Research

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

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.

Fundamental questions we ask include:
1) How do microbial communities assemble?
2) How do microbial phylogenetic or functional trajectories shift across environmental gradients?
3) How will microbially-mediated processes change with global change factors?

To address these questions, our lab uses an integrative approach combining large scale experiments, synthetic microbial systems, theoretical modeling, and functional ‘omics. We are primarily focused on two major systems to develop our research program: soils and synthetic sourdough starter communities.

(1) Modeling approaches to elucidate the functional contributions and evolutionary strategies of soil microbes.

Current research is focused on using metagenome-resolved genomics to quantify the functional attributes and ecological strategies of the dominant soil bacterial taxa, in combination with soil edaphic measurements and climatic properties, across a broad range of natural soils. Previous research mapped the dominant soil bacteria globally (Delgado-Baquerizo et al., 2018) and modeled the ecological and functional niches of soil protists (Oliverio at el., 2020, Science Advances).

(2) Linking belowground soil systems to ecological processes and environmental change

Leveraging soil geochemical data along with ‘omics approaches to quantify the functional attributes of soil bacteria and their potential contributions to ecosystem processes. Current research is focused on understanding these ecological strategies and relationships to ecosystem processes in the context of decomposition of leaf litter across a dozen NEON (National Ecological Observatory Network) sites that span a broad range of geographic, climatic, and soil environments. Previous research has investigated which soil microbes respond to changes in soil temperature (Oliverio et al., 2017, Global Change Biology), and microbial contributions to phosphorus cycling in natural soil systems (Oliverio et al., 2020, mBio).

(3) Determining the molecular mechanisms that drive the eco-evolutionary dynamics of microbial systems via synthetic microbial communities.

We also use a lab-based synthetic microbial ‘model’ system that is easily culturable and can be highly replicated in a lab setting to address fundamental questions in assembly of communities and study microbiome dynamics. Current research in this area is focused on leveraging sourdough starters as a model system to relate community composition and assembly to emergent functional properties (and in particular, understanding the functional roles of acetic acid bacterial strains) and to explore eco-evolutionary dynamics in the context of heritability and directed evolution. Previously, in collaboration with colleagues at Tufts and NC State, we gathered starters from 500 community scientists to profile their microbial composition and functional properties, and also began to develop sourdough starters as a model system for looking at biotic interactions(Landis & Oliverio et al., 2021, eLife).