What functional roles differentiate fungi in the plant soil microbiome?
Collaborators: PMI Consortium (Oak Ridge National Lab)
In forest soils, dozens of fungal species can share the same root system, but cryptically play very different jobs. Using genome-resolved metatranscriptomics from natural microbial communities of Populus , I track when and where fungi turn on genes for carbon use, nutrient foraging, and stress tolerance across seasons and environmental gradients. This approach reveals “cryptic” symbionts—like dark endophytes and fine-root associates—that are functionally important but often overlooked in standard surveys.
My lab scales this work from whole rhizospheres down to individual colonized root tips, pairing single-tip and spatial transcriptomics with greenhouse bioassays. By mapping which enzymes, transporters, and signaling pathways are deployed during colonization, nutrient exchange, and competition, we identify the ecological mechanisms that differentiate coexisting fungi and link them to host performance and forest soil health.
How do fungal functional roles evolve across the landscape and time?
Collaborators: Hoffman Lab (Bielefeld University); Brown Lab (University of Utah)
To understand why fungal communities differ from site to site, we need to know how their functional “toolkits” evolve with climate, soil, and host identity. In the porcini mushroom Boletus edulis, I use one of the largest population-genomic datasets for any symbiotic fungus—hundreds of genomes plus reference-quality assemblies—to study how structural variants, mobile elements, and copy-number changes in key gene families track environment and host associations.
In parallel, I use the ectomycorrhizal genus Laccaria as a genus-scale model for symbiotic trait evolution, building pan-genomes to quantify how effectors, CAZymes, and transporters are gained, lost, and repurposed across species and habitats. By integrating these genomes with metatranscriptomes from colonized Populus roots, my group links genomic variation to realized function in situ—generating trait maps that connect landscape heterogeneity to patterns of fungal diversity and symbiotic performance.
How has the fungal symbiosis toolkit diversified over deep time?
The extreme diversity of ectomycorrhizal fungi did not arise overnight—it reflects tens of millions of years of host shifts, niche transitions, and genomic innovation. Focusing on the porcini family Boletaceae (>2,000 species), I combine dense taxon sampling from herbaria and tropical field collections with genome-scale phylogenetics to reconstruct when and where major radiations occurred, and how they intersect with Earth’s geological and biogeographic history.
Building on a fully resolved Boletaceae backbone phylogeny, my lab is now generating comparative genomic resources across the family to track evolution in core symbiosis genes and genome architecture. By pairing these data with ancestral host reconstructions and available transcriptomes, we test which components of the fungal “symbiosis toolkit” are conserved, which diversify with new hosts or environments, and how these deep-time processes set the stage for the cryptic ecological differentiation we observe in today’s forest soils.
