Microbial diversity studies of Spanish bentonites: Comparison of clone libraries and Illumina-sequencing based methods

The long-term disposal of radioactive wastes in a deep geological repository (DGR) is the accepted international solution for the treatment and management of these special residues, mainly produced by the nuclear energy industry. The present work describes the structure and composition of microbial communities in Spanish bentonites, considered as natural analogue of the bentonite-engineered barrier, by two different culture- independent approaches based on the 16S ribosomal RNA gene analysis: clone libraries and Illumina sequencing platform. These two techniques showed a high microbial diversity of the bentonite samples studied. The microbial community was dominated by Proteobacteria and Bacteroidetes, and contained bacteria potentially involved in the possible microbial deterioration processes of DGR safety case including transformations of clay minerals, mobilization/immobilization of radionuclides, etc. When analysing all of the datasets from the samples en masse we observed high similarity between the clone libraries and Illumina datasets in terms of dominant groups and the community profiles at the phylum level, while significant differences in the proportion of some phyla and class between the samples were observed. Illumina-sequencing was more sensitive to Bacteroidetes, while in the case of Gammaproteobacteria class, the traditional clone library was much more efficient. The structure and composition of the microbial communities present in the bentonites samples will be discussed in term of geochemistry and mineralogy of the clays, and also on their impact in the safety case of DGR. The results obtained indicate that the combination of both molecular techniques provide an accurate and boarder view of the microbial communities present in complex environmental samples.