Date of Award

January 2019

Document Type


Degree Name

Doctor of Philosophy (PhD)



First Advisor

Brian J. Darby


Enrichment of ecosystems with excess nutrients often results in microbial communities with an overabundance of just one or a few species, such as algae in eutrophic waters, or micro- invertebrates in organically amended soils. To explain this, the Growth Rate Hypothesis postulates that rapid growth rates are constrained by cellular ribosome concentrations and that nitrogen and phosphorous act as limiting nutrients. However, the genetic mechanism to the Growth Rate Hypothesis has not been clearly identified. The objective of this work is to test the hypothesis that rRNA copy number variance is the causative genetic mechanism of the Growth Rate Hypothesis because it codes for vital and phosphorus-rich ribosomal RNA and appears in repeats that vary in copy number between organisms. In the first chapter, I suggest that there are three pieces of evidence needed to confirm this hypothesis: 1) that rRNA copy numbers are phylogenetically autocorrelated, 2) that nutrient enrichment disproportionately benefits high-copy number species, and 3) that rRNA copy number is positively correlated with rapid intrinsic population growth rate and generation time. The second chapter tested the hypothesis that rRNA operon copy number is a heritable trait with variation, as evidenced by phylogenetic auto-correlation in bacteria, archaea, and nematodes, using rRNA copy numbers obtained from publicly available databases as well as from experimental findings. Prokaryote copy number was phylogenetically autocorrelated as a whole. Copy number also clustered in most phyla, which indicates that copy number is under selection and therefore a viable mechanism for the Growth Rate Hypothesis. The third and fourth chapters tested the hypothesis that nematodes and bacteria with high copy number benefit from nutrient enrichment more so than species with low copy number. I examined the abundance and distribution of nematode and bacteria from Illumina sequencing for long term enrichment plot samples, short term soil core mesocosm experiments from the spring, and short term mesocosms experiments from the fall. High copy number prokaryotes and fast-growing nematodes had significant responses to nutrient enrichment that differed across season and nutrient type, which indicates that copy number operated as the genetic mechanism for the Growth Rate Hypothesis. The fifth chapter tested the hypothesis that rRNA gene copy number is positively correlated with growth metrics in enrichment type soil nematodes. I measured life-history traits and sequenced copy number and found a significant positive correlation. The correlation indicates that fast-growing nematodes have high copy number, linking copy number to nutrient enrichment from the soil core experiments.