Super-generalist predation in a model microbe Dictyostelium discoideum

This project will study how organisms evolve to be either generalist or specialist predators using an amoeba, Dictyostelium discoideum, that preys on bacteria. This amoeba can eat many different bacterial species, despite their wide variety of defenses. The project will seek to determine whether the amoebas see all edible bacteria as equivalent, or the degree to which they must handle different bacteria in different ways.

For bacteria that they do handle in different ways, it will ask whether the amoeba’s changes in strategy are effective. This work will determine amoeba genes that important in handling prey and will test the idea that these genes evolve particularly rapidly because they must respond to changing bacterial strategies. Since bacteria can cause disease, provide services in our microbiomes, and have impacts on agriculture and nutrient cycling, a better understand their predators is needed.

The study will involve the training of undergraduates from diverse backgrounds, along with graduate students and a post-doctoral scholar. The project team will reach out to share its knowledge with diverse groups via public talks and popular articles, a booth at the Ferguson Farmer’s market, a blog, and a computer project for university classes, and a Behavior and Evolution Day for high school students.

The researchers will investigate the extent to which D. discoideum handles distinct prey differently using a panel of 15 diverse bacteria species. This array of prey species will be explored by four methods: studies of costs to amoebas of switching between prey species, responses to experimental evolution of amoebas on different prey, amoeba transcriptomic changes on different prey, and selection of amoeba gene knockout libraries on different prey.

Each of these four studies will be analyzed by similar multivariate statistical and clustering methods, giving four independent takes on which prey species are handled similarly. The researchers will use the results of the transcriptomics and the knockout selections in two further ways. First, the knockout selection results – do gene knockouts increase or decrease amoeba fitness on each prey – will be used to test how broadly adaptive the transcriptional changes on different prey are.

Second, those genes that most strongly show adaptive changes in this sense will define a set of “predation genes” which will be tested to see if predation drives evolutionary arms races. This project is co-funded by the Behavioral Systems program in the Division of Integrative Organismal Systems.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.