In shales of all ages, the presence of organic matter within the shale matrix typically leads to depletion of oxygen in the pore waters. The reason is bacterial degradation of organic matter by aerobic bacteria. Once the sediment is anoxic, organic matter degradation is largely continued by sulfate reducing bacteria (available nitrate and manganese and iron oxides will be reduced prior to that step) that produce hydrogen sulfide which then can form iron sulfides with iron that has gone into solution.
The iron sulfides that form can be directly precipitated pyrite (FeS2), or can be various metastable iron monosulfides that later on react to form pyrite. In addition, under low pH conditions marcasite (FeS2), a pyrite polymorph, may form instead of pyrite. Although thought of as metastable, marcasite has been detected in sedimentary rocks as old as Ordovician.
The morphology of the iron sulfides and the texture of the surrounding shale matrix can give information about the timing of pyrite (or marcasite) formation in the sediment, as well as about the conditions of formation. Iron sulfides may also enclose and preserve microbes that were present within the pore spaces of the sediment.
Overall, distribution, morphology, and type of iron sulfides in shales and mudstones carries a lot of useful information about the early diagenetic history of these rocks. Very little of it has yet been utilized to arrive at a better understanding of these rocks. The references below are examples of how we use of iron sulfides in our shale studies.