Deep-Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp

Abstract

Bacterial Halanaerobium strains become the dominant persisting microbial community member in produced fluids across geographically distinct hydraulically fractured shales. Halanaerobium is believed to be inadvertently introduced into this environment during the drilling and fracturing process and must therefore tolerate large changes in pressure, temperature, and salinity. Here, we used a Halanaerobium strain isolated from a natural gas well in the Utica Point Pleasant formation to investigate metabolic and physiological responses to growth under high-pressure subsurface conditions. Laboratory incubations confirmed the ability of Halanaerobium congolense strain WG8 to grow under pressures representative of deep shale formations (21 to 48 MPa). Under these conditions, broad metabolic and physiological shifts were identified, including higher abundances of proteins associated with the production of extracellular polymeric substances. Confocal laser scanning microscopy indicated that extracellular polymeric substance (EPS) production was associated with greater cell aggregation when biomass was cultured at high pressure. Changes in Halanaerobium central carbon metabolism under the same conditions were inferred from nuclear magnetic resonance (NMR) and gas chromatography measurements, revealing large per-cell increases in production of ethanol, acetate, and propanol and cessation of hydrogen production. These metabolic shifts were associated with carbon flux through 1,2-propanediol in response to slower fluxes of carbon through stage 3 of glycolysis. Together, these results reveal the potential for bioclogging and corrosion (via organic acid fermentation products) associated with persistent Halanaerobium growth in deep, hydraulically fractured shale ecosystems, and offer new insights into cellular mechanisms that enable these strains to dominate deep-shale microbiomes.IMPORTANCE The hydraulic fracturing of deep-shale formations for hydrocarbon recovery accounts for approximately 60% of U.S. natural gas production. Microbial activity associated with this process is generally considered deleterious due to issues associated with sulfide production, microbially induced corrosion, and bioclogging in the subsurface. Here we demonstrate that a representative Halanaerobium species, frequently the dominant microbial taxon in hydraulically fractured shales, responds to pressures characteristic of the deep subsurface by shifting its metabolism to generate more corrosive organic acids and produce more polymeric substances that cause "clumping" of biomass. While the potential for increased corrosion of steel infrastructure and clogging of pores and fractures in the subsurface may significantly impact hydrocarbon recovery, these data also offer new insights for microbial control in these ecosystems.

Keywords: Halanaerobium; biofilms; high pressure; hydraulic fracturing; metabolomics; shale.

FIG 1

H. congolense WG8 growth at high pressure. Growth rates (red) and corresponding cell densities (gray) across a pressure gradient (0.1 to 48 MPa) are shown. Growth rate and cell densities decreased as incubation pressure increased.

FIG 2

Major fermentation products excreted by H. congolense WG8 detected using NMR and gas chromatography. (A) The heat map shows the Z score (the number of standard deviations away from the mean) of normalized concentrations. Bolded product names signify differences in concentrations between treatments where P < 0.05. (B) Fold changes in per-cell fermentation products. All positive values represent increased production under high-pressure growth conditions. Asterisks represent statistically significant changes in fermentation product formation (P < 0.05).

FIG 3

Predicted carbon flux through H. congolense WG8 when grown under pressure (21, 35, and 48 MPa) using proteomic and NMR analyses. H. congolense WG8 is a strict fermenter, and glucose was the substrate provided during growth experiments. Major fermentation products are acetate, ethanol, formate, lactate, propanol, carbon dioxide, and hydrogen gas (only when grown at 0.1 MPa). The production of 1,2 propanediol is hypothesized to be a result of the methylglyoxal bypass, which may become important during high-pressure growth because activity of triose phosphate isomerase (protein 5) decreases under pressure. 1,2-Propanediol and other alcohols converted into aldehydes are processed in a microcompartment to contain toxic aldehyde intermediates. The arrow size represents the increased abundance of a protein under 1, 2, or 3 high-pressure growth conditions. Arrows outlined in black represent statistically significant changes in protein abundance (P < 0.05). Arrow colors are based on Z-score values calculated from protein abundances. Proteins: 1, phosphotransferase; 2, glucose-6-phosphate isomerase; 3, phosphofructokinase; 4, fructose bisphosphate aldolase; 5, triose phosphate isomerase; 6, glyceraldehyde-3-phosphate dehydrogenase; 7, 3-phosphoglycerate kinase; 8, phosphoglycerate mutase; 9, enolase; 10, pyruvate kinase; 11, lactate dehydrogenase; 12, pyruvate formate lyase; 13, pyruvate-ferredoxin oxidoreductase; 14, aldehyde dehydrogenase; 15, alcohol dehydrogenase; 16, phosphotransacetylase; 17, acetate kinase. Methyl glyoxal bypass: 18, methylglyoxal synthase; 19, glyoxalase; 20, methylglyoxal reductase; 21, 1,2-propanediol dehydrogenase. Microcompartment: 22, propanediol dehydratase; 23, alcohol dehydrogenase; 24, propionaldehyde dehydrogenase; 25, phosphotransacetylase; 26, propionate kinase; 27, hydrogenase.

FIG 4

Proteins potentially involved in stress response and associated EPS formation in H. congolense WG8. Black outlined boxes represent a significant difference (P < 0.05, Student’s t test) in protein abundances between low- and high-pressure conditions. Boxes without outlines represent changes in protein concentration that were not statistically significant (P > 0.05, Student’s t test).

FIG 5

Confocal scanning laser microscopy analysis of Halanaerobium grown at high and low pressure. The bar graph represents the average amount of extracellular polymeric substance produced by the cells in three biological replicates grown at high and low pressure (P < 0.05, Student’s t test). The confocal image panel shows examples of Halanaerobium biofilms. Syto59 (red) was used to stain nucleic acids, while Alexa Fluor 488-ConA (green) was used to stain α-mannopyranosyl and α-glucopyranosyl residues within the EPS matrix.

FIG 6

Proposed mechanism for diol dehydratase-catalyzed reactions. This mechanism involved a free radical-induced rearrangement of -OH groups to generate aldehydes and ketones. Reaction 1 is believed to be the most common route to generate propionaldehyde from 1,2-propanediol. Propionaldehyde is converted to 1-propanol. Reaction 2 could be induced under high-pressure conditions, leading to the formation of acetone from 1,2-propanediol. Acetone may be an isopropanol precursor. Ado^• denotes the 5′-deoxyadenosyl radical supplied by the coenzyme B₁₂.