Ziming Yang

Anaerobic Mercury Methylation and Demethylation by Geobacter bemidjiensis Bem.

Microbial methylation and demethylation are two competing processes controlling the net production and bioaccumulation of neurotoxic methylmercury (MeHg) in natural ecosystems. Although mercury (Hg) methylation by anaerobic microorganisms and demethylation by aerobic Hg-resistant bacteria have both been extensively studied, little attention has been given to MeHg degradation by anaerobic bacteria, particularly the iron-reducing bacterium Geobacter bemidjiensis Bem. Here we report, for the first time, that the strain G. bemidjiensis Bem can mediate a suite of Hg transformations, including Hg(II) reduction, Hg(0) oxidation, MeHg production and degradation under anoxic conditions. Results suggest that G. bemidjiensis utilizes a reductive demethylation pathway to degrade MeHg, with elemental Hg(0) as the major reaction product, possibly due to the presence of genes encoding homologues of an organomercurial lyase (MerB) and a mercuric reductase (MerA). In addition, the cells can strongly sorb Hg(II) and MeHg, reduce or oxidize Hg, resulting in both time and concentration-dependent Hg species transformations. Moderate concentrations (10-500 μM) of Hg-binding ligands such as cysteine enhance Hg(II) methylation but inhibit MeHg degradation. These findings indicate a cycle of Hg methylation and demethylation among anaerobic bacteria, thereby influencing net MeHg production in anoxic water and sediments.

The removal of selenate to low ppb levels from flue gas desulfurization brine using the H2-based membrane biofilm reactor (MBfR)

The H(2)-based membrane biofilm reactor (MBfR) was shown to consistently remove nitrate, nitrite, and selenate at high efficiencies from flue-gas desulfurization brine. Selenate was removed to <50 ppb which is the National Pollutant Discharge Elimination System (NPDES) criteria for the brine to be released into the environment. When selenate was removed to <50 ppb, nitrate and nitrite were still present in the mg/L range which suggests that selenate is able to be secondarily reduced to low levels when nitrate and nitrite serve as the main electron acceptors for bacterial growth. SO(4)(2-) was not removed and therefore did not compete with nitrate and selenate reduction for the available H(2).

Geochemical drivers of organic matter decomposition in arctic tundra soils

Climate change is warming tundra ecosystems in the Arctic, resulting in the decomposition of previously-frozen soil organic matter (SOM) and release of carbon (C) to the atmosphere; however, the processes that control SOM decomposition and C emissions remain highly uncertain. In this study, we evaluate geochemical factors that influence microbial production of carbon dioxide (CO2) and methane (CH4) in the seasonally-thawed active layer of interstitial polygonal tundra near Barrow, Alaska. We report spatial and seasonal patterns of dissolved gases in relation to the geochemical properties of Fe and organic C in soil and soil solution, as determined using spectroscopic and chromatographic techniques. The chemical composition of soil water collected during the annual thaw season varied significantly with depth. Soil water in the middle of the active layer contained abundant Fe(III), and aromatic-C and low-molecular-weight organic acids derived from SOM decomposition. At these depths, CH4 was positively correlated with the ratio of Fe(III) to total Fe in waterlogged transitional and low-centered polygons but negatively correlated in the drier flat- and high-centered polygons. These observations contradict the expectation that CH4 would be uniformly low where Fe(III) was high due to inhibition of methanogenesis by Fe(III)-reduction reactions. Our results suggest that vertically-stratified Fe redox reactions influence respiration/fermentation of SOM and production of substrates (e.g., low-molecular-weight organic acids) for methanogenesis, but that these effects vary with soil moisture. We infer that geochemical differences induced by water saturation dictate microbial products of SOM decomposition, and Fe geochemistry is an important factor regulating methanogenesis in anoxic tundra soils.

Organic Oxidations Using Geomimicry

Oxidations of phenylacetic acid to benzaldehyde, benzyl alcohol to benzaldehyde, and benzaldehyde to benzoic acid have been observed, in water as the solvent and using only copper(II) chloride as the oxidant. The reactions are performed at 250 °C and 40 bar, conditions that mimic hydrothermal reactions that are geochemically relevant. Speciation calculations show that the oxidizing agent is not freely solvated copper(II) ions, but complexes of copper(II) with chloride and carboxylate anions. Measurements of the reaction stoichiometries and also of substituent effects on reactivity allow plausible mechanisms to be proposed. These oxidation reactions are relevant to green chemistry in that they proceed in high chemical yield in water as the solvent and avoid the use of toxic heavy metal oxidizing reagents.

Hydrothermal Photochemistry as a Mechanistic Tool in Organic Geochemistry: The Chemistry of Dibenzyl Ketone

Hydrothermal organic transformations under geochemically relevant conditions can result in complex product mixtures that form via multiple reaction pathways. The hydrothermal decomposition reactions of the model ketone dibenzyl ketone form a mixture of reduction, dehydration, fragmentation, and coupling products that suggest simultaneous and competitive radical and ionic reaction pathways. Here we show how Norrish Type I photocleavage of dibenzyl ketone can be used to independently generate the benzyl radicals previously proposed as the primary intermediates for the pure hydrothermal reaction. Under hydrothermal conditions, the benzyl radicals undergo hydrogen atom abstraction from dibenzyl ketone and para-coupling reactions that are not observed under ambient conditions. The photochemical method allows the primary radical coupling products to be identified, and because these products are generated rapidly, the method also allows the kinetics of the subsequent dehydration and Paal-Knorr cyclization reactions to be measured. In this way, the radical and ionic thermal and hydrothermal reaction pathways can be studied separately.

Effect of NaCl on nitrate removal from ion-exchange spent brine in the membrane biofilm reactor (MBfR)

The H(2)-based membrane biofilm reactor was used to remove nitrate from synthetic ion-exchange brine at NaCl concentrations from ∼3 to 30 g/L. NaCl concentrations below 20 g/L did not affect the nitrate removal flux as long as potassium was available to generate osmotic tolerance for high sodium, the H(2) pressure was adequate, and membrane fouling was eliminated. Operating pHs of 7-8 and periodic citric acid washes controlled membrane fouling and enabled reactor operation for 650 days. At 30 psig H(2) and high nitrate loading rates of 15 to 80 g/m(2) d, nitrate removal fluxes ranged from 2.5 to ∼6 g/m(2) d, which are the highest fluxes observed when treating 30 g/L IX brine. However, percent removals were low, and the H(2) pressure probably limited the removal flux.

Microbial community and functional gene changes in Arctic tundra soils in a microcosm warming experiment

Microbial decomposition of soil organic carbon (SOC) in thawing Arctic permafrost is important in determining greenhouse gas feedbacks of tundra ecosystems to climate. However, the changes in microbial community structure during SOC decomposition are poorly known. Here we examine these changes using frozen soils from Barrow, Alaska, USA, in anoxic microcosm incubation at −2 and 8°C for 122 days. The functional gene array GeoChip was used to determine microbial community structure and the functional genes associated with SOC degradation, methanogenesis, and Fe(III) reduction. Results show that soil incubation after 122 days at 8°C significantly decreased functional gene abundance (P < 0.05) associated with SOC degradation, fermentation, methanogenesis, and iron cycling, particularly in organic-rich soil. These observations correspond well with decreases in labile SOC content (e.g., reducing sugar and ethanol), methane and CO2 production, and Fe(III) reduction. In contrast, the community functional structure was largely unchanged in the −2°C incubation. Soil type (i.e., organic vs. mineral) and the availability of labile SOC were among the most significant factors impacting microbial community structure. These results demonstrate the important roles of microbial community in SOC degradation and support previous findings that SOC in organic-rich Arctic tundra is highly vulnerable to microbial degradation under warming.

Variability of heavy metal content in soils of typical Tibetan grasslands

Relatively high contents of heavy metals were recently reported in the high-altitude Tibetan Plateau (TP) environment, but the source and distribution characteristics of heavy metals in grassland environments of the TP remain unclear. Here, we report the contents of Hg, Cd, As, Pb, Ni, Cr, Cu, and Zn in soils of typical grasslands from the western to eastern parts of the TP, and the factors regulating accumulation of these heavy metals in the soil. Results show a large degree of variability of the eight heavy metals in the topsoil (0–20 cm) of different grasslands of the TP. Distribution characteristics of the heavy metals in the subsoil (20–40 cm) from the different grasslands were similar to those in the topsoil. Concentrations of As, Cd, Cu, and Zn in grassland soil tended to decrease as longitude increased, whereas Hg content displayed an increasing trend with increasing longitude after 88°E. These observations may be related to different sources of the heavy metals in the soils. Our results suggest that Cu, Zn, Cr, Cd, Ni, and As were mainly derived from natural sources, whereas anthropogenic activities could be responsible for the accumulation of Pb and Hg in the soil. Positive correlation between average annual rainfall amounts and soil Hg content may suggest the contribution of precipitation to soil Hg content. However, accumulation and distribution of heavy metals in the grasslands also depend on soil characteristics which could influence the mobility of heavy metals. These findings have important implications for an understanding of the occurrence and accumulation of soil heavy metals in grasslands of high-altitude environments.

Response to Comment on "Anaerobic Mercury Methylation and Demethylation by Geobacter Bemidjiensis Bem".

Demethylation by Geobacter Bemidjiensis Bem” W offer our response to comments by Regnell regarding the calculations of methylation/demethylation rates reported in our paper “Anaerobic Mercury Methylation and Demethylation by Geobacter bemidjiensis Bem”. We disagree with the proposed approach, resulting in the calculated demethylation rate being nearly 2 orders of magnitude slower for methylmercury (MeHg) added externally than for MeHg produced internally. The kinetics of bacterial mercury (Hg) methylation or demethylation is the result of many coupled processes (i.e., Hg sorption, reduction, oxidation, methylation, and demethylation) and thus is far more complex than described by the rate equations in the comment by Regnell. Furthermore, environmental factors, such as presence of small thiols and culture conditions, affect Hg(II) bioavailability and its uptake, thus impacting the observed methylation and demethylation rates. Without a full understanding of all these processes and mechanisms, any presented kinetic model for calculating methylation or demethylation rates and comparing them with others may prove to be a fruitless exercise in data fitting. We now address these points in detail below. First, Regnell noted that “the observation that more Hg(0) than MeHg was produced from HgCl2 suggests that the rate of demethylation (Kdemeth) was higher than the rate of methylation (Kmeth), unless Hg 0 was a result mainly of direct reduction of the added Hg”. However, his subsequent analysis assumed that Hg(0) is a product of demethylation only. We clearly attributed formation of Hg(0) primarily to biological reduction of Hg(II) in the methylation assay (see our original manuscript p. 4368), since G. bemidjiensis is a known metal-reducing bacterium. In fact, when MeHg was added as the sole source of Hg, we observed lower amounts of Hg(0) produced than MeHg degraded, due to oxidation of Hg(0) (see Figure 2 in Lu et al.). Second, Regnell’s model assumed that in the Hg(II) methylation assay all added Hg is available for bacterial methylation, and that demethylation competes with methylation with Kmeth decreasing linearly from 0.03 to 0.015 h −1 over time during demethylation. This assumption is incorrect because ∼38% of the added Hg(II) was rapidly reduced to Hg(0), as described above. More importantly, studies have shown that in pure cultures Hg methylation often exhibits a plateau or a maximum, usually within a few hours or a day, despite the presence of a large quantity of inorganic Hg in the system. Although the mechanism of this stalled methylation is not fully understood, and is a subject of future investigations related to Hg bioavailability, we can reasonably assume a near zero MeHg production after 8 h Hg(II) incubation. Given these considerations, we calculated Kmeth by fitting the data as a pseudo-first-order reaction for the first 8 h, assuming that methylation is limited by the amount of bioavailable Hg, which is subsequently converted to MeHg (∼1.2 nM). As a result, our estimated methylation rate was about 30 times higher than the value obtained by Regnell. After 8 h, MeHg concentration decreased linearly with time. The data thus fitted well with a zero-order kinetics. This linear relationship also holds true when MeHg is added as the sole source of Hg in demethylation assays (see Figure 2 in Lu et al.). Lastly, demethylation rates calculated by Regnell differed by nearly 2 orders of magnitude for MeHg added externally and for MeHg produced internally by the cells. These results seem quite unrealistic. They would imply that indigenously produced MeHg and exogenously added MeHg would end up in different pools or have different availabilities to cells for demethylation. However, our results indicate that the exogenously added MeHg is rapidly absorbed and degraded by the cells (see Figure 3b and Figure 2a in Lu et al.). Similarly, in a study of Hg methylation and demethylation by the sulfate-reducing bacterium Desulfobulbus propionicus (DSM6523) with isotope labeled Hg(II) and MeHg, Bridou et al. observed only a 2-fold difference in demethylation rates between MeHg added externally and MeHg produced internally. The discrepancy here again illustrates that, while different assumptions could be made and different kinetic rate expressions could be used, the calculated methylation or demethylation rates may be only meaningful and comparable if the mechanisms of these processes are well understood, and all the experimental and environmental conditions are fully considered. Xia Lu*,†,‡ Yurong Liu‡,§ Alexander Johs‡ Linduo Zhao‡ Tieshan Wang† Ziming Yang‡ Hui Lin‡ Dwayne A. Elias Eric M. Pierce‡ Liyuan Liang‡,⊥ Tamar Barkay Baohua Gu*,‡ †School of Nuclear Science and Technology, Lanzhou University, Lanzhou, China ‡Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey 08901, United States

Molecular Insights into Arctic Soil Organic Matter Degradation under Warming

Molecular composition of the Arctic soil organic carbon (SOC) and its susceptibility to microbial degradation are uncertain due to heterogeneity and unknown SOC compositions. Using ultrahigh-resolution mass spectrometry, we determined the susceptibility and compositional changes of extractable dissolved organic matter (EDOM) in an anoxic warming incubation experiment (up to 122 days) with a tundra soil from Alaska (United States). EDOM was extracted with 10 mM NH4HCO3 from both the organic- and mineral-layer soils during incubation at both -2 and 8 °C. Based on their O:C and H:C ratios, EDOM molecular formulas were qualitatively grouped into nine biochemical classes of compounds, among which lignin-like compounds dominated both the organic and the mineral soils and were the most stable, whereas amino sugars, peptides, and carbohydrate-like compounds were the most biologically labile. These results corresponded with shifts in EDOM elemental composition in which the ratios of O:C and N:C decreased, while the average C content in EDOM, molecular mass, and aromaticity increased after 122 days of incubation. This research demonstrates that certain EDOM components, such as amino sugars, peptides, and carbohydrate-like compounds, are disproportionately more susceptible to microbial degradation than others in the soil, and these results should be considered in SOC degradation models to improve predictions of Arctic climate feedbacks.