The effect of biogenic Fe(II) on the stability and sorption of Co(II)EDTA22 to goethite and a subsurface sediment

Laboratory experiments were conducted with suspensions of goethite (α-FeOOH) and a subsurface sediment to assess the influence of bacterial iron reduction on the fate of Co(II)EDTA2-, a representative metal-ligand complex of intermediate stability (log KCo(II)EDTA = 17.97). The goethite was synthetic (ca. 55 m2/g) and the sediment was a Pleistocene age, Fe(III) oxide-containing material from the Atlantic coastal plain (Milford). Shewanella alga strain BrY, a dissimilatory iron reducing bacterium (DIRB), was used to promote Fe(III) oxide reduction. Sorption isotherms and pH adsorption edges were measured for Co2+, Fe2+, Co(II)EDTA2-, and Fe(II)EDTA2- on the two sorbents in 0.001 mol/L Ca(ClO4)2 to aid in experiment interpretation. Anoxic suspensions of the sorbents in PIPES buffer at pH 6.5–7.0 were spiked with Co(II)EDTA2- (10-5 mol/L, 60Co and 14EDTA labeled), inoculated with BrY (1–6 X 108 organisms/mL), and the headspace filled with a N2/H2 gas mix. The experiments were conducted under non-growth conditions. The medium did not contain PO43- (with one exception), trace elements, or vitamins. The tubes were incubated under anoxic conditions at 25°C for time periods in excess of 100 d. Replicate tubes were sacrificed and analyzed at desired time periods for pH, Fe(II)TOT, Fe(aq)2+ , 60Co, and 14EDTA. Abiotic analogue experiments were conducted where Fe(aq)2+ was added in increasing concentration to Co(II)EDTA2-/mineral suspensions to simulate the influence of bacterial Fe(II) evolution. The DIRB generated Fe(II) from both goethite and the Milford sediment that was strongly sorbed by mineral surfaces. Aqueous Fe2+ increased during the experiment as surfaces became saturated; Fe(aq)2+ induced the dissociation of Co(II)EDTA2- into a mixture of Co2+, Co(II)EDTA2-, and Fe(II)EDTA2- (log KFe(II)EDTA = 15.98). The extent of dissociation of Co(II)EDTA2- was greater in the subsurface sediment because it sorbed Fe(II) less strongly than did goethite. The post dissociation sorption behavior of Co2+ was dependent on pH and the intrinsic sorptivity of the solid phases. Dissociation generally lead to an increase in the sorption (e.g., Kd) of Co2+ relative to EDTA4- (form unspecified). Sorbed biogenic Fe(II) competed with free Co(aq) 2+ and reduced its sorption relative to unreduced material. It is concluded that cationic radionuclides such as 60Co or 239/240Pu, which may be mobilized from disposed wastes by complexation with EDTA4-, may become immobilized in groundwater zones where dissimilatory bacterial iron reduction is operative

Effect of light intensity and wavelength on concentration of plant secondary metabolites in the leaves of Flourensia cernua

Flourensia cernua (tarbush) is a shrub that has encroached into grasslands in many areas of the northern Chihuahuan Desert and contains high levels of carbon-based secondary compounds. Concentrations of secondary compounds are affected by numerous biotic and abiotic influences, including amount and wavelength of solar radiation. However, responses to shade and ultraviolet light restriction are inconsistent among plant species and compound class. We conducted a three-year study to evaluate the effect of shade and UV light restriction on total phenolic and terpene concentrations in tarbush. Sixty plants were randomly assigned to one of three treatments (control, UV light restriction, or 50% incident light restriction). Mean concentrations of total phenolics and total volatiles in tarbush were 82.4 and 12.5 mg/g DM, respectively. Total phenolics did not differ between UV-restricted and control plants, but were lower in shaded plants than the other treatments (P \u3c 0.05). Total volatiles tended to be greater for the UV-restricted treatment than control plants (P = 0.056), with shaded plants not different from either treatment. Treatment effects were detected for 18 individual compounds (P \u3c 0.05). Our results partially support the hypothesis that UV restriction and shading alter carbon-based secondary chemical concentrations

Direct involvement of ombB, omaB, and omcB genes in extracellular reduction of Fe(III) by Geobacter sulfurreducens PCA

The tandem gene clusters orfR-ombB-omaB-omcB and orfS-ombC-omaC-omcC of the metal-reducing bacterium Geobacter sulfurreducens PCA are responsible for trans-outer membrane electron transfer during extracellular reduction of Fe(III)-citrate and ferrihydrite [a poorly crystalline Fe(III) oxide]. Each gene cluster encodes a putative transcriptional factor (OrfR/OrfS), a porin-like outer-membrane protein (OmbB/OmbC), a periplasmic c-type cytochrome (c-Cyt, OmaB/OmaC) and an outer-membrane c-Cyt (OmcB/OmcC). The individual roles of OmbB, OmaB and OmcB in extracellular reduction of Fe(III), however, have remained either uninvestigated or controversial. Here, we showed that replacements of ombB, omaB, omcB and ombB-omaB with an antibiotic gene in the presence of ombC-omaC-omcC had no impact on reduction of Fe(III)-citrate by G. sulfurreducens PCA. Disruption of ombB, omaB, omcB and ombB-omaB in the absence of ombC-omaC-omcC, however, severely impaired the bacterial ability to reduce Fe(III)-citrate as well as ferrihydrite. These results unequivocally demonstrate an overlapping role of ombB-omaB-omcB and ombC-omaC-omcC in extracellular Fe(III) reduction by G. sulfurreducens PCA. Involvement of both ombB-omaB-omcB and ombC-omaC-omcC in extracellular Fe(III) reduction reflects the importance of these trans-outer membrane protein complexes in the physiology of this bacterium. Moreover, the kinetics of Fe(III)-citrate and ferrihydrite reduction by these mutants in the absence of ombC-omaC-omcC were nearly identical, which suggests that absence of any protein subunit eliminates function of OmaB/OmbB/OmcB protein complex. Finally, orfS was found to have a negative impact on the extracellular reduction of Fe(III)-citrate and ferrihydrite in G. sulfurreducens PCA probably by serving as a transcriptional repressor

The Crystal Structure of the Extracellular 11-heme Cytochrome UndA Reveals a Conserved 10-heme Motif and Defined Binding Site for Soluble Iron Chelates

Members of the genus Shewanella translocate deca- or undeca-heme cytochromes to the external cell surface thus enabling respiration using extracellular minerals and polynuclear Fe(III) chelates. The high resolution structure of the first undeca-heme outer membrane cytochrome, UndA, reveals a crossed heme chain with four potential electron ingress/egress sites arranged within four domains. Sequence and structural alignment of UndA and the deca-heme MtrF reveals the extra heme of UndA is inserted between MtrF hemes 6 and 7. The remaining UndA hemes can be superposed over the heme chain of the decaheme MtrF, suggesting that a ten heme core is conserved between outer membrane cytochromes. The UndA structure has also been crystallographically resolved in complex with substrates, an Fe(III)-nitrilotriacetate dimer or an Fe(III)-citrate trimer. The structural resolution of these UndA-Fe(III)-chelate complexes provides a rationale for previous kinetic measurements on UndA and other outer membrane cytochromes

Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process

In a recent study of denitrification dynamics in hyporheic zone sediments, we observed a significant time lag (up to several days) in enzymatic response to the changes in substrate concentration. To explore an underlying mechanism and understand the interactive dynamics between enzymes and nutrients, we developed a trait-based model that associates a community’s traits with functional enzymes, instead of typically used species guilds (or functional guilds). This enzyme-based formulation allows to collectively describe biogeochemical functions of microbial communities without directly parameterizing the dynamics of species guilds, therefore being scalable to complex communities. As a key component of modeling, we accounted for microbial regulation occurring through transcriptional and translational processes, the dynamics of which was parameterized based on the temporal profiles of enzyme concentrations measured using a new signature peptide-based method. The simulation results using the resulting model showed several days of a time lag in enzymatic responses as observed in experiments. Further, the model showed that the delayed enzymatic reactions could be primarily controlled by transcriptional responses and that the dynamics of transcripts and enzymes are closely correlated. The developed model can serve as a useful tool for predicting biogeochemical processes in natural environments, either independently or through integration with hydrologic flow simulators

Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process

In a recent study of denitrification dynamics in hyporheic zone sediments, we observed a significant time lag (up to several days) in enzymatic response to the changes in substrate concentration. To explore an underlying mechanism and understand the interactive dynamics between enzymes and nutrients, we developed a trait-based model that associates a community’s traits with functional enzymes, instead of typically used species guilds (or functional guilds). This enzyme-based formulation allows to collectively describe biogeochemical functions of microbial communities without directly parameterizing the dynamics of species guilds, therefore being scalable to complex communities. As a key component of modeling, we accounted for microbial regulation occurring through transcriptional and translational processes, the dynamics of which was parameterized based on the temporal profiles of enzyme concentrations measured using a new signature peptide-based method. The simulation results using the resulting model showed several days of a time lag in enzymatic responses as observed in experiments. Further, the model showed that the delayed enzymatic reactions could be primarily controlled by transcriptional responses and that the dynamics of transcripts and enzymes are closely correlated. The developed model can serve as a useful tool for predicting biogeochemical processes in natural environments, either independently or through integration with hydrologic flow simulators

Design and Construction of Deinococcus Radiodurans for Biodegradation of Organic Toxins at Radioactive DOE Waste Sites

Seventy million cubic meters of ground and three trillion liters of groundwater have been contaminated by leaking radioactive waste generated in the United States during the Cold War. A cleanup technology is being developed based on the extremely radiation resistant bacterium Deinococcus radiodurans that is being engineered to express bioremediating functions. Research aimed at developing D. radiodurans for organic toxin degradation in highly radioactive waste sites containing radionuclides, heavy metals, and toxic organic compounds was started by this group.Work funded by the existing grant has already contributed to eleven papers on the fundamental biology of D. radiodurans and its design for bioremediation of highly radioactive waste environment

Design and Construction of Deinococcus radiodurans for Biodegradation of Organic Toxins at Radioactive DOE Waste Sites

Immense volumes of radioactive waste, generated from nuclear weapons production during the Cold War, were disposed directly to the ground. The current expense of remediating these polluted sites is driving the development of alternative remediation strategies using microorganisms. The bacterium Deinococcus radiodurans is the most radiation resistant organism known and can grow in highly irradiating (>60 Gray/h) environments (1). Numerous microorganisms (e.g., Pseudomonas sp.) have been described, and studied in detail, for their ability to transform and degrade a variety of organic pollutants (e.g., toluene), present at many radioactive DOE waste sites. Detoxification of the organic toxins at these sites is an important goal in remediating or stabilizing contaminated sites as well as preventing their further dissemination. The aim of this project is to engineer strains of D. radiodurans that are capable of degrading organic/aromatic hydrocarbons present in radioactive mixed waste sites--sites that contain mixtures of toxic organic compounds, radionuclides and heavy metals. Conventional bioremediating organisms are unable to survive at many of these sites because of their sensitivity to radiation. Generally, microorganisms are sensitive to the damaging effects of ionizing radiation, and most of the bacteria currently being studied as candidates for bioremediation are no exception. For example, Pseudomonas sp. is very sensitive to radiation (more sensitive than E. coli) and is not suited to remediate radioactive wastes. Therefore, radiation resistant microorganisms that can remediate toxic organic compounds need to be found in nature or engineered in the laboratory to address this problem

Pore-Scale Characterization of Biogeochemical Controls on Iron and Uranium Speciation under Flow Conditions

Etched silicon microfluidic pore network models (micromodels) with controlled chemical and redox gradients, mineralogy, and microbiology under continuous flow conditions are used for the incremental development of complex microenvironments that simulate subsurface conditions. We demonstrate the colonization of micromodel pore spaces by an anaerobic Fe(III)-reducing bacterial species (Geobacter sulfurreducens) and the enzymatic reduction of a bioavailable Fe(III) phase within this environment. Using both Xray microprobe and X-ray absorption spectroscopy, we investigate the combined effects of the precipitated Fe(III) phases and the microbial population on uranium biogeochemistry under flow conditions. Precipitated Fe(III) phases within the micromodel were most effectively reduced in the presence of an electron shuttle (AQDS), and Fe(II) ions adsorbed onto the precipitated mineral surface without inducing any structural change. In the absence of Fe(III), U(VI) was effectively reduced by the microbial population to insoluble U(IV), which was precipitated in discrete regions associated with biomass. In the presence of Fe(III) phases, however, both U(IV) and U(VI) could be detected associated with biomass, suggesting reoxidation of U(IV) by localized Fe(III) phases. These results demonstrate the importance of the spatial localization of biomass and redox active metals, and illustrate the key effects of pore-scale processes on contaminant fate and reactive transport

Influence of Mass Transfer on Bioavailability and Kinetic Rate of Uranium(VI) Biotransformation

This research is investigating the influence of mass transfer process on the rate and extent of microbial reduction of U(VI) associated with intragrain domains in the Hanford subsurface sediments. The project will develop instrumental techniques to characterize microscopic mass transfer process at the sediment grain scale and to develop kinetic data and process models that describe microbial reduction of intragrain U(VI). Scientific knowledge and process models developed from this research will enhance our understanding on the future behavior of in-ground U(VI) at Hanford and other DOE sites where sediments contain U(VI) in intragrain domains or fracture-matrix systems