A 3-m thick sediment sequence, found in a limestone mine located in the south of Italy at a depth of ca. 25–30 m from the current ground level, was investigated. Samples from 5 layers were analysed by X-ray diffraction, elemental analysis, Inductively Coupled Plasma Mass Spectrometry and micromorphology. Microbial DNA was analysed by 16S rRNA gene metabarcoding. The main mineral compounds found in the 5 layers were calcite (70–80%) and clay minerals in layers #1 and #5, goethite (75%) and hematite in layer #2, manganese (66%) and iron oxides in layer #3, and almost exclusively goethite in layer #4. Micromorphology data allowed to shed light in understanding whether these sediments formed by subsequent weathering of carbonates and silicates or by migration of soil sediments from the surface, or also by the accumulation of shallow marine sediments occurring between the middle Pliocene and the lower Pleistocene, when the extreme western sector of this area underwent strong subsidence. From the microbiological point of view, upon the 16S rRNA gene analysis, these 5 layers appear to cluster in three groups. Overall, such a distribution suggests that, both in the top (#1) and two bottom layers (#4 and #5), different communities would have undergone in situ reproduction and colonization exploiting metabolically the substrate, whereas the two mid layers would have received bacterial convection by passive transport of percolating waters. At the same time, micromorphological data show that each layer preserved its distinct features to be related to the environmental condition at the time of deposition. The chemical, mineralogical and micromorphological features of the layers and the known physiology of the microbial taxa thereby encountered highlight the possible role of the latter in elucidating the occurrence of certain mineral species as well as the biogeochemistry of elements like Mn and Fe in sediment layers.
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