Keystone species are widely distributed across aquatic and terrestrial ecosystems and are fundamental in preserving the structure, diversity, and stability of an ecological community due to its disproportionately large impact on its community relative to its biomass. As biodiversity of ecosystems becomes more threatened with urbanization and habitat destruction, it is imperative to understand a keystone species' role in maintaining ecosystem function. One of the ways to do so is by examining their significance and connection to the ecosystem food web. Within North American freshwater ecosystems is the pebble nest-building minnow, the bluehead chub (Nocomis leptocephalus; "chub"). Chubs provide spawning habitat for not only themselves, but for other minnows, collectively called "nest associates". In this work, I observe the predatory and potential mutualistic interactions between chubs, nest associates, and their predators. In Chapter 1, I observe spawning nests to identify the predators of adult chubs, nest associates, and embryos. I further investigate how nest visibility covariates including minnow activity, minnow abundance, nest size (area), and nest growth affect predator encounter rate to spawning nests. I found a total of 23 diverse taxa to prey on the adult minnows and minnow embryos on chub spawning nests, 14 predators of which had not been reported in literature. One of these predators was the common snapping turtle (Chelydra serpentina; "turtle"). Additionally, I found that activity, abundance, nest size (area), and nest growth had a significant effect on predator encounter rate, attracting predators to seek spawning nests for prey. In Chapter 2, I investigate the effect of ambient temperature on turtle epizoic coverage during the spawning season and provide preliminary evidence of a potential cleaning symbiotic mutualism between the turtle and minnows. I found that epizoic coverage decreases during the duration of a minnow spawning season after an initial increase with early summer warming, and my results also present unique and shared bacterial communities across three sources, the ambient environment, gut contents of minnows, and turtles. The results additionally revealed there to be bacterial communities unique between minnows and turtles that were not identified in the ambient environment. Overall, this study is first to systematically document predators of chub spawning nests and first to provide preliminary evidence of a cleaning symbiotic mutualism between a freshwater turtle and minnow species (or freshwater turtles and fish in general), which, thus far, has not been explored in freshwater ecosystems. This work demonstrates that chub spawning nests are a crucial entity of the freshwater food web structure across Nocomis' distribution range and reveals that chub spawning nests create an interconnection between a diversity of fauna in a freshwater ecosystem. / Master of Science / Ecological communities often include species that are essential in ensuring the overall stability and biodiversity of an ecosystem. These species, otherwise called keystone species, play a crucial role in facilitating interconnections within the ecosystem's food web. The bluehead chub (Nocomis leptocephalus; "chub") is an example of a keystone minnow found in North American freshwater streams. This minnow engages in a complex, distinguished act when it reproduces, making mounded, pebble nests using only its mouth. Chubs are not the only minnow species interested in this engineering complexity. Various minnow species called "nest associates" reproduce on the nests as well, providing an appearance of a mutualism: all species involved benefit from the interaction. While this interaction has been observed, there is limited research identifying predators of chub nests and if there are potential mutualisms with any of these predators. In this work, I identify predatory and mutualistic interactions between chubs, nest associates, and their predators. In Chapter 1, I identify predators of chub nests and observe variables that attract these predators to the nests. In Chapter 2, I explore a potential, mutualistic interaction between these minnows and an identified predator from this research, the common snapping turtle (Chelydra serpentina; "turtle"), whereby minnows feed on potentially harmful growth of algae and bacteria on turtles, while turtles benefit from the cleaning. For Chapter 1, my results revealed that a chub nest is a hotspot for predator diversity, showing 23 diverse taxa as predators, in which 14 of the identified taxa are novel for ecological literature. Additionally, variables that were observed to attract predators to chub nests were minnow activity, minnow abundance, nest size (area), and nest growth. Results for Chapter 2 demonstrated that there are unique bacterial communities between turtles and minnows that are not found in the stream environment, therefore providing preliminary evidence of mutualistic interaction between the coexisting species. Overall, this study is the first to systematically document predators of chub nests. This study is also first to investigate a mutualistic interaction between minnows and turtles in a freshwater ecosystem, an area that has not been previously explored, unlike similar interactions in marine ecosystems. Cohesively, the keystone species, the chub, and their reproductive nests, are important for the aquatic food web structure and the interconnectedness to their overall ecosystem function. This research further stewards scientific knowledge about how important Nocomis are to natural freshwater ecosystems.

Our understanding of microbial evolution is largely dependent on available genomic data of diverse organisms. Yet, genome-sequencing efforts have mostly ignored the diverse uncultivable majority in favor of cultivable and sociologically relevant organisms. In this thesis, I have applied and developed cultivation independent methods to explore microbial diversity and obtain genomic data in an unbiased manner. The obtained genomes were then used to study the evolution of mitochondria, Rickettsiales and Haloarchaea. Metagenomic binning of oceanic samples recovered draft genomes for thirteen novel Alphaproteobacteria-related lineages. Phylogenomics analyses utilizing the improved taxon sample suggested that mitochondria are not related to Rickettsiales but rather evolved from a proteobacterial lineage closely related to all sampled alphaproteobacteria. Single-cell genomics and metagenomics of lake and oceanic samples, respectively, identified previously unobserved Rickettsiales-related lineages. They branched early relative to characterized Rickettsiales and encoded flagellar genes, a feature once thought absent in this order. Flagella are most likely an ancestral feature, and were independently lost during Rickettsiales diversification. In addition, preliminary analyses suggest that ATP/ADP translocase, the marker for energy parasitism, was acquired after the acquisition of type IV secretion systems during the emergence of the Rickettsiales. Further exploration of the oceanic samples yielded the first draft genomes of Marine Group IV archaea, the closest known relatives of the Haloarchaea. The halophilic and generally aerobic Haloarchaea are thought to have evolved from an anaerobic methanogenic ancestor. The MG-IV genomes allowed us to study this enigmatic evolutionary transition. Preliminary ancestral reconstruction analyses suggest a gradual loss of methanogenesis and adaptation to an aerobic lifestyle, respectively. The thesis further presents a new amplicon sequencing method that captures near full-length 16S and 23S rRNA genes of environmental prokaryotes. The method exploits PacBio's long read technology and the frequent proximity of these genes in prokaryotic genomes. Compared to traditional partial 16S amplicon sequencing, our method classifies environmental lineages that are distantly related to reference taxa more confidently. In conclusion, this thesis provides new insights into the origins of mitochondria, Rickettsiales and Haloarchaea and illustrates the power of cultivation independent methods with respect to the study of microbial evolution.