General Expertise

Fungal evolution; Plant microbiomes; Truffle biology; Plant-fungal-bacterial interactions; Microbiome ecology and evolution


Research Areas

Our research makes use of phylogenetics, high-throughput sequencing, isotope tracers and –omics approaches to better understand:

(1) phylogenetic and functional diversity of plant-associated fungi

(2) environmental and genetic factors that structure microbiome communities

(3) the evolution and functional relevance of bacterial symbionts of fungi

Our lab research has applications pertinent to agriculture, forestry, biodiversity and the sustainability of Earth’s life support systems.


Current Projects

  • Phylogenetic and functional diversity of tripartite plant-fungal-bacterial symbioses

This project investigates the diversity, evolution and functions
within a lineage of fungi, the Mucoromycota, implicated in terrestrialization
of Earth. These fungi co-evolved with plants through innovations that
include growth habits within the plant and on its surface. Intriguing, many
of the plant-associated genera of these fungi carry specific bacterial
endosymbionts within their cells only known from fungi. The evolution and
functional ecology of these endobacteria remains unclear. This project will
compare and analyze entire genomes to identify co-evolved symbiosis traits
in plant-fungi-bacteria partners and assess the impact of bacterial
endosymbionts on the function of their fungal host and its interaction with plants.

  • Impact of production system, plant species and stress on whole plant microbiome and productivity

Sustainable agriculture production is intimately linked to microorganisms that associate with plants, known as the plant microbiomes.  Our research will reveal foundational knowledge on fungal, oomycete and bacterial microbiome characteristics of woody plant (poplar) and herbaceous (wheat/corn/soy;) agronomic crops grown under three production systems (conventional; organic; no-till). We will also investigate how applications of fungicides, herbicides and insecticides impact plant and soil microbiomes. 

  • Great Lakes Bioenergy Research Center (GLBRC) – Harnessing the switchgrass microbiome

The GLBRC is addressing interrelated knowledge gaps that currently limit the industrial scale production of specialty biofuels and bioproducts from purpose-grown bioenergy crops, in order to develop a new generation of sustainable lignocellulosic biorefineries. The Bonito lab is working to characterize the switchgrass microbiome and its impact on plant physiology in collaboration with other researchers in the GLBRC.