Structural analysis of microbiomes from salt caverns used for underground gas storage

Salt caverns are a safe and well-proven reservoir for large-scale natural gas storage and hence, a potential hydrogen storage. Contrary to natural gas, hydrogen is a favorable energy source for many microorganisms. Microorganisms are ubiquitously abundant in the upper lithosphere and therefore expected to be present also in subsurface geological formations potentially selected for H2 storage, such as salt caverns. Thus, future salt cavern hydrogen storage requires monitoring of the cavern microbiome, to evaluate and prevent unwanted microbial activities. In this study, we analyzed the microbiomes of brines sampled from the bottom of five German natural gas storage caverns. All brines were colonized by microorganisms in considerable cell numbers ranging from 2 × 106 cells ml−1 to 7 × 106 cells ml−1. The structures of the microbiomes were characterized by 16S rRNA gene amplicon sequencing. A core community detected in all five studied caverns consists of members affiliated to the Halobacteria, Halanaerobiales and Balneolales. Further, a phylotype belonging to the extremely halophilic, lithoautotrophic and sulfate-reducing genus Desulfovermiculus was found. Examination of microbial activity also included measuring hydrochemical parameters in order to assess the salt concentrations and the availability of nutrients and potential microbial carbon sources or metabolites. NaCl (4.7 M) was the main salt and sulfate (at average 40.8 mM) the main electron acceptor; methanol (up to 37.5 mM) and ethanol (up to 6.9 mM) were of anthropogenic origin and found in higher concentrations. Some putative microbial metabolites were found in lower concentrations (butyrate, ≤0.7 mM; formate, ≤0.08 mM; acetate, ≤0.5 mM; lactate, ≤0.06 mM); their potential relation to microbial activity is discussed. We propose a guideline for sampling and subsequent chemical and molecular biological analysis for future characterization of microbial communities of salt cavern brines.