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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.

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.

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.