Ecological and evolutionary consequences of microbial community responses to environmental change

Global changes such as increased frequency of fire, drought, and nitrogen deposition, perturb microorganisms and the higher trophic life forms they support. Microorganisms play key roles in carbon and nutrient cycling, which are important to agriculture and ecosystem health. Although microorganisms are pivotal in an ecosystem's response to environmental changes, little is known about how abundant and diverse microbial communities adapt to such changes. The overarching aim of my thesis is to investigate how bacterial communities respond to global change and in particular, their ability to quickly adapt to environmental perturbations. I first investigated how microbial responses to global changes are influenced by interactions with plant communities using the Loma Ridge Global Change Experiment, a decade-long experiment that manipulates rainfall and nitrogen levels across two adjacent ecosystems (Chapter 1). My findings underscore the importance of plant–microbe interactions when considering the transferability of the results of global change experiments across ecosystems. Next, I investigated traits found on plasmids, a type of mobile genetic element (MGE) that can facilitate rapid evolution in bacteria. I asked what are the ecologically-relevant plasmid genes that may serve as reservoirs of environmental-adaptive traits in bacteria (Chapter 2). The findings of this chapter suggest that plasmid traits may contribute to host adaptation in environmental microbiomes. Lastly, I extended this work to a cosmopolitan soil taxon, Curtobacterium, an abundant genus of bacteria in southern California ecosystems. This taxon shows marked shifts in relative abundance in response to simulated drought and is amenable to culturing, providing a tractable system for investigating both genotypic and phenotypic characteristics of this organism. Previous experiments have shown Curtobacterium rapidly evolve via de novo mutations in response to environmental changes. I asked what MGE and associated traits are found in Curtobacterium, and determined whether MGE and traits showed any environment- versus clade- specific genomic signatures (Chapter 3). The findings of this chapter highlight the potential of traits found on plasmids to be mobilized within the bacterial communities where these Curtobacterium were isolated. Overall, my thesis work highlights the importance for considering the intersection of evolution and ecology in understanding how microbial communities adapt to environmental changes