Earth & Environmental Sciences

We recently reported the discovery of phenylacetate decarboxylase (PhdB), representing one of only ten glycyl-radical-enzyme reaction types known, and a promising biotechnological tool for first-time biochemical synthesis of toluene from renewable resources. Here, we used experimental and computational data to evaluate the plausibility of three candidate PhdB mechanisms, involving either attack at the phenylacetate methylene carbon or carboxyl group [via H-atom abstraction from COOH or single-electron oxidation of COO^- (Kolbe-type decarboxylation)]. In vitro experimental data included assays with F-labeled phenylacetate, kinetic studies, and tests with site-directed PhdB mutants; computational data involved estimation of reaction energetics using density functional theory (DFT). The DFT results indicated that all three mechanisms are thermodynamically challenging (beyond the range of many known enzymes in terms of endergonicity or activation energy barrier), reflecting the formidable demands on PhdB for catalysis of this reaction. Evidence that PhdB was able to bind α,α-difluorophenylacetate but was unable to catalyze its decarboxylation supported the enzyme's abstraction of a methylene H atom. Diminished activity of H327A and Y691F mutants was consistent with proposed proton donor roles for His327 and Tyr691. Collectively, these and other data most strongly support PhdB attack at the methylene carbon.

Abstract. Microtopographic features, such as polygonal ground, are characteristic sources of landscape heterogeneity in the Alaskan Arctic coastal plain. Here, we analyze the effects of snow redistribution (SR) and lateral subsurface processes on hydrologic and thermal states at a polygonal tundra site near Barrow, Alaska. We extended the land model integrated in the E3SM to redistribute incoming snow by accounting for microtopography and incorporated subsurface lateral transport of water and energy (ELM-3D v1.0). Multiple 10-year-long simulations were performed for a transect across a polygonal tundra landscape at the Barrow Environmental Observatory in Alaska to isolate the impact of SR and subsurface process representation. When SR was included, model predictions better agreed (higher R2, lower bias and RMSE) with observed differences in snow depth between polygonal rims and centers. The model was also able to accurately reproduce observed soil temperature vertical profiles in the polygon rims and centers (overall bias, RMSE, and R2 of 0.59 ∘C, 1.82 ∘C, and 0.99, respectively). The spatial heterogeneity of snow depth during the winter due to SR generated surface soil temperature heterogeneity that propagated in depth and time and led to ∼ 10 cm shallower and ∼ 5 cm deeper maximum annual thaw depths under the polygon rims and centers, respectively. Additionally, SR led to spatial heterogeneity in surface energy fluxes and soil moisture during the summer. Excluding lateral subsurface hydrologic and thermal processes led to small effects on mean states but an overestimation of spatial variability in soil moisture and soil temperature as subsurface liquid pressure and thermal gradients were artificially prevented from spatially dissipating over time. The effect of lateral subsurface processes on maximum thaw depths was modest, with mean absolute differences of ∼ 3 cm. Our integration of three-dimensional subsurface hydrologic and thermal subsurface dynamics in the E3SM land model will facilitate a wide range of analyses heretofore impossible in an ESM context.

In this paper, we present progress made in a study aimed at increasing the understanding of the relative contributions of different mechanisms that may be causing the seismicity occurring at The Geysers geothermal field, California. The approach we take is to integrate: (1) coupled reservoir geomechanical numerical modeling, (2) data from recently upgraded and expanded NCPA/Calpine/LBNL seismic arrays, and (3) tens of years of archival InSAR data from monthly satellite passes. We have conducted a coupled reservoir geomechanical analysis to study potential mechanisms induced by steam production. Our simulation results corroborate co-locations of hypocenter field observations of induced seismicity and their correlation with steam production as reported in the literature. Seismic and InSAR data are being collected and processed for use in constraining the coupled reservoir geomechanical model.

Abstract. Microtopographic features, such as polygonal ground, are characteristic sources of landscape heterogeneity in the Alaskan Arctic coastal plain. Here, we analyze the effects of snow redistribution (SR) and lateral subsurface processes on hydrologic and thermal states at a polygonal tundra site near Barrow, Alaska. We extended the land model integrated in the E3SM to redistribute incoming snow by accounting for microtopography and incorporated subsurface lateral transport of water and energy (ELM-3D v1.0). Multiple 10-year-long simulations were performed for a transect across a polygonal tundra landscape at the Barrow Environmental Observatory in Alaska to isolate the impact of SR and subsurface process representation. When SR was included, model predictions better agreed (higher R2, lower bias and RMSE) with observed differences in snow depth between polygonal rims and centers. The model was also able to accurately reproduce observed soil temperature vertical profiles in the polygon rims and centers (overall bias, RMSE, and R2 of 0.59 ∘C, 1.82 ∘C, and 0.99, respectively). The spatial heterogeneity of snow depth during the winter due to SR generated surface soil temperature heterogeneity that propagated in depth and time and led to ∼ 10 cm shallower and ∼ 5 cm deeper maximum annual thaw depths under the polygon rims and centers, respectively. Additionally, SR led to spatial heterogeneity in surface energy fluxes and soil moisture during the summer. Excluding lateral subsurface hydrologic and thermal processes led to small effects on mean states but an overestimation of spatial variability in soil moisture and soil temperature as subsurface liquid pressure and thermal gradients were artificially prevented from spatially dissipating over time. The effect of lateral subsurface processes on maximum thaw depths was modest, with mean absolute differences of ∼ 3 cm. Our integration of three-dimensional subsurface hydrologic and thermal subsurface dynamics in the E3SM land model will facilitate a wide range of analyses heretofore impossible in an ESM context.

In this paper, we present progress made in a study aimed at increasing the understanding of the relative contributions of different mechanisms that may be causing the seismicity occurring at The Geysers geothermal field, California. The approach we take is to integrate: (1) coupled reservoir geomechanical numerical modeling, (2) data from recently upgraded and expanded NCPA/Calpine/LBNL seismic arrays, and (3) tens of years of archival InSAR data from monthly satellite passes. We have conducted a coupled reservoir geomechanical analysis to study potential mechanisms induced by steam production. Our simulation results corroborate co-locations of hypocenter field observations of induced seismicity and their correlation with steam production as reported in the literature. Seismic and InSAR data are being collected and processed for use in constraining the coupled reservoir geomechanical model.

Copper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarchaeales. The CuMMO proteins in Ca. Angelarchaeales are more similar in structure to those in Nitrososphaerales than those of bacteria, and contain all functional residues required for general monooxygenase activity. Ca. Angelarchaeales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirK) 2-domain cupredoxin proteins co-located with electron transport machinery. Ca. Angelarchaeales also encode significant capacity for peptide/amino acid uptake and degradation and share numerous electron transport mechanisms with the Nitrososphaerales. Ca. Angelarchaeales are detected at high relative abundance in some of the environments where their genomes originated from. While the exact substrate specificities of the novel CuMMOs identified here have yet to be determined, activity on ammonia is possible given their metabolic and ecological context. The identification of an archaeal CuMMO outside of the Nitrososphaerales significantly expands the known diversity of CuMMO enzymes in archaea and suggests previously unaccounted organisms contribute to critical global nitrogen and/or carbon cycling functions.