This dissertation integrates environmental metagenomes with extensive geochemical metadata for the development and application of multidimensional biogeochemical metrics. Analysis techniques including a Markov cluster-based evolutionary distance between whole communities, oligonucleotide signature-based taxonomic binning and principal component analysis of geochemical parameters allow for the determination of correlations between microbial community dynamics and environmental parameters. Together, these techniques allow for the taxonomic classification and functional analysis of the evolution of hot spring communities. Further, these techniques provide insight into specific geochemistry-biology interactions which enable targeted analyses of community taxonomic and functional diversity. Finally, analysis of synonymous substitution rates among physically separated microbial communities provides insights into microbial dispersion patterns and the roles of environmental geochemistry and community metabolism on DNA transfer among hot spring communities.
The data presented here confirms temperature and pH as the primary factors shaping the evolutionary trajectories of microbial communities. However, the integration of extensive geochemical metadata reveals new links between geochemical parameters and the distribution and functional diversification of communities. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial community functional composition and inter-community DNA transfer rates. Finally, the taxonomic classification and clustering techniques developed within this dissertation will facilitate future genomic and metagenomic studies through enhanced community profiling obtainable via Markov clustering, longer oligonucleotide signatures and insight into PCR primer biases.
Geology and its tangential studies, collectively known and referred to in this thesis as geosciences, have been paramount to the transformation and advancement of society, fundamentally changing the way we view, interact and live with the surrounding natural and built environment. It is important to recognize the value and importance of this interdisciplinary scientific field while reconciling its ties to imperial and colonizing extractive systems which have led to harmful and invasive endeavors. This intersection among geosciences, (environmental) justice studies, and decolonization is intended to promote inclusive pedagogical models through just and equitable methodologies and frameworks as to prevent further injustices and promote recognition and healing of old wounds. By utilizing decolonial frameworks and highlighting the voices of peoples from colonized and exploited landscapes, this annotated syllabus tackles the issues previously described while proposing solutions involving place-based education and the recentering of land within geoscience pedagogical models. (abstract)