Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost.

Climate change is rapidly transforming Arctic landscapes where increasing soil temperatures speed up permafrost thaw. This exposes large carbon stocks to microbial decomposition, possibly worsening climate change by releasing more greenhouse gases. Understanding how microbes break down soil carbon, especially under the anaerobic conditions of thawing permafrost, is important to determine future changes. Here, we studied the microbial community dynamics and soil carbon decomposition potential in permafrost and active layer soils under anaerobic laboratory conditions that simulated an Arctic summer thaw. The microbial and viral compositions in the samples were analyzed based on metagenomes, metagenome-assembled genomes, and metagenomic viral contigs (mVCs). Following the thawing of permafrost, there was a notable shift in microbial community structure, with fermentative Firmicutes and Bacteroidota taking over from Actinobacteria and Proteobacteria over the 60-day incubation period. The increase in iron and sulfate-reducing microbes had a significant role in limiting methane production from thawed permafrost, underscoring the competition within microbial communities. We explored the growth strategies of microbial communities and found that slow growth was the major strategy in both the active layer and permafrost. Our findings challenge the assumption that fast-growing microbes mainly respond to environmental changes like permafrost thaw. Instead, they indicate a common strategy of slow growth among microbial communities, likely due to the thermodynamic constraints of soil substrates and electron acceptors, and the need for microbes to adjust to post-thaw conditions. The mVCs harbored a wide range of auxiliary metabolic genes that may support cell protection from ice formation in virus-infected cells. IMPORTANCE: As the Arctic warms, thawing permafrost unlocks carbon, potentially accelerating climate change by releasing greenhouse gases. Our research delves into the underlying biogeochemical processes likely mediated by the soil microbial community in response to the wet and anaerobic conditions, akin to an Arctic summer thaw. We observed a significant shift in the microbial community post-thaw, with fermentative bacteria like Firmicutes and Bacteroidota taking over and switching to different fermentation pathways. The dominance of iron and sulfate-reducing bacteria likely constrained methane production in the thawing permafrost. Slow-growing microbes outweighed fast-growing ones, even after thaw, upending the expectation that rapid microbial responses to dominate after permafrost thaws. This research highlights the nuanced and complex interactions within Arctic soil microbial communities and underscores the challenges in predicting microbial response to environmental change.

Activity assays of NnlA homologs suggest the natural product N-nitroglycine is degraded by diverse bacteria.

Linear nitramines (R-N(R')NO2; R' = H or alkyl) are toxic compounds, some with environmental relevance, while others are rare natural product nitramines. One of these natural product nitramines is N-nitroglycine (NNG), which is produced by some Streptomyces strains and exhibits antibiotic activity towards Gram-negative bacteria. An NNG degrading heme enzyme, called NnlA, has recently been discovered in the genome of Variovorax sp. strain JS1663 (Vs NnlA). Evidence is presented that NnlA and therefore, NNG degradation activity is widespread. To achieve this objective, we characterized and tested the NNG degradation activity of five Vs NnlA homologs originating from bacteria spanning several classes and isolated from geographically distinct locations. E. coli transformants containing all five homologs converted NNG to nitrite. Four of these five homologs were isolated and characterized. Each isolated homolog exhibited similar oligomerization and heme occupancy as Vs NnlA. Reduction of this heme was shown to be required for NnlA activity in each homolog, and each homolog degraded NNG to glyoxylate, NO2- and NH4+ in accordance with observations of Vs NnlA. It was also shown that NnlA cannot degrade the NNG analog 2-nitroaminoethanol. The combined data strongly suggest that NnlA enzymes specifically degrade NNG and are found in diverse bacteria and environments. These results imply that NNG is also produced in diverse environments and NnlA may act as a detoxification enzyme to protect bacteria from exposure to NNG.

Inhibition of Methylmercury and Methane Formation by Nitrous Oxide in Arctic Tundra Soil Microcosms.

Climate warming causes permafrost thaw predicted to increase toxic methylmercury (MeHg) and greenhouse gas [i.e., methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O)] formation. A microcosm incubation study with Arctic tundra soil over 145 days demonstrates that N2O at 0.1 and 1 mM markedly inhibited microbial MeHg formation, methanogenesis, and sulfate reduction, while it slightly promoted CO2 production. Microbial community analyses indicate that N2O decreased the relative abundances of methanogenic archaea and microbial clades implicated in sulfate reduction and MeHg formation. Following depletion of N2O, both MeHg formation and sulfate reduction rapidly resumed, whereas CH4 production remained low, suggesting that N2O affected susceptible microbial guilds differently. MeHg formation strongly coincided with sulfate reduction, supporting prior reports linking sulfate-reducing bacteria to MeHg formation in the Arctic soil. This research highlights complex biogeochemical interactions in governing MeHg and CH4 formation and lays the foundation for future mechanistic studies for improved predictive understanding of MeHg and greenhouse gas fluxes from thawing permafrost ecosystems.

Reduction of a Heme Cofactor Initiates N-Nitroglycine Degradation by NnlA.

Linear nitramines are potentially carcinogenic environmental contaminants. The NnlA enzyme from Variovorax sp. strain JS1663 degrades the nitramine N-nitroglycine (NNG)-a natural product produced by some bacteria-to glyoxylate and nitrite (NO2-). Ammonium (NH4+) was predicted as the third product of this reaction. A source of nonheme FeII was shown to be required for initiation of NnlA activity. However, the role of this FeII for NnlA activity was unclear. This study reveals that NnlA contains a b-type heme cofactor. Reduction of this heme-either by a nonheme iron source or dithionite-is required to initiate NnlA activity. Therefore, FeII is not an essential substrate for holoenzyme activity. Our data show that reduced NnlA (FeII-NnlA) catalyzes at least 100 turnovers and does not require O2. Finally, NH4+ was verified as the third product, accounting for the complete nitrogen mass balance. Size exclusion chromatography showed that NnlA is a dimer in solution. Additionally, FeII-NnlA is oxidized by O2 and NO2- and stably binds carbon monoxide (CO) and nitric oxide (NO). These are characteristics shared with heme-binding PAS domains. Furthermore, a structural homology model of NnlA was generated using the PAS domain from Pseudomonas aeruginosa Aer2 as a template. The structural homology model suggested His73 is the axial ligand of the NnlA heme. Site-directed mutagenesis of His73 to alanine decreased the heme occupancy of NnlA and eliminated NNG activity, validating the homology model. We conclude that NnlA forms a homodimeric heme-binding PAS domain protein that requires reduction for initiation of the activity. IMPORTANCE Linear nitramines are potential carcinogens. These compounds result from environmental degradation of high-energy cyclic nitramines and as by-products of carbon capture technologies. Mechanistic understanding of the biodegradation of these compounds is critical to inform strategies for their remediation. Biodegradation of NNG by NnlA from Variovorax sp. strain JS 1663 requires nonheme iron, but its role is unclear. This study shows that nonheme iron is unnecessary. Instead, our study reveals that NnlA contains a heme cofactor, the reduction of which is critical for activating NNG degradation activity. These studies constrain the proposals for NnlA reaction mechanisms, thereby informing mechanistic studies of degradation of anthropogenic nitramine contaminants. In addition, these results will inform future work to design biocatalysts to degrade these nitramine contaminants.

Unravelling biogeochemical drivers of methylmercury production in an Arctic fen soil and a bog soil.

Arctic tundra soils store a globally significant amount of mercury (Hg), which could be transformed to the neurotoxic methylmercury (MeHg) upon warming and thus poses serious threats to the Arctic ecosystem. However, our knowledge of the biogeochemical drivers of MeHg production is limited in these soils. Using substrate addition (acetate and sulfate) and selective microbial inhibition approaches, we investigated the geochemical drivers and dominant microbial methylators in 60-day microcosm incubations with two tundra soils: a circumneutral fen soil and an acidic bog soil, collected near Nome, Alaska, United States. Results showed that increasing acetate concentration had negligible influences on MeHg production in both soils. However, inhibition of sulfate-reducing bacteria (SRB) completely stalled MeHg production in the fen soil in the first 15 days, whereas addition of sulfate in the low-sulfate bog soil increased MeHg production by 5-fold, suggesting prominent roles of SRB in Hg(II) methylation. Without the addition of sulfate in the bog soil or when sulfate was depleted in the fen soil (after 15 days), both SRB and methanogens contributed to MeHg production. Analysis of microbial community composition confirmed the presence of several phyla known to harbor microorganisms associated with Hg(II) methylation in the soils. The observations suggest that SRB and methanogens were mainly responsible for Hg(II) methylation in these tundra soils, although their relative contributions depended on the availability of sulfate and possibly syntrophic metabolisms between SRB and methanogens.

Benchmarking SARS CoV-2 Infection in the Workplace to Support Continuity of Operations.

OBJECTIVE: The COVID-19 pandemic jeopardizes continuity of operations of workplaces and the health and safety of workers. Exemplar workplace-related SARS-CoV-2 benchmarks are described and illustrated with empirical data. METHODS: Benchmarks were collected over a 9-month period on a large workplace (N = 5500+). These ranged from quantitative indices associated with RT-qPCR targeted testing and random surveillance screening, surveillance for new variants of SARS-CoV-2, intensive contact tracing, case management, return to work procedures, to monitoring of antibody seropositive status. RESULTS: Data and analyses substantiated effectiveness of interventions. This was evidenced in suppressed infection rates, rapid case identification and isolation, acceptance of the program by employees, documentation of presumptive immunity, and working relationships with senior management. CONCLUSIONS: These SARS-CoV-2 exemplar benchmarks provided an evidence-base for practice and contributed strategically to organizational decisions.

Anaerobic respiration pathways and response to increased substrate availability of Arctic wetland soils.

The availability of labile carbon (C) compounds in Arctic wetland soils is expected to increase due to thawing permafrost and increased fermentation as a result of decomposition of organic matter with warming. How microbial communities respond to this change will affect the balance of CO2 and CH4 emitted during anaerobic organic matter decomposition, and ultimately the net radiative forcing of greenhouse gas emissions from these soils. While soil water content limits aerobic respiration, the factors controlling methanogenesis and anaerobic respiration are poorly defined in suboxic Arctic soils. We conducted incubation experiments on two tundra soils from field sites on the Seward Peninsula, Alaska, with contrasting pH and geochemistry to determine the pathways of anaerobic microbial respiration and changes with increasing substrate availability upon warming. In incubation of soils from the circumneutral Teller site, the ratio of CO2 to CH4 dropped from 10 to <2 after 60 days, indicating rapid depletion of alternative terminal electron acceptors (TEAs). Addition of acetate stimulated production of CO2 and CH4 in a nearly 1 : 1 ratio, consistent with methanogenesis, and the composition of the microbial community shifted to favor clades capable of utilizing the added acetate such as the Fe(iii)-reducing Geobacter and the methanogenic archaea Methanosarcina. In contrast, both CO2 and CH4 production declined with acetate addition during incubation of soils from the more acidic Council site, and fermentative microorganisms increased in abundance despite the high availability of fermentation products. These results demonstrate that the degree to which increasing substrate availability stimulates greenhouse gas production in tundra wetlands will vary widely depending on soil pH and geochemistry.

Temporal, Spatial, and Temperature Controls on Organic Carbon Mineralization and Methanogenesis in Arctic High-Centered Polygon Soils.

Warming temperatures in continuous permafrost zones of the Arctic will alter both hydrological and geochemical soil conditions, which are strongly linked with heterotrophic microbial carbon (C) cycling. Heterogeneous permafrost landscapes are often dominated by polygonal features formed by expanding ice wedges: water accumulates in low centered polygons (LCPs), and water drains outward to surrounding troughs in high centered polygons (HCPs). These geospatial differences in hydrology cause gradients in biogeochemistry, soil C storage potential, and thermal properties. Presently, data quantifying carbon dioxide (CO2) and methane (CH4) release from HCP soils are needed to support modeling and evaluation of warming-induced CO2 and CH4 fluxes from tundra soils. This study quantifies the distribution of microbial CO2 and CH4 release in HCPs over a range of temperatures and draws comparisons to previous LCP studies. Arctic tundra soils were initially characterized for geochemical and hydraulic properties. Laboratory incubations at -2, +4, and +8°C were used to quantify temporal trends in CO2 and CH4 production from homogenized active layer organic and mineral soils in HCP centers and troughs, and methanogen abundance was estimated from mcrA gene measurements. Results showed that soil water availability, organic C, and redox conditions influence temporal dynamics and magnitude of gas production from HCP active layer soils during warming. At early incubation times (2-9 days), higher CO2 emissions were observed from HCP trough soils than from HCP center soils, but increased CO2 production occurred in center soils at later times (>20 days). HCP center soils did not support methanogenesis, but CH4-producing trough soils did indicate methanogen presence. Consistent with previous LCP studies, HCP organic soils showed increased CO2 and CH4 production with elevated water content, but HCP trough mineral soils produced more CH4 than LCP mineral soils. HCP mineral soils also released substantial CO2 but did not show a strong trend in CO2 and CH4 release with water content. Knowledge of temporal and spatial variability in microbial C mineralization rates of Arctic soils in response to warming are key to constraining uncertainties in predictive climate models.

Temperature sensitivity of mineral-enzyme interactions on the hydrolysis of cellobiose and indican by ß-glucosidase.

Extracellular enzymes are mainly responsible for depolymerizing soil organic matter (SOM) in terrestrial ecosystems, and soil minerals are known to affect enzyme activity. However, the mechanisms and the effects of mineral-enzyme interactions on enzymatic degradation of organic matter remain poorly understood. In this study, we examined the adsorption of fungal ß-glucosidase enzyme on minerals and time-dependent changes of enzymatic reactivity, measured by the degradation of two organic substrates (i.e., cellobiose and indican) under both cold (4 °C) and warm (20 and 30 °C) conditions. Hematite, kaolinite, and montmorillonite were used, to represent three common soil minerals with distinctly different surface charges and characteristics. ß-glucosidase was found to sorb more strongly onto hematite and kaolinite than montmorillonite. All three minerals inhibited enzyme degradation of cellobiose and indican, likely due to the inactivation or hindrance of enzyme active sites. The mineral-bound ß-glucosidase retained its specificity for organic substrate degradation, and increasing temperature from 4 to 30 °C enhanced the degradation rates by 2-4 fold for indican and 5-9 fold for cellobiose. These results indicate that enzyme adsorption, mineral type, temperature, and organic substrate specificity are important factors influencing enzymatic reactivity and thus have important implications in further understanding and modeling complex enzyme-facilitated SOM transformations in terrestrial ecosystems.

Expression of benzoyl-CoA metabolism genes in the lignocellulolytic host Caldicellulosiruptor bescii.

Genes responsible for the anaerobic catabolism of benzoate in the thermophilic archaeon Ferroglobus placidus were expressed in the thermophilic lignocellulose-degrading bacterium Caldicellulosiruptor bescii, as a first step to engineering this bacterium to degrade this lignin metabolite. The benzoyl-CoA ligase gene was expressed individually, and in combination with benzoyl-CoA reductase and a putative benzoate transporter. This effort also assessed heterologous expression from a synthetically designed operon whereby each coding sequence was proceeded by a unique C. bescii ribosome binding site sequence. The F. placidicus benzoyl-CoA ligase gene was expressed in C. bescii to produce a full-length protein with catalytic activity. A synthetic 6-gene operon encoding three enzymes involved in benzoate degradation was also successfully expressed in C. bescii as determined by RNA analysis, though the protein products of only four of the genes were detected. The discord between the mRNA and protein measurements, especially considering the two genes lacking apparent protein abundance, suggests variable effectiveness of the ribosome binding site sequences utilized in this synthetic operon. The engineered strains did not degrade benzoate. Although the heterologously expressed gene encoding benzoyl-CoA ligase yielded a protein that was catalytically active in vitro, expression in C. bescii of six benzoate catabolism-related genes combined in a synthetic operon yielded mixed results. More effective expression and in vivo activity might be brought about by validating and using different ribosome binding sites and different promoters. Expressing additional pathway components may alleviate any pathway inhibition and enhance benzoyl-CoA reductase activity.

Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales.

Soils contain a tangle of minerals, water, nutrients, gases, plant roots, decaying organic matter, and microorganisms which work together to cycle nutrients and support terrestrial plant growth. Most soil microorganisms live in periodically interconnected communities closely associated with soil aggregates, i.e., small (<2 mm), strongly bound clusters of minerals and organic carbon that persist through mechanical disruptions and wetting events. Their spatial structure is important for biogeochemical cycling, and we cannot reliably predict soil biological activities and variability by studying bulk soils alone. To fully understand the biogeochemical processes at work in soils, it is necessary to understand the micrometer-scale interactions that occur between soil particles and their microbial inhabitants. Here, we review the current state of knowledge regarding soil aggregate microbial communities and identify areas of opportunity to study soil ecosystems at a scale relevant to individual cells. We present a framework for understanding aggregate communities as "microbial villages" that are periodically connected through wetting events, allowing for the transfer of genetic material, metabolites, and viruses. We describe both top-down (whole community) and bottom-up (reductionist) strategies for studying these communities. Understanding this requires combining "model system" approaches (e.g., developing mock community artificial aggregates), field observations of natural communities, and broader study of community interactions to include understudied community members, like viruses. Initial studies suggest that aggregate-based approaches are a critical next step for developing a predictive understanding of how geochemical and community interactions govern microbial community structure and nutrient cycling in soil.

Epigenetic Footprints of CRISPR/Cas9-Mediated Genome Editing in Plants.

CRISPR/Cas9 has been widely applied to various plant species accelerating the pace of plant genome editing and precision breeding in crops. Unintended effects beyond off-target nucleotide mutations are still somewhat unexplored. We investigated the degree and patterns of epigenetic changes after gene editing. We examined changes in DNA methylation in genome-edited promoters of naturally hypermethylated genes (AT1G72350 and AT1G09970) and hypomethylated genes (AT3G17320 and AT5G28770) from Arabidopsis. Transgenic plants were developed via Agrobacterium-mediated floral dip transformation. Homozygous edited lines were selected from segregated T2 plants by an in vitro digestion assay using ribonucleoprotein complex. Bisulfite sequencing comparisons were made between paired groups of edited and non-edited plants to identify changes in DNA methylation of the targeted loci. We found that directed mutagenesis via CRISPR/Cas9 resulted in no unintended morphological or epigenetic alterations. Phenotypes of wild-type, transgenic empty vector, and transgenic edited plants were similar. Epigenetic profiles revealed that methylation patterns of promoter regions flanking target sequences were identical among wild-type, transgenic empty vector, and transgenic edited plants. There was no effect of mutation type on epigenetic status. We also evaluated off-target mutagenesis effects in the edited plants. Potential off-target sites containing up to 4-bp mismatch of each target were sequenced. No off-target mutations were detected in candidate sites. Our results showed that CRISPR/Cas9 did not leave an epigenetic footprint on either the immediate gene-edited DNA and flanking DNA or introduce off-target mutations.

Improved ZnS nanoparticle properties through sequential NanoFermentation.

Sequential NanoFermentation (SNF) is a novel process which entails sparging microbially produced gas containing H2S from a primary reactor through a concentrated metal-acetate solution contained in a secondary reactor, thereby precipitating metallic sulfide nanoparticles (e.g., ZnS, CuS, or SnS). SNF holds an advantage over single reactor nanoparticle synthesis strategies, because it avoids exposing the microorganisms to high concentrations of toxic metal and sulfide ions. Also, by segregating the nanoparticle products from biological materials, SNF avoids coating nanoparticles with bioproducts that alter their desired properties. Herein, we report the properties of ZnS nanoparticles formed from SNF as compared with ones produced directly in a primary reactor (i.e., conventional NanoFermentation, or "CNF"), commercially available ZnS, and ZnS chemically synthesized by bubbling H2S gas through a Zn-acetate solution. The ZnS nanoparticles produced by SNF provided improved optical properties due to their smaller crystallite size, smaller overall particle sizes, reduced biotic surface coatings, and reduced structural defects. SNF still maintained the advantages of NanoFermentation technology over chemical synthesis including scalability, reproducibility, and lower hazardous waste burden.

Characterization of iron oxide nanoparticle films at the air-water interface in Arctic tundra waters.

Massive amounts of organic carbon have accumulated in Arctic permafrost and soils due to anoxic and low temperature conditions that limit aerobic microbial respiration. Alternative electron acceptors are thus required for microbes to degrade organic carbon in these soils. Iron or iron oxides have been recognized to play an important role in carbon cycle processes in Arctic soils, although the exact form and role as an electron acceptor or donor remain poorly understood. Here, Arctic biofilms collected during the summers of 2016 and 2017 from tundra surface waters on the Seward Peninsula of western Alaska were characterized with a suite of microscopic and spectroscopic methods. We hypothesized that these films contain redox-active minerals bound to biological polymers. The major components of the films were found to be iron oxide nanoparticle aggregates associated with extracellular polymeric substances. The observed mineral phases varied between films collected in different years with magnetite (Fe2+Fe23+O4) nanoparticles (<5nm) predominantly identified in the 2016 films, while for films collected in 2017 ferrihydrite-like amorphous iron oxyhydroxides were found. While the exact formation mechanism of these Artic iron oxide films remains to be explored, the presence of magnetite and other iron oxide/oxyhydroxide nanoparticles at the air-water interface may represent a previously unknown source of electron acceptors for continual anaerobic microbial respiration of organic carbon within poorly drained Arctic tundra.

Cryomilled zinc sulfide: A prophylactic for Staphylococcus aureus-infected wounds.

Bacterial pathogens that colonize wounds form biofilms, which protect the bacteria from the effect of host immune response and antibiotics. This study examined the effectiveness of newly synthesized zinc sulfide in inhibiting biofilm development by Staphylococcus aureus ( S. aureus) strains. Zinc sulfide (ZnS) was anaerobically biosynthesized to produce CompA, which was further processed by cryomilling to maximize the antibacterial properties to produce CompB. The effect of the two compounds on the S. aureus strain AH133 was compared using zone of inhibition assay. The compounds were formulated in a polyethylene glycol cream. We compared the effect of the two compounds on biofilm development by AH133 and two methicillin-resistant S. aureus clinical isolates using the in vitro model of wound infection. Zone of inhibition assay revealed that CompB is more effective than CompA. At 15 mg/application, the formulated cream of either compound inhibited biofilm development by AH133, which was confirmed using confocal laser scanning microscopy. At 20 mg/application, CompB inhibited biofilm development by the two methicillin-resistant S. aureus clinical isolates. To further validate the effectiveness of CompB, mice were treated using the murine model of wound infection. Colony forming cell assay and in vivo live imaging results strongly suggested the inhibition of S. aureus growth.

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.

Impacts of Methane on Carbon Dioxide Storage in Brine Formations.

In the context of geological carbon sequestration (GCS), carbon dioxide (CO2 ) is often injected into deep formations saturated with a brine that may contain dissolved light hydrocarbons, such as methane (CH4 ). In this multicomponent multiphase displacement process, CO2 competes with CH4 in terms of dissolution, and CH4 tends to exsolve from the aqueous into a gaseous phase. Because CH4 has a lower viscosity than injected CO2 , CH4 is swept up into a 'bank' of CH4 -rich gas ahead of the CO2 displacement front. On the one hand, this may provide a useful tracer signal of an approaching CO2 front. On the other hand, the emergence of gaseous CH4 is undesirable because it poses a leakage risk of a far more potent greenhouse gas than CO2 if the cap rock is compromised. Open fractures or faults and wells could result in CH4 contamination of overlying groundwater aquifers as well as surface emissions. We investigate this process through detailed numerical simulations for a large-scale GCS pilot project (near Cranfield, Mississippi) for which a rich set of field data is available. An accurate cubic-plus-association equation-of-state is used to describe the non-linear phase behavior of multiphase brine-CH4 -CO2 mixtures, and breakthrough curves in two observation wells are used to constrain transport processes. Both field data and simulations indeed show the development of an extensive plume of CH4 -rich (up to 90 mol%) gas as a consequence of CO2 injection, with important implications for the risk assessment of future GCS projects.

Influence of Structural Defects on Biomineralized ZnS Nanoparticle Dissolution: An in-Situ Electron Microscopy Study.

The dissolution of metal sulfides, such as ZnS, is an important biogeochemical process affecting fate and transport of trace metals in the environment. However, current studies of in situ dissolution of metal sulfides and the effects of structural defects on dissolution are lacking. Here we have examined the dissolution behavior of ZnS nanoparticles synthesized via several abiotic and biological pathways. Specifically, we have examined biogenic ZnS nanoparticles produced by an anaerobic, metal-reducing bacterium Thermoanaerobacter sp. X513 in a Zn-amended, thiosulfate-containing growth medium in the presence or absence of silver (Ag), and abiogenic ZnS nanoparticles were produced by mixing an aqueous Zn solution with either H2S-rich gas or Na2S solution. The size distribution, crystal structure, aggregation behavior, and internal defects of the synthesized ZnS nanoparticles were examined using high-resolution transmission electron microscopy (TEM) coupled with X-ray energy dispersive spectroscopy. The characterization results show that both the biogenic and abiogenic samples were dominantly composed of sphalerite. In the absence of Ag, the biogenic ZnS nanoparticles were significantly larger (i.e., ∼10 nm) than the abiogenic ones (i.e., ∼3-5 nm) and contained structural defects (e.g., twins and stacking faults). The presence of trace Ag showed a restraining effect on the particle size of the biogenic ZnS, resulting in quantum-dot-sized nanoparticles (i.e., ∼3 nm). In situ dissolution experiments for the synthesized ZnS were conducted with a liquid-cell TEM (LCTEM), and the primary factors (i.e., the presence or absence structural defects) were evaluated for their effects on the dissolution behavior using the biogenic and abiogenic ZnS nanoparticle samples with the largest average particle size. Analysis of the dissolution results (i.e., change in particle radius with time) using the Kelvin equation shows that the defect-bearing biogenic ZnS nanoparticles (γ = 0.799 J/m2) have a significantly higher surface energy than the abiogenic ZnS nanoparticles (γ = 0.277 J/m2). Larger defect-bearing biogenic ZnS nanoparticles were thus more reactive than the smaller quantum-dot-sized ZnS nanoparticles. These findings provide new insight into the factors that affect the dissolution of metal sulfide nanoparticles in relevant natural and engineered scenarios, and have important implications for tracking the fate and transport of sulfide nanoparticles and associated metal ions in the environment. Moreover, our study exemplified the use of an in situ method (i.e., LCTEM) to investigate nanoparticle behavior (e.g., dissolution) in aqueous solutions.

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.