Current Research 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. The USDA-funded 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.

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

The  DOE-funded 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 harness the switchgrass and sorghum microbiome and to improve plant productivity and resilience 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 NSF-funded 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 USDA SARE-funded 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.

MIM:Collaborative Research: The impact of the fungal microbiome in metal tolerance and soil biogeochemical transformations

Fungi and bacteria are microorganisms that often live in a close association and play a key role in transforming and detoxifying metals in the environment. In spite of this importance, there is relatively little understanding of how the interactions between bacteria and fungi influence the transformation and/or detoxification of metals. The goal of this NSF-funded project is to address this knowledge gap by identifying how fungal-bacterial interactions affect metal transformation. This will be achieved through a novel multidisciplinary research approach employing advanced, state-of-the-science analytical techniques. Knowledge gained through this project will allow the engineered control of metal transformations for a wide range of applications in environmental cleanup, biorefining, production of nanoparticles, and other beneficial applications.

Bacterial-Fungal Interactions and their role in Soil Functioning

This DOE-funded Science Focal Area program integrates a wide range of experts in the fields of fungal and bacterial biology and ecology, genomics and bioinformatics, proteomics, metabolomics and metabolic flux analysis (MFA), cell-cell interactions, in situ molecular-scale imaging, and system modeling.

Improved Method for Identifying Causative Antigen in Hypersensitivity Pneumonitis

Hypersensitivity pneumonitis (HP) is a difficult disease to identify the causative agent. There have been over 300 antigens, including animal proteins, bacteria, fungi, and low molecular weight chemicals identified as agent(s) important in the etiology of HP. Symptomatic treatment generally involves the use of corticosteroids. The most effective treatment is for patients to avoid exposure to the causal antigen, which has the potential to stabilize and reverse the patient's disease, and in one study significantly reduced mortality. In this NIH-funded project, a cross- disciplinary patient-centered approach is being used to determine the causative antigen in patients with hypersensitivity pneumonitis.