<p>  Non-model microorganisms offer a wealth of biotechnological potential that may be leveraged to address a variety of global grand challenges. These include challenges in carrying out complex or altogether new chemistries, discovery and production of bioactive molecules, sustainable production of biochemicals and bioproducts from renewable feedstocks, and improving agricultural practices for responsible management of carbon. Specifically, using renewable plant biomass as a substrate for production of fuels and or chemicals offers a near ubiquitous supply that does not compete with food or petrochemicals. Alternatively, identifying new natural products will be essential to addressing the ever-increasing occurrence of antibiotic resistance. Non-model organisms may provide elegant solutions to many of these challenges, whether by possessing new or more efficient strategies to depolymerize lignocellulose, by encoding enzymes with increased stabilities and or specific activities, or perhaps by containing rich biosynthetic capabilities for production of previously unidentified natural products, among others. Yet efforts to leverage non-model microorganisms for their diverse biotechnological potential remain limited to a variety of often difficult, yet not insurmountable challenges.</p> <p>     In this work, I propose anaerobic gut fungi (Neocallimastigomycota) as a robust microbial system that may be leveraged to efficiently depolymerize crude lignocellulose, increase animal nutrition, or identify novel natural products. To this end, I detail the first chromosomally resolved genome assembly of anaerobic fungi (<em>Piromyces communis </em>var. <em>indianae</em> UH3-1). I investigate the genome organization of this isolate and describe how acquisition of Carbohydrate Active EnZymes (CAZymes) contribute to the robust lignocellulolytic activity of gut fungi. I then detail efforts to build a nascent genetic engineering toolbox for these anaerobic organisms. With the acquisition of the first chromosomally resolved genome assemblies, I identify a basic set of genetic parts needed for a genetic engineering toolkit. I show these parts are functional and detail methods to enable higher throughput testing in vivo. I subsequently detail efforts to construct the first preliminary CRISPR tools for anaerobic fungi as these will be essential to establish precise DNA targeting in future strain engineering efforts. I then describe the role of epigenetics in anaerobic fungi, detailing the extent to which it may be leveraged to control gene expression. Finally, I provide a discussion of this work and describe how it may guide future efforts to domesticate these organisms. Collectively, this work provides the first chromosomally resolved genome assembly as a resource for the community, along with genetic tools and techniques to begin domesticating these non-model organisms. Importantly, this work reveals that despite the challenges associated with anaerobic microbes of relatively high complexity, they are not insurmountable, and thus efforts to domesticate them are feasible.</p>

<p dir="ltr">In a rapidly changing world, human actions and natural events are reshaping ecosystems and presenting new challenges for conservation efforts. Within this context, unraveling the recent ecosystem transformations and their implications on a fine scale is required. The impacts of such changes are not always sudden but often gradual and sometimes as a result of historical events. With the recent advancement in technologies, the resolution of information by genome sequences spans from millions of years ago (hindcasting) to future generations (forecasting). Aquatic ecosystems pose their own challenges when it comes to ecosystem changes and the types of data required to assess impact and help inform conservation efforts. My dissertation comprises three chapters focused on using genomic techniques to generate data valuable for the conservation and management of aquatic ecosystems. Each of the three chapters is a distinct manuscript in terms of scientific publications, where Chapter 1 has already been published, Chapter 2 has been submitted to a journal, revised, and is now awaiting publication, and Chapter 3 is in preparation for submission to a peer-reviewed journal. In Chapter 1, dietary DNA from harvested North American river otter (<i>Lontra canadensis</i>)<i> </i>was used to determine whether metabarcoding of stomach content could be used to identify fish prey species consumed. In Chapter 2, DNA sequencing of endangered pupfish species in the Tularosa Basin of New Mexico was studied; before my work, it was nominally comprised of a single species, the White Sands pupfish (<i>Cyprinodon tularosa</i>). The results indicate a rapid speciation event occurred within about the last ~5000 years, driven primarily by genetic drift. Chapter 3 extends Chapter 2 by assessing the dynamics of genomic diversity over space and time while evaluating the short-term evolutionary dynamics (~18 generations) of the two native pupfish populations. This temporal study aimed to determine if the extraordinarily rapid evolution over the last ~5000 years (observed in Chapter 2) could be detected over timescales more relevant to conservation and management efforts. Overall, this dissertation used genomic sequence data from metabarcoding of the COI gene region in the otter stomach content as well as pool sequencing and whole genome resequencing of pupfish to provide key biological insights into the conservation of these aquatic species. This dissertation also provides insights into avenues for further study and highlights the significant role that conservation genomics can play in the future. The findings presented in the three chapters are discussed within the context of species’ conservation and management.</p>