Biogeochemical and Phylogenetic Signals of Proterozoic and Phanerozoic Microbial Metabolisms

Danielle Gruen, Ph.D., 2018
Gregory Fournier, Advisor

Life is ubiquitous on Earth, but quantifying the distribution and fluxes of microbial metabolisms in Earth’s carbon cycle is difficult, especially in spatially- and temporally-remote environments. This thesis develops and employs novel geochemical and phylogenetic approaches to illuminate diagnostic signals of microbial metabolisms on geologic timescales. Field studies, laboratory experiments, and computational models explain how methanogens produce unique nonequilibrium methane clumped isotopologue (13CH3D) signals which may be driven by enzymatic reactions, the C-H bond inherited from substrate precursors, isotope exchange, and environmental processes. Phylogenetic analyses of methyl-corrinoid proteins in methylotrophic methanogens suggests that substrate specificity evolved via a complex history involving horizontal gene transfer (HGT). Furthermore, this work identifies a previously unrecognized HGT involving chitinases (ChiC/D), used to tether fossil-calibrated ages within fungi to bacterial lineages. Molecular clock analyses show that multiple clades of bacteria likely acquired chitinase homologs from fungi via HGT during the late Neoproterozoic into the early Paleozoic. Recipient terrestrial bacterial clades diversified ∼400-500 Ma, consistent with the dispersal of chitinase genes throughout the microbial world in direct response to the evolution and expansion of detrital-chitin producing groups including arthropods. Taken together, this work may improve our understanding of the coevolution of life and Earth processes.