Microscopy evidence of bacterial microfossils in phosphorite crusts of the Peruvian shelf: Implications for phosphogenesis mechanisms

Phosphorites are sedimentary formations enriched in Ca-phosphate minerals. The precipitation of these minerals is thought to be partly mediated by the activity of microorganisms. The vast majority of studies on phosphorites have focused on a petrological and geochemical characterization of these rocks. However, detailed descriptions are needed at the sub-micrometer scale at which crucial information can be retrieved about traces of past or modern microbial activities. Here, scanning electron microscopy (SEM) analyses of a recent phosphorite crust from the upwelling-style phosphogenesis area off Peru revealed that it contained a great number of rod-like and coccus-like shaped micrometer-sized (~1.1μm and 0.5μm, respectively) objects, referred to as biomorphs. Some of these biomorphs were filled with carbonate fluoroapatite (CFA, a calcium-phosphate phase common in phosphorites); some were empty; some were surrounded by one or two layers of pyrite. Transmission electron microscopy (TEM) and energy dispersive X-ray spectrometry (EDXS) analyses were performed on focused ion beam (FIB) milled ultrathin foils to characterize the texture of CFA and pyrite in these biomorphs at the few nanometer scale. Non-pyritized phosphatic biomorphs were surrounded by a thin (5-15nm thick) rim appearing as a void on TEM images. Bundles of CFA crystals sharing the same crystallographic orientations (aligned along their c-axis) were found in the interior of some biomorphs. Pyrite formed a thick (~35-115nm) layer with closely packed crystals surrounding the pyritized biomorphs, whereas pyrite crystals at distance from the biomorphs were smaller and distributed more sparsely. Scanning transmission X-ray microscopy (STXM) analyses performed at the C K-edge provided maps of organic and inorganic carbon in the samples. Inorganic C, mainly present as carbonate groups in the CFA lattice, was homogeneously distributed, whereas organic C was concentrated in the rims of the phosphatic biomorphs. Finally, STXM analyses at the Fe L_2,3-edges together with TEM-EDXS analyses, revealed that some pyritized biomorphs experienced partial oxidation. The mineralogical features of these phosphatic biomorphs are very similar to those formed by bacteria having precipitated phosphate minerals intra- and extracellularly in laboratory experiments. Similarly, pyritized biomorphs resemble bacteria encrusted by pyrite. We therefore interpret phosphatic and pyritized biomorphs present in the Peruvian phosphorite crust as microorganisms fossilized near the boundary of zones of sulfate reduction. The implications of these observations are then discussed in the light of the different possible and non-exclusive microbially-driven phosphogenesis mechanisms that have been proposed in the past: (i) Organic matter mineralization, in particular mediated by iron reducing bacteria and/or sulfate-reducing bacteria (SRB), (ii) reduction of iron-(oxyhydr)oxides by iron-reducing bacteria and/or SRB, and (iii) polyphosphate metabolism in sulfide-oxidizing bacteria, possibly associated with SRB.