Using a tiny symbiosis to answer big questions about how host-microbe interactions evolve

Understanding how the microbiome evolves, and how the microbiome shapes host evolution, requires measuring host and microbe phenotypes and fitness across multiple host genotypes (G), microbial genotypes or community compositions (also often represented by G), and environments (E). When measuring outcomes across these multiple sources of variation, experiments quickly become very large, especially when we want to estimate G x G, G x E, or G x G x E interaction effects, which are often of substantial interest. For example, there must be G x G effects for both host and microbial fitness for hosts and microbes to co-evolve, while local adaptation of hosts, microbes, or both implies G x E or G x G x E effects. My lab has developed a new experimental system to manipulate many host genotypes and microbiomes across environmental gradients at high throughput using tiny, fast-growing aquatic plants (duckweeds in the genus Lemna) and their microbiota. I will describe the results of several recent experiments in this system that quantify the main and interactive effects of host genetic variation, microbial community composition variation, and environmental variation on host and microbe fitness, thereby shedding light on how host-microbe interactions evolve.