Date of Award

Spring 1-1-2019

Document Type


Degree Name

Doctor of Philosophy (PhD)

First Advisor

Noah Fierer

Second Advisor

Kenneth Krauter

Third Advisor

Robin Dowell

Fourth Advisor

Shelley Copely

Fifth Advisor

Eduardo Rocha


Soil is essential for much of life on earth. Microbes are ubiquitous in this environment – billions of microbial cells can occupy one gram of soil. Soil microbes participate in carbon sequestration, nutrient cycling, and soil formation - all critical ecosystem processes, yet are poorly understood. A key factor in this knowledge gap is the low proportion of cultivated soil microbes – by one estimate 1/3 of soil dwelling bacteria and archaea do not have a cultured representative of their phylum. In my thesis research, I have studied the bacteria and archaea that live in soil using culture-independent techniques; specifically studying the unique ecological strategies they employ to excel in what can be a challenging habitat. First, I described how microbial communities change with soil depth; I found that as soil depth increases soil microbes become even more mysterious - candidate phyla and uncultured groups flourish in the low nutrient environment of deep soils. Here, I assembled two genomes from the candidate phylum AD3 and describe the strategies it employs to survive in deep soils. Second, I examined one particular soil bacterium - Ca. Udaeobacter copiosus. I show that Ca. U. copiosus is incredibly abundant and widespread in soils across the globe, all while relying on a reduced genome with many putative auxotrophies. This observation stands in contrast to prevailing theories that to succeed in soil, bacteria and archaea must possess vast metabolic versatility to take advantage of the diverse, yet limited nutrient sources characteristic of soil. Lastly, I describe a rearrangement of the rRNA operon where the 16S and 23S rRNA genes are “unlinked” and transcribed separately. I show that this rearrangement is common in many environmental bacteria and archaeal groups, and is especially widespread in soil - in one sample 41% of rRNA genes were unlinked. Together, these studies shed a measure of light on the uncultivated majority dwelling in soil, showing that uncultured environmental taxa adopt unique strategies to succeed in this environment, and in some cases harbor biology that stands apart from what we have learned from model organisms like Bacillus subtilis and Escherichia coli.