Carbonate mounds are preserved in the late Oxfordian Smackover Formation in southwest Alabama. A shallow-marine mound on the Saint Stephens ridge, which separated the Mississippi interior salt basin and the Manila embayment, is dominated by thrombolite (clotted microbialite). Small foraminifera and coccoid calcimicrobes entombed within the thrombolite record an endocommensal community that lived a fugitive existence while the thrombolite was growing. Disarticulated ostracodes, fragmentary larger foraminifera, molluscan debris, and thalassinidean fecal pellets (Parafavreina and Helicerina) embedded in the thrombolite are interpreted as detrital.

Laminar and “birds-eye” fenestrae contain the remains of at least two distinct low-diversity cryptic microbial communities. Where endocommensal coccoid calcimicrobes are common in the lower part of the mound they also encrust fenestral walls and are the only preserved cryptic organisms. Higher in the mound, a pioneer community of encrusting microorganisms is preserved as microcrystalline clots; laminated or structureless rinds with or without internal voids; pendant drapes; and irregular, stalagmitic, or stalactitic blobs. These objects do not preserve morphological features of the organisms that produced them. An erect microorganism overgrew the pioneers and is preserved as a fringe of inclusion-rich early cement. Thalassinidean fecal pellets within fenestrae are allochthonous, but probably delivered valuable nutrients to cryptic habitats.

Coccoid calcimicrobes occupy small, poorly connected “birds-eye” fenestrae low in the mound whereas a morphologically more diverse microcrystalline community occupies larger, better connected “birds-eye” and laminar fenestrae higher in the mound. Changes in pore-water oxygenation or nutrient supply may have driven succession of cryptic communities within the mound.