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.

Keywords: ATEX; UGS; deep aquifer; downhole sampler; geological storage; microorganisms.

Figure 1

Use of the LEUTERT OPS downhole sampler to collect microorganisms from a deep aquifer. (A) Descriptive diagram of the downhole sampler; (B) Deployment of the sampler on site: the sampler is inserted into a chamber. Then, the chamber is connected to the wellhead before it is opened, and the sampler descends into the well.

Figure 2

Enumeration and cell survival during the sampling campaign. The black circles represent total cell counts. For each of these counts, the cells with intact membranes, qualified as living cells, are represented in green, while the cells with lysed membranes, qualified as dead cells, are shown in red. As the well is artesian throughout the procedure, the volume of water purged is represented with blue triangles. DS: downhole sampling; WHS: wellhead sampling.

Figure 3

Heatmap showing the distributions of 108 bacterial OTUs in the formation water collected at the wellhead (WHS) and with the downhole samplers (DS) after a biomass concentration with filters with a porosity of 0.22 μm and 0.1 μm from the 0.22 μm-eluate. The taxa associated with the OTUs are presented to the left of the figure and in Supplementary Table S1.

Figure 4

Jaccard’s analysis of the beta diversity and comparison representation of the dominant bacterial families based on the 16S rRNA gene (v3-v4) in different formation water samples from the downhole sampler (DS, red) and the wellhead sampler (WHS, blue). The deep aquifer bacterial community was obtained by 0.22 μm filtration or 0.1 μm filtration from the 0.22 μm eluate.