NSF Postdoctoral Fellowship in Biology FY 2020

Rohwer, Robin Rebecca, Madison WI

Investigators

Abstract

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2020, Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment and Phenotypes. The fellowship supports research and training of the Fellow that will contribute to the area of Rules of Life in innovative ways. Ecology and evolution are the frameworks through which scientists understand how organisms adapt to a changing environment. Ecology describes the abundance of different species over time, while evolution describes the abundance of different genes within a species over time. However, for microbes the definition of a species is unclear. Scientists hotly debate the criteria that should be used to group microbes into the same species, and shifting these criteria will determine whether observed changes in abundance reflect changes among species (ecology) or changes within species (evolution). This uncertainty around a microbial species blurs the boundary between ecology and evolution. This project will examine ecological and evolutionary processes across a range of species resolutions to identify unifying principles of ecology and evolution. The Fellow will search for these unifying principles using a 20-year microbial time series from a freshwater lake. The Fellow will create interactive data visualizations and incorporate them into outreach programs and course materials for diverse, public audiences that include scientists and educators. The 20-year microbial time series includes 500 metagenomes from Lake Mendota (WI, USA). The Fellow will assemble genomes from these metagenomes, and group them into "genome groups" that approximate a wide range of phylogenetic delineations from sub-species to phyla. First, the Fellow will quantify the standing genetic variation by comparing the gene contents of a genome group's core genome to its accessory genome. Analyzing annotated accessory genes may reveal functional impacts of genetic variation. Second, the Fellow will identify temporal changes in the abundance of different genome groups. Correlating genome group abundance with accessory gene abundance may reveal functional characteristics contributing to ecological success. Third, the Fellow will identify changes in allele frequencies in the finely resolved genome groups. Focusing on single nucleotide variants that change protein structure, and correlating these with the genome group's abundance, may reveal functional characteristics contributing to evolutionary success. To communicate these complex topics with the public, the Fellow will create interactive, mobile-friendly websites using the R-Shiny package. This will allow students, including those underrepresented in scientific disciplines, to move a slider to see how adjusting the phylogenetic resolution changes results. 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.