A deep continental aquifer downhole sampler for microbiological studies

Abstract

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.

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

“…While these sulfate reducers have already been identified in this aquifer, some have also been identified in other UGS sites in aquifers, such as members of the Desulforamulus genus and microorganisms close to the strain formerly named Desulfotomaculum profundi Bs107 (Aüllo et al 2016 , Berlendis et al 2016 ). In addition to these microorganisms, others persist in these simplified communities and have already been identified in a previous study carried out on this aquifer ( Burkhoderiaceae, Pseudomonadaceae , and Rhizobiaceae ; Ranchou-Peyruse et al 2023 ). Their survival can be explained by a fermentative metabolism, as in the case of members of the genus Pseudoclostridium (ASV44-16S) and the phylogenetic group DTU014 (ASV68-16S; Dyksma et al 2020 ).…”

De novoevolution of transmissible tumors in Hydra

“…The analyses presented here were performed with the R software (version 4.2.2) [29] and the graphical representations were realized with the "GGplot2" package [30]. The sequencing data for the microbiome were checked for their quality and processed via the FROGS analysis pipeline developed by the GenoToul genomic platform in the Galaxy interface [31].…”

Physicochemical and microbiological effects of geological biomethane storage in deep aquifers: introduction of O2 as a cocontaminant

“…Two underground samplings were performed to recover 0.578 L and 0.556 L of water containing autochthonous microorganisms. Samplings were carried out from the site using two downhole samplers equipped with a PDS Sampler (Leutert Bottom Hole Positive Displacement Sampler 33 ). Formation water was also sampled from the wellhead and was filter-sterilized (PES 47 mm membranes, 0.1 μm, Sartorius) under anoxic conditions and stored at 4 °C before use.…”

“…25 One example is mineral oxidation, which depends on the nature of the solid phase. 9,22,[31][32][33] Recently, a study with 1% O 2 was carried out since it corresponds to the maximum quantity found in biomethane. 9,16 The results indicated the deleterious effect of O 2 on microbial life.…”