Understanding the functioning of the subsurface biosphere in Icelandic aquifers used for gas storage

The Institut de physique du globe de Paris (IPGP, Université de Paris), the Laboratoire de Géologie de Lyon (LGL) at Université Claude Bernard Lyon1 and the “Microbiology of Extreme Environments” research unit of the University of Western Britany (UBO) are working in close collaboration to decipher the functioning of deep biota in Icelandic aquifers used for gas storage. With the recognition that the vast majority of microorganisms on Earth lives in the subsurface, where they rely mainly on water-rock reactions for their energy and carbon supply, far from carbon inputs from photosynthesis, this raises questions regarding underground storage and any geoengineering operation targeting the subsurface such as carbon capture and storage, underground energy storage or geothermal exploitation. One aspect of the S4CE project is to understand the role of subsurface microorganisms in such operations.

The subsurface is known to host a wide variety of microorganisms with various survival strategies. However, these microorganisms are often considered to be carbon and energy limited. When sources of carbon, such as carbon dioxide, CO2, or electron donors, such as hydrogen sulfide, H2S, are injected into the subsurface at temperatures below ~120°C (i.e. the current known limit for life), bioavailable resources are provided to the system which can promote the growth of endemic communities. Carbon dioxide ± H2S injections related to carbon capture and storage technologies have already been shown to promote fast and pronounced microbial reactivity in basalts, including growth (e.g., Trias et al. 2017, Nature Communications, 1063). It comprised the bloom of endemic iron- and sulfur-oxidizing autotrophic (i.e. CO2– utilizing) bacteria such as species of the genera Sideroxydans and Thiobacillus. The goal of IPGP, LGL and UBO is to determine how the growth of rock-dwelling microorganisms influences the way injected CO2 and reduced sulfur compounds are processed and retained in rocks at subsurface conditions and if during their growth microorganisms influence (bio)geochemical reactions including rock alteration. While part of this goal can be achieved through DNA sequencing of microbes inhabiting subsurface aquifers such as the ones associated with Hellisheidi and Nesjavellir powerplants in Iceland, IPGP and LGL are also running analogical experiments in the lab including in vitro simulation of key metabolisms at high pressure (LGL) and flow-through experiments with enriched microbial consortia (IPGP) to overall constrain how non-sterile rocky systems react to the percolation of CO2 and H2S.

 

Rock alteration experiments, where minerals are exposed to fluids at specific temperatures and pressures, are used to determine how rock-forming minerals change over time. Such experiments can include microorganisms, but very often when they do so, they use monocultures, which poorly mimic the diversity of microbial life found in Nature. Rachael L. Moore from IPGP (Paris, France) in partnership with the BRGM (Orléans, France) and the Université de Pau et des Pays de l’Adour (Pau, France) searched for a way to address this missing knowledge gap and assessed biologically mediated rock alteration under high CO2 partial pressure using a reactive percolation device (Figure 1) and a consortium of microorganisms originally derived from the basaltic aquifer close to the Hellisheidi powerplant. In order to identify if microorganisms influence alteration of minerals it is necessary to also observe how minerals can alter in a sterile environment. At low temperatures, this is nearly impossible to observe in natural systems since microbial organisms, or traces of their metabolisms, are ubiquitous in the environment. When designing the two experiments to bridge this knowledge gap the goal was to have one completely sterile experiment at low-temperatures, and one experiment with a microbial inoculate. Even though we took significant steps to ensure sterility (including sterilizing the rock, parts of the instrument), in the end we have found evidence of a growing microbial community in the “sterile” experiment. At this time, we cannot identify the origin of this community; it could have come from the water used during the experiment, the rock, the instrument or some other sources. These findings suggest that in any places microbial life can quickly adapt to rather hostile conditions when supplied with a source of energy and other nutrients.

Fig. 1: Schematic of the BIOREP device used to run the reactive percolation experiments in the presence of an enriched, deep surface, microbial consortia. The reactor was filled with a sequence of basalt plugs (grey rectangles).

Fig. 1: Schematic of the BIOREP device used to run the reactive percolation experiments in the presence of an enriched, deep surface, microbial consortia. The reactor was filled with a sequence of basalt plugs (grey rectangles).

As an important role of S-oxidizing Thiobacillus species was suggested after CO2 injection associated with the CarbFix1 project (Trias et al., 2017), the LGL team in Lyon began to study the metabolic activity of a Thiobacillus species closely related to the uncultivated one revealed by metagenomic approaches carried out by the IPGP team during gas injections. The mesophilic bacteria Thiobacillus thioparus was selected among the available cultivable strains. Jorge Osman N. determined its metabolic activity as a function of hydrostatic pressure between ambient pressure and 100 bar using a high-pressure device named ‘Andrea’. He measured sulfur oxidation rate using in situ Raman spectroscopy. Figure 2 displays the evolution Raman spectra of the culture medium as a function of pressure after 244 h of metabolic activity of Thiobacillus thioparus that oxidizes thiosulfate (S2O32-) in sulfate (SO42-). It shows that the production of sulfate by T. thioparus stopped between 30 to 40 bar and therefore that T. thioparus is actively metabolizing thiosulfate in the subsurface down to 300 m depth approximately.

Fig. 2: Selected Raman spectra of T. thioparus culture after 244 h (A) from ambient pressure to 100 bar and (B) 15, 20 and 30 bar.

Fig. 2: Selected Raman spectra of T. thioparus culture after 244 h (A) from ambient pressure to 100 bar and (B) 15, 20 and 30 bar. 

The LGL in Lyon (France) hosts a high-pressure lab and a variety of pressure vessels and equipments to investigate the Earth’s subsurface – kilobar down to the lower mantle – megabar. Some of them are equipped with optical windows and can be coupled to Raman spectrometers to measure the evolution of molecular vibrations or molecular species as a function of pressure. They are also transparent to the hard X-rays generated by synchrotron sources, that allow X-ray diffraction or X-ray Near Edge Absorption Spectroscopy (XANES), the latter allowing the investigation of redox changes. Diamond anvil cells with symmetric anvils may reach pressures as high as a megabar, the smaller the culet, the higher the pressure. Some diamond anvil cells have a thin diamond window replacing one anvil and allow to smoothly scan pressures between ambient and ten kilobars. The ‘Andrea’ device used in the present study is a large volume tube equipped with a sapphire window (Figure 3). Members of the high-pressure team investigate the deep interior of the Earth and planets and their habitability, hydrothermal processes at ocean ridges or subseafloor, and microbial activities of the subsurface.

Andrea Cell device: used for studies with living organisms or corrosive liquid., The pressurizing fluid and the experimental volume fluid can be decoupled through a separator (cylindrical assembly in the center of the above assembly). This separator (a free piston) is designed to operate up to 4000 bar for a maximum temperature of 100°C. Building materials allow sterilization by autoclave. The entire assembly is fixed on a support whose design is compatible with conventional optical microscope stages.

Fig. 3: Andrea Cell device: used for studies with living organisms or corrosive liquid., The pressurizing fluid and the experimental volume fluid can be decoupled through a separator (cylindrical assembly in the center of the above assembly). This separator (a free piston) is designed to operate up to 4000 bar for a maximum temperature of 100°C. Building materials allow sterilization by autoclave. The entire assembly is fixed on a support whose design is compatible with conventional optical microscope stages.

 

 

 

 

 

Authors: Jorge Osman R., Rachael L. Moore, Isabelle Daniel, Bénédicte Ménez