CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough

Abstract

Geologic carbon dioxide (CO2) sequestration drives physical and geochemical changes in deep subsurface environments that impact indigenous microbial activities. The combined effects of pressurized CO2 on a model sulfate-reducing microorganism, Desulfovibrio vulgaris, have been assessed using a suite of genomic and kinetic measurements. Novel high-pressure NMR time-series measurements using 13C-lactate were used to track D. vulgaris metabolism. We identified cessation of respiration at CO2 pressures of 10 bar, 25 bar, 50 bar, and 80 bar. Concurrent experiments using N2 as the pressurizing phase had no negative effect on microbial respiration, as inferred from reduction of sulfate to sulfide. Complementary pressurized batch incubations and fluorescence microscopy measurements supported NMR observations, and indicated that non-respiring cells were mostly viable at 50 bar CO2 for at least 4 h, and at 80 bar CO2 for 2 h. The fraction of dead cells increased rapidly after 4 h at 80 bar CO2. Transcriptomic (RNA-Seq) measurements on mRNA transcripts from CO2-incubated biomass indicated that cells up-regulated the production of certain amino acids (leucine, isoleucine) following CO2 exposure at elevated pressures, likely as part of a general stress response. Evidence for other poorly understood stress responses were also identified within RNA-Seq data, suggesting that while pressurized CO2 severely limits the growth and respiration of D. vulgaris cells, biomass retains intact cell membranes at pressures up to 80 bar CO2. Together, these data show that geologic sequestration of CO2 may have significant impacts on rates of sulfate reduction in many deep subsurface environments where this metabolism is a key respiratory process.

The geomicrobiology of CO2 geosequestration: a focused review on prokaryotic community responses to field-scale CO2 injection

“…It is therefore crucial that we understand the molecular mechanisms (i.e., genomic, metagenomic, transcriptomic, metabolomic, and proteomic) behind biofilm formation, biofilm-induced calcium carbonate precipitation (Phillips et al, 2013 ), and general microbial tolerance to CO 2 stress, in order to control and utilize microorganisms for remediation purposes, such as long-term sealing of fractures in subsurface storage reservoirs. A recent study analyzing the transcriptome of a model sulfate-reducing microorganism, Desulfovibrio vulgaris , identified that cells up-regulated the transcription of certain amino-acids related to osmotic stress responses, and genes associated with chemotaxis (e.g., flagella subunits), in response to elevated CO 2 pressures (Wilkins et al, 2014 ). However, scientists are routinely tasked with collecting adequate amounts of quality nucleic acid, in the form of biomass, from the deep subsurface to conduct the aforementioned omics measurements; modifying the U-tube system to collect significantly larger volumes of subsurface waters may be one option.…”

Earth as a Microbial Habitat

“…Although the impacts of these perturbations have not been extensively investigated, laboratory and field data have indicated that indigenous microorganisms are impacted, with shifts in community composition and biomass abundances reported (Morozova et al, 2010;Mu et al, 2014). At a CO 2 injection test site in Ketzin, Germany, community shifts from sulfate-reducing bacteria to methanogenic archaea were observed in groundwater following CO 2 injection, while cessation of metabolic activity of sulfate-reducing bacteria has been reported in laboratory cultures exposed to CO 2 at elevated pressures (Frerichs et al, 2013;Wilkins et al, 2014b). Given that leakage of sequestered CO 2 from these reservoirs is a major concern, it has been suggested that both biofilm formation (Mitchell et al, 2009) and microbially catalyzed mineral precipitation (Mitchell et al, 2010) may offer an opportunity to reduce caprock permeability through the blocking of small fractures and pores.…”

Interplay between microorganisms and geochemistry in geological carbon storage

“…GCS reservoirs will commonly be anoxic, with heterogeneous mineralogy and microbiology and elevated pressure, temperature, and salinity. Many recent laboratory studies were performed under relevant conditions (e.g., Dupraz et al, 2013;Mayumi et al, 2013;Ohtomo et al, 2013;Peet et al, 2015;Wilkins et al, 2014). However, most of what we know about the impact of high pressure CO 2 on microbiology stems from food industry research into CO 2 as a sterilizing agent (e.g., Amanatidou et al, 1999;Spilimbergo et al, 2002;Watanabe et al, 2003;Zhang et al, 2006).…”

“…Changes in conditions following CO 2 injection will impose stress on indigenous microorganisms, potentially triggering changes in community composition (Mu et al, 2014;Peet et al, 2015;Wilkins et al, 2014). Where CO 2 exists as a supercritical phase, it may dissolve cell membranes and cause cell death (Dillow et al, 1999;White et al, 2006).…”