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Subsurface Microbial contribution to Dark CO2 fixation in geological storage sites. Community structure and dynamics

Final Report Summary - DARK ENERGY (Subsurface Microbial contribution to Dark CO2 fixation in geological storage sites. Community structure and dynamics.)

In an attempt to assess the feasibility of in situ CO2 mineralization in basaltic rocks, a field-scale Carbon Capture and Storage (CCS) project, CarbFix, has begun in 2007 at Hellisheidi, SW Iceland ( The injection site is adjacent to a geothermal power plant, which produces up to 40,000 tons of CO2 per year for injection into subsurface basalts at a depth of 400–800 m and temperatures up to ~50°C. The Hellisheidi site has, in addition to the injection wells (HN-02), several strategically located wells for monitoring the geochemical evolution of the groundwater. In 2012 two injections of CO2 dissolved in groundwater were performed: first 175 tons of pure industrial CO2 were injected between January and March 2012 and second, 73 tons of the CO2-H2S-H2 gas mix released by the power plant were injected between June and August 2012.

1. Pure CO2 injections
The IPGP group, Géobiosphère actuelle et primitive has been monitoring the microbial diversity in the different available wells since 2008, using bacterial and archaeal 16S rRNA gene cloning and sequencing and deep sequencing (454 pyrosequencing) and more recently, through this project, through qPCR and metagenomics analyses of taxonomic and functional groups. Results show that there is a diverse and abundant community before the injection. Potentially thermophilic bacteria belonging to the phyla Thermotogae, Deinococcus-Thermus and Firmicutes, and hyperthermophilic archaea belonging to the phyla Euryarchaeota and Thaumarchaeota are present (aquifer waters can be up to 80°C). A large proportion of Proteobacteria and Actinobacteria was also detected, as well as microorganisms belonging to the phyla Nitrospirae, Bacteriodetes and Chlorobi. Other groups detected were the sulphate-reducing bacteria (Desulfuromonas), hydrogen-oxidizing bacteria (Hydrogenophaga, Hydrogenophilus) and sulfate oxidizers (Thiobacillus). Archaea were dominated by Euryarchaeota and by Thaumarchaeota. A large portion of the microorganisms belong to new species since the 75% of the archaeal sequences retrieved and 44% of the bacterial ones showed less than 97% identity to the sequences of cultures microorganisms. Eukaryotes could not be detected in any of the analyzed samples.
The CO2 injection reduced the diversity and richness of the microbial communities. Two OTUs became dominant immediately after injection (the autotrophic Fe and S oxidizer Sideroxydans sp.), and two months later (the sulfate-reducing bacteria Desulfotomaculum sp.) respectively, showing a fast response of the microbial community to the pure CO2 injection. The increase of autotrophic microbial groups after the first injection suggests that a fraction of the injected CO2 is fixed by the microbial communities for primary production, which has never been taken into account in the currently-used predictive thermo/geochemical numerical models that do not consider the possibility of efficient carbon reduction in the subsurface. Host-basalt dissolution was key in releasing nutrients and energy sources sustaining autotrophic and heterotrophic growths with possible consequences of the stimulated microbial activities on mineral storage. Overall, the rapid bacterial response to the injection of pure CO2-charged water which was evidenced at month scales was ruled by several additive factors that interacted all together and favored bacterial growth (i.e. basalt dissolution and associated ions release, carbon availability). Although further studies are needed to quantify biologically-fixed carbon, the composition of the dissolving host rock undoubtedly shaped the stimulated microbial metabolisms that in turn have changed the chemistry of the basaltic aquifer, with potential impact on secondary mineralizations including carbonatation. As the success of CCS projects relying on mineral storage will depend on the efficiency of fluid-rock interactions governing carbonatation, the fast reactivity of deep ecosystems and the associated biogeochemical reactions have hence to be considered to ensure long term and safe storage in the form of solid carbonate. Although CO2 conversion into biomass may offer an alternative pathway for CO2 subsurface entrapment, carbon storage as biomass is not desirable as: 1) no long-term stability of the biologically stored carbon can be ensured, and 2) controlling the geographic distribution of this biomass along with associated biogeochemical pathways is very unlikely. These statements are valid for both mafic and ultramafic rocks, serpentinized peridotites being similarly considered as target of prime interest for CCS but also as large microbial habitat.

2. Gas mix injections
On the other hand, the CO2-H2-H2S injections caused a decrease of the injectivity index. Back-flushing of the injection well by airlift pumping was performed for remediation. The microbial diversity and the mineralogy of the collected materials performed in order to understand the causes of clogging reveal an increase of gene copy numbers (detected by qPCR) and a loss of diversity, in comparison to pre-clogging communities. The endemic Betaproteobacteria sulfur-oxidizing Thiobacillus sp. and the Deltaproteobacteria sulfur reducing Desulfurivibrio sp. were the main representatives of the bacterial communities, as revealed by 454-pyrosequencing. Microscopic observations evidenced that H2S reacted with the Fe-bearing basaltic minerals to abiotically form submicrometric Fe-sulfides, and then oxidized by Thiobacillus that formed to adhere to this substrate, a dense biofilm aggregating individual Fe-sulfides. Oxidation byproducts were in turn used by iron-metabolizing bacteria, forming large crusts of cell-entombing Fe-oxi-hydroxides. The overall process, interpreted as the result of the stimulation at depth of specific activities, converted submicrometric Fe-sulfides into compact microbially-induced mineralizations, up to hundreds of micrometers in size, likely filling the basalt porosity, with a deleterious impact on the injectivity.

3. Drilling at the Hellisheidi injection site
The study of the microbial communities in the groundwater is the most straightforward and has been used for the first approach mainly due to the difficulty of sampling the subsurface and the unavailability of drilling. However, the microorganisms are present not only in the groundwater but also at the surface of the rocks, where they grow in the form of biofilms, utilizing the minerals as a substrate. The biofilms formed on these surfaces, form complex and diverse communities with direct implications in the system functioning (e.g. silicate dissolution or carbonate nucleation) and also in CO2 fixation. I have participated in the drilling operations that have taken place at Hellisheidi during October-November 2014. This sampling experience has allowed us to understand that the microbial communities have developed in the form of biofilms after the gas injection. A greenish layer of biofilm (as confirmed by Confocal Scanning Laser Microscope imaging) has been found between 400 and 500 m in almost all the cores retrieved. This ubiquitous biofilms at these depths have not been described before, and we believe is consequence of the CO2 injection, since deep communities are usually C limited and the injection could have stimulated the development of the biofilms.

4. Concluding remarks
The present work has shown that microbial communities in basaltic environments are highly impacted by gas injections and that Carbon Capture and Storage technologies need to take into account the living component in the subsurface.