, Jordi

2004-01-01

Theoretical models predict that the relative importance of facilitation and competition may vary inversely across gradients of abiotic stress. However, these predictions have not been thoroughly tested in the field, especially in semi-arid environments. In this study, we evaluated how the net effect of the tussock grass Stipa tenacissima on the shrub Pistacia lentiscus varied across a gradient of abiotic stress in semi-arid Mediterranean steppes. We fitted the relationship between accumulated rainfall and the relative neighbour index (our measures of abiotic stress and of the net effect of S. tenacissima on P. lentiscus, respectively), which varied across this gradient, to a quadratic model. Competitive interactions dominated at both extremes of the gradient. Our results do not support established theory. Instead, they suggest that a shift from facilitation to competition under high abiotic stress conditions is likely to occur when the levels of the most limiting resource are so low that the benefits provided by the facilitator cannot overcome its own resource uptake. PMID:15504009

bHLH106 Integrates Functions of Multiple Genes through Their G-Box to Confer Salt Tolerance on Arabidopsis.

PubMed

Ahmad, Aftab; Niwa, Yasuo; Goto, Shingo; Ogawa, Takeshi; Shimizu, Masanori; Suzuki, Akane; Kobayashi, Kyoko; Kobayashi, Hirokazu

2015-01-01

An activation-tagging methodology was applied to dedifferentiated calli of Arabidopsis to identify new genes involved in salt tolerance. This identified salt tolerant callus 8 (stc8) as a gene encoding the basic helix-loop-helix transcription factor bHLH106. bHLH106-knockout (KO) lines were more sensitive to NaCl, KCl, LiCl, ABA, and low temperatures than the wild-type. Back-transformation of the KO line rescued its phenotype, and over-expression (OX) of bHLH106 in differentiated plants exhibited tolerance to NaCl. Green fluorescent protein (GFP) fused with bHLH106 revealed that it was localized to the nucleus. Prepared bHLH106 protein was subjected to electrophoresis mobility shift assays against E-box sequences (5'-CANNTG-3'). The G-box sequence 5'-CACGTG-3' had the strongest interaction with bHLH106. bHLH106-OX lines were transcriptomically analyzed, and resultant up- and down-regulated genes selected on the criterion of presence of a G-box sequence. There were 198 genes positively regulated by bHLH106 and 36 genes negatively regulated; these genes possessed one or more G-box sequences in their promoter regions. Many of these genes are known to be involved in abiotic stress response. It is concluded that bHLH106 locates at a branching point in the abiotic stress response network by interacting directly to the G-box in genes conferring salt tolerance on plants.

Biotic and abiotic factors predicting the global distribution and population density of an invasive large mammal

PubMed Central

Lewis, Jesse S.; Farnsworth, Matthew L.; Burdett, Chris L.; Theobald, David M.; Gray, Miranda; Miller, Ryan S.

2017-01-01

Biotic and abiotic factors are increasingly acknowledged to synergistically shape broad-scale species distributions. However, the relative importance of biotic and abiotic factors in predicting species distributions is unclear. In particular, biotic factors, such as predation and vegetation, including those resulting from anthropogenic land-use change, are underrepresented in species distribution modeling, but could improve model predictions. Using generalized linear models and model selection techniques, we used 129 estimates of population density of wild pigs (Sus scrofa) from 5 continents to evaluate the relative importance, magnitude, and direction of biotic and abiotic factors in predicting population density of an invasive large mammal with a global distribution. Incorporating diverse biotic factors, including agriculture, vegetation cover, and large carnivore richness, into species distribution modeling substantially improved model fit and predictions. Abiotic factors, including precipitation and potential evapotranspiration, were also important predictors. The predictive map of population density revealed wide-ranging potential for an invasive large mammal to expand its distribution globally. This information can be used to proactively create conservation/management plans to control future invasions. Our study demonstrates that the ongoing paradigm shift, which recognizes that both biotic and abiotic factors shape species distributions across broad scales, can be advanced by incorporating diverse biotic factors. PMID:28276519

Abiotic dechlorination in rock matrices impacted by long-term exposure to TCE.

PubMed

Schaefer, Charles E; Towne, Rachael M; Lippincott, David R; Lacombe, Pierre J; Bishop, Michael E; Dong, Hailiang

2015-01-01

Field and laboratory tests were performed to evaluate the abiotic reaction of trichloroethene (TCE) in sedimentary rock matrices. Hydraulically conductive fractures, and the rock directly adjacent to the hydraulically conductive fractures, within a historically contaminated TCE bedrock aquifer were used as the basis for this study. These results were compared to previous work using rock that had not been exposed to TCE (Schaefer et al., 2013) to assess the impact of long-term TCE exposure on the abiotic dechlorination reaction, as the longevity of these reactions after long-term exposure to TCE was hitherto unknown. Results showed that potential abiotic TCE degradation products, including ethane, ethene, and acetylene, were present in the conductive fractures. Using minimally disturbed slices of rock core at and near the fracture faces, laboratory testing on the rocks confirmed that abiotic dechlorination reactions between the rock matrix and TCE were occurring. Abiotic daughter products measured in the laboratory under controlled conditions were consistent with those measured in the conductive fractures, except that propane also was observed as a daughter product. TCE degradation measured in the laboratory was well described by a first order rate constant through the 118-d study. Observed bulk first-order TCE degradation rate constants within the rock matrix were 1.3×10(-8) s(-1). These results clearly show that abiotic dechlorination of TCE is occurring within the rock matrix, despite decades of exposure to TCE. Furthermore, these observed rates of TCE dechlorination are expected to have a substantial impact on TCE migration and uptake/release from rock matrices. Copyright © 2014 Elsevier Ltd. All rights reserved.

Improvement of peanut (Arachis hypogaea L.) transformation efficiency and determination of transgene copy number by relative quantitative real-time PCR

USDA-ARS?s Scientific Manuscript database

The biolistic method is reliable for delivering genes of interest into various species. Low transformation efficiency has been a limiting factor for its application. The DNA coating agent protamine was shown to improve transformation efficiency in rice, while a reduction of plasmid DNA in the bomb...

Multiple DC, single AC converter with a switched DC transformer

DOEpatents

Donnelly, M.K.; Hammerstrom, D.J.

1997-05-20

The invention is an improvement of the PASC inverter, wherein the improvements include the reduction from two shorting gates per transformer to one shorting gate per transformer and replacement of active control of the shorting gate with passive control of the shorting gate. Further advantages are obtained through the use of anti-parallel gate sets. 14 figs.

Multiple DC, single AC converter with a switched DC transformer

DOEpatents

Donnelly, Matthew K.; Hammerstrom, Donald J.

1997-01-01

The invention is an improvement of the PASC inverter, wherein the improvements include the reduction from two shorting gates per transformer to one shorting gate per transformer and replacement of active control of the shorting gate with passive control of the shorting gate. Further advantages are obtained through the use of anti-parallel gate sets.

Poverty Reduction in Zambia: A Conceptual Analysis of the Zambian Poverty Reduction Strategy Paper

ERIC Educational Resources Information Center

Imboela, Bruce Lubinda

2005-01-01

Poverty reduction strategy papers (PRSPs) present a recipient country's program of intent for the utilization of World Bank loans and grants to alleviate debt under the bank's programs of action for poverty reduction in highly indebted poor countries (HIPCs). This article argues that structural transformation is a prerequisite for poverty…

A study of renal blood flow regulation using the discrete wavelet transform

NASA Astrophysics Data System (ADS)

Pavlov, Alexey N.; Pavlova, Olga N.; Mosekilde, Erik; Sosnovtseva, Olga V.

2010-02-01

In this paper we provide a way to distinguish features of renal blood flow autoregulation mechanisms in normotensive and hypertensive rats based on the discrete wavelet transform. Using the variability of the wavelet coefficients we show distinctions that occur between the normal and pathological states. A reduction of this variability in hypertension is observed on the microscopic level of the blood flow in efferent arteriole of single nephrons. This reduction is probably associated with higher flexibility of healthy cardiovascular system.

Evidence for the Existence of Autotrophic Nitrate-Reducing Fe(II)-Oxidizing Bacteria in Marine Coastal Sediment

PubMed Central

Laufer, Katja; Røy, Hans; Jørgensen, Bo Barker

2016-01-01

ABSTRACT Nitrate-reducing Fe(II)-oxidizing microorganisms were described for the first time ca. 20 years ago. Most pure cultures of nitrate-reducing Fe(II) oxidizers can oxidize Fe(II) only under mixotrophic conditions, i.e., when an organic cosubstrate is provided. A small number of nitrate-reducing Fe(II)-oxidizing cultures have been proposed to grow autotrophically, but unambiguous evidence for autotrophy has not always been provided. Thus, it is still unclear whether or to what extent Fe(II) oxidation coupled to nitrate reduction is an enzymatically catalyzed and energy-yielding autotrophic process or whether Fe(II) is abiotically oxidized by nitrite from heterotrophic nitrate reduction. The aim of the present study was to find evidence for the existence of autotrophic nitrate-reducing Fe(II) oxidizers in coastal marine sediments. Microcosm incubations showed that with increasing incubation times, the stoichiometric ratio of reduced nitrate/oxidized Fe(II) [NO3−reduced/Fe(II)oxidized] decreased, indicating a decreasing contribution of heterotrophic denitrification and/or an increasing contribution of autotrophic nitrate-reducing Fe(II) oxidation over time. After incubations of sediment slurries for >10 weeks, nitrate-reducing activity ceased, although nitrate was still present. This suggests that heterotrophic nitrate reduction had ceased due to the depletion of readily available organic carbon. However, after the addition of Fe(II) to these batch incubation mixtures, the nitrate-reducing activity resumed, and Fe(II) was oxidized, indicating the activity of autotrophic nitrate-reducing Fe(II) oxidizers. The concurrent reduction of 14C-labeled bicarbonate concentrations unambiguously proved that autotrophic C fixation occurred during Fe(II) oxidation and nitrate reduction. Our results clearly demonstrated that autotrophic nitrate-reducing Fe(II)-oxidizing bacteria were present in the investigated coastal marine sediments. IMPORTANCE Twenty years after the discovery of nitrate-reducing Fe(II) oxidizers, it is still controversially discussed whether autotrophic nitrate-reducing Fe(II)-oxidizing microorganisms exist and to what extent Fe(II) oxidation in this reduction/oxidation process is enzymatically catalyzed or which role abiotic side reactions of Fe(II) with reactive N species play. Most pure cultures of nitrate-reducing Fe(II) oxidizers are mixotrophic; i.e., they need an organic cosubstrate to maintain their activity over several cultural transfers. For the few existing autotrophic isolates and enrichment cultures, either the mechanism of nitrate-reducing Fe(II) oxidation is not known or evidence for their autotrophic lifestyle is controversial. In the present study, we provide evidence for the existence of autotrophic nitrate-reducing Fe(II) oxidizers in coastal marine sediments. The evidence is based on stoichiometries of nitrate reduction and Fe(II) oxidation determined in microcosm incubations and the incorporation of carbon from CO2 under conditions that favor the activity of nitrate-reducing Fe(II) oxidizers. PMID:27496777

The hysteretic evapotranspiration - vapor pressure deficit relation

NASA Astrophysics Data System (ADS)

Zhang, Q.; Manzoni, S.; Katul, G. G.; Porporato, A. M.; Yang, D.

2013-12-01

Diurnal hysteresis between evapotranspiration (ET) and vapor pressure deficit (VPD) was reported in many ecosystems but justification for its onset and magnitude remain incomplete with biotic and abiotic factors invoked as possible explanations. To place these explanations within a mathematical framework, ';rate-dependent' hysteresis originating from a phase angle difference between periodic input and output time series is first considered. Lysimeter evaporation (E) measurements from wet bare soils and model calculations using the Penman equation demonstrate that the E-VPD hysteresis emerges without any biotic effects due to a phase angle difference (or time lag) between net radiation the main driver of E, and VPD. Modulations originating from biotic effects on the ET-VPD hysteresis were then considered. The phase angle difference representation earlier employed was mathematically transformed into a storage problem and applied to the soil-plant system. The transformed system shows that soil moisture storage within the root zone can produce an ET-VPD hysteresis prototypical of those generated by phase-angle differences. To explore the interplay between all the lags in the soil-plant-atmosphere system and phase angle differences among forcing and response variables, a detailed soil-plant-atmosphere continuum (SPAC) model was developed and applied to a grassland ecosystem. The results of the SPAC model suggest that the hysteresis magnitude depends on the radiation-VPD lag. The soil moisture dry-down simulations also suggest that modeled root water potential and leaf water potential are both better indicators of the hysteresis magnitude than soil moisture, suggesting that plant water status is the main factor regulating the hysteretic relation between ET and VPD. Hence, the genesis and magnitude of the ET-VPD hysteresis are controlled directly by both biotic factors and abiotic factors such as time lag between radiation and VPD originating from boundary layer processes. Measured eddy covariance evapotranspiration (ET) and vapor pressure deficit (VPD) time series normalized by their maximum values collected in a grassland ecosystem. The magnitude of the hysteresis is quantified as the area enveloped by the ET-VPD relation (Ahys). The arrows together with time ticks indicate the progression of the diurnal cycle from sunrise to sunset.

Quantitative determination of polyphosphate in sediments using Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy and partial least squares regression.

PubMed

Khoshmanesh, Aazam; Cook, Perran L M; Wood, Bayden R

2012-08-21

Phosphorus (P) is a major cause of eutrophication and subsequent loss of water quality in freshwater ecosystems. A major part of the flux of P to eutrophic lake sediments is organically bound or of biogenic origin. Despite the broad relevance of polyphosphate (Poly-P) in bioremediation and P release processes in the environment, its quantification is not yet well developed for sediment samples. Current methods possess significant disadvantages because of the difficulties associated with using a single extractant to extract a specific P compound without altering others. A fast and reliable method to estimate the quantitative contribution of microorganisms to sediment P release processes is needed, especially when an excessive P accumulation in the form of polyphosphate (Poly-P) occurs. Development of novel approaches for application of emerging spectroscopic techniques to complex environmental matrices such as sediments significantly contributes to the speciation models of P mobilization, biogeochemical nutrient cycling and development of nutrient models. In this study, for the first time Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy in combination with partial least squares (PLS) was used to quantify Poly-P in sediments. To reduce the high absorption matrix components in sediments such as silica, a physical extraction method was developed to separate sediment biological materials from abiotic particles. The aim was to achieve optimal separation of the biological materials from sediment abiotic particles with minimum chemical change in the sample matrix prior to ATR-FTIR analysis. Using a calibration set of 60 samples for the PLS prediction models in the Poly-P concentration range of 0-1 mg g(-1) d.w. (dry weight of sediment) (R(2) = 0.984 and root mean square error of prediction RMSEP = 0.041 at Factor-1) Poly-P could be detected at less than 50 μg g(-l) d.w. Using this technique, there is no solvent extraction or chemical treatment required, sample preparation is minimal and simple, and the analysis time is greatly reduced. The results from this study demonstrated the potential of ATR FT-IR spectroscopy as an alternative method to study Poly-P in sediments.

A Continuous Flow Column Study of the Anaerobic Transformation of a CAH Mixture of Tetrachloroethene and Carbon Tetrachloride Using Formate as an Electron Donor

NASA Astrophysics Data System (ADS)

Semprini, L.; Azizian, M. F.; Kim, Y.

2011-12-01

Many groundwater sites are contaminated with mixtures of chlorinated aliphatic hydrocarbons (CAHs) that represent a challenge when biological remediation processes are being considered. This is especially challenging when high concentrations of CAHs are present.Trichloromethane (CF), for example, has been observed to inhibit and potentially exert toxicity on reductive dehalogenation of tetrachloroethene (PCE) and trichloroethene (TCE). Results will be presented from a continuous flow column study where the simultaneous transformation of PCE and carbon tetrachloride (CT) was achieved. The column was packed with a quartz sand and bioaugmented with the Evanite Culture (EV) that is capable of transforming PCE to ethene. The column was fed a synthetic groundwater that was amended with PCE to achieve an influent concentration near its solubility limit (0.10 mM) and formate (1.5 mM) that reacts to produce hydrogen as the ultimate electron donor. The column was operated for over 1600 days prior to the addition of CT. During this period PCE was transformed mainly to vinyl chloride (VC) and ethene (ETH) and minor amounts of cis-dichloroethene (cis-DCE) and TCE. The transformation extent achieved based on the column effluent concentrations ranged from about 50% ETH, 30% VC, and 20 cis-DCE up to 80% ETH and 20% VC. When the column was fed sulfate, it was completely transformed via sulfate reduction. Ferrous iron production from ferric iron reduction was observed early in the study. Acetate was also formed as a result of homoacetogenesis from hydrogen utilization. CT addition (0.015 mM) was started at 1600 days while PCE addition was continued. During the first 25 days of CT addition, CT concentrations gradually increased to 50% of the injection concentration and chloromethane (CM) and CF were observed as transformation products. CT concentrations then decreased with over 98% transformation achieved.CM was removed to below the detection limit and CF concentration decreases to about 0.003 mM, representing 20% of the CT transformed. Other transformation products have not been identified. Neither methane nor carbon monoxide have been detected as transformation products. The transformation of PCE to ethene actually improved after the addition of CT. Thus, neither CT nor CF are inhibiting the reductive dehalogenation of PCE. The improvement in PCE transformation extent coincided with an increase in the aqueous hydrogen concentration from 5 nM, prior to CT addition, to 150 nM after CT addition. This increase in hydrogen was associated with the inhibition in acetate production and the increase in formate concentrations from below detection to 1.0 mM after CT addition. The results indicate that there are likely benefits in adding formate to produce hydrogen when contaminants are present that can inhibit fermentation. The results from the column study are consistent with our observations in batch reactors using the EV culture.

Integer cosine transform for image compression

NASA Technical Reports Server (NTRS)

Cheung, K.-M.; Pollara, F.; Shahshahani, M.

1991-01-01

This article describes a recently introduced transform algorithm called the integer cosine transform (ICT), which is used in transform-based data compression schemes. The ICT algorithm requires only integer operations on small integers and at the same time gives a rate-distortion performance comparable to that offered by the floating-point discrete cosine transform (DCT). The article addresses the issue of implementation complexity, which is of prime concern for source coding applications of interest in deep-space communications. Complexity reduction in the transform stage of the compression scheme is particularly relevant, since this stage accounts for most (typically over 80 percent) of the computational load.

Differential sensitivity to regional-scale drought in six central US grasslands.

PubMed

Knapp, Alan K; Carroll, Charles J W; Denton, Elsie M; La Pierre, Kimberly J; Collins, Scott L; Smith, Melinda D

2015-04-01

Terrestrial ecosystems often vary dramatically in their responses to drought, but the reasons for this are unclear. With climate change forecasts for more frequent and extensive drought in the future, a more complete understanding of the mechanisms that determine differential ecosystem sensitivity to drought is needed. In 2012, the Central US experienced the fourth largest drought in a century, with a regional-scale 40% reduction in growing season precipitation affecting ecosystems ranging from desert grassland to mesic tallgrass prairie. This provided an opportunity to assess ecosystem sensitivity to a drought of common magnitude in six native grasslands. We tested the prediction that drought sensitivity is inversely related to mean annual precipitation (MAP) by quantifying reductions in aboveground net primary production (ANPP). Long-term ANPP data available for each site (mean length = 16 years) were used as a baseline for calculating reductions in ANPP, and drought sensitivity was estimated as the reduction in ANPP per millimeter reduction in precipitation. Arid grasslands were the most sensitive to drought, but drought responses and sensitivity varied by more than twofold among the six grasslands, despite all sites experiencing 40% reductions in growing season precipitation. Although drought sensitivity generally decreased with increasing MAP as predicted, there was evidence that the identity and traits of the dominant species, as well as plant functional diversity, influenced sensitivity. A more comprehensive understanding of the mechanisms leading to differences in drought sensitivity will require multi-site manipulative experiments designed to assess both biotic and abiotic determinants of ecosystem sensitivity.

Arbuscular Mycorrhizal Fungal 14-3-3 Proteins Are Involved in Arbuscule Formation and Responses to Abiotic Stresses During AM Symbiosis

PubMed Central

Sun, Zhongfeng; Song, Jiabin; Xin, Xi’an; Xie, Xianan; Zhao, Bin

2018-01-01

Arbuscular mycorrhizal (AM) fungi are soil-borne fungi belonging to the ancient phylum Glomeromycota and are important symbionts of the arbuscular mycorrhiza, enhancing plant nutrient acquisition and resistance to various abiotic stresses. In contrast to their significant physiological implications, the molecular basis involved is poorly understood, largely due to their obligate biotrophism and complicated genetics. Here, we identify and characterize three genes termed Fm201, Ri14-3-3 and RiBMH2 that encode 14-3-3-like proteins in the AM fungi Funneliformis mosseae and Rhizophagus irregularis, respectively. The transcriptional levels of Fm201, Ri14-3-3 and RiBMH2 are strongly induced in the pre-symbiotic and symbiotic phases, including germinating spores, intraradical hyphae- and arbuscules-enriched roots. To functionally characterize the Fm201, Ri14-3-3 and RiBMH2 genes, we took advantage of a yeast heterologous system owing to the lack of AM fungal transformation systems. Our data suggest that all three genes can restore the lethal Saccharomyces cerevisiae bmh1 bmh2 double mutant on galactose-containing media. Importantly, yeast one-hybrid analysis suggests that the transcription factor RiMsn2 is able to recognize the STRE (CCCCT/AGGGG) element present in the promoter region of Fm201 gene. More importantly, Host-Induced Gene Silencing of both Ri14-3-3 and RiBMH2 in Rhizophagus irregularis impairs the arbuscule formation in AM symbiosis and inhibits the expression of symbiotic PT4 and MST2 genes from plant and fungal partners, respectively. We further subjected the AM fungus-Medicago truncatula association system to drought or salinity stress. Accordingly, the expression profiles in both mycorrhizal roots and extraradical hyphae reveal that these three 14-3-3-like genes are involved in response to drought or salinity stress. Collectively, our results provide new insights into molecular functions of the AM fungal 14-3-3 proteins in abiotic stress responses and arbuscule formation during AM symbiosis. PMID:29556216

Assessing coastal wetland vulnerability to sea-level rise along the northern Gulf of Mexico coast: Gaps and opportunities for developing a coordinated regional sampling network

PubMed Central

Griffith, Kereen T.; Larriviere, Jack C.; Feher, Laura C.; Cahoon, Donald R.; Enwright, Nicholas M.; Oster, David A.; Tirpak, John M.; Woodrey, Mark S.; Collini, Renee C.; Baustian, Joseph J.; Breithaupt, Joshua L.; Cherry, Julia A.; Conrad, Jeremy R.; Cormier, Nicole; Coronado-Molina, Carlos A.; Donoghue, Joseph F.; Graham, Sean A.; Harper, Jennifer W.; Hester, Mark W.; Howard, Rebecca J.; Krauss, Ken W.; Kroes, Daniel E.; Lane, Robert R.; McKee, Karen L.; Mendelssohn, Irving A.; Middleton, Beth A.; Moon, Jena A.; Piazza, Sarai C.; Rankin, Nicole M.; Sklar, Fred H.; Steyer, Greg D.; Swanson, Kathleen M.; Swarzenski, Christopher M.; Vervaeke, William C.; Willis, Jonathan M.; Wilson, K. Van

2017-01-01

Coastal wetland responses to sea-level rise are greatly influenced by biogeomorphic processes that affect wetland surface elevation. Small changes in elevation relative to sea level can lead to comparatively large changes in ecosystem structure, function, and stability. The surface elevation table-marker horizon (SET-MH) approach is being used globally to quantify the relative contributions of processes affecting wetland elevation change. Historically, SET-MH measurements have been obtained at local scales to address site-specific research questions. However, in the face of accelerated sea-level rise, there is an increasing need for elevation change network data that can be incorporated into regional ecological models and vulnerability assessments. In particular, there is a need for long-term, high-temporal resolution data that are strategically distributed across ecologically-relevant abiotic gradients. Here, we quantify the distribution of SET-MH stations along the northern Gulf of Mexico coast (USA) across political boundaries (states), wetland habitats, and ecologically-relevant abiotic gradients (i.e., gradients in temperature, precipitation, elevation, and relative sea-level rise). Our analyses identify areas with high SET-MH station densities as well as areas with notable gaps. Salt marshes, intermediate elevations, and colder areas with high rainfall have a high number of stations, while salt flat ecosystems, certain elevation zones, the mangrove-marsh ecotone, and hypersaline coastal areas with low rainfall have fewer stations. Due to rapid rates of wetland loss and relative sea-level rise, the state of Louisiana has the most extensive SET-MH station network in the region, and we provide several recent examples where data from Louisiana’s network have been used to assess and compare wetland vulnerability to sea-level rise. Our findings represent the first attempt to examine spatial gaps in SET-MH coverage across abiotic gradients. Our analyses can be used to transform a broadly disseminated and unplanned collection of SET-MH stations into a coordinated and strategic regional network. This regional network would provide data for predicting and preparing for the responses of coastal wetlands to accelerated sea-level rise and other aspects of global change. PMID:28902904

Assessing coastal wetland vulnerability to sea-level rise along the northern Gulf of Mexico coast: Gaps and opportunities for developing a coordinated regional sampling network

USGS Publications Warehouse

Osland, Michael J.; Griffith, Kereen T.; Larriviere, Jack C.; Feher, Laura C.; Cahoon, Donald R.; Enwright, Nicholas M.; Oster, David A.; Tirpak, John M.; Woodrey, Mark S.; Collini, Renee C.; Baustian, Joseph J.; Breithaupt, Joshua L.; Cherry, Julia A; Conrad, Jeremy R.; Cormier, Nicole; Coronado-Molina, Carlos A.; Donoghue, Joseph F.; Graham, Sean A.; Harper, Jennifer W.; Hester, Mark W.; Howard, Rebecca J.; Krauss, Ken W.; Kroes, Daniel; Lane, Robert R.; Mckee, Karen L.; Mendelssohn, Irving A.; Middleton, Beth A.; Moon, Jena A.; Piazza, Sarai; Rankin, Nicole M.; Sklar, Fred H.; Steyer, Gregory D.; Swanson, Kathleen M.; Swarzenski, Christopher M.; Vervaeke, William; Willis, Jonathan M; Van Wilson, K.

2017-01-01

Coastal wetland responses to sea-level rise are greatly influenced by biogeomorphic processes that affect wetland surface elevation. Small changes in elevation relative to sea level can lead to comparatively large changes in ecosystem structure, function, and stability. The surface elevation table-marker horizon (SET-MH) approach is being used globally to quantify the relative contributions of processes affecting wetland elevation change. Historically, SET-MH measurements have been obtained at local scales to address site-specific research questions. However, in the face of accelerated sea-level rise, there is an increasing need for elevation change network data that can be incorporated into regional ecological models and vulnerability assessments. In particular, there is a need for long-term, high-temporal resolution data that are strategically distributed across ecologically-relevant abiotic gradients. Here, we quantify the distribution of SET-MH stations along the northern Gulf of Mexico coast (USA) across political boundaries (states), wetland habitats, and ecologically-relevant abiotic gradients (i.e., gradients in temperature, precipitation, elevation, and relative sea-level rise). Our analyses identify areas with high SET-MH station densities as well as areas with notable gaps. Salt marshes, intermediate elevations, and colder areas with high rainfall have a high number of stations, while salt flat ecosystems, certain elevation zones, the mangrove-marsh ecotone, and hypersaline coastal areas with low rainfall have fewer stations. Due to rapid rates of wetland loss and relative sea-level rise, the state of Louisiana has the most extensive SET-MH station network in the region, and we provide several recent examples where data from Louisiana’s network have been used to assess and compare wetland vulnerability to sea-level rise. Our findings represent the first attempt to examine spatial gaps in SET-MH coverage across abiotic gradients. Our analyses can be used to transform a broadly disseminated and unplanned collection of SET-MH stations into a coordinated and strategic regional network. This regional network would provide data for predicting and preparing for the responses of coastal wetlands to accelerated sea-level rise and other aspects of global change.

Assessing coastal wetland vulnerability to sea-level rise along the northern Gulf of Mexico coast: Gaps and opportunities for developing a coordinated regional sampling network.

PubMed

Osland, Michael J; Griffith, Kereen T; Larriviere, Jack C; Feher, Laura C; Cahoon, Donald R; Enwright, Nicholas M; Oster, David A; Tirpak, John M; Woodrey, Mark S; Collini, Renee C; Baustian, Joseph J; Breithaupt, Joshua L; Cherry, Julia A; Conrad, Jeremy R; Cormier, Nicole; Coronado-Molina, Carlos A; Donoghue, Joseph F; Graham, Sean A; Harper, Jennifer W; Hester, Mark W; Howard, Rebecca J; Krauss, Ken W; Kroes, Daniel E; Lane, Robert R; McKee, Karen L; Mendelssohn, Irving A; Middleton, Beth A; Moon, Jena A; Piazza, Sarai C; Rankin, Nicole M; Sklar, Fred H; Steyer, Greg D; Swanson, Kathleen M; Swarzenski, Christopher M; Vervaeke, William C; Willis, Jonathan M; Wilson, K Van

2017-01-01

Coastal wetland responses to sea-level rise are greatly influenced by biogeomorphic processes that affect wetland surface elevation. Small changes in elevation relative to sea level can lead to comparatively large changes in ecosystem structure, function, and stability. The surface elevation table-marker horizon (SET-MH) approach is being used globally to quantify the relative contributions of processes affecting wetland elevation change. Historically, SET-MH measurements have been obtained at local scales to address site-specific research questions. However, in the face of accelerated sea-level rise, there is an increasing need for elevation change network data that can be incorporated into regional ecological models and vulnerability assessments. In particular, there is a need for long-term, high-temporal resolution data that are strategically distributed across ecologically-relevant abiotic gradients. Here, we quantify the distribution of SET-MH stations along the northern Gulf of Mexico coast (USA) across political boundaries (states), wetland habitats, and ecologically-relevant abiotic gradients (i.e., gradients in temperature, precipitation, elevation, and relative sea-level rise). Our analyses identify areas with high SET-MH station densities as well as areas with notable gaps. Salt marshes, intermediate elevations, and colder areas with high rainfall have a high number of stations, while salt flat ecosystems, certain elevation zones, the mangrove-marsh ecotone, and hypersaline coastal areas with low rainfall have fewer stations. Due to rapid rates of wetland loss and relative sea-level rise, the state of Louisiana has the most extensive SET-MH station network in the region, and we provide several recent examples where data from Louisiana's network have been used to assess and compare wetland vulnerability to sea-level rise. Our findings represent the first attempt to examine spatial gaps in SET-MH coverage across abiotic gradients. Our analyses can be used to transform a broadly disseminated and unplanned collection of SET-MH stations into a coordinated and strategic regional network. This regional network would provide data for predicting and preparing for the responses of coastal wetlands to accelerated sea-level rise and other aspects of global change.

ABP9, a maize bZIP transcription factor, enhances tolerance to salt and drought in transgenic cotton.

PubMed

Wang, Chunling; Lu, Guoqing; Hao, Yuqiong; Guo, Huiming; Guo, Yan; Zhao, Jun; Cheng, Hongmei

2017-09-01

ABP9 , encoding a bZIP transcription factor from maize, enhances tolerance to multiple stresses and may participate in the ABA signaling pathway in transgenic cotton by altering physiological and biochemical processes and stress-related gene expression. Abiotic stresses, such as soil salinity and drought, negatively affect growth, development, and yield in cotton. Gene ABP9, which encodes a bZIP transcription factor, binds to the abscisic acid (ABA)-responsive-element (ABRE2) motif of the maize catalase1 gene. Its expression significantly improves tolerance in Arabidopsis to multiple abiotic stresses, but little is known about its role in cotton. In the present study, the ABP9 gene was introduced into upland cotton (Gossypium hirsutum L.) cultivar R15 by Agrobacterium tumefaciens-mediated transformation, and 12 independent transgenic cotton lines were obtained. Cotton plants over-expressing ABP9 have enhanced tolerance to salt and osmotic stress. Under stress, they developed better root systems in a greenhouse and higher germination, reduced stomatal aperture, and stomatal density in a growth chamber. Under drought conditions, survival rate and relative water content (RWC) of transgenic cotton were higher than those of R15 plants. Under salt and osmotic stresses, chlorophyll, proline, and soluble sugar contents significantly increased in transgenic cotton leaves and the malondialdehyde (MDA) content was lower than in R15. Overexpression of ABP9 also enhanced oxidative stress tolerance, reduced cellular levels of reactive oxygen species (ROS) through increased activities of antioxidative enzymes, and alleviated oxidative damage to cell. Interestingly, ABP9 over-expressing cotton was more sensitive to exogenous ABA than R15 at seed germination, root growth, stomatal aperture, and stomatal density. Moreover, ABP9 overexpression upregulated significantly the transcription levels of stress-related genes such as GhDBP2, GhNCED2, GhZFP1, GhERF1, GhHB1, and GhSAP1 under salt treatment. Conjointly, these results showed that overexpression of ABP9 conferred enhanced tolerance to multiple abiotic stresses in cotton. The stress-tolerant transgenic lines provide valuable resources for cotton breeding.

Arbuscular Mycorrhizal Fungal 14-3-3 Proteins Are Involved in Arbuscule Formation and Responses to Abiotic Stresses During AM Symbiosis.

PubMed

Sun, Zhongfeng; Song, Jiabin; Xin, Xi'an; Xie, Xianan; Zhao, Bin

2018-01-01

Arbuscular mycorrhizal (AM) fungi are soil-borne fungi belonging to the ancient phylum Glomeromycota and are important symbionts of the arbuscular mycorrhiza, enhancing plant nutrient acquisition and resistance to various abiotic stresses. In contrast to their significant physiological implications, the molecular basis involved is poorly understood, largely due to their obligate biotrophism and complicated genetics. Here, we identify and characterize three genes termed Fm201 , Ri14-3-3 and RiBMH2 that encode 14-3-3-like proteins in the AM fungi Funneliformis mosseae and Rhizophagus irregularis , respectively. The transcriptional levels of Fm201 , Ri14-3-3 and RiBMH2 are strongly induced in the pre-symbiotic and symbiotic phases, including germinating spores, intraradical hyphae- and arbuscules-enriched roots. To functionally characterize the Fm201 , Ri14-3-3 and RiBMH2 genes, we took advantage of a yeast heterologous system owing to the lack of AM fungal transformation systems. Our data suggest that all three genes can restore the lethal Saccharomyces cerevisiae bmh1 bmh2 double mutant on galactose-containing media. Importantly, yeast one-hybrid analysis suggests that the transcription factor RiMsn2 is able to recognize the STRE (CCCCT/AGGGG) element present in the promoter region of Fm201 gene. More importantly, Host-Induced Gene Silencing of both Ri14-3-3 and RiBMH2 in Rhizophagus irregularis impairs the arbuscule formation in AM symbiosis and inhibits the expression of symbiotic PT4 and MST2 genes from plant and fungal partners, respectively. We further subjected the AM fungus- Medicago truncatula association system to drought or salinity stress. Accordingly, the expression profiles in both mycorrhizal roots and extraradical hyphae reveal that these three 14-3-3-like genes are involved in response to drought or salinity stress. Collectively, our results provide new insights into molecular functions of the AM fungal 14-3-3 proteins in abiotic stress responses and arbuscule formation during AM symbiosis.

Wavelet packets for multi- and hyper-spectral imagery

NASA Astrophysics Data System (ADS)

Benedetto, J. J.; Czaja, W.; Ehler, M.; Flake, C.; Hirn, M.

2010-01-01

State of the art dimension reduction and classification schemes in multi- and hyper-spectral imaging rely primarily on the information contained in the spectral component. To better capture the joint spatial and spectral data distribution we combine the Wavelet Packet Transform with the linear dimension reduction method of Principal Component Analysis. Each spectral band is decomposed by means of the Wavelet Packet Transform and we consider a joint entropy across all the spectral bands as a tool to exploit the spatial information. Dimension reduction is then applied to the Wavelet Packets coefficients. We present examples of this technique for hyper-spectral satellite imaging. We also investigate the role of various shrinkage techniques to model non-linearity in our approach.

Understanding the Interaction of Peptides and Proteins with Abiotic Surfaces: Towards Water-Free Biologics

DTIC Science & Technology

2018-02-03

peptides immobilized on abiotic surfaces depends upon a) the chemical and physical nature of the abiotic surface; b) the physicochemical properties of... dependent model of protein aggregation, aggregation proceeds only after a lag phase in which the concentration of energetically unfavorable nuclei reaches...time dependent kinetics or dynamics at such interfaces. This paper focuses on these three most important advantages of SFG and reviews some of the

Molecular characterization of organic matter mobilized from Bangladeshi aquifer sediment: tracking carbon compositional change during microbial utilization

NASA Astrophysics Data System (ADS)

Pracht, Lara E.; Tfaily, Malak M.; Ardissono, Robert J.; Neumann, Rebecca B.

2018-03-01

Bioavailable organic carbon in aquifer recharge waters and sediments can fuel microbial reactions with implications for groundwater quality. A previous incubation experiment showed that sedimentary organic carbon (SOC) mobilized off sandy sediment collected from an arsenic-contaminated and methanogenic aquifer in Bangladesh was bioavailable; it was transformed into methane. We used high-resolution mass spectrometry to molecularly characterize this mobilized SOC, reference its composition against dissolved organic carbon (DOC) in surface recharge water, track compositional changes during incubation, and advance understanding of microbial processing of organic carbon in anaerobic environments. Organic carbon mobilized off aquifer sediment was more diverse, proportionately larger, more aromatic, and more oxidized than DOC in surface recharge. Mobilized SOC was predominately composed of terrestrially derived organic matter and had characteristics signifying that it evaded microbial processing within the aquifer. Approximately 50 % of identified compounds in mobilized SOC and in DOC from surface recharge water contained sulfur. During incubation, after mobilized SOC was converted into methane, new organosulfur compounds with high S-to-C ratios and a high nominal oxidation state of carbon (NOSC) were detected. We reason that these detected compounds formed abiotically following microbial reduction of sulfate to sulfide, which could have occurred during incubation but was not directly measured or that they were microbially synthesized. Most notably, microbes transformed all carbon types during incubation, including those currently considered thermodynamically unviable for microbes to degrade in anaerobic conditions (i.e., those with a low NOSC). In anaerobic environments, energy yields from redox reactions are small and the amount of energy required to remove electrons from highly reduced carbon substrates during oxidation decreases the thermodynamic favorability of degrading compounds with a low NOSC. While all compound types were eventually degraded during incubation, NOSC and compound size controlled the rates of carbon transformation. Large, more thermodynamically favorable compounds (e.g., aromatics with a high NOSC) were targeted first, while small, less thermodynamically favorable compounds (e.g., alkanes and olefinics with a low NOSC) were used last. These results indicate that in anaerobic conditions, microbial communities are capable of degrading and mineralizing all forms of organic matter, converting larger energy-rich compounds into smaller energy-poor compounds. However, in an open system, where fresh carbon is continually supplied, the slower degradation rate of reduced carbon compounds would enable this portion of the organic carbon pool to build up, explaining the apparent persistence of compounds with a low NOSC in anaerobic environments.

Production of Eight Different Hydride Complexes and Nitrite Release from 2,4,6-Trinitrotoluene by Yarrowia lipolytica▿ †

PubMed Central

Ziganshin, Ayrat M.; Gerlach, Robin; Borch, Thomas; Naumov, Anatoly V.; Naumova, Rimma P.

2007-01-01

2,4,6-Trinitrotoluene (TNT) transformation by the yeast strain Yarrowia lipolytica AN-L15 was shown to occur via two different pathways. Direct aromatic ring reduction was the predominant mechanism of TNT transformation, while nitro group reduction was observed to be a minor pathway. Although growth of Y. lipolytica AN-L15 was inhibited initially in the presence of TNT, TNT transformation was observed, indicating that the enzymes necessary for TNT reduction were present initially. Aromatic ring reduction resulted in the transient accumulation of eight different TNT-hydride complexes, which were characterized using high-performance liquid chromatography, UV-visible diode array detection, and negative-mode atmospheric pressure chemical ionization mass spectrometry (APCI-MS). APCI-MS analysis revealed three different groups of TNT-hydride complexes with molecular ions at m/z 227, 228, and 230, which correspond to TNT-mono- and dihydride complexes and protonated dihydride isomers, respectively. One of the three protonated dihydride complex isomers detected appears to release nitrite in the presence of strain AN-L15. This release of nitrite is of particular interest since it can provide a pathway towards complete degradation and detoxification of TNT. PMID:17933928

Damage detection on sudden stiffness reduction based on discrete wavelet transform.

PubMed

Chen, Bo; Chen, Zhi-wei; Wang, Gan-jun; Xie, Wei-ping

2014-01-01

The sudden stiffness reduction in a structure may cause the signal discontinuity in the acceleration responses close to the damage location at the damage time instant. To this end, the damage detection on sudden stiffness reduction of building structures has been actively investigated in this study. The signal discontinuity of the structural acceleration responses of an example building is extracted based on the discrete wavelet transform. It is proved that the variation of the first level detail coefficients of the wavelet transform at damage instant is linearly proportional to the magnitude of the stiffness reduction. A new damage index is proposed and implemented to detect the damage time instant, location, and severity of a structure due to a sudden change of structural stiffness. Numerical simulation using a five-story shear building under different types of excitation is carried out to assess the effectiveness and reliability of the proposed damage index for the building at different damage levels. The sensitivity of the damage index to the intensity and frequency range of measurement noise is also investigated. The made observations demonstrate that the proposed damage index can accurately identify the sudden damage events if the noise intensity is limited.

Empowering biotechnology in southern Africa: establishment of a robust transformation platform for the production of transgenic industry-preferred cassava.

PubMed

Chetty, C C; Rossin, C B; Gruissem, W; Vanderschuren, H; Rey, M E C

2013-01-25

Knowledge and technology transfer to African laboratories and farmers is an important objective for achieving food security and sustainable crop production on the sub-Saharan African continent. Cassava (Manihot esculenta Crantz) is a vital source of calories for more than a billion people in developing countries, and its potential industrial use for starch and bioethanol in the tropics is increasingly being recognized. However, cassava production remains constrained by the susceptibility of the crop to several biotic and abiotic stresses. For more than a decade, biotechnology has been considered an attractive tool to improve cassava as it substantially circumvents the limitations of traditional breeding, which is particularly time-consuming and tedious because of the high heterozygosity of the crop. A major constraint to the development of biotechnological approaches for cassava improvement has been the lack of an efficient and robust transformation and regeneration system. Despite some success achieved in genetic modification of the model cassava cultivar Tropical Manihot Series (TMS), TMS 60444, in some European and U.S. laboratories, the lack of a reproducible and robust protocol has not allowed the establishment of a routine transformation system in sub-Saharan Africa. In this study, we optimized a robust and efficient protocol developed at ETH Zurich to successfully establish transformation of a commercially cultivated South African landrace, T200, and compared this with the benchmark model cultivar TMS 60444. Results from our study demonstrated high transformation rates for both T200 (23 transgenic lines from 100 friable embryogenic callus (FEC) clusters) compared with TMS 60444 (32 transgenic lines from 100 FEC clusters). The success in transforming landraces or farmer-preferred cultivars has been limited, and the high transformation rate of an industry-preferred landrace in this study is encouraging for a feasible transformation program for cassava improvement in South Africa (SA), which can potentially be extended to other countries in southern Africa. The successful establishment of a robust cassava transformation and regeneration system in SA demonstrates the relevance of technology transfer to sub-Saharan Africa and highlights the importance of developing suitable and reliable techniques before their transfer to laboratories offering less optimal conditions. Copyright © 2012 Elsevier B.V. All rights reserved.

Evaluation of Silicone Fluid for Replacement of PCB Coolants in Railway Industry

DOT National Transportation Integrated Search

1979-06-01

Electrical performance evaluations were made on a railway transformer which was retrofilled with 50 cs polydimethylsiloxane. Comparisons of the data from the PCB-filled transformer retrofilled with the silicone oil indicated no reduction in operating...

Incorporating exposure to pitch canker disease to support management decisions of Pinus pinaster Ait. in the face of climate change.

PubMed

Serra-Varela, María Jesús; Alía, Ricardo; Pórtoles, Javier; Gonzalo, Julián; Soliño, Mario; Grivet, Delphine; Raposo, Rosa

2017-01-01

Climate change is gravely affecting forest ecosystems, resulting in large distribution shifts as well as in increasing infection diseases and biological invasions. Accordingly, forest management requires an evaluation of exposure to climate change that should integrate both its abiotic and biotic components. Here we address the implications of climate change in an emerging disease by analysing both the host species (Pinus pinaster, Maritime pine) and the pathogen's (Fusarium circinatum, pitch canker) environmental suitability i.e. estimating the host's risk of habitat loss and the disease`s future environmental range. We constrained our study area to the Spanish Iberian Peninsula, where accurate climate and pitch canker occurrence databases were available. While P. pinaster is widely distributed across the study area, the disease has only been detected in its north-central and north-western edges. We fitted species distribution models for the current distribution of the conifer and the disease. Then, these models were projected into nine Global Climate Models and two different climatic scenarios which totalled to 18 different future climate predictions representative of 2050. Based on the level of agreement among them, we created future suitability maps for the pine and for the disease independently, which were then used to assess exposure of current populations of P. pinaster to abiotic and biotic effects of climate change. Almost the entire distribution of P. pinaster in the Spanish Iberian Peninsula will be subjected to abiotic exposure likely to be driven by the predicted increase in drought events in the future. Furthermore, we detected a reduction in exposure to pitch canker that will be concentrated along the north-western edge of the study area. Setting up breeding programs is recommended in highly exposed and productive populations, while silvicultural methods and monitoring should be applied in those less productive, but still exposed, populations.

Incorporating exposure to pitch canker disease to support management decisions of Pinus pinaster Ait. in the face of climate change

PubMed Central

Serra-Varela, María Jesús; Alía, Ricardo; Pórtoles, Javier; Gonzalo, Julián; Soliño, Mario; Grivet, Delphine; Raposo, Rosa

2017-01-01

Climate change is gravely affecting forest ecosystems, resulting in large distribution shifts as well as in increasing infection diseases and biological invasions. Accordingly, forest management requires an evaluation of exposure to climate change that should integrate both its abiotic and biotic components. Here we address the implications of climate change in an emerging disease by analysing both the host species (Pinus pinaster, Maritime pine) and the pathogen’s (Fusarium circinatum, pitch canker) environmental suitability i.e. estimating the host’s risk of habitat loss and the disease`s future environmental range. We constrained our study area to the Spanish Iberian Peninsula, where accurate climate and pitch canker occurrence databases were available. While P. pinaster is widely distributed across the study area, the disease has only been detected in its north-central and north-western edges. We fitted species distribution models for the current distribution of the conifer and the disease. Then, these models were projected into nine Global Climate Models and two different climatic scenarios which totalled to 18 different future climate predictions representative of 2050. Based on the level of agreement among them, we created future suitability maps for the pine and for the disease independently, which were then used to assess exposure of current populations of P. pinaster to abiotic and biotic effects of climate change. Almost the entire distribution of P. pinaster in the Spanish Iberian Peninsula will be subjected to abiotic exposure likely to be driven by the predicted increase in drought events in the future. Furthermore, we detected a reduction in exposure to pitch canker that will be concentrated along the north-western edge of the study area. Setting up breeding programs is recommended in highly exposed and productive populations, while silvicultural methods and monitoring should be applied in those less productive, but still exposed, populations. PMID:28192454

A LATIN-based model reduction approach for the simulation of cycling damage

NASA Astrophysics Data System (ADS)

Bhattacharyya, Mainak; Fau, Amelie; Nackenhorst, Udo; Néron, David; Ladevèze, Pierre

2017-11-01

The objective of this article is to introduce a new method including model order reduction for the life prediction of structures subjected to cycling damage. Contrary to classical incremental schemes for damage computation, a non-incremental technique, the LATIN method, is used herein as a solution framework. This approach allows to introduce a PGD model reduction technique which leads to a drastic reduction of the computational cost. The proposed framework is exemplified for structures subjected to cyclic loading, where damage is considered to be isotropic and micro-defect closure effects are taken into account. A difficulty herein for the use of the LATIN method comes from the state laws which can not be transformed into linear relations through an internal variable transformation. A specific treatment of this issue is introduced in this work.

Reductive dehalogenation of carbon tetrachloride by Escherichia coli K-12

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

Criddle, C.S.; DeWitt, J.T.; McCarty, P.L.

1990-11-01

The formation of radicals from carbon tetrachloride (CT) is often invoked to explain the product distribution resulting from its transformation. Radicals formed by reduction of CT presumably react with constituents of the surrounding milieu to give the observed product distribution. The patterns of transformation observed in this work were consistent with such as hypothesis. In cultures of Escherichia coli K-12, the pathways and rates of CT transformation were dependent on the electron acceptor condition of the media. Use of oxygen and nitrate as electron acceptors generally prevented CT metabolism. At low oxygen levels ({approximately}1%), however, transformation of ({sup 14}C)CT tomore » {sup 14}CO{sub 2} and attachment to cell material did occur, in accord with reports of CT fate in mammalian cell cultures. Under fumarate-respiring conditions, ({sup 14}C)CT was recovered as {sup 14}CO{sub 2}, chloroform, and a nonvolatile fraction. In contrast, fermenting conditions resulted in more chloroform, more cell-bound {sup 14}C, and almost no {sup 14}CO{sub 2}. Rates of transformation of CT were faster under fermenting conditions than under fumarate-respiring conditions. Transformation rates also decreased over time, suggesting the gradual exhaustion of transformation activity. This loss was modeled with a simple exponential decay term.« less

Acid transformation of bauxite residue: Conversion of its alkaline characteristics.

PubMed

Kong, Xiangfeng; Li, Meng; Xue, Shengguo; Hartley, William; Chen, Chengrong; Wu, Chuan; Li, Xiaofei; Li, Yiwei

2017-02-15

Bauxite residue (BR) is a highly alkaline solid hazardous waste produced from bauxite processing for alumina production. Alkaline transformation appears to reduce the environmental risk of bauxite residue disposal areas (BRDAs) whilst potentially providing opportunities for the sustainable reuse and on-going management of BR. Mineral acids, a novel citric acid and a hybrid combination of acid-gypsum treatments were investigated for their potential to reduce residue pH and total alkalinity and transform the alkaline mineral phase. XRD results revealed that with the exception of andradite, the primary alkaline solid phases of cancrinite, grossular and calcite were transformed into discriminative products based on the transformation used. Supernatants separated from BR and transformed bauxite residue (TBR) displayed distinct changes in soluble Na, Ca and Al, and a reduction in pH and total alkalinity. SEM images suggest that mineral acid transformations promote macro-aggregate formation, and the positive promotion of citric acid, confirming the removal or reduction in soluble and exchangeable Na. NEXAFS analysis of Na K-edge revealed that the chemical speciation of Na in TBRs was consistent with BR. Three acid treatments and gypsum combination had no effect on Na speciation, which affects the distribution of Na revealed by sodium STXM imaging. Copyright © 2016 Elsevier B.V. All rights reserved.

Candida parapsilosis: A versatile biocatalyst for organic oxidation-reduction reactions.

PubMed

Chadha, Anju; Venkataraman, Sowmyalakshmi; Preetha, Radhakrishnan; Padhi, Santosh Kumar

2016-10-01

This review highlights the importance of the biocatalyst, Candida parapsilosis for oxidation and reduction reactions of organic compounds and establishes its versatility to generate a variety of chiral synthons. Appropriately designed reactions using C. parapsilosis effect efficient catalysis of organic transformations such as deracemization, enantioselective reduction of prochiral ketones, imines, and kinetic resolution of racemic alcohols via selective oxidation. This review includes the details of these biotransformations, catalyzed by whole cells (wild type and recombinant strains), purified enzymes (oxidoreductases) and immobilized whole cells of C. parapsilosis. The review presents a bioorganic perspective as it discusses the chemo, regio and stereoselectivity of the biocatalyst along with the structure of the substrates and optical purity of the products. Fermentation scale biocatalysis using whole cells of C. parapsilosis for several biotransformations to synthesize important chiral synthons/industrial chemicals is included. A comparison of C. parapsilosis with other whole cell biocatalysts for biocatalytic deracemization and asymmetric reduction of carbonyl and imine groups in the synthesis of a variety of enantiopure products is presented which will provide a basis for the choice of a biocatalyst for a desired organic transformation. Thus, a wholesome perspective on the present status of C. parapsilosis mediated organic transformations and design of new reactions which can be considered for large scale operations is provided. Taken together, C. parapsilosis can now be considered a 'reagent' for the organic transformations discussed here. Copyright © 2016 Elsevier Inc. All rights reserved.

Identification of tissue-specific, abiotic stress-responsive gene expression patterns in wine grape (Vitis vinifera L.) based on curation and mining of large-scale EST data sets

PubMed Central

2011-01-01

Background Abiotic stresses, such as water deficit and soil salinity, result in changes in physiology, nutrient use, and vegetative growth in vines, and ultimately, yield and flavor in berries of wine grape, Vitis vinifera L. Large-scale expressed sequence tags (ESTs) were generated, curated, and analyzed to identify major genetic determinants responsible for stress-adaptive responses. Although roots serve as the first site of perception and/or injury for many types of abiotic stress, EST sequencing in root tissues of wine grape exposed to abiotic stresses has been extremely limited to date. To overcome this limitation, large-scale EST sequencing was conducted from root tissues exposed to multiple abiotic stresses. Results A total of 62,236 expressed sequence tags (ESTs) were generated from leaf, berry, and root tissues from vines subjected to abiotic stresses and compared with 32,286 ESTs sequenced from 20 public cDNA libraries. Curation to correct annotation errors, clustering and assembly of the berry and leaf ESTs with currently available V. vinifera full-length transcripts and ESTs yielded a total of 13,278 unique sequences, with 2302 singletons and 10,976 mapped to V. vinifera gene models. Of these, 739 transcripts were found to have significant differential expression in stressed leaves and berries including 250 genes not described previously as being abiotic stress responsive. In a second analysis of 16,452 ESTs from a normalized root cDNA library derived from roots exposed to multiple, short-term, abiotic stresses, 135 genes with root-enriched expression patterns were identified on the basis of their relative EST abundance in roots relative to other tissues. Conclusions The large-scale analysis of relative EST frequency counts among a diverse collection of 23 different cDNA libraries from leaf, berry, and root tissues of wine grape exposed to a variety of abiotic stress conditions revealed distinct, tissue-specific expression patterns, previously unrecognized stress-induced genes, and many novel genes with root-enriched mRNA expression for improving our understanding of root biology and manipulation of rootstock traits in wine grape. mRNA abundance estimates based on EST library-enriched expression patterns showed only modest correlations between microarray and quantitative, real-time reverse transcription-polymerase chain reaction (qRT-PCR) methods highlighting the need for deep-sequencing expression profiling methods. PMID:21592389

Why some plant species are rare.

PubMed

Wieger Wamelink, G W; Wamelink, G W Weiger; Goedhart, Paul W; Frissel, Joep; Frissel, Josep Y

2014-01-01

Biodiversity, including plant species diversity, is threatened worldwide as a result of anthropogenic pressures such as an increase of pollutants and climate change. Rare species in particular are on the verge of becoming extinct. It is still unclear as to why some plant species are rare and others are not. Are they rare due to: intrinsic reasons, dispersal capacity, the effects of management or abiotic circumstances? Habitat preference of rare plant species may play an important role in determining why some species are rare. Based on an extensive data set of soil parameters we investigated if rarity is due to a narrow habitat preference for abiotic soil parameters. For 23 different abiotic soil parameters, of which the most influential were groundwater-table, soil-pH and nutrient-contents, we estimated species responses for common and rare species. Based on the responses per species we calculated the range of occurrence, the range between the 5 and 95 percentile of the response curve giving the habitat preference. Subsequently, we calculated the average response range for common and rare species. In addition, we designed a new graphic in order to provide a better means for presentation of the results. The habitat preferences of rare species for abiotic soil conditions are significantly narrower than for common species. Twenty of the twenty-three abiotic parameters showed on average significantly narrower habitat preferences for rare species than for common species; none of the abiotic parameters showed on average a narrower habitat preference for common species. The results have major implications for the conservation of rare plant species; accordingly management and nature development should be focussed on the maintenance and creation of a broad range of environmental conditions, so that the requirements of rare species are met. The conservation of (abiotic) gradients within ecosystems is particularly important for preserving rare species.

Biotic and abiotic degradation of CL-20 and RDX in soils.

PubMed

Crocker, Fiona H; Thompson, Karen T; Szecsody, James E; Fredrickson, Herbert L

2005-01-01

The caged cyclic nitramine 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) is a new explosive that has the potential to replace existing military explosives, but little is known about its environmental toxicity, transport, and fate. We quantified and compared the aerobic environmental fate of CL-20 to the widely used cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in surface and subsurface soil microcosms. Soil-free controls and biologically attenuated soil controls were used to separate abiotic processes from biologically mediated processes. Both abiotic and biological processes significantly degraded CL-20 in all soils examined. Apparent abiotic, first-order degradation rates (k) for CL-20 were not significantly different between soil-free controls (0.018 < k < 0.030 d(-1)) and biologically attenuated soil controls (0.003 < k < 0.277 d(-1)). The addition of glucose to biologically active soil microcosms significantly increased CL-20 degradation rates (0.068 < k < 1.22 d(-1)). Extents of mineralization of (14)C-CL-20 to (14)CO(2) in biologically active soil microcosms were 41.1 to 55.7%, indicating that the CL-20 cage was broken, since all carbons are part of the heterocyclic cage. Under aerobic conditions, abiotic degradation rates of RDX were generally slower (0 < k < 0.032 d(-1)) than abiotic CL-20 degradation rates. In biologically active soil microcosms amended with glucose aerobic RDX degradation rates varied between 0.010 and 0.474 d(-1). Biodegradation was a key factor in determining the environmental fate of RDX, while a combination of biotic and abiotic processes was important with CL-20. Our data suggest that CL-20 should be less recalcitrant than RDX in aerobic soils.

Effect of jasmonic acid and yeast extract elicitation on low-molecular antioxidants and antioxidant activity of marjoram (Origanum majorana L.).

PubMed

Złotek, Urszula

2017-01-01

Elicitation, which is a way of inducing plant secondary metabolism, may be an effective method for improving the quality of plant food. The aim of this study was to determine how the application of jasmonic acid (as an abiotic elicitor) and yeast extract (as a biotic elicitor) influences the production of some bioactive compounds in marjoram and the antioxidant activity of this herb. Elicitation with 0.01 µM and 1 µM jasmonic acid as well as 0.1% and 1% yeast extracts was used for improving the health-benefiting quality of marjoram. The study focused on the effects of eliciting the level of some phytochemicals and the antioxidant activity of marjoram. There were no significant differences in total phenolic content between the elicited and control plants. In turn, the elicitation with 0.1% and 1% yeast extracts caused 1.8- and 2.5-fold increases in the ascorbic acid content in marjoram leaves, respectively. Both biotic and abiotic elicitation resulted in elevation of chlorophyll content, but only the abiotic elicitor (jasmonic acid) caused a significant increase (by over 50%) in the carotenoid content of marjoram leaves. The antiradical activity of marjoram was increased by the abiotic and biotic elicitation, whereas only the abiotic elicitation resulted in improving the reducing power of this herb. In conclusion, biotic and abiotic elicitation could be an effective strategy for improving the level of some phytochemicals, as well as the antioxidant activity of marjoram. A particularly valuable finding obtained in this study is that natural elicitors e.g. yeast extract can be equally effective in elevating the content of some bioactive compounds in herbs e.g. marjoram as an abiotic one.

Elucidating the Role of Carbon Sources on Abiotic and Biotic Release of Arsenic into Cambodian Aquifers

NASA Astrophysics Data System (ADS)

Koeneke, M.

2017-12-01

Arsenic (As) is a naturally occurring contaminant in Cambodia that has been contaminating well-water sources of millions of people. Commonly, studies look into the biotic factors that cause the arsenic to be released from aquifer sediments to groundwater. However, abiotic release of As from sediments, though little studied, may also play key roles in As contamination of well water. The goal of this research is to quantitatively compare organic-carbon mediated abiotic and biotic release of arsenic from sediments to groundwater. Batch anaerobic incubation experiments under abiotic (sodium azide used to immobilize microbes) and biotic conditions were conducted using Cambodian aquifer sediments, four different organic carbon sources (sodium lactate, sodium citrate, sodium oxalate, and humic acid), and six different carbon concentrations (0, 1, 2.5, 5, 10, 25mg C/L). Dissolved arsenic, iron(Fe), and manganese(Mn) concentrations in the treatments were measured 112 days . In addition, sediment and solution carbon solution was measured . Collectively, these show how different carbon sources, different carbon concentrations, and how abiotic and biotic factors impact the release of arsenic from Cambodian sediments into aquifers. Overall, an introduction of organic carbon to the soil increases the amount of As released from the sediment. The biotic + abiotic and abiotic conditions seemed to play a minimal role in the amount of As released. Dissolved species analysis showed us that 100% of the As was As(V), Our ICP-MS results vary due to the heterogeneity of samples, but when high levels are Fe are seen in solution, we also see high levels of As. We also see higher As concentrations when there is a smaller amount of Mn in solution.

Abiotic stresses affect differently the intron splicing and expression of chloroplast genes in coffee plants (Coffea arabica) and rice (Oryza sativa).

PubMed

Nguyen Dinh, Sy; Sai, Than Zaw Tun; Nawaz, Ghazala; Lee, Kwanuk; Kang, Hunseung

2016-08-20

Despite the increasing understanding of the regulation of chloroplast gene expression in plants, the importance of intron splicing and processing of chloroplast RNA transcripts under stress conditions is largely unknown. Here, to understand how abiotic stresses affect the intron splicing and expression patterns of chloroplast genes in dicots and monocots, we carried out a comprehensive analysis of the intron splicing and expression patterns of chloroplast genes in the coffee plant (Coffea arabica) as a dicot and rice (Oryza sativa) as a monocot under abiotic stresses, including drought, cold, or combined drought and heat stresses. The photosynthetic activity of both coffee plants and rice seedlings was significantly reduced under all stress conditions tested. Analysis of the transcript levels of chloroplast genes revealed that the splicing of tRNAs and mRNAs in coffee plants and rice seedlings were significantly affected by abiotic stresses. Notably, abiotic stresses affected differently the splicing of chloroplast tRNAs and mRNAs in coffee plants and rice seedlings. The transcript levels of most chloroplast genes were markedly downregulated in both coffee plants and rice seedlings upon stress treatment. Taken together, these results suggest that coffee and rice plants respond to abiotic stresses via regulating the intron splicing and expression of different sets of chloroplast genes. Copyright © 2016 Elsevier GmbH. All rights reserved.

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

Wu, T.; Griffin, A. M.; Gorski, C. A.

Dissimilatory microbial reduction of solid-phase Fe(III)-oxides and Fe(III)-bearing phyllosilicates (Fe(III)-phyllosilicates) is an important process in anoxic soils, sediments, and subsurface materials. Although various studies have documented the relative extent of microbial reduction of single-phase Fe(III)-oxides and Fe(III)-phyllosilicates, detailed information is not available on interaction between these two processes in situations where both phases are available for microbial reduction. The goal of this research was to use the model dissimilatory iron-reducing bacterium (DIRB) Geobacter sulfurreducens to study Fe(III)-oxide vs. Fe(III)-phyllosilicate reduction in a range of subsurface materials and Fe(III)-oxide stripped versions of the materials. Low temperature (12K) Mossbauer spectroscopy was usedmore » to infer changes in the relative abundances of Fe(III)-oxide, Fe(III)-phyllosilicate, and phyllosilicate-associated Fe(II) (Fe(II)-phyllosilicate). A Fe partitioning model was employed to analyze the fate of Fe(II) and assess the potential for abiotic Fe(II)-catalyzed reduction of Fe(III)-phyllosilicates. The results showed that in most cases Fe(III)- oxide utilization dominated (70-100 %) bulk Fe(III) reduction activity, and that electron transfer from oxide-derived Fe(II) played only a minor role (ca. 10-20 %) in Fe partitioning. In addition, the extent of Fe(III)-oxide reduction was positively correlated to surface area-normalized cation exchange capacity and the phyllosilicate-Fe(III)/total Fe(III) ratio, which suggests that the phyllosilicates in the natural sediments promoted Fe(III)-oxide reduction by binding of oxide-derived Fe(II), thereby enhancing Fe(III)-oxide reduction by reducing or delaying the inhibitory effect that Fe(II) accumulation on oxide and DIRB cell surfaces has on Fe(III)-oxide reduction. In general our results suggest that although Fe(III)-oxide reduction is likely to dominate bulk Fe(III) reduction in most subsurface sediments, Fe(II) binding by phyllosilicates is likely to play a key role in controlling the long-term kinetics of Fe(III)-oxide reduction.« less

WRKY Proteins: Signaling and Regulation of Expression during Abiotic Stress Responses

PubMed Central

Banerjee, Aditya

2015-01-01

WRKY proteins are emerging players in plant signaling and have been thoroughly reported to play important roles in plants under biotic stress like pathogen attack. However, recent advances in this field do reveal the enormous significance of these proteins in eliciting responses induced by abiotic stresses. WRKY proteins act as major transcription factors, either as positive or negative regulators. Specific WRKY factors which help in the expression of a cluster of stress-responsive genes are being targeted and genetically modified to induce improved abiotic stress tolerance in plants. The knowledge regarding the signaling cascade leading to the activation of the WRKY proteins, their interaction with other proteins of the signaling pathway, and the downstream genes activated by them are altogether vital for justified targeting of the WRKY genes. WRKY proteins have also been considered to generate tolerance against multiple abiotic stresses with possible roles in mediating a cross talk between abiotic and biotic stress responses. In this review, we have reckoned the diverse signaling pattern and biological functions of WRKY proteins throughout the plant kingdom along with the growing prospects in this field of research. PMID:25879071

A membraneless single compartment abiotic glucose fuel cell

NASA Astrophysics Data System (ADS)

Slaughter, Gymama; Sunday, Joshua

2014-09-01

A simple energy harvesting strategy has been developed to selectively catalyze glucose in the presence of oxygen in a glucose/O2 fuel cell. The anode consists of an abiotic catalyst Al/Au/ZnO, in which ZnO seed layer was deposited on the surface of Al/Au substrate using hydrothermal method. The cathode is constructed from a single rod of platinum with an outer diameter of 500 μm. The abiotic glucose fuel cell was studied in phosphate buffer solution (pH 7.4) containing 5 mM glucose at a temperature of 22 °C. The cell is characterized according to its open-circuit voltage, polarization profile, and power density plot. Under these conditions, the abiotic glucose fuel cell possesses an open-circuit voltage of 840 mV and delivered a maximum power density of 16.2 μW cm-2 at a cell voltage of 495 mV. These characteristics are comparable to biofuel cell utilizing a much more complex system design. Such low-cost lightweight abiotic catalyzed glucose fuel cells have a great promise to be optimized, miniaturized to power bio-implantable devices.

WRKY proteins: signaling and regulation of expression during abiotic stress responses.

PubMed

Banerjee, Aditya; Roychoudhury, Aryadeep

2015-01-01

WRKY proteins are emerging players in plant signaling and have been thoroughly reported to play important roles in plants under biotic stress like pathogen attack. However, recent advances in this field do reveal the enormous significance of these proteins in eliciting responses induced by abiotic stresses. WRKY proteins act as major transcription factors, either as positive or negative regulators. Specific WRKY factors which help in the expression of a cluster of stress-responsive genes are being targeted and genetically modified to induce improved abiotic stress tolerance in plants. The knowledge regarding the signaling cascade leading to the activation of the WRKY proteins, their interaction with other proteins of the signaling pathway, and the downstream genes activated by them are altogether vital for justified targeting of the WRKY genes. WRKY proteins have also been considered to generate tolerance against multiple abiotic stresses with possible roles in mediating a cross talk between abiotic and biotic stress responses. In this review, we have reckoned the diverse signaling pattern and biological functions of WRKY proteins throughout the plant kingdom along with the growing prospects in this field of research.

Relative Importance of Biotic and Abiotic Forces on the Composition and Dynamics of a Soft-Sediment Intertidal Community

PubMed Central

Barbeau, Myriam A.

2016-01-01

Top-down, bottom-up, middle-out and abiotic factors are usually viewed as main forces structuring biological communities, although assessment of their relative importance, in a single study, is rarely done. We quantified, using multivariate methods, associations between abiotic and biotic (top-down, bottom-up and middle-out) variables and infaunal population/community variation on intertidal mudflats in the Bay of Fundy, Canada, over two years. Our analysis indicated that spatial structural factors like site and plot accounted for most of the community and population variation. Although we observed a significant relationship between the community/populations and the biotic and abiotic variables, most were of minor importance relative to the structural factors. We suggest that community and population structure were relatively uncoupled from the structuring influences of biotic and abiotic factors in this system because of high concentrations of resources that sustain high densities of infauna and limit exploitative competition. Furthermore, we hypothesize that the infaunal community primarily reflects stochastic spatial events, namely a “first come, first served” process. PMID:26790098

Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.

PubMed

Priest, Henry D; Fox, Samuel E; Rowley, Erik R; Murray, Jessica R; Michael, Todd P; Mockler, Todd C

2014-01-01

Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

Lack of anodic capacitance causes power overshoot in microbial fuel cells.

PubMed

Peng, Xinhong; Yu, Han; Yu, Hongbing; Wang, Xin

2013-06-01

Power overshoot commonly makes the performance evaluation of microbial fuel cells (MFCs) inaccurate. Here, three types of carbon with different capacitance (ultracapacitor activated carbon (UAC), plain activated carbon (PAC) and carbon black (CB)) rolled on stainless steel mesh (SSM) as anodes to investigate the relationship between overshoot and anodic capacitance. It was not observed in all cycles of UAC-MFCs (from Cycle 2 to 4) due to the largest abiotic capacitance (Cm(abiotic)) of 2.1F/cm(2), while this phenomenon was eliminated in PAC-MFCs (Cm(abiotic)=1.6 F/cm(2)) from Cycle 3 and in CB-MFCs (Cm(abiotic)=0.5F/cm(2)) from Cycle 4, indicated that the Cm(abiotic) of the anode stored charges and functioned as electron shuttle to overcome the power overshoot. With bacterial colonization, the transient charge storage in biofilm resulted in a 0.1-0.4F/cm(2) increase in total capacitance for anodes, which was the possible reason for the elimination of power overshoot in PAC/CB-MFCs after multi cycle acclimation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Advances in crop proteomics: PTMs of proteins under abiotic stress.

PubMed

Wu, Xiaolin; Gong, Fangping; Cao, Di; Hu, Xiuli; Wang, Wei

2016-03-01

Under natural conditions, crop plants are frequently subjected to various abiotic environmental stresses such as drought and heat wave, which may become more prevalent in the coming decades. Plant acclimation and tolerance to an abiotic stress are always associated with significant changes in PTMs of specific proteins. PTMs are important for regulating protein function, subcellular localization and protein activity and stability. Studies of plant responses to abiotic stress at the PTMs level are essential to the process of plant phenotyping for crop improvement. The ability to identify and quantify PTMs on a large-scale will contribute to a detailed protein functional characterization that will improve our understanding of the processes of crop plant stress acclimation and stress tolerance acquisition. Hundreds of PTMs have been reported, but it is impossible to review all of the possible protein modifications. In this review, we briefly summarize several main types of PTMs regarding their characteristics and detection methods, review the advances in PTMs research of crop proteomics, and highlight the importance of specific PTMs in crop response to abiotic stress. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Overexpression of SlGRAS40 in Tomato Enhances Tolerance to Abiotic Stresses and Influences Auxin and Gibberellin Signaling

PubMed Central

Liu, Yudong; Huang, Wei; Xian, Zhiqiang; Hu, Nan; Lin, Dongbo; Ren, Hua; Chen, Jingxuan; Su, Deding; Li, Zhengguo

2017-01-01

Abiotic stresses are major environmental factors that inhibit plant growth and development impacting crop productivity. GRAS transcription factors play critical and diverse roles in plant development and abiotic stress. In this study, SlGRAS40, a member of the tomato (Solanum lycopersicum) GRAS family, was functionally characterized. In wild-type (WT) tomato, SlGRAS40 was upregulated by abiotic stress induced by treatment with D-mannitol, NaCl, or H2O2. Transgenic tomato plants overexpressing SlGRAS40 (SlGRAS40-OE) were more tolerant of drought and salt stress than WT. SlGRAS40-OE plants displayed pleiotropic phenotypes reminiscent of those resulting from altered auxin and/or gibberellin signaling. A comparison of WT and SlGRAS40-OE transcriptomes showed that the expression of a large number of genes involved in hormone signaling and stress responses were modified. Our study of SlGRAS40 protein provides evidence of how another GRAS plays roles in resisting abiotic stress and regulating auxin and gibberellin signaling during vegetative and reproductive growth in tomato. PMID:29018467

Insularity and the determinants of lizard population density.

PubMed

Buckley, Lauren B; Jetz, Walter

2007-06-01

The relative effects of resource availability and partitioning on animal population density are unresolved yet central to ecology and conservation. Species-depauperate islands offer an intriguing test case. Across 643 lizard populations from around the world, local abundances are one order of magnitude higher on islands than on mainlands, even when controlled for resource availability. On mainlands, predator and competitor richness only weakly correlate with lizard densities. On islands, sharp reductions in predator and competitor richness are the dominant drivers of lizard abundance. Our results demonstrate the dramatic effect insularity has on the interplay between biotic and abiotic control of animal abundances and the heightened sensitivity of island communities to species' losses and gains.

Cloning and characterization of a novel stress-responsive WRKY transcription factor gene (MusaWRKY71) from Musa spp. cv. Karibale Monthan (ABB group) using transformed banana cells.

PubMed

Shekhawat, Upendra K Singh; Ganapathi, Thumballi R; Srinivas, Lingam

2011-08-01

WRKY transcription factor proteins play significant roles in plant stress responses. Here, we report the cloning and characterization of a novel WRKY gene, MusaWRKY71 isolated from an edible banana cultivar Musa spp. Karibale Monthan (ABB group). MusaWRKY71, initially identified using in silico approaches from an abiotic stress-related EST library, was later extended towards the 3' end using rapid amplification of cDNA ends technique. The 1299-bp long cDNA of MusaWRKY71 encodes a protein with 280 amino acids and contains a characteristic WRKY domain in the C-terminal half. Although MusaWRKY71 shares good similarity with other monocot WRKY proteins the substantial size difference makes it a unique member of the WRKY family in higher plants. The 918-bp long 5' proximal region determined using thermal asymmetric interlaced-polymerase chain reaction has many putative cis-acting elements and transcription factor binding motifs. Subcellular localization assay of MusaWRKY71 performed using a GFP-fusion platform confirmed its nuclear targeting in transformed banana suspension cells. Importantly, MusaWRKY71 expression in banana plantlets was up-regulated manifold by cold, dehydration, salt, ABA, H2O2, ethylene, salicylic acid and methyl jasmonate treatment indicating its involvement in response to a variety of stress conditions in banana. Further, transient overexpression of MusaWRKY71 in transformed banana cells led to the induction of several genes, homologues of which have been proven to be involved in diverse stress responses in other important plants. The present study is the first report on characterization of a banana stress-related transcription factor using transformed banana cells.

Rapid analysis of diclofenac and some of its transformation products in the three-spined stickleback, Gasterosteus aculeatus, by liquid chromatography-tandem mass spectrometry.

PubMed

Daniele, Gaëlle; Fieu, Maëva; Joachim, Sandrine; Bado-Nilles, Anne; Baudoin, Patrick; Turies, Cyril; Porcher, Jean-Marc; Andres, Sandrine; Vulliet, Emmanuelle

2016-06-01

Pharmaceuticals are emerging organic contaminants ubiquitously present in the environment due to incessant input into the aquatic compartment mainly resulting from incomplete removal in wastewater treatment plants. One of the major preoccupations concerning pharmaceuticals released into surface waters is their potential for bioaccumulation in biota, possibly leading to deleterious effects on ecosystems especially as they could affect a broad variety of organisms living in or depending on the aquatic environment. Thus, the development of accurate and sensitive methods is necessary to detect these compounds in aquatic ecosystems. Considering this need, this study deals with the analytical development of a methodology to quantify traces of diclofenac together with some of its biotic and abiotic transformation products in whole-body tissue of three-spined stickleback. A simple and reliable extraction method based on a modified QuEChERS extraction is implemented on 200 mg of fish. The detection and quantification of the ten target compounds are performed using liquid chromatography-tandem mass spectrometry. The whole process was successfully validated regarding linearity, recovery, repeatability, and reproducibility. The method limits of detection and quantification do not exceed 1 ng/g. To reproduce environmental conditions, we measured the concentration of DCF and its transformation products in three-spined sticklebacks after a 6-month exposure in mesocosms at several levels of DCF ranging from 0.05 to 4.1 μg/L. The phase I metabolite 4'-hydroxydiclofenac was detected in fish samples exposed at the highest DCF concentration. Graphical abstract Analysis of diclofenac and some of its transformation products in the three-spined stickleback, Gasterosteus aculeatus, by QuEChERS extraction followed by LC-MS/MS.

Optimized satellite image compression and reconstruction via evolution strategies

NASA Astrophysics Data System (ADS)

Babb, Brendan; Moore, Frank; Peterson, Michael

2009-05-01

This paper describes the automatic discovery, via an Evolution Strategy with Covariance Matrix Adaptation (CMA-ES), of vectors of real-valued coefficients representing matched forward and inverse transforms that outperform the 9/7 Cohen-Daubechies-Feauveau (CDF) discrete wavelet transform (DWT) for satellite image compression and reconstruction under conditions subject to quantization error. The best transform evolved during this study reduces the mean squared error (MSE) present in reconstructed satellite images by an average of 33.78% (1.79 dB), while maintaining the average information entropy (IE) of compressed images at 99.57% in comparison to the wavelet. In addition, this evolved transform achieves 49.88% (3.00 dB) average MSE reduction when tested on 80 images from the FBI fingerprint test set, and 42.35% (2.39 dB) average MSE reduction when tested on a set of 18 digital photographs, while achieving average IE of 104.36% and 100.08%, respectively. These results indicate that our evolved transform greatly improves the quality of reconstructed images without substantial loss of compression capability over a broad range of image classes.

Multiadaptive Bionic Wavelet Transform: Application to ECG Denoising and Baseline Wandering Reduction

NASA Astrophysics Data System (ADS)

Sayadi, Omid; Shamsollahi, Mohammad B.

2007-12-01

We present a new modified wavelet transform, called the multiadaptive bionic wavelet transform (MABWT), that can be applied to ECG signals in order to remove noise from them under a wide range of variations for noise. By using the definition of bionic wavelet transform and adaptively determining both the center frequency of each scale together with the[InlineEquation not available: see fulltext.]-function, the problem of desired signal decomposition is solved. Applying a new proposed thresholding rule works successfully in denoising the ECG. Moreover by using the multiadaptation scheme, lowpass noisy interference effects on the baseline of ECG will be removed as a direct task. The method was extensively clinically tested with real and simulated ECG signals which showed high performance of noise reduction, comparable to those of wavelet transform (WT). Quantitative evaluation of the proposed algorithm shows that the average SNR improvement of MABWT is 1.82 dB more than the WT-based results, for the best case. Also the procedure has largely proved advantageous over wavelet-based methods for baseline wandering cancellation, including both DC components and baseline drifts.

The Nitrogen Cycle Before the Rise of Oxygen

NASA Astrophysics Data System (ADS)

Ward, L. M.; Hemp, J.; Fischer, W. W.

2016-12-01

The nitrogen cycle on Earth today is driven by a complex network of microbially-mediated transformations. Atmospheric N2 is fixed into biologically available forms that can either be incorporated into biomass or utilized for bioenergetic redox reactions. The cycle is kept in balance by the return of fixed nitrogen to the atmospheric N2 pool by anammox and denitrification. The early evolution and history of the nitrogen cycle is not well resolved, particularly before the evolution of oxygenic photosynthesis and rise of atmospheric oxygen ca. 2.3 Gya. Ammonia oxidation is a biochemically difficult reaction requiring activation of ammonia using O2 or oxidized nitrogen species that are produced using O2. Before the rise of oxygen, when O2 was largely unavailable, nitrification could not proceed, trapping fixed nitrogen in reduced forms such as ammonia and biomass. Without production of nitrite and nitrate, anammox and denitrification could not occur, preventing return of fixed nitrogen to the N2 pool and leaving the nitrogen cycle unclosed. While it has been hypothesized that ammonia oxidation could be driven anaerobically by processes such as phototrophy or iron reduction, these metabolisms have not been recovered in extant microorganisms, and would require complex unknown biochemical mechanisms. Furthermore, phylogenetic data for the key organisms and biochemical pathways involved in denitrification and anammox suggest that these metabolisms postdate the rise of oxygen. This is particularly clear for steps utilizing enzymes in the Heme-Copper Oxidoreductase superfamily, which appear to have originally evolved for O2 reduction at non-negligible substrate concentrations. Together, this suggests that the Archean nitrogen cycle was not closed, and that nitrogen fixed to reduced forms—either through biological nitrogen fixation or abiotic processes—was not easily returned to the atmospheric N2 pool. In principle, this could have stripped the atmosphere of N2 over timescales of hundreds of Myr, which is consistent with recent paleopressure estimates that suggest < 0.5 bar by late Archean time. The modern, N2-rich atmosphere and (largely) closed biological nitrogen cycle may therefore not have evolved until Proterozoic time, after the rise of oxygen.

Biogenic nanosilver synthesized in Metarhizium robertsii waste mycelium extract – As a modulator of Candida albicans morphogenesis, membrane lipidome and biofilm

PubMed Central

Budzyńska, Aleksandra; Bernat, Przemysław

2018-01-01

Due to low efficacy of classic antimicrobial drugs, finding new active preparations attracts much attention. In this study an innovative, cost-effective and environmentally friendly method was applied to produce silver nanoparticles (AgNPs) using filamentous fungi Metarhizium robertsii biomass waste. It was shown that these NPs possess prominent antifungal effects against C. albicans, C. glabrata and C. parapsilosis reference strains. Further detailed studies were performed on C. albicans ATCC 90028. AgNPs kill curve (CFU method and esterase-mediated reduction of fluorescein diacetate); fractionally inhibitory concentration index (FICI) with fluconazole (FLC); effect on fungal cell membrane permeability (propidium iodide (PI) staining), membrane lipids profile (HPLC-MS), yeast morphotypes and intracellular reactive oxygen species level (H2DCFDA probe) were investigated. Anti-adhesive and anti-biofilm properties of AgNPs (alone and in combination with FLC) were also tested. Biosafety of AgNPs use was assessed in vitro in cytotoxicity tests against L929 fibroblasts, pulmonary epithelial A549 cell line, and red blood cells. Significant reduction in the viability of yeast cells treated with AgNPs was shown within 6 h. The proportion of C. albicans PI-positive cells increased in a dose and time-dependent manner. Changes in the qualitative and quantitative profile of cell membrane lipids, including significant decline in the quantity of most phospholipid species containing C18:2 and an increase in the amount of phospholipids containing C18:1 acyl species were observed after yeast exposure to AgNPs. CLSM images showed an enhancement in ROS intracellular accumulation in C. albicans treated with biogenic nanosilver. C. albicans transformation from yeast to hyphal forms was also reduced. AgNPs decreased adhesion of yeast to abiotic surfaces, as well as acted synergistically with FLC against sessile population. At fungicidal and fungistatic concentrations, they were non-toxic to mammalian cells. Obtained results confirm suitability of our “green synthesis” method to produce AgNPs with therapeutic potential against fungal infections. PMID:29554119

Transgenic cotton: from biotransformation methods to agricultural application.

PubMed

Zhang, Baohong

2013-01-01

Transgenic cotton is among the first transgenic plants commercially adopted around the world. Since it was first introduced into the field in the middle of 1990s, transgenic cotton has been quickly adopted by cotton farmers in many developed and developing countries. Transgenic cotton has offered many important environmental, social, and economic benefits, including reduced usage of pesticides, indirect increase of yield, minimizing environmental pollution, and reducing labor and cost. Agrobacterium-mediated genetic transformation method is the major method for obtaining transgenic cotton. However, pollen tube pathway-mediated method is also used, particularly by scientists in China, to breed commercial transgenic cotton. Although transgenic cotton plants with disease-resistance, abiotic stress tolerance, and improved fiber quality have been developed in the past decades, insect-resistant and herbicide-tolerant cotton are the two dominant transgenic cottons in the transgenic cotton market.

CHROTRAN 1.0: A mathematical and computational model for in situ heavy metal remediation in heterogeneous aquifers

NASA Astrophysics Data System (ADS)

Hansen, Scott K.; Pandey, Sachin; Karra, Satish; Vesselinov, Velimir V.

2017-12-01

Groundwater contamination by heavy metals is a critical environmental problem for which in situ remediation is frequently the only viable treatment option. For such interventions, a multi-dimensional reactive transport model of relevant biogeochemical processes is invaluable. To this end, we developed a model, chrotran, for in situ treatment, which includes full dynamics for five species: a heavy metal to be remediated, an electron donor, biomass, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, bio-fouling, and biomass death. Our software implementation handles heterogeneous flow fields, as well as arbitrarily many chemical species and amendment injection points, and features full coupling between flow and reactive transport. We describe installation and usage and present two example simulations demonstrating its unique capabilities. One simulation suggests an unorthodox approach to remediation of Cr(VI) contamination.

CHROTRAN: a mathematical and computational model for in situ heavy metal remediation in heterogeneous aquifers

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

Hansen, Scott; Pandey, Sachin; Karra, Satish

Groundwater contamination by heavy metals is a critical environmental problem for which in situ remediation is frequently the only viable treatment option. For such interventions, a three-dimensional reactive transport model of relevant biogeochemical processes is invaluable. To this end, we developed a model, CHROTRAN, for in situ treatment, which includes full dynamics for five species: a heavy metal to be remediated, an electron donor, biomass, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, bio-fouling and biomass death.more » Our software implementation handles heterogeneous flow fields, arbitrarily many chemical species and amendment injection points, and features full coupling between flow and reactive transport. We describe installation and usage and present two example simulations demonstrating its unique capabilities. One simulation suggests an unorthodox approach to remediation of Cr(VI) contamination.« less

Prediction of Bicarbonate Requirements for Enhanced Reductive Bioremediation of Chlorinated Solvent-Contaminated Sites

NASA Astrophysics Data System (ADS)

Robinson, C.; Barry, D. A.

2008-12-01

Enhanced anaerobic dechlorination is a promising technology for in situ remediation of chlorinated ethene DNAPL source areas. However, the build-up of organic acids and HCl in the source zone can lead to significant groundwater acidification. The resulting pH drop inhibits the activity of the dechlorinating microorganisms and thus may stall the remediation process. Source zone remediation requires extensive dechlorination, such that it may be common for soil's natural buffering capacity to be exceeded, and for acidic conditions to develop. In these cases bicarbonate addition (e.g., NaHCO3, KHCO3) is required for pH control. As a design tool for treatment strategies, we have developed BUCHLORAC, a Windows Graphical User Interface based on an abiotic geochemical model that allows the user to predict the acidity generated during dechlorination and associated buffer requirements for their specific operating conditions. BUCHLORAC was motivated by the SABRE (Source Area BioREmediation) project, which aims to evaluate the effectiveness of enhanced reductive dechlorination in the treatment of chlorinated solvent source zones.

CHROTRAN: a mathematical and computational model for in situ heavy metal remediation in heterogeneous aquifers

DOE PAGES

Hansen, Scott; Pandey, Sachin; Karra, Satish; ...

2017-04-25

Groundwater contamination by heavy metals is a critical environmental problem for which in situ remediation is frequently the only viable treatment option. For such interventions, a three-dimensional reactive transport model of relevant biogeochemical processes is invaluable. To this end, we developed a model, CHROTRAN, for in situ treatment, which includes full dynamics for five species: a heavy metal to be remediated, an electron donor, biomass, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, bio-fouling and biomass death.more » Our software implementation handles heterogeneous flow fields, arbitrarily many chemical species and amendment injection points, and features full coupling between flow and reactive transport. We describe installation and usage and present two example simulations demonstrating its unique capabilities. One simulation suggests an unorthodox approach to remediation of Cr(VI) contamination.« less