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A large majority of the OTUs defined was present in the different microcosms, and sequences from the 10 most abundant and best-shared OTUs represented 50 to 84% of the total number of sequences (Table ?Table33). However, bacterial diversity shows a shift in terms of taxonomy between the consortium maintained on acetate and the consortia grown on the rock substrates (Tables ?Tables22�C4). Initially, the inoculum presents a very low bacterial diversity, since the 10 most abundant OTUs represent over 92% of the total Bacteria (Table ?Table44), as opposed to the acetate control (ca. 66%) or the unsterilized rock-containing microcosms (ca. 60 to 72%). The low Chao and Shannon Roxadustat concentration indexes of this sample (Table  ?Table22) confirmed this observation. When maintained on acetate (positive control), the bacterial diversity of the inoculum does not evolve strikingly. Although more OTUs were defined in the control compared to the inoculum (51 vs. 40 OTUs, respectively), 9 out of the 10 most abundant and best-shared OTUs are maintained (Table ?Table33) and the diversity profiles are very similar (Figure ?Figure33), with Bacteroidetes representing half of the total Bacteria present (Table ?Table22). Parabacteroides is the only genus of this phylum detected in all our microcosms (Table ?Table55). In the positive control and inoculum, this genus is represented by two major OTUs accounting for ca. 36 and 54% of the total bacterial diversity, respectively. Table 2 Bacterial diversity at the phylum level in the microcosms prepared from the immature shale (7 m depth). Table 3 Proportion of the 10 most abundant and best-shared OTUs from the microcosms prepared with the immature shale-derived substrates. Table 4 Proportion of the 10 most abundant OTUs for each sample. FIGURE 3 Comparative bacterial diversity after 155 days of incubation in the different microcosms containing substrates prepared from the immature shale sample, and in the acetate-grown consortia (control and inoculum). BR, Bulk Rock; R1, Residue 1; R2, Residue ... Table 5 Taxonomic affiliation of the OTUs defined for the different substrates prepared from the immature shale sample, and for the acetate-grown consortia (control and inoculum). A second diversity profile was observed in all the unsterilized rock samples (BR, R1, and R2). For a number of sequences normalized to the sample least covered, we observed an increase in the richness (Chao index) in the microcosm containing the Residue 2 (Table ?Table22). Bacterial diversity does not show a strong reduction trend in the BR, R1, and R2 microcosms since the Shannon index remains stable (Table ?Table22). However, a few variations in the OTU numbers and taxonomy were observed.