A deep continental aquifer downhole sampler for microbiological studies

In order to be effective, microbiological studies of deep aquifers must be free from surface microbial contaminants (atmosphere/ soil) and infrastructures allowing access to formation water (wellheads, well completions). Many microbiological studies are based on water samples obtained after more or less rinsing of the well without guaranteeing the absence of contaminants (biofilms). The protocol described in this paper presents the adaptation for microbiological studies of deep aquifers of a commercial downhole sampler (Positive Displacement Sampler, PDSshort, Leutert, Germany) used until now for physicochemical and analytical chemistry studies (determination of dissolved gases, isotopy, etc.). Analyzes of taxonomic diversity based on high-throughput sequencing of the bacterial 16S rRNA gene were compared and discussed for different water samples taken at the surface at the wellhead (WHS) or at depth using the downhole sampler (DS). Here, the results show that even after extensive rinsing, the water collected at the wellhead is not free of microbial contaminants and the downhole sampler procedure is the only way to ensure the purity of the sampled water samples. In addition, the downhole sampler allows the formation water and the autochthonous microbial community to be maintained at pressure in situ up to the laboratory. With the advent of metagenomics and metatranscriptomics methods, the non-contamination of the sample and its representativeness are key to guarantee the best results and their interpretations which will allow us to understand the functioning of deep biosphere.