A: Biogenic high-Mg calcite minerals observed under light microscopy (phase contrast).

<p>B: Light micrograph of the carbonate crystal section stained with the nucleic acid dye SYBR Gold showing specific yellow-green fluorescence of bacteria (b) and viruses (v). C: three-dimensional presentation of an AFM image of a section of a biogenic calcium carbonate mineral showing a topographic anomaly caused by an included particle emerging 30–40 nm above the crystal surface interpreted as a viruses, the panel also includes a topographic presentation along the broken white line. D: AFM height image of a 500 × 500 nm surface area of a biogenic calcium carbonate grain. E: same area as in panel D but according a phase image representation.</p

TEM image of cross-sections of high-Mg calcite showing apparent polyhedral-like viruses marked v (A) and bacteria marked b (E), and their elemental composition shown for the same fields in (B, C, D) and (F, G, H), respectively.

<p>The XEDS maps of nitrogen (B, F), phosphorus (C, G), and calcium (D, H), respectively, showing that viruses and bacteria contain nitrogen and phosphorus, with calcium mainly located in the mineral part of the high-Mg calcite grain (Ca,Mg)CO₃.</p

Virus observed in different depth layers (see below) and different fractions of the microbial mat dominated by diatoms, <i>Coleofasciculus chthonoplastes</i>, and <i>Chloroflexus</i>-like bacteria (CLB), sampled in September 2007.

<p>A: Virus counts in the extracted water fraction (pore water and water soaked into the extracellular polymer matrix). B: Virus attached to solid organic and mineral matter. (circles = without acidification, squares = after 10 min of acidification, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130552#sec002" target="_blank">Methods</a>). C: Virus associated with extracted and purified carbonate grains observed on the outside of the carbonate grains (circles) and after 10 min of acidification (squares). See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130552#sec002" target="_blank">Methods</a> for details. Description of the different layers: I: the yellow brown toplayer (0–1 ± 0.1 mm depth) was dominated by the diatom species belonging to the genera <i>Frustula</i>, <i>Cymbella</i>, <i>Denticula</i>, <i>Nitzschia</i>; II: layer B (1 ± 0.1 mm to 2.3 ± 0.2 mm depth) comprised bundles of <i>C</i>. <i>chthonoplastes</i> and filaments of CLB; III: layer (2.3 ± 0.2 mm to 3.9 ± 0.2 mm depth) corresponding to a transition zone with <i>C</i>. <i>chthonoplastes</i> and filaments of CLB, some of them showing signs of degradation; IV: deeply black coloured sediment (3.9 ± 0.3 mm to 5 ± 0.3 mm depth); V: layer (5 ± 0.3 mm to 6.4 ± 0.4 mm depth) was grey coloured with a lot of sand grains, other mineral particles. Biogenic high-Mg calcite grains were observed by microscopy in layers I, II, III, and IV.</p

TEM image of cross-sections of high-Mg calcite showing apparent polyhedral-like viruses marked v (A) and bacteria marked b (E), and their elemental composition shown for the same fields in (B, C, D) and (F, G, H), respectively.

<p>The XEDS maps of nitrogen (B, F), phosphorus (C, G), and calcium (D, H), respectively, showing that viruses and bacteria contain nitrogen and phosphorus, with calcium mainly located in the mineral part of the high-Mg calcite grain (Ca,Mg)CO₃.</p

Biogenic calcite, extracted from the microbial mats, observed in scanning electron microscopy linked with energy dispersive X-ray spectrometry and in atomic force microscopy.

<p>A: SEM picture of a cross section of carbonate grains showing a surface area of about 50 × 40 µm cutting through two agglomerates of very small globules and large crystals. B and C: Maps of calcium (B) and magnesium (C) obtained by EDS analysis in the same area. D-E: High-resolution images showing the variety in size and shape of mineral grains and crystals that compose biogenic calcium carbonate agglutinates. The arrows point towards smaller agglomerates of roundish micro-grains. F: EDS spectrum of the (Ca,Mg)CO₃ grain for the location indicated by the blue dots in A and D (note that the high Si peak, due to the glass slide, masks the Si present in the clay colloids which also comprise Al and K). G: Details of an agglomerate of roundish micro-grains showing micromorphologies of very small rounded globules. H, I: AFM (in intermittent contact mode) images of a 1 × 1 µm surface area showing the globular structure of the individual (Ca,Mg)CO₃ micro-grains and presented as height (H) and phase (I) images. J, K: AFM images of a 4 × 4 µm surface area in the cross section in AFM showing topography (J) and phase (K) images at a magnification comparable to that used for SEM. White arrows point to viruses that have been studied at higher magnification, i.e., the viruses illustrated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130552#pone.0130552.g004" target="_blank">Fig 4D–4E</a>.</p

Virus observed in different depth layers (see below) and different fractions of the microbial mat dominated by diatoms, <i>Coleofasciculus chthonoplastes</i>, and <i>Chloroflexus</i>-like bacteria (CLB), sampled in March 2007.

<p>Left panel (A): Virus counts in the extracted water fraction (pore water and water soaked into the extracellular polymer matrix). Right panel (B): Virus attached to solid organic and mineral matter. (circles = without acidification, squares = after 10 min of acidification, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130552#sec002" target="_blank">Methods</a>). Description of the different layers: I: the top layer from 0 to 0.8 ± 0.2 mm depth, comprised dense populations of diatoms of the genera: <i>Frustula</i>, <i>Cymbella</i>, <i>Denticula</i>, <i>Nitzschia</i> and few bundles of <i>C</i>. <i>chthonoplastes</i> and filaments of CLB; II: layer from 0.8 ± 0.2 mm to 1.5 ± 0.2 mm depth that separated very well from the top layer and comprised lesser densities of diatoms with high quantities biogenic high-Mg calcite grains (cf. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130552#pone.0130552.g003" target="_blank">Fig 3</a>); III: locally a very fine layer was observed at 1.5 ± 0.3 mm depth that was particularly enriched in biogenic high-Mg calcite embedded in an organic matrix; IV: A layer located below the high densities of biogenic calcium carbonate crystals occurred layer B from 1.5 ± 0.3 mm to 2.6 ± 0.3 mm depth which comprising bundles of <i>C</i>. <i>chthonoplastes</i> and filaments of CLB; V: layer from 2.6 ± 0.3 mm to 4 ± 0.3 mm depth corresponded to a transition zone where large amounts of mineral particles sand grains and biogenic calcite occurred intertwined with of <i>C</i>. <i>chthonoplastes</i> and filaments of CLB; VI: layer comprising black coloured sediment ranging from 4 ± 0.3 mm to 6 ± 0.5 mm depth.</p

S10 Fig -

Panel b. (panel of the fossil). From top to bottom, photograph and survey of ancient anthropic traces in black, animal traces in blue, surface of the fossil section in green, numbering of the traces. The clear traces are in continuous line, when the trace is deep the line is thicker. Traces that are more difficult to read are dashed. (TIF)</p

La Roche-Cotard site.

A. Map of La Roche-Cotard with its four loci: LRC I, LRC II, LRC III and LRC IV. In blue: location of anthropogenic marks. B. Profiles of slope sections (red lines in A) with location of sediments extracted in 1846.</p

Experimental determination of the direction of finger flutings.

A. Experiment: some crushed is prepared tuff, then placed in a small flat container, moistened a bit, beat and grooved with a finger on its surface. Result: on the bottom of the trace, some reliefs like scales lifted up in the opposite direction of the finger passage are observable. The black arrow indicates the direction of the trace; white arrows the scales. B. Circular Panel, trace C1a. The scales are visible on the bottom of trace (white arrows) and show the direction of the finger fluting. (TIF)</p

Analysis of the Triangular Panel and especially of its left part.

a). Survey of the finger flutings of the totality of the panel. It permit to situate the left part of the panel which has been studied particularly and specially the three preserved triangles A, B and C. b). Orthophoto from the photogrammetry of the left part of the panel. The two triangles A and B are clearly visible, the triangle C with some difficulty due to its alteration. c). The same surface with its contour lines which give the surface relief. The lines are equidistant sections (1mm) parallel to the average plane of the panel, not horizontal. d). A coloured model representing the microrelief of the panel. Red indicates concave surface (relative to the observer’s axis of vision), blue indicates convex surface. Thick line at 0 of the scale indicates flatness of the surface. The units of bending intensity are given in colour range from -0.18 (convex) to +0.08 (concave) for curvature, i.e., from 8 mm to 10 mm for radii of curve. The colour range on the right shows the range and gradation of the panel’s colouration: red and yellow are the concave surfaces (for the observer), green and blue the convex surfaces and, at the limit of yellow and green, the areas without curvature. e). Detail of the groove along the left side of the triangle A. Arrow 1 shows the beginning of the strong slope, Arrow 2 shows a narrow band corresponding to the part of the groove on the side of the triangle. Arrow 3 shows a red band corresponding to the deep part of the groove, Arrow 4 shows a wide yellow stripe corresponding to the other side of the groove with a very gentle slope. (Y. Egels, see S4 Text). (TIF)</p