Deep-sea diagenesis resulting in chert-nodule formation has been studied by scanning electron microscopy, light microscopy, X-ray diffraction, and electron microprobe analysis of core material recovered by the Deep-Sea Drilling Project (DSDP). Nodules in Tertiary chalk are generally cristobalite-rich, except where metastable silica has converted to quartz. At high magnification, fractures through nodules appear smooth, with little indication of intergranular pore space. Several transition zones may separate chert nodules from unsilicified host rock. For example, in DSDP sample 7/64.1/11/CC, a nodule is surrounded by a weakly silicified chalk zone several centimeters wide, in which interstices are partly filled with 10-micron-diameter cristobalite microspherulites (lepisph res). In a high-silica zone directly adjacent to the nodule, lepispheres are more numerous and exhibit hollow centers. At the chalk-chert boundary, the chalk groundmass has been largely replaced by isotrophic silica, which occludes pore openings but not the hollow centers of the lepispheres. These can be traced for several millimeters into the nodule. Chalcedony within foraminiferal chambers is present in cherts and silicified chalks, but is more common toward the centers of nodules. Fracture surfaces, however, reveal no differences in ultramorphology between ground-masses composed of isotropic silica and those of chalcedonic quartz.

Growth of chert nodules causes dissolution and displacement of most (but not all) of the organic calcite which forms the chalk. Some displaced carbonate in reprecipitated as ultra-fine, euhedral calcite grains within chalk interstices adjacent to nodules. These are probably the supposed calcium-silicate intermediary mineral grains, which some investigators have reported at chert-chalk boundaries. Calcite also may be precipitated as secondary overgrowths on radial prisms of some planktonic foraminiferal tests. This produces characteristic euhedral terminations on inner and outer chamber surfaces.

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