Microbial chemolithotrophic oxidation of pyrite in a subsurface shale weathering environment: Geologic considerations and potential mechanisms.

Oxidative weathering of pyrite plays an important role in the biogeochemical cycling of Fe and S in terrestrial environments. While the mechanism and occurrence of biologically accelerated pyrite oxidation under acidic conditions are well established, much less is known about microbially mediated pyrite oxidation at circumneutral pH. Recent work (Percak-Dennett et al., 2017, Geobiology, 15, 690) has demonstrated the ability of aerobic chemolithotrophic microorganisms to accelerate pyrite oxidation at circumneutral pH and proposed two mechanistic models by which this phenomenon might occur. Here, we assess the potential relevance of aerobic microbially catalyzed circumneutral pH pyrite oxidation in relation to subsurface shale weathering at Susquehanna Shale Hills Critical Zone Observatory (SSHCZO) in Pennsylvania, USA. Specimen pyrite mixed with native shale was incubated in groundwater for 3 months at the inferred depth of in situ pyrite oxidation. The colonized materials were used as an inoculum for pyrite-oxidizing enrichment cultures. Microbial activity accelerated the release of sulfate across all conditions. 16S rRNA gene sequencing and metagenomic analysis revealed the dominance of a putative chemolithoautotrophic sulfur-oxidizing bacterium from the genus Thiobacillus in the enrichment cultures. Previously proposed models for aerobic microbial pyrite oxidation were assessed in terms of physical constraints, enrichment culture geochemistry, and metagenomic analysis. Although we conclude that subsurface pyrite oxidation at SSCHZO is largely abiotic, this work nonetheless yields new insight into the potential pathways by which aerobic microorganisms may accelerate pyrite oxidation at circumneutral pH. We propose a new "direct sulfur oxidation" pathway, whereby sulfhydryl-bearing outer membrane proteins mediate oxidation of pyrite surfaces through a persulfide intermediate, analogous to previously proposed mechanisms for direct microbial oxidation of elemental sulfur. The action of this and other direct microbial pyrite oxidation pathways have major implications for controls on pyrite weathering rates in circumneutral pH sedimentary environments where pore throat sizes permit widespread access of microorganisms to pyrite surfaces.

Methane concentrations in streams reveal gas leak discharges in regions of oil, gas, and coal development.

As natural gas has grown in importance as a global energy source, leakage of methane (CH4) from wells has sometimes been noted. Leakage of this greenhouse gas is important because it affects groundwater quality and, when emitted to the atmosphere, climate. We hypothesized that streams might be most contaminated by CH4 in the northern Appalachian Basin in regions with the longest history of hydrocarbon extraction activities. To test this, we searched for CH4-contaminated streams in the basin. Methane concentrations ([CH4]) for 529 stream sites are reported in New York, West Virginia and (mostly) Pennsylvania. Despite targeting contaminated areas, the median [CH4], 1.1 µg/L, was lower than a recently identified threshold indicating potential contamination, 4.0 µg/L. [CH4] values were higher in a few streams because they receive high-[CH4] groundwaters, often from upwelling seeps. By analogy to the more commonly observed type of groundwater seep known as abandoned mine drainage (AMD), we introduce the term, "gas leak discharge" (GLD) for these waters where they are not associated with coal mines. GLD and AMD, observed in all parts of the study area, are both CH4-rich. Surprisingly, the region of oldest and most productive oil/gas development did not show the highest median for stream [CH4]. Instead, the median was statistically highest where dense coal mining was accompanied by conventional and unconventional oil and gas development, emphasizing the importance of CH4 contamination from coal mines into streams.

Exploring How to Use Groundwater Chemistry to Identify Migration of Methane near Shale Gas Wells in the Appalachian Basin.

Methane (CH4) enters waters in hydrocarbon-rich basins because of natural processes and problems related to oil and gas wells. As a redox-active greenhouse gas, CH4 degrades water or emits to the atmosphere and contributes to climate change. To detect if methane migrated from hydrocarbon wells (i.e., anomalous methane), we examined 20 751 methane-containing groundwaters from the Upper Appalachian Basin (AB). We looked for concentrations (mg/L) that indicated AB brine salts (chloride concentrations ([Cl]) > 30; [Ca]/[Na] < 0.52) to detect natural methane, and we looked for concentrations of redox-active species ([SO4] ≥ 6; [Fe] ≥ 0.3) to detect anomalous methane. These indicators highlight natural contamination by methane-containing brines or recent onset of microbial oxidation of methane coupled to iron- or sulfate-reduction. We hypothesized that only waters recently contaminated by methane still exhibit high iron and sulfate concentrations. Of the AB samples, 17 (0.08%) from 12 sites indicated potential contamination. All were located in areas with high densities of shale-gas or conventional oil/gas wells. In contrast, in southwestern Pennsylvania where brines are shallow and coal, oil, and gas all have been extracted extensively, no sites of recent methane migration were detectable. Such indicators may help screen for contamination in some areas even without predrill measurements.

Links between physical and chemical weathering inferred from a 65-m-deep borehole through Earth's critical zone.

As bedrock weathers to regolith - defined here as weathered rock, saprolite, and soil - porosity grows, guides fluid flow, and liberates nutrients from minerals. Though vital to terrestrial life, the processes that transform bedrock into soil are poorly understood, especially in deep regolith, where direct observations are difficult. A 65-m-deep borehole in the Calhoun Critical Zone Observatory, South Carolina, provides unusual access to a complete weathering profile in an Appalachian granitoid. Co-located geophysical and geochemical datasets in the borehole show a remarkably consistent picture of linked chemical and physical weathering processes, acting over a 38-m-thick regolith divided into three layers: soil; porous, highly weathered saprolite; and weathered, fractured bedrock. The data document that major minerals (plagioclase and biotite) commence to weather at 38 m depth, 20 m below the base of saprolite, in deep, weathered rock where physical, chemical and optical properties abruptly change. The transition from saprolite to weathered bedrock is more gradational, over a depth range of 11-18 m. Chemical weathering increases steadily upward in the weathered bedrock, with intervals of more intense weathering along fractures, documenting the combined influence of time, reactive fluid transport, and the opening of fractures as rock is exhumed and transformed near Earth's surface.