Graduation Year


Document Type




Degree Name

Doctor of Philosophy (Ph.D.)

Degree Granting Department

Biology (Integrative Biology)

Major Professor

Christina Richards, Ph.D.

Committee Member

Gordon Fox, Ph.D.

Committee Member

Kathleen Scott, Ph.D.

Committee Member

Aaron Schrey, Ph.D.


coastal ecosystems, gene expression, molecular ecology, transgenics


Although the “genome as a blueprint” metaphor has been pervasive in biology, recent advances in molecular biology have revealed a complex network of regulatory machinery that dynamically regulated molecular processes in response to environmental conditions. However, these patterns, as well as the evolutionary processes that underlie them, remain understudied in natural conditions. In 2010, the Deepwater Horizon oil spill released an estimated 4.9 million barrels of oil into the Gulf of Mexico, making landfall on salt marsh habitat dominated by the foundation species Spartina alterniflora. Despite the severe impacts to phenotype and fitness, S. alterniflora proved remarkably resilient in the face of the crude oil stress. Despite the tragedy of the Deepwater Horizon oil spill, the event represented a unique opportunity to explore the molecular mechanisms of oil tolerance in this highly resilient species. To understand how organisms regulate gene expression in natural settings and to identify best practices in genome-wide expression studies, we first surveyed a ten-year span of transcriptome-wide gene expression studies. We then confirmed the hypothesis that crude oil exposure would induce differential gene expression in affected populations, and whole-transcriptome microarray identified 3,622 genes that responded exclusively to oil stress. To confirm the function of candidate genes involved in resilience to oil stress, we used a highly-differentially expressed subset of these genes to construct gene interaction networks and identify target genes. We obtained T-DNA insertion genotypes of the emerging model grass species Brachypodium distachyon that were disrupted in these target genes for functional confirmation, but were unable to detect significant modulation of oil response through these heterologous knockouts. Finally, we isolated the phenotypic effects of crude oil exposure through greenhouse trials and found evidence that crude oil may have acted as a selective pressure, rather than an inducer of plasticity. Together, these studies identify novel patterns of gene expression in response to a severe but unpredictable stressor that has widespread impacts on a foundational salt marsh grass species. In addition, this dissertation represents a pathway to understanding functional genomics in non-model systems without extensive genomic resources.