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Microbial degradation of organic matter is a key driver of subsurface biogeochemistry. Here, we present a bioenergetics-informed kinetic model for the anaerobic degradation of macromolecular organic matter that accounts for extracellular hydrolysis, fermentation, and respiration. The catabolic energy generated by fermentation and respiration is allocated to biomass growth, production of extracellular hydrolytic enzymes, and cellular maintenance. Microbial cells are assumed to exist in active or dormant states with marked differences in maintenance energy requirements. Dormant cells are further assumed to fulfill their maintenance energy requirements by utilizing their own biomass instead of relying on external substrates. When the catabolic Gibbs energy production for a given functional group of microorganisms exceeds the total maintenance energy requirement of the active cells, biomass growth, re-activation of dormant cells, and production of extracellular hydrolytic enzymes are possible. The latter, in turn, allows the microbial community to access more of the available external organic substrates. In the opposite case, active cells decay or become dormant. We apply the model to simulate the anaerobic degradation of cellulose by a hypothetical microbial community consisting of cellulolytic fermenting bacteria and sulfate-reducing bacteria, under conditions representative of those encountered in water-saturated subsurface environments.

Previous work has shown that about 10% of total clay-bound Fe(III) in unaltered nontronite NAu-1 is bioreducible, although it remains unclear how much of the bioreducible Fe pool persists after repeated oscillations between anoxic and oxic conditions. Here, we report on results from an experiment where we monitored the abundance of bioreducible Fe(III) in NAu-1 over three consecutive redox cycles using chemical extractions and Fe isotope analysis to document the changes in the nature and extent of Fe atom exchange. During each cycle, NAu-1 was reduced biotically by Shewanella oneidensis MR-1 and then re-oxidized abiotically by O2 via aeration. By the third reduction period (RP3), the bacteria were only able to reduce 5.7% of the total clay Fe, that is, 40% less than during the first reduction period (RP1). The decrease in bioreducible Fe(III) is attributed to preferential reductive dissolution of Fe(III) from the finest clay particles. Extrapolation of the observed trend implies that, once the reducible Fe of the finest clay particles is removed, around 4% of the total Fe of the clay remains permanently redox-active, presumably as Fe atoms within the octahedral mineral structure that are accessible to the bacteria. The proposed particle size-dependent evolution of bioreducible Fe(III) from RP1 to RP3 is supported by the observed increasing crystalline domain size, preferential Fe dissolution from the smallest aggregates, and decreasing Fe isotope fractionation factors between aqueous Fe(II) and structural Fe(III) and between solid-bound Fe(II) and structural Fe(III). Our results imply that, in redox dynamic environments, the fraction of insoluble clay-bound Fe that is potentially renewable for use by Fe-reducing bacteria is a function of the evolving size distribution of the clay particles.

International audience; Global climate warming disproportionately affects high-latitude and mountainous terrestrial ecosystems. Warming is accompanied by permafrost thaw, shorter winters, earlier snowmelt, more intense soil freeze-thaw cycles, drier summers, and longer fire seasons. These environmental changes in turn impact surface water and groundwater flow regimes, water quality, greenhouse gas emissions, soil stability, vegetation cover, and soil (micro)biological communities. Warming also facilitates agricultural expansion, urban growth, and natural resource development, adding growing anthropogenic pressures to cold regions" landscapes, soil health, and biodiversity. Further advances in the predictive understanding of how cold regions" critical zone processes, functions, and ecosystem services will continue to respond to climate warming and land use changes require multiscale monitoring technologies coupled with integrated observational and modeling tools. We highlight some of the major challenges, knowledge gaps, and opportunities in cold region critical zone research, with an emphasis on subsurface processes and responses in both natural and agricultural ecosystems.

Petroleum hydrocarbon (PHC) contamination is a global environmental issue. Understanding the key factors and mechanisms controlling the fate and mobility of PHCs in soils and aquifers is critical for environmental risk assessment, the development of remediation strategies, and policy decisions. This study focuses on the effects of soil composition and temperature on the sorption and desorption of two representative aromatic PHC compounds: benzene and naphthalene. The experiments were carried out using artificial sandy loam soil mixtures with temperatures ranging from 3 to 25℃. As expected, the sorption capacities of the soils were primarily controlled by the organic carbon (OC) content, while barely affected by the clay content. The sorption data for benzene and naphthalene followed linear to near-linear isotherms. Naphthalene sorption further increased with decreasing temperature, whereas temperature had little effect on benzene sorption. The latter was consistent with the very small magnitude of the sorption enthalpy of benzene. Under imposed dynamic temperature fluctuations, naphthalene sorption and desorption were shown to be reversible: model simulations demonstrated minimal kinetic limitation of the temperature-dependent soil-water partitioning. Our results imply that even in simple artificial soil systems, temperature variations can have complex, but predictable, effects on the soil-pore water partitioning of PHCs and, hence, on their mobility and bioavailability. Understanding the role of temperature is thus a prerequisite to unraveling the coupled abiotic and biotic processes that modulate the fate of PHCs in real-world soils.

Water table fluctuations generate temporally and spatially dynamic physicochemical conditions that drive biogeochemical hot spots and hot moments in the vadose zone. However, their role in the cycling of soil C remains poorly known. Here, we present results from unvegetated column experiments filled with 45 cm of artificial soil containing 10% humus, and inoculated with a natural microbial extract. In one series of three replicate columns, five cycles, each consisting of a 4‐wk drainage followed by a 4‐wk imbibition period, were imposed, whereas in a second series, the water table remained static. Depth‐resolved O2 concentration profiles and headspace CO2 effluxes were markedly different between the two regimes. In the fluctuating regime, drainage periods yielded 2.5 times greater CO2 effluxes than imbibition periods. At the end of the experiment, the fluctuating water table columns exhibited a distinct zone of organic C (OC) depletion in the depth interval of 8–20 cm that was not observed under the static regime. Although this zone showed elevated levels of adenosine triphosphate (ATP), the microbial biomass was actually lower than at the corresponding depth interval of the static regime. A vertically stratified microbial community established in all columns that depended on oxygenation with depth. The 16S ribosomal RNA (rRNA) gene analyses showed a slightly higher diversity in the soil exposed to moisture fluctuations, but there was no clear difference in major taxa and microbial community composition between treatments. These results thus suggest that the localized enhancement of OC degradation induced by the water table fluctuations was driven by a more active, rather than a more abundant or compositionally very different, microbial community.

The final publication is available at Elsevier via https://dx.doi.org/10.1016/j.gca.2018.08.023 © 2018. This open-access version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/

Spectral induced polarization signatures have been used as proxies for microbial abundance in subsurface environments, by taking advantage of the charged properties of microbial cell membranes. The method's applicability, however, remains qualitative, and signal interpretation ambiguous. The adoption of spectral induced polarization as a robust geo‐microbiological tool for monitoring microbial dynamics in porous media requires the development of quantitative relationships between biogeochemical targets and spectral induced polarization parameters, such as biomass density and imaginary conductivity (σ″). Furthermore, deriving cell density information from electrical signals in porous media necessitates a detailed understanding of the nature of the cell membrane surface charge dynamics. We present results from a fully saturated sand‐filled column reactor experiment where Shewanella oneidensis growth during nitrate reduction to ammonium was monitored using spectral induced polarization. While our results further confirm the direct dependence of σ″ on changing cell density, Cole–Cole derived relaxation times also record the changing surface charging properties of the cells, ascribed to toxic stress due to nitrite accumulation. Concurrent estimates of cell size yield the first measurement‐derived estimation of the apparent surface ion diffusion coefficient for cells (Ds = 5.4 ±1.3 µm2 s−1), strengthening the link between spectral induced polarization and electrochemical cell polarization. Our analysis provides a theoretical framework on which to build σ″–cell density relations using bench‐scale experiments, leading to eventual robust non‐destructive monitoring of in situ microbial growth dynamics., Canada Excellence Research Chair programme, Waterloo‐Technion University Cooperation Programme

Overburden and tailings materials from oil sands production were used as construction materials as part of a novel attempt to create a self-sustaining, peat accumulating fen-upland ecosystem. To evaluate the potential for elemental release from the construction materials, total elemental concentrations in the tailings sand, petroleum coke and peat used to construct a fen ecosystem were determined using microwave-assisted acid digestions and compared to a leaching experiment conducted under environmentally-relevant conditions. A comparison of solid phase to aqueous Na, Ca, S and Mg concentrations showed they were highly leachable in the materials. Given that the concentrations of these elements can affect plant community structure, it is important to understand their leachability and mobility as they migrate between materials used to construct the system. To that end, a mass balance of aqueous Na, Ca, S and Mg was conducted based on leaching experiments and materials analysis coupled with existing data from the constructed system. The data indicate that there is a large pool of leachable Na, Ca, S and Mg in the system, estimated at 27 t of Na, 14 t of Ca, 37.3 t of S and 8.8 t of Mg. Since recharge mainly drives the fen-upland system water regime, and discharge in the fen, evapo-accumulation of these solutes on the surface may occur.

We report on stable Fe isotope fractionation during microbial and chemical reduction of structural Fe(III) in nontronite NAu-1. (56)Fe/(54)Fe fractionation factors between aqueous Fe(II) and structural Fe(III) ranged from -1.2 to +0.8‰. Microbial (Shewanella oneidensis and Geobacter sulfurreducens) and chemical (dithionite) reduction experiments revealed a two-stage process. Stage 1 was characterized by rapid reduction of a finite Fe(III) pool along the edges of the clay particles, accompanied by a limited release to solution of Fe(II), which partially adsorbed onto basal planes. Stable Fe isotope compositions revealed that electron transfer and atom exchange (ETAE) occurred between edge-bound Fe(II) and octahedral (structural) Fe(III) within the clay lattice, as well as between aqueous Fe(II) and structural Fe(III) via a transient sorbed phase. The isotopic fractionation factors decreased with increasing extent of reduction as a result of the depletion of the finite bioavailable Fe(III) pool. During stage 2, microbial reduction was inhibited while chemical reduction continued. However, further ETAE between aqueous Fe(II) and structural Fe(III) was not observed. Our results imply that the pool of bioavailable Fe(III) is restricted to structural Fe sites located near the edges of the clay particles. Blockage of ETAE distinguishes Fe(III) reduction of layered clay minerals from that of Fe oxyhydroxides, where accumulation of structural Fe(II) is much more limited.

Thallium (Tl) is emerging as a metal of concern in countries such as China due to its release during the natural weathering of Tl-bearing ore deposits and mining activities. Despite the high toxicity of Tl, few studies have examined the reductive dissolution of Tl mineral phases by microbial populations. In this study we examined the dissolution of synthetic Tl(I)-jarosite, (H(3)O)(0.29)Tl(0.71)Fe(2.74)(SO(4))(2)(OH)(5.22)(H(2)O)(0.78), by Shewanella putrefaciens CN32 using batch experiments under anaerobic circumneutral conditions. Fe(II) concentrations were measured over time and showed Fe(II) production (4.6 mM) in inoculated samples by 893 h not seen in mineral and dead cell controls. Release of aqueous Tl was enhanced in inoculated samples whereby maximum concentrations in inoculated and cell-free samples reached 3.2 and 2.1 mM, respectively, by termination of the experiment. Complementary batch Tl/S. putrefaciens sorption experiments were conducted under experimentally relevant pH (5 and 6.3) at a Tl concentration of 35 μM and did not show significant Tl accumulation by either live or dead cells. Therefore, in contrast to many metals such as Pb and Cd, S. putrefaciens does not represent a sink for Tl in the environment and Tl is readily released from Tl-jarosite during both abiotic and biotic dissolution.

Globally arsenic (As) is a ubiquitous trace element derived from the natural weathering of As-bearing rock. With the onset of reducing conditions, the prevalence of aqueous As(III) may be intensified through biotic and abiotic processes. Here we evaluate the stability of arsenic bearing Ca–Fe hydroxide phases collected from exposed tailings at Ketza River mine, Yukon, Canada, during the reductive dissolution of both acid treated and untreated samples by Shewanella putrefaciens 200R and Shewanella sp. ANA-3. Samples were acid treated in order to remove Ca–Fe oxide coatings and evaluate the influence of these coatings on the rates of microbial Fe(III) and As(V) reduction. Environmental scanning electron microscope (ESEM) micrographs of the solid phase show significant differences in the chemistry and physical morphology of the material by the bacteria over time and are especially evident in the acid treated samples. Moreover, while solution chemistry showed similar As(III) respiration rates of the inoculated acid treated samples for both ANA3 and 200R at ~ 1.1 × 10 −6 μM·s − 1 ·m − 2 , the Fe(II) respiration rates differed at 1.4 × 10 − 7 and 9.5 × 10 − 8 μM·s − 1 ·m −2 respectively, thus suggesting strain specific metal reduction metabolic pathways Additionally, the enhanced metal reduction observed in the acid treated inoculated samples suggests that the presence of the Ca–Fe hydroxide phase in the untreated samples acted as a barrier, inhibiting the bacteria from accessing the metals. This has implications for increased mobilization of metals by metal reducing bacteria within areas of increased acidity, such as acid mine drainage sites and industrial tailings ponds that can come into contact with surface and ground water sources.

Jarosites (MFe(3)(SO(4))(2)(OH)(6)) are precipitated in the Zn industry to remove impurities during the extraction process and contain metals such as Pb and Ag. Jarosite wastes are often confined to capped tailings ponds, thereby creating potential for anaerobic reductive dissolution by microbial populations. This study demonstrates the reductive dissolution of synthetic Pb-jarosite (PbFe(6)(SO(4))(4)(OH)(12)) by a subsurface dissimilatory Fe reducing bacterium (Shewanella putrefaciens CN32) using batch experiments under anaerobic circumneutral conditions. Solution chemistry, pH, Eh, and cell viability were monitored over time and illustrated the reduction of released structural Fe(III) from the Pb-jarosite to Fe(II). Inoculated samples containing Pb-jarosite also demonstrated decreased cellular viability coinciding with increased Pb concentrations. SEM images showed progressive nucleation of electron dense nanoparticles on the surface of bacteria, identified by TEM/EDS as intracellular crystalline precipitates enriched in Pb and P. The intracellular precipitation of Pb by S. putrefaciens CN32 observed in this study provides potential new insight into the biogeochemical cycling of Pb in reducing environments.

The release of U from the mineral meta-autunite {l_brace}Ca[(UO{sub 2})(PO{sub 2})](H{sub 2}O){sub 6}{r_brace} was evaluated using spectroscopy, aqueous geochemistry, and electron microscopy in a minimal media with the dissimilatory metal-reducing bacterium Shewanella putrefaciens 200R. The onset of anaerobic conditions resulted in the rapid release of U and phosphate to solution followed by the reprecipitation of meta-autinite. Spectroscopy measurements (XANES) indicated that the U was not released via reduction during the bacterial incubations, but instead dissolution was promoted by uptake and immobilization of P by the bacterial cells. Our results suggest that U(VI) in 'refractory' P mineral phases may be mobilized from U mill tailings and/or U disposal sites and that the nutrient status (P) of the geologic setting may be a predictor for the lability of U in these environments.

Environmental contextRedox potential is a controlling variable in aquatic chemistry. Through time series data, we show that microbial exudates released by bacteria may control trends in redox potential observed in natural waters. In particular, electron transfer between these exudates and the electrode could explain the values measured in the presence of abundant oxidants such as oxygen and nitrate. AbstractRedox electrodes are commonly used to measure redox potentials (EH) of natural waters. The recorded EH values are usually interpreted in terms of the dominant inorganic redox couples. To further advance the interpretation of measured EH distributions along temporal and spatial redox gradients, we performed a series of reactor experiments in which oxidising and reducing conditions were alternated by switching between sparging with air and N2. Starting from a simple electrolyte solution and ending with a complex biogeochemical system, common groundwater solutes, metabolic substrates (NO3− and C3H5O3−), bacteria (Shewanella oneidensis MR-1) and goethite (α-FeOOH(s)) were tested by increasing the system complexity with each subsequent experiment. This systematic approach yielded a redox cascade ranging from +500 to −350 mV (pH ~7.4). The highest and lowest EH values registered by the platinum (Pt) electrode agreed with Nernstian redox potentials predicted for the O2/H2O2 and FeOOH/Fe2+(aq) couples respectively. Electrode poisoning by the organic pH buffer (MOPS) and addition of bacteria to the aerated solutions resulted in marked decreases in measured EH values. The latter effect is attributed to the release of flavins by Shewanella oneidensis MR-1 to the medium. As expected, equilibrium with the non-electroactive NO3−/NO2−/NH4+ redox couples could not account for the EH values recorded during dissimilatory nitrate reduction to ammonium (DNRA). However, the observed EH range for DNRA coincided with that bracketed by EH values measured in separate abiotic solutions containing either the oxidised (+324 ± 29 mV) or reduced (−229 ± 40 mV) forms of flavins. The results therefore suggest that the Pt electrode detected the presence of the electroactive flavins, even at submicromolar concentrations. In particular, flavins help explain the fairly low EH values measured in the presence of strong oxidants, such as O2 and NO3−.

Jarosites are produced during metallurgical processing, on oxidized sulfide deposits, and in acid mine drainage environments. Despite the environmental relevance of jarosites, few studies have examined their biogeochemical stability. This study demonstrates the simultaneous reduction of structural Fe(III) and aqueous As(V) during the dissolution of synthetic Pb-As jarosite (PbFe(3)(SO(4),AsO(4))(2)(OH)(6)) by Shewanella putrefaciens using batch experiments under anaerobic circumneutral conditions. Fe(III) reduction occurred immediately in inoculated samples while As(V) reduction was observed after 72 h. XANES spectra showed As(III) (14.7%) in the solid phase at 168 h coincident with decreased aqueous As(V). At 336 h, XANES spectra and aqueous speciation analysis demonstrated 20.2% and 3.0% of total As was present as As(III) in the solid and aqueous phase, respectively. In contrast, 12.4% of total Fe was present as aqueous Fe(II) and was below the detection limits of XANES in the solid phase. TEM-EDS analysis at 336 h showed secondary precipitates enriched in Fe and O with minor amounts of As and Pb. Based on experimental data and thermodynamic modeling, we suggest that structural Fe(III) reduction was thermodynamically driven while aqueous As(V) reduction was triggered by detoxification induced to offset the high As(V) (328 μM) concentrations released during dissolution.