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.

Check out the project website here.


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.


Phylogenomics of Pezizales and evolutionary transitions between saprotrophy and symbioses with animals, plants and bacteria.

Pezizales are an early diverging lineage of Ascomycetes that include morels and truffles and is diverse but undersampled, understudied, and unresolved in terms of genus and family-level relationships.The objective of this research is to generate a phylogenomic framework to resolve higher level evolutionary relationships in Pezizales in order to generate and test hypotheses on fungal genomic traits related to fruiting body form, nutritional ecology and plant-animal-bacterial symbioses. This  international collaboration  with BSF-PI Segula Masaphy from Israel will facilitate reciprocal international student training and field forays focused on sampling and collection of Pezizales in order to reconstruct a genome-based phylogeny of the Pezizales, stabilize taxonomy, and improve understanding of the microbiome contribution to Pezizales trophic ecology.


Cultivating a morel mushroom industry in the North Central United States.

Morels (Morchella spp.) are iconic spring mushrooms in the North-Central Region of the United States and a high-value commodity in food markets. This project aims to develop morel cultivation in forest, low- and high-tunnel systems, and will compare yield and market considerations among these systems. Project results from consumer surveys and panel focus groups will help in estimating market demand along with demographics and preferences pertaining to different morel production methods and species. Results from outdoor morel cultivation research will establish a new knowledge base for a novel, agronomically and economically sustainable crop and co-cropping systems for the North-Central Region.