Silicification steps in chert deduced from fossil fungus hyphae
deutsche Version

Chalzedony differing locally in hue and brightness allows a complex sequence of silicification stages to be reconstructed from Fig.1. This is made easier and more convincing by the presence of fungus hyphae which obviously became covered with a whitish coating which contrasts against a dark brown matrix. Hyphae found outside plant matter must have grown and become silicified in water. As another conspicuous feature, the stack of levels resembling agates with horizontal banding indicates discontinuous silicification, which will be explained below. The sequence of events which materialized on the small area on the cut face of the Rhynie chert sample shown here begins with a former swamp gas bubble trapped among plant parts.

complex silica deposits in Rhynie chert

Fig.1: Complex-structured fill within a former swamp gas bubble in Rhynie chert. (Lengthwise
section of the early land plant Aglaophyton above left.) Note the level deposits, slightly tilted towards each other. Width of the image 10mm.

Fig.2: Detail of Fig.1. Note the hyphae of some aquatic fungus coated with whitish chalzedony whose thickness varies with height above bottom. Width of the image 4mm.

complex silica deposits in Rhynie chert
differentially coated fungus hyphae
Fig.3 (on the right): Detail of Figs.1,2. Note the two small cross-sections of pale coated fungus hyphae, diameter about 40Ám, in the lower dark stratum. Width of the image 1.6mm.

The apparent succession of events which brought about what is seen in Fig.1 and details thereof is listed here:

(1) A patch of Lower Devonian vegetation became upset and inundated in silica-rich water.
(2) A swamp gas bubble got trapped among plant parts.
(3) The silica solution became supersaturated and turned into silica gel rapidly ere the plants could rot.
(4) With silica gel formation, the gas bubble became stabilized.
(5) After this early silica deposition had essentially ended, the gas slowly escaped by diffusion through the surrounding gel while water entered in the same way.
(6) Other than the surrounding gel, the now water-filled cavity provided a habitat for some aquatic fungus to thrive. A loose tangle of fungus hyphae spread throughout the water.
(7) Much later than the light-weight and hence quickly moving water molecules, the heavier silica molecules or complexes entered by diffusion and slowly increased the silica concentration there.
(8) Apparently the solution became supersaturated again, only slightly since the water did not turn into gel as it did before, see (3).
(9) The silica complexes or clusters were still so small that they got pushed about by thermal motion such that their concentration remained homogeneous throughout the water. Silica deposition began with the formation of a thin white coating on available substrates, that is the cavity walls and the fungus hyphae. The result of this first silicification step inside the water-filled cavity is seen as a thin white layer and as coatings of about 20Ám in the lowermost part. (The hyphae are so thin that the diameter of the coated hypha equals twice the coating thickness.) Two cross-sections of coated hyphae are vaguely seen in Fig.3 as small pale spots.
(10) Apparently, as the silica clusters became larger, they settled to form a comparatively heavy suspension with a well-defined boundary against the lighter solution above. This must have been a fast process since the diameter of the upper coated hypha is not larger than that of the one at the bottom of the fill: If the level had risen more slowly, the upper hypha would have acquired a thicker coating while it was not yet immersed in the settled suspension. The dark stain of the suspension could possibly be due to the decay products of microbes living in the water.
(11) The accumulation of dark suspension stopped. It solidified and became the lower stratum of dark silica gel, now chalcedony, in Fig.1.
(12) Again with slight supersaturation, the process described in (9) repeated itself in the cavity of reduced size. The whitish lining and coatings are obviously much thicker this time. This means that their deposition went on for some time without being interfered by new-formed dark suspension.
(13) Eventually, suspension formation as described in (10) repeated itself at a slower pace. The rising level stopped the growth of the whitish lining and hypha coatings as soon as it reached them.
(14) The level of settled suspension rose so slowly this time that there was more time available for the growth of coatings on the hyphae higher up. This is evident in Fig.2 where the diameter of coated hyphae is 130Ám below and 200Ám above in the second dark stratum, which is bounded by the next white line whose origin is explained below.
(15) Meanwhile the solidifying swamp had got a slight tilt. The new interface level has been choosen as the horizontal direction in these pictures so that the old level is slightly tilted against the new one.
(16) Again, the accumulation of dark suspension stopped. Same as before with the lowermost stratum, it solidified and became the second stratum of dark silica gel.

(17) In the silica solution above, a third lining of whitish silica gel was deposited around the new cavity walls, and since three coated hyphae, seen in Fig.2 as cross-sections, partially stuck out, they, too, became covered by the third white lining. This is a peculiar type of coating: lower half thin, upper half thick.
(18) A third cycle of accumulation of dark suspension ended the deposition of white gel again.
(19) Same as described in (16), a third dark stratum was formed. 

(20) All the time while the lower strata were formed and solidified, the hyphae higher up in the water-filled cavity surrounded themselves with ever thicker coatings which fused into a coherent mass of white gel with a few pockets of water in between.
(21) Eventually, suspension formation and solidification ended further deposition of white gel there, too. By that time, the thickest coating had reached a diameter of 270Ám, hence a diameter of the coated hypha of 540Ám, as seen in Fig.1 on top.

The succession of processes which led to the agate-like fill and coated fungus hyphae in this former cavity may be confusing so that a summary is appropriate: Watery suspensions of silica clusters segregate if the particles are so big that they settle into a fluid precipitate with a horizontal interface against the water above. Any horizontal plane faces in cherts, often thought to be former water levels, are former interfaces between fluids. They could not have been former water levels since mm-size water surfaces against air would be spherical bubbles.
Successively formed suspensions may vary in aspect but in the present case it is always the same dark brown, the cause of which can be guessed and may be foumd out with higher magnification.

The white precipitate is not a settled suspension since it appears as hypha coatings, too. Plane white layers could have been deposited only with the brown suspension below being in a solid state, and without new brown particles being formed. Hence, the production of dark suspension must repeatedly have stopped for a while, then started anew later. Similar discontinuities in silicification are well known from banded agates, where the "bands" seem to have been deposited separately.
From the sorting of the coated hyphae according to diameter, with thicker coatings positioned higher up than thinner ones, it can be concluded that hypha growth was restricted to an early time span when the silica concentration in the water-filled cavity was so low that no coating was formed. Otherwise, if new hyphae had grown in the later stages, too, no relation between coating diameter and height above the bottom of the former cavity would be observed.
Finally it can be stated that the Rhynie chert sample shown here, with whitish coatings and dark horizontal strata, offers evidence of discontinuous silicification whose cause remains obscure.
Sample: Rh12/91, (0.31kg, Part5: slab 6-7mm), found near Smithston in 2006. 

                        H.-J. Weiss       2015,  2016,  2018
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