An uncommon variety of Rhynie chert
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cavity in chalcedony with quartz fill
Judging from numerous own finds and from samples seen in collections and as images in publications, the vast majority of them are more or less dull dark if looked at from afar and reveal their rich detail, if there is, under the microscope, preferably with transparent light [1,2]. Those with much different aspect are rare, as the one described here with bright yellow fills in former cavities in the chalcedony: Fig.1. (The bright yellow has turned dull ochre with time on and near the surface of this old chert layer fragment.)

Fig.1: Rhynie chert, former cavity filled with a granular quartz deposit of yellow aspect, with dark lining, probably of microbial origin, 40Ám. Width of the image 1cm.

What has been called here a lining of the cavity can as well be called a coating on the surface of the bluish chalcedony. As a probable scenario, inundated plant debris and other substrates in silica-rich water triggered the deposition of silica gel with irregular surface and bulging protrusions.
Apparently the deposition ended when most of the dissolved silica was used up. Subsequently a layer of microbial slime grew on the gel surface and became silicified later, with microbes enclosed (Figs.2-4).
cavity in chalcedony with quartz fill
cavity lininglining
Figs.2-4: Similar as Fig.1, with dark or pale lining,  with tiny black dots
(2Ám) seen scattered around the boundary of the gray area in the "eye". Fig.4: 0.4mm.

Obviously the dark aspect is not an intrinsic property of the coating or lining of about 40Ám thickness. It seems to be a secondary phenomenon, in the present case caused by a black stain taken on by a smaller or larger fraction of the particles which the layer seems to contain, producing shades varying from pale brown to black. Individual black dots are often seen a few Ám above the layer, which probably indicates that their position had been fixed by organic gel before silicification.
There seems to be a connection with similar coatings and deposits which are conspicuous only if stained dark, as often seen with parts of tissue of Aglaophyton and Ventarura.
After nearly all of the initially supplied dissolved silica had been used up in gel formation, and the gels in the bulk and the coatings and the silicified plants had become such solid matter on their path of transformation into chalcedony that cracks had been able to run through as if the whole were brittle, slow diffusional influx of silica caused the growth of what is now seen as a deposit of quartz crystals of yellow aspect, filling cracks and cavities alike (Fig.5).

crack and cavity with same fill
Fig.5 (left): Wide crack running through silica gel and crossing a cavity with dark lining. Note the absence of any lining on the crack faces. The small black level fill above right indicates the up-direction during silicification. Width of the image 5mm.

4 types of former cavities in chert
The former cavities of unusual aspect due to their dark lining and yellow fill in Figs.1-7,10 differ much from the more common former cavities in the chert which most often can be traced back to gas bubbles which got stuck among submerged plant debris or microbial mats in silica-rich water (Figs.6,8,10). Apparently the bubbles remained empty while everything around turned into silica gel. Later the gas escaped by diffusion and water entered likewise. Usually, fungus hyphae thrived in the water-filled cavities, now seen coated with bluish chalcedony (and quartz, Fig.8), later often completely enclosed, as in Fig.10.

Fig.6 (right): Chert with former cavities of various origin, now filled with chalcedony or quartz. Note the lengthwise cut nearly along the symmetry plane of a complete trigonotarbid or its moult, rare big species (on the left). Width of the image 17mm.

Several types of former cavities can be distinguished in Fig.6:
 -  spaces without silica gel, water-filled, now filled with quartz, here yellow,
 -  gas bubbles in swamp matter (below right), now filled with bluish chalcedony,
 -  the empty hulk of a big terrestrial arachnid [2], with agate-like fill,
 -  a void in Aglaophyton (above), now filled with bluish chalcedony.
Another type of former cavity is seen in Fig.7:
 -  crescent-shaped narrow cavities due to shrinkage of embedded plant shoots,
    now filled with chalcedony and quartz.

Note that there are two characteristic features of the first-mentioned type of cavity: distinct linings, absence of hyphae. The latter fact seems to indicate that either there had never been hyphae because all organic matter was sealed within solid gel and thus inaccessible to fungi or else if there had been hyphae, influx of dissolved silica was so slow and late that the hyphae did not become coated with gel and hence vanished before the cavity gradually got filled with quartz.
crescent-shaped gaps due to shrinkage
Fig.7: Two sections of Aglaophyton
once enclosed in silica gel, then slightly shrunken and detached before silicification. Width of the image 17mm.

Obviously the plants
in Fig.7 have shrunk away from their enclosure of silica gel, which indicates delayed silicification inside, probably due to the presence of the cuticle, so that the tissue was degrading and shrinking even after the enclosure had become rather solid.
Several tiny details on the sections are due to fungi in the live plant.
cavity traversed by coated hyphae
Fig.8: Cavity with coated fungus hyphae, thickness 0.2mm.

The hyphae of aquatic fungi are common in the Rhynie chert, notably in places where silicification was so slow that free water persisted for some time. Gas bubbles which later became filled with water were suitable places for growing hyphae. Much later the cavities would either become filled with chalcedony or quartz as in Fig.6 (below) or the water would vanish after the once delicate hyphae had been coated and turned into rods crossing the now empty cavity, which makes an impressive sight (Fig.8).

The presence of fungi in this Lower Devonian habitat reveals itself in the Rhynie chert also in other ways. Cells with dark fill, loosely aligned as a concentric ring on cross-sections (Fig.7), are a characteristic feature of the symbiotic fungus Glomites rhyniensis [3]. Quite different fungus parts are the vesicles summarily called chlamydospores. Some of them are seen on the plant section in Fig.6. Occasionally something is attached to them which looks like the collapsed remains of an older vesicle, and rather seldom the attached object and the connecting tube are still in good shape (Fig.9, see Addendum below). 
chlamydospore with attachment
Fig.9 (right): Fungus chlamydospore inside
Aglaophyton with attached object of similar size. Width of the combined object 0.9mm.
cavities of different origin with different fills
Fig.10 (left): Former cavities of different origin,
 with enigmatic partial fills. Width of the image 4.5mm.

Fungus hyphae grown in water-filled cavities are also seen in Fig.10, although less spectacular than in Fig.8.
Stacks of level layers are not rare in the Rhynie chert. The layers below left had obviously been deposited in a globular water-filled former bubble after a few hyphae had grown there and had got a transparent coating of silica gel, now seen as bluish chalcedony looking like wormholes in the layered deposit below. A straight hypha is faintly seen below the pocket of granular quartz on the left. Bluish inclusions in the dark level fills of other former cavities above left are coated hyphae, too. 
What is seen on the right half of Fig.10 is of the same type as the quartz-filled cavities in Figs.1-7 except for the fact that it is not quite filled and never had been. There are more of such cavities partially filled with quartz grains which did not assemble at the bottom, which is an unexplained phenomenon.
Other uncommon details are mentioned here only briefly:
There are long slender bristles (not seen here), thickness about 2Ám, on the legs of the
rare big trigonotarbid species in Fig.6.
The spore capsule of Aglaophyton, part of which is seen in Fig.6 above right, lacks the typical feature, the palisade wall aspect of the outer capsule wall. This may be due to the fact that it is a juvenile sporangium, judging from the observation that all spores are still in tetrads, a stage less often seen preserved in chert.
Obviously this small sample of Rhynie chert, conspicuous for its cavities with yellow fill and distinct dark lining, offers an unexpectedly rich trove of detail, more or less understood or still enigmatic.
Sample: Rh7/10 (0.23kg), found in 2003 by
Sieglinde Weiss near Milton of Noth. The pictures have been taken with incident light.

Fungus formations as in Fig.9 have been thoroughly described in [4] as "acaulosporoid glomeromycotan spores" forming "spore-saccule complexes". The spore is thought to develop sideways on the tail of a saccule. This means that the visual impressions from Fig.9 above and from Fig.5 in Rhynie Chert News 55 , which suggest a straight connection by a thick tube, should be regarded as mere illusions. Apparently the deeper question why a big spore develops from an equally big saccule on a thin hypha is dealt with in the ample fungus literature referred to in [4].

H.-J. Weiss    2014

[1]  N.H. Trewin, C.M. Rice (eds.): The Rhynie hot-spring system: Geology, biota, and mineralisation.
       Trans. Roy. Soc. Edinburgh, Earth Sci. 94(2004 for 2003) Part4, 283-529.
[2] H. Kerp, H. Hass : De Onder-Devonische Rhynie Chert,
    Grondboor & Hamer 58(2004), 33-51.
[3]  T.N. Taylor et al.: Fossil arbuscular mycorrhizae from the Early Devonian,
     Mycologia 87(1995), 560-73.
[4]  N. Dotzler, Ch. Walker, M. Krings, H. Hass, H. Kerp, T.N. Taylor, R. Agerer:
      Acaulosporoid glomeromycotan spores with a germination shield from ... Rhynie chert.
      Mycol. Progress (2009) 8, 9-18.
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