Background Uranium-mineralized sandy aquifer, planned for a mining by in situ recovery (U ISR), harbors a reservoir of bacterial life that may influence the biogeochemical cycles surrounding the Uranium roll front deposits. Since microorganisms are likely to play an important role at all stages of U ISR, a better knowledge of the resident bacteria before any ISR actuations is essential to face environmental quality assessment. The focus here was made on the characterization of the resident microbiome of an aquifer surrounding uranium roll-front deposit that is part of an ISR facility project at Zoovch Ovoo (Mongolia). Water samples were collected following the natural redox zonation inherited in the aquifer, including the native mineralized orebody, and both the upstream and downstream compartments.Results An imposed chemical zonation for all sensitive redox elements through the roll-front system was observed in all water samples. High-throughput sequencing showed that the bacterial community structure was shaped by the redox gradient and the oxygen availability. Several interesting bacteria were observed including sulphate-reducing (e.g. Desulfovibrio, Nitrospira), iron-reducing (e.g. Gallionella, Sideroxydans) iron-oxidizing (e.g. Rhodobacter, Albidiferax, Ferribacterium), and nitrate-reducing bacteria (e.g. Pseudomonas, Aquabacterium), which may be also involved in metal reduction (e.g. Desulfovibrio, Ferribacterium, Pseudomonas, Albidiferax, Caulobacter, Zooglea). The taxa residing in each aquifer compartment followed a strong redox zonation differentiation, although as a whole the population of each water section seems to define an ecologically functional ecosystem containing suitable microorganisms that are probably prone to promote the remediation of the acidified aquifer by natural attenuation. Co-occurrence patterns confirmed a strong correlations among the bacterial genera suggesting either a shared and preferred environmental conditions or the performance of functions similar or complementary to each other.Conclusions Assessing the composition, and structure of the resident bacterial communities is a prerequisite for understanding the natural attenuation and predicting bacterial input in the improvement of ISR efficiency.

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