Research

Our research spans systems biology, genomics, bioinformatics, microbial evolution and ecology.

Our lab is interested in elucidating the molecular mechanisms that drive eco-evolutionary dynamics in microbial systems and the consequences of these relationships on system-level functions. To address these questions, our lab uses an integrative approach combining large scale experiments, synthetic microbial systems, theoretical modeling, and functional ‘omics.

Microbial ecology and evolution

We use a diverse suite of tools including ‘omics (i.e. metagenomics, metatranscriptomics, genomics), metabolomics, and culturing to link microbes to nutrient transformations and broader biogeochemical cycling in belowground ecosystems. Current research in this area is focused on the role of soil micronutrients (e.g. Shepherd & Oliverio, 2024) and how soil microbial eukaryotes regulate key aspects of belowground microbiomes.

Eco-evolutionary dynamics of microbial systems.

We use a lab-based synthetic microbial ‘model’ systems that are easily culturable and can be highly replicated to address fundamental questions evolution and ecology (Landis & Oliverio et al., 2021, eLife). Current research in this area is focused on using sourdough starters to explore eco-evolutionary dynamics.

Elucidating the genomics and functional contributions of microbial eukaryotes.

We have a particular interest in protists. We have looked at their functional contributions to (Oliverio et al., 2020 Science Advances) aquatic geothermal spring systems (Rappaport & Oliverio, 2023 Nature Comms; Oliverio et al., 2018 ISMEJ). We are interested in obtaining protist genomes and transcriptomes to further resolve the ecology and evolution of protists.