Figure 3: Vertical transect of the microbial mat from Lagoa Vermelha under natural lake conditions showing the different microbial and mineral components.

(a) Cross-section of a microbial mat showing stratified layers of carbonate precipitation alternating with microbial community layers. Numbers on the right side correspond to the sampled organic layers. (b–m) Bright-field TEM images showing the different mineralization stages occurring in the successive layers in the living microbial mat: (b–d) layer 1, which is mainly constituted by oxygenic photosynthetic organisms³⁸, did not show any evidence of (per)mineralization, but cyanobacteria (see the intact thylakoid membranes inside the cell (b, black arrow)), fibrillar EPS (dashed arrows) and virus-like particles (white arrows) were all common. Layer 2 is dominated by phototrophic sulphide oxidizers³⁸ and displayed the early (amorphous Mg-Si) permineralization stages (e–g) occurring within EPS (black dashed arrow) and around some prokaryotic cells (black arrows), whereas algal cell walls and other prokaryotes remained non-mineralized (white arrow). Virus-like particles were still recognizable (g). Note that early permineralization corresponds to the oxic–anoxic transition in the mat. (h–j) Layer 4 showed an increase in _amMg-Si precipitates (black arrows), while prokaryotes containing intracellular inclusions remained non-mineralized (white arrows). Early mineralization of virus-like particles also occurred in this layer (j). (k–m) Layer 5 showed abundant prokaryotic cells containing inclusions (white arrow), likely SRB as they dominated the deepest part of the microbial mat³⁸. Empty cells were mineralized and displayed more crystalline parts (dashed arrow). Some virus-like particles remained non-mineralized (black arrow). Scale bar, 2 μm (e–f,h–i,k), 1 μm (l), 500 nm (b–c,g), 200 nm (d,j,m).