Doctoral Dissertations

Date of Award


Degree Type


Degree Name

Doctor of Philosophy



Major Professor

Annette S. Engel

Committee Members

Linda Kah, Chris Fedo, Mark Radosevich


One of the most challenging questions in paleobiology is how bone transforms from a living tissue into a fossil. In life, the gastrointestinal tract microbiome of an animal promotes host health. But, in death, these microbial communities, as well as soil communities, begin to degrade tissue, including bones. Using the American alligator from coastal wetland habitats as a model system, the gastrointestinal tract microbiome was found to contain microbial communities consisting of Fusobacteria, Proteobacteria, Bacteroidetes, and Firmicutes, with variations based on tissue type along the length of the digestive tract. The overall dominance of Fusobacteria is distinct from any other tetrapod studied to date and is suggestive of a retained ancestral condition that may be controlled by conservative host morphology, behavior, and niche occupation. Alligators are crown archosaurs that have occupied similar wetland habitats since their divergence in the Late Triassic, with an accompanying crocodylian fossil record that is replete with bones preserved in wetland environments. Following alligator death, structural and chemical changes to alligator bone, including transformations into more thermodynamically stable mineral phases, occur within days to weeks when bone is exposed to indigenous soil and water microbial communities, as well as from abiotic processes controlled by habitat geochemistry. Direct exposure to indigenous microbial communities slows alteration, which may be critical for stability of bone over geologic time. Despite different compositional chemistries, experimentally treated and fossil bones of varying ages converge on a common mineral lattice arrangement at the atomic-level that may facilitate bone preservation.

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