Biofilm and carbonate trace metals as biomarkers : tentatively tracking enzymatic pathways in geobiological objects

The redox evolution of Earth and the evolution of life are tightly coupled through the progressive bioavailability of transition metals. As microbial metabolisms emerged and diversified, newly available metals were incorporated into oxydoreductase enzymes, reshaping global biogeochemical cycles and the redox state of the atmosphere and oceans. This evolutionary history is preserved in microbial metallomes, which record the metals integrated into metabolic nanomachinery over geological time and thus provide potential proxies for paleo-metabolic reconstructions.

Here, we imaged trace-metal distributions in commercial enzymes, modern carbonate spherules from microbial mats of the Dead Sea shores, and Archean mineralized biofilms from the 2.72 Ga Tumbiana formation using synchrotron-based XRF and particle-induced X-ray emission (PIXE), and integrate sedimentological, mineralogical, and geochemical constraints to infer the nature of the microbial metabolisms involved. Beyond this comparative approach, we aim to assess whether mineralized microbial systems retain diagnostic signatures of ancient metabolic pathways and redox conditions.

In practice, trace-metal measurements in enzymes are feasible, as demonstrated by our synchrotron-based analyses of carbonic anhydrase and associated calcium carbonate, which show systematic Zn enrichment. In modern arsenic-rich microbial mats from the Dead Sea, carbonate (aragonite) spherules and needles are enriched in Sr and Ni, likely linking carbonate precipitation to urease activity, which contains two Ni²⁺ ions per active site. Despite strong arsenic enrichment in the extracellular polymeric substances (EPS) driven by seasonal arsenic pulses in spring waters (Thomas et al., 2024), arsenic is excluded from the carbonate crystal lattice. In arsenic-rich Tumbiana stromatolitic laminae, PIXE analyses of layers containing nanopyrite and carbonaceous matter reveal complex but potentially syngenetic metal distributions. Multivariate discrimination identifies metal signatures in carbonaceous horizons dominated by As, Cu, and Mo. Taking into account both passive abiotic metal enrichment and previous interpreted metabolic signatures inferred for  the Tumbiana Formation stromatolites (i.e.  arsenic reduction and oxidation, nitrification and denitrification, sulfate reduction, anaerobic oxidation of methane ; Marin-Carbonne et al., 2018; Sforna et al., 2014; Thomazo et al., 2011) metallomic signatures may be in agreement with microbial arsenic and nitrogen cycling (Sforna et al., 2014). Given the complexity and different nature of metal accumulation in those enzymes, carbonates or modern and fossilized biofilms, extracting a metabolic signature associated to a metallome remains elusive without integrating lab-based approaches. Further work is therefore needed to constrain metal circulation and immobilization in organic matter (EPS, biofilm) and mineralizing phases to better assess biosignatures associated to metals and their isotopes in such objects.

Marin-Carbonne et al. (2018). Sulfur isotope’s signal of nanopyrites enclosed in 2.7 Ga stromatolitic organic remains reveal microbial sulfate reduction. Geobiology, 16(2), 121–138. 

Sforna et al. (2014). Evidence for arsenic metabolism and cycling by microorganisms 2.7 billion years ago. Nature Geoscience, 7(11), 811–815. 

Thomas et al. (2024). Combined Genomic and Imaging Techniques Show Intense Arsenic Enrichment Caused by Detoxification in a Microbial Mat of the Dead Sea Shore. Geochemistry, Geophysics, Geosystems, 25(3), e2023GC011239. 

Thomazo et al., (2011). Extreme 15N-enrichments in 2.72-Gyr-old sediments: Evidence for a turning point in the nitrogen cycle. Geobiology, 9(2), 107–120.