Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer

Anthropogenic impacts on the terrestrial subsurface biosphere

The terrestrial subsurface is estimated to be the largest reservoir of microbial life on Earth. However, the subsurface also harbours economic, industrial and environmental resources, on which humans heavily rely, including diverse energy sources and formations for the storage of industrial waste and carbon dioxide for climate change mitigation. As a result of this anthropogenic activity, the subsurface landscape is transformed, including the subsurface biosphere. Through the creation of new environments and the introduction of substrates that fuel microbial life, the structure and function of subsurface microbiomes shift markedly. These microbial changes often have unintended effects on overall ecosystem function and are frequently challenging to manage from the surface of the Earth. In this Review, we highlight emerging research that investigates the impacts of anthropogenic activity on the terrestrial subsurface biosphere. We explore how humans alter the constraints on microbial life in the subsurface through drilling, mining, contamination and resource extraction, along with the resulting impacts of microorganisms on resource recovery and subsurface infrastructure.

Multi-approach assessment of groundwater biogeochemistry: Implications for the site characterization of prospective spent nuclear fuel repository sites

The disposal of spent nuclear fuel in deep subsurface repositories using multi-barrier systems is considered to be the most promising method for preventing radionuclide leakage. However, the stability of the barriers can be affected by the activities of diverse microbes in subsurface environments. Therefore, this study investigated groundwater geochemistry and microbial populations, activities, and community structures at three potential spent nuclear fuel repository construction sites. The microbial analysis involved a multi-approach including both culture-dependent, culture-independent, and sequence-based methods for a comprehensive understanding of groundwater biogeochemistry. The results from all three sites showed that geochemical properties were closely related to microbial population and activities. Total number of cells estimates were strongly correlated to high dissolved organic carbon; while the ratio of adenosine-triphosphate:total number of cells indicated substantial activities of sulfate reducing bacteria. The 16S rRNA gene sequencing revealed that the microbial communities differed across the three sites, with each featuring microbes performing distinctive functions. In addition, our multi-approach provided some intriguing findings: a site with a low relative abundance of sulfate reducing bacteria based on the 16S rRNA gene sequencing showed high populations during most probable number incubation, implying that despite their low abundance, sulfate reducing bacteria still played an important role in sulfate reduction within the groundwater. Moreover, a redundancy analysis indicated a significant correlation between uranium concentrations and microbial community compositions, which suggests a potential impact of uranium on microbial community. These findings together highlight the importance of multi-methodological assessments in better characterizing groundwater biogeochemical properties for the selection of potential spent nuclear fuel disposal sites.

Assessment of the in situ biomethanation potential of a deep aquifer used for natural gas storage

The dihydrogen (H2) sector is undergoing development and will require massive storage solutions. To minimize costs, the conversion of underground geological storage sites, such as deep aquifers, used for natural gas storage into future underground hydrogen storage sites is the favored scenario. However, these sites contain microorganisms capable of consuming H2, mainly sulfate reducers and methanogens. Methanogenesis is, therefore expected but its intensity must be evaluated. Here, in a deep aquifer used for underground geological storage, 17 sites were sampled, with low sulfate concentrations ranging from 21.9 to 197.8 µM and a slow renewal of formation water. H2-selected communities mainly were composed of the families Methanobacteriaceae and Methanothermobacteriaceae and the genera Desulfovibrio, Thermodesulfovibrio, and Desulforamulus. Experiments were done under different conditions, and sulfate reduction, as well as methanogenesis, were demonstrated in the presence of a H2 or H2/CO2 (80/20) gas phase, with or without calcite/site rock. These metabolisms led to an increase in pH up to 10.2 under certain conditions (without CO2). The results suggest competition for CO2 between lithoautotrophs and carbonate mineral precipitation, which could limit microbial H2 consumption.

Microbiological insight into various underground gas storages in Vienna Basin focusing on methanogenic Archaea

In recent years, there has been a growing interest in extending the potential of underground gas storage (UGS) facilities to hydrogen and carbon dioxide storage. However, this transition to hydrogen storage raises concerns regarding potential microbial reactions, which could convert hydrogen into methane. It is crucial to gain a comprehensive understanding of the microbial communities within any UGS facilities designated for hydrogen storage. In this study, underground water samples and water samples from surface technologies from 7 different UGS objects located in the Vienna Basin were studied using both molecular biology methods and cultivation methods. Results from 16S rRNA sequencing revealed that the proportion of archaea in the groundwater samples ranged from 20 to 58%, with methanogens being the predominant. Some water samples collected from surface technologies contained up to 87% of methanogens. Various species of methanogens were isolated from individual wells, including Methanobacterium sp., Methanocalculus sp., Methanolobus sp. or Methanosarcina sp. We also examined water samples for the presence of sulfate-reducing bacteria known to be involved in microbially induced corrosion and identified species of the genus Desulfovibrio in the samples. In the second part of our study, we contextualized our data by comparing it to available sequencing data from terrestrial subsurface environments worldwide. This allowed us to discern patterns and correlations between different types of underground samples based on environmental conditions. Our findings reveal presence of methanogens in all analyzed groups of underground samples, which suggests the possibility of unintended microbial hydrogen-to-methane conversion and the associated financial losses. Nevertheless, the prevalence of methanogens in our results also highlights the potential of the UGS environment, which can be effectively leveraged as a bioreactor for the conversion of hydrogen into methane, particularly in the context of Power-to-Methane technology.

A deep continental aquifer downhole sampler for microbiological studies

To be effective, microbiological studies of deep aquifers must be free from surface microbial contaminants and from infrastructures allowing access to formation water (wellheads, well completions). Many microbiological studies are based on water samples obtained after rinsing a well without guaranteeing the absence of contaminants from the biofilm development in the pipes. The protocol described in this paper presents the adaptation, preparation, sterilization and deployment of a commercial downhole sampler (PDSshort, Leutert, Germany) for the microbiological studying of deep aquifers. The ATEX sampler (i.e., explosive atmospheres) can be deployed for geological gas storage (methane, hydrogen). To validate our procedure and confirm the need to use such a device, cell counting and bacterial taxonomic diversity based on high-throughput sequencing for different water samples taken at the wellhead or at depth using the downhole sampler were compared and discussed. The results show that even after extensive rinsing (7 bore volumes), the water collected at the wellhead was not free of microbial contaminants, as shown by beta-diversity analysis. The downhole sampler procedure was the only way to ensure the purity of the formation water samples from the microbiological point of view. In addition, the downhole sampler allowed the formation water and the autochthonous microbial community to be maintained at in situ pressure for laboratory analysis. The prevention of the contamination of the sample and the preservation of its representativeness are key to guaranteeing the best interpretations and understanding of the functioning of the deep biosphere.