Effects of natural non-volcanic CO2 leakage on soil microbial community composition and diversity.

Geological carbon capture and storage (CCS) can reduce anthropogenic CO2 emissions, but questions exist about impacts at the surface if CO2 leaks from deep storage reservoirs. To examine potential impacts on soils, previous studies have investigated the geochemistry and microbiology of volcanic soils hosting high fluxes of CO2 rich gas. This study builds on those previous investigations by considering impacts of CO2 leakage at a non-volcanic site, where deep geogenic CO2 leaks from a cracked well casing. At the site, we collected 26 soil cores adjacent to soil gas monitoring wells. Based on measured CO2 fluxes, the soil samples fall into two groups 1) high CO2 (flux = 304.6 ± 272.1 g m-2 d-1, conc. = 29.1 ± 34 %) and 2) low CO2 (flux = 15.8 ± 6.1 g m-2 d-1, conc. = 0.8 ± 0.9 %). Soil pH was significantly lower (p < 0.05) in high flux group samples (4.6 ± 0.3) than the low flux ones (5.3 ± 0.7). Beta diversity calculations using 16S rRNA gene sequences and redundancy analysis (RDA) revealed clear clustering of microbial communities relative to CO2 flux and significant correlations of community composition with pH and organic carbon content. In the high flux soils, abundant microbial groups included Acidobacteriota, Ktedonobacteria, and SC-I-84 in the phylum Proteobacteria, as well as Nitrososphaeria, a genus of ammonia oxidizing archaea. Compared to volcanic sites described previously, our non-volcanic site had slight differences in soil geochemical properties and gradual shifts in community compositions between CO2 hotspots and background locations. Moreover, the elevated abundance of SC-I-84 has not been reported in studies of volcanic sites. This study improves our ability to predict potential environmental impacts of geological CCS by expanding the range of conditions over which existing CO2 leakage has been observed.

Effect of CO2 on biogeochemical reactions and microbial community composition in bioreactors with deep groundwater and basalt.

Changes in subsurface microbiology following CO2 injection have the potential to impact carbon trapping in CO2 storage reservoirs. However, much remains to be learned about responses of natural microbial consortia to elevated CO2 in basaltic systems. This study asks: how will microbes from deep (700 m) groundwater change along a gradient in CO2 (0-20 psi) in batch reactor systems containing basalt chips and groundwater amended with lactate? Reactors incubated for 87 days at 23 °C. Results for reactors with low CO2 (0 and 3 psi) differed considerably from those with high CO2 (10 and 20 psi). In reactors with low CO2, pH was >6.5 and lactate started to be used within 24 days. By 40 days, lactate was completely consumed and acetate increased to ~4 mM. As lactate was consumed, sulfate decreased from 0.16 to 0 mM after 40 days. In contrast, in reactors with high CO2, pH was <6.5, lactate and sulfate concentrations varied little and acetate was not produced. Biogeochemical modeling and community analyses indicate that differences between reactors with low and high CO2 reflect tolerances of reactor microbes to CO2 exposure. Communities in the low CO2 reactors carried out syntrophic lactate oxidation coupled with methanogenesis and sulfate reduction. Bacteroidota and Firmicutes became dominant phyla after 24 days and groups capable of sulfate reduction and methanogenesis were detected. In reactors with high CO2, however, biogeochemical activity was insignificant, no groups capable of sulfate reducion or methanogenesis were observed, and the community became less diverse during the incubation. These findings show that the response of microbial consortia can vary sharply along a CO2 gradient, creating significant differences in community composition and biogeochemistry, and that the timescale of basalt weathering is likely not rapid enough to prevent significant stress following a rapid increase in CO2 abundance.

Influences of pH and substrate supply on the ratio of iron to sulfate reduction.

Iron reduction and sulfate reduction often occur simultaneously in anoxic systems, and where that is the case, the molar ratio between the reactions (i.e., Fe/SO42- reduced) influences their impact on water quality and carbon storage. Previous research has shown that pH and the supply of electron donors and acceptors affect that ratio, but it is unclear how their influences compare and affect one another. This study examines impacts of pH and the supply of acetate, sulfate, and goethite on the ratio of iron to sulfate reduction in semi-continuous sediment bioreactors. We examined which parameter had the greatest impact on that ratio and whether the parameter influences depended on the state of each other. Results show that pH had a greater influence than acetate supply on the ratio of iron to sulfate reduction, and that the impact of acetate supply on the ratio depended on pH. In acidic reactors (pH 6.0 media), the ratio of iron to sulfate reduction decreased from 3:1 to 2:1 as acetate supply increased (0-1 mM). In alkaline reactors (pH 7.5 media), iron and sulfate were reduced in equal proportions, regardless of acetate supply. Secondly, a comparison of experiments with and without sulfate shows that the extent of iron reduction was greater if sulfate reduction was occurring and that the effect was larger in alkaline reactors than acidic reactors. Thus, the influence of sulfate supply on iron reduction extent also depended on pH and suggests that iron reduction grows more dependent on sulfate reduction as pH increases. Our results compare well to trends in groundwater geochemistry and provide further evidence that pH is a major control on iron and sulfate reduction in systems with crystalline (oxyhydr)oxides. pH not only affects the ratio between the reactions but also the influences of other parameters on that ratio.

Predicting algal blooms: Are we overlooking groundwater?

Significant advances in understanding and predicting freshwater algal bloom dynamics have emerged in response to both increased occurrence and financial burden of nuisance and harmful blooms. Several factors have been highlighted as key controls of bloom occurrence, including nutrient dynamics, local hydrology, climatic perturbations, watershed geomorphology, biogeochemistry, food-web control, and algal competition. However, a major research gap continues to be the degree to which groundwater inputs modulate microbial biomass production and food-web dynamics at the terrestrial-aquatic interface. We present a synthesis of groundwater related algal bloom literature, upon which we derive a foundational hypothesis: long residence times cause groundwater to be geochemically and biologically distinct from surface water, allowing groundwater inputs to modulate algal bloom dynamics (growth, decline, toxicity) through its control over in-stream water chemistry. Distinct groundwater chemistry can support or prevent algal blooms, depending on specific local conditions. We highlight three mechanisms that influence the impact of groundwater discharge on algal growth: 1) redox state of the subsurface, 2) extent of water-rock interactions, and 3) stability of groundwater discharge. We underscore that in testing hypotheses related to groundwater control over algal blooms, it is critical to understand how changes in land use, water management, and climate will influence groundwater dynamics and, thus, algal bloom probabilities. Given this challenge, we argue that advances in both modeling and data integration, including genomics data and integrated process-based models that capture groundwater dynamics, are needed to illuminate mechanistic controls and improve predictions of algal blooms.

Influence of pH on the balance between methanogenesis and iron reduction.

Methanogenesis and iron reduction play major roles in determining global fluxes of greenhouse gases. Despite their importance, environmental factors that influence their interactions are poorly known. Here, we present evidence that pH significantly influences the balance between each reaction in anoxic environments that contain ferric (oxyhydr)oxide minerals. In sediment bioreactors that contained goethite as a source of ferric iron, both iron reduction and methanogenesis occurred but the balance between them varied significantly with pH. Compared to bioreactors receiving acidic media (pH 6), electron donor oxidation was 85% lower for iron reduction and 61% higher for methanogenesis in bioreactors receiving alkaline media (pH 7.5). Thus, methanogenesis displaced iron reduction considerably at alkaline pH. Geochemistry data collected from U.S. aquifers demonstrate that a similar pattern also exists on a broad spatial scale in natural settings. In contrast, in bioreactors that were not augmented with goethite, clay minerals served as the source of ferric iron and the balance between each reaction did not vary significantly with pH. We therefore conclude that pH can regulate the relative contributions of microbial iron reduction and methanogenesis to carbon fluxes from terrestrial environments. We further propose that the availability of ferric (oxyhydr)oxide minerals influences the extent to which the balance between each reaction is sensitive to pH. The results of this study advance our understanding of environmental controls on microbial methane generation and provide a basis for using pH and the occurrence of ferric minerals to refine predictions of greenhouse gas fluxes.

Dissolved fulvic acids from a high arsenic aquifer shuttle electrons to enhance microbial iron reduction.

It was demonstrated more than two decades ago that microorganisms use humic substances, including fulvic acid (FA), as electron shuttles during iron (Fe) reduction in anaerobic soils and sediments. The relevance of this mechanism for the acceleration of Fe(III) reduction in arsenic-laden groundwater environments is gaining wider attention. Here we provide new evidence that dissolved FAs isolated from sediment-influenced surface water and groundwater in the Bengal Basin were capable of electron shuttling between Geobacter metallireducens and Fe(III). Moreover, all four Bangladesh sediment-derived dissolved FAs investigated in this study had higher electron accepting capacity (176 to 245µmol/g) compared to aquatic FAs, such as Suwanee River Fulvic Acid (67µmol/g). Our direct evidence that Bangladesh FAs are capable of intermediate electron transfer to Fe(III) supports other studies that implicate electron shuttling by sediment-derived aqueous humics to enhance Fe reduction and, in turn, As mobility. Overall, the finding of greater electron accepting capacity by dissolved FAs from groundwater and other sediment-influenced environments advances our understanding of mechanisms that control Fe reduction under conditions where electron transfer is the rate limiting step.

Geochemical Influence on Microbial Communities at CO2-Leakage Analog Sites.

Microorganisms influence the chemical and physical properties of subsurface environments and thus represent an important control on the fate and environmental impact of CO2 that leaks into aquifers from deep storage reservoirs. How leakage will influence microbial populations over long time scales is largely unknown. This study uses natural analog sites to investigate the long-term impact of CO2 leakage from underground storage sites on subsurface biogeochemistry. We considered two sites with elevated CO2 levels (sample groups I and II) and one control site with low CO2 content (group III). Samples from sites with elevated CO2 had pH ranging from 6.2 to 4.5 and samples from the low-CO2 control group had pH ranging from 7.3 to 6.2. Solute concentrations were relatively low for samples from the control group and group I but high for samples from group II, reflecting varying degrees of water-rock interaction. Microbial communities were analyzed through clone library and MiSeq sequencing. Each 16S rRNA analysis identified various bacteria, methane-producing archaea, and ammonia-oxidizing archaea. Both bacterial and archaeal diversities were low in groundwater with high CO2 content and community compositions between the groups were also clearly different. In group II samples, sequences classified in groups capable of methanogenesis, metal reduction, and nitrate reduction had higher relative abundance in samples with relative high methane, iron, and manganese concentrations and low nitrate levels. Sequences close to Comamonadaceae were abundant in group I, while the taxa related to methanogens, Nitrospirae, and Anaerolineaceae were predominant in group II. Our findings provide insight into subsurface biogeochemical reactions that influence the carbon budget of the system including carbon fixation, carbon trapping, and CO2 conversion to methane. The results also suggest that monitoring groundwater microbial community can be a potential tool for tracking CO2 leakage from geologic storage sites.

Uranium mobility and accumulation along the Rio Paguate, Jackpile Mine in Laguna Pueblo, NM.

The mobility and accumulation of uranium (U) along the Rio Paguate, adjacent to the Jackpile Mine, in Laguna Pueblo, New Mexico was investigated using aqueous chemistry, electron microprobe, X-ray diffraction and spectroscopy analyses. Given that it is not common to identify elevated concentrations of U in surface water sources, the Rio Paguate is a unique site that concerns the Laguna Pueblo community. This study aims to better understand the solid chemistry of abandoned mine waste sediments from the Jackpile Mine and identify key hydrogeological and geochemical processes that affect the fate of U along the Rio Paguate. Solid analyses using X-ray fluorescence determined that sediments located in the Jackpile Mine contain ranges of 320 to 9200 mg kg-1 U. The presence of coffinite, a U(iv)-bearing mineral, was identified by X-ray diffraction analyses in abandoned mine waste solids exposed to several decades of weathering and oxidation. The dissolution of these U-bearing minerals from abandoned mine wastes could contribute to U mobility during rain events. The U concentration in surface waters sampled closest to mine wastes are highest during the southwestern monsoon season. Samples collected from September 2014 to August 2016 showed higher U concentrations in surface water adjacent to the Jackpile Mine (35.3 to 772 µg L-1) compared with those at a wetland 4.5 kilometers downstream of the mine (5.77 to 110 µg L-1). Sediments co-located in the stream bed and bank along the reach between the mine and wetland had low U concentrations (range 1-5 mg kg-1) compared to concentrations in wetland sediments with higher organic matter (14-15%) and U concentrations (2-21 mg kg-1). Approximately 10% of the total U in wetland sediments was amenable to complexation with 1 mM sodium bicarbonate in batch experiments; a decrease of U concentration in solution was observed over time in these experiments likely due to re-association with sediments in the reactor. The findings from this study provide new insights about how hydrologic events may affect the reactivity of U present in mine waste solids exposed to surface oxidizing conditions, and the influence of organic-rich sediments on U accumulation in the Rio Paguate.

Thermodynamic and Kinetic Response of Microbial Reactions to High CO2.

Geological carbon sequestration captures CO2 from industrial sources and stores the CO2 in subsurface reservoirs, a viable strategy for mitigating global climate change. In assessing the environmental impact of the strategy, a key question is how microbial reactions respond to the elevated CO2 concentration. This study uses biogeochemical modeling to explore the influence of CO2 on the thermodynamics and kinetics of common microbial reactions in subsurface environments, including syntrophic oxidation, iron reduction, sulfate reduction, and methanogenesis. The results show that increasing CO2 levels decreases groundwater pH and modulates chemical speciation of weak acids in groundwater, which in turn affect microbial reactions in different ways and to different extents. Specifically, a thermodynamic analysis shows that increasing CO2 partial pressure lowers the energy available from syntrophic oxidation and acetoclastic methanogenesis, but raises the available energy of microbial iron reduction, hydrogenotrophic sulfate reduction and methanogenesis. Kinetic modeling suggests that high CO2 has the potential of inhibiting microbial sulfate reduction while promoting iron reduction. These results are consistent with the observations of previous laboratory and field studies, and highlight the complexity in microbiological responses to elevated CO2 abundance, and the potential power of biogeochemical modeling in evaluating and quantifying these responses.

Broad-Scale Evidence That pH Influences the Balance Between Microbial Iron and Sulfate Reduction.

Understanding basic controls on aquifer microbiology is essential to managing water resources and predicting impacts of future environmental change. Previous theoretical and laboratory studies indicate that pH can influence interactions between microorganisms that reduce ferric iron and sulfate. In this study, we test the environmental relevance of this relationship by examining broad-scale geochemical data from anoxic zones of aquifers. We isolated data from the U.S. Geological Survey National Water Information System for 19 principal aquifer systems. We then removed samples with chemical compositions inconsistent with iron- and sulfate-reducing environments and evaluated the relationships between pH and other geochemical parameters using Spearman's rho rank correlation tests. Overall, iron concentration and the iron-sulfide concentration ratio of groundwater share a statistically significant negative correlation with pH (P < 0.0001). These relationships indicate that the significance of iron reduction relative to sulfate reduction tends to increase with decreasing pH. Moreover, thermodynamic calculations show that, as the pH of groundwater decreases, iron reduction becomes increasingly favorable relative to sulfate reduction. Hence, the relative significance of each microbial reaction may vary in response to thermodynamic controls on microbial activity. Our findings demonstrate that trends in groundwater geochemistry across different regional aquifer systems are consistent with pH as a control on interactions between microbial iron and sulfate reduction. Environmental changes that perturb groundwater pH can affect water quality by altering the balance between these microbial reactions.

Solute Concentrations Influence Microbial Methanogenesis in Coal-bearing Strata of the Cherokee Basin, USA.

Microorganisms have contributed significantly to subsurface energy resources by converting organic matter in hydrocarbon reservoirs into methane, the main component of natural gas. In this study, we consider environmental controls on microbial populations in coal-bearing strata of the Cherokee basin, an unconventional natural gas resource in southeast Kansas, USA. Pennsylvanian-age strata in the basin contain numerous thin (0.4-1.1 m) coalbeds with marginal thermal maturities (0.5-0.7% R o ) that are interbedded with shale and sandstone. We collected gas, water, and microbe samples from 16 commercial coalbed methane wells for geochemical and microbiological analysis. The water samples were Na-Cl type with total dissolved solids (TDS) content ranging from 34.9 to 91.3 g L(-1). Gas dryness values [C1/(C2 + C3)] averaged 2640 and carbon and hydrogen isotope ratios of methane differed from those of carbon dioxide and water, respectively, by an average of 65 and 183‰. These values are thought to be consistent with gas that formed primarily by hydrogenotrophic methanogenesis. Results from cultivation assays and taxonomic analysis of 16S rRNA genes agree with the geochemical results. Cultivable methanogens were present in every sample tested, methanogen sequences dominate the archaeal community in each sample (avg 91%), and few archaeal sequences (avg 4.2%) were classified within Methanosarcinales, an order of methanogens known to contain methylotrophic methanogens. Although hydrogenotrophs appear dominant, geochemical and microbial analyses both indicate that the proportion of methane generated by acetoclastic methanogens increases with the solute content of formation water, a trend that is contrary to existing conceptual models. Consistent with this trend, beta diversity analyses show that archaeal diversity significantly correlates with formation water solute content. In contrast, bacterial diversity more strongly correlates with location than solute content, possibly as a result of spatial variation in the thermal maturity of the coalbeds.

Effect of permeable biofilm on micro- and macro-scale flow and transport in bioclogged pores.

Simulations of coupled flow around and inside biofilms in pores were conducted to study the effect of porous biofilm on micro- and macro-scale flow and transport. The simulations solved the Navier-Stokes equations coupled with the Brinkman equation representing flow in the pore space and biofilm, respectively, and the advection-diffusion equation. Biofilm structure and distribution were obtained from confocal microscope images. The bulk permeability (k) of bioclogged porous media depends on biofilm permeability (kbr) following a sigmoidal curve on a log-log scale. The upper and lower limits of the curve are the k of biofilm-free media and of bioclogged media with impermeable biofilms, respectively. On the basis of this, a model is developed that predicts k based solely on kbr and biofilm volume ratio. The simulations show that kbr has a significant impact on the shear stress distribution, and thus potentially affects biofilm erosion and detachment. The sensitivity of flow fields to kbr directly translated to effects on the transport fields by affecting the relative distribution of where advection and diffusion dominated. Both kbr and biofilm volume ratio affect the shape of breakthrough curves.

Variation in energy available to populations of subsurface anaerobes in response to geological carbon storage.

Microorganisms can strongly influence the chemical and physical properties of the subsurface. Changes in microbial activity caused by geological CO(2) storage, therefore, have the potential to influence the capacity, injectivity, and integrity of CO(2) storage reservoirs and ultimately the environmental impact of CO(2) injection. This analysis uses free energy calculations to examine variation in energy available to Fe(III) and SO(4)(2-) reducers and methanogens because of changes in the bulk composition of brine and shallow groundwater following subsurface CO(2) injection. Calculations were performed using data from two field experiments, the Frio Formation experiment and an experiment at the Zero Emission Research and Technology test site. Energy available for Fe(III) reduction increased significantly during CO(2) injection in both experiments, largely because of a decrease in pH from near-neutral levels to just below 6. Energy available to SO(4)(2-) reducers and methanogens varied little. These changes can lead to a greater rate of microbial Fe(III) reduction following subsurface CO(2) injection in reservoirs where Fe(III) oxides or oxyhydroxides are available and the rate of Fe(III) reduction is limited by energy available prior to injection.

Microbiological response to well pumping.

To better constrain sampling strategies for observing biologically sensitive parameters in ground water, we vigorously pumped for 120 h a lightly pumped well completed in a confined glacial aquifer while observing how various physical and chemical parameters evolve in the water produced. The parameters commonly monitored when sampling a well stabilized within about an hour, after 5 wellbore volumes were produced; these parameters include temperature, pH, dissolved oxygen, oxidation-reduction potential (Eh), and electrical conductivity. The concentrations of ferrous iron, sulfide, and sulfate and various biological or biologically sensitive parameters, including the concentrations of dissolved hydrogen and methane, direct cell counts, and the microbial community profile, in contrast, required more than 8 h or 36 well volumes to stabilize. We interpret this result to mean that the zone of influence of the wellbore on biologic processes in the aquifer extends beyond the commonly recognized zone where physical properties are affected. A second period of adjustment of these biologically sensitive parameters began after about 50 h of pumping, following displacement of 230 wellbore volumes, and continued to the end of the experiment. During this period, the cell density and the composition of the microbial community suspended in the water samples changed. This finding indicates that the microbial community in and near the wellbore changed in response to pumping and the changes affected aspects of the composition of water produced from the well. The study demonstrates the importance of allowing adequate pumping time when sampling ground water for the analysis of biologically sensitive parameters.