Research

What does a plant get back for the carbon it spends on its fungal partners?

The exchange of plant carbon for microbial nutrients drives carbon into soils and nutrients into plants. My overarching question: how do plants and microbes vary in that exchange, what governs the variation, and how does it shape ecosystem functioning?

I work through the model–experiment (ModEx) loop. I measure process rates with radio- and stable-isotope tracers, build functional classifications for the plants and fungi involved, test the consequences in large field manipulations, and fold the results into process-based models. The plant–arbuscular mycorrhizal fungus (AMF) symbiosis is my main testbed.

The premise is simple: thin-rooted plants take up nutrients from soil easily, so thick-rooted plants outsource more of that uptake to fungi — and they get more from edaphophilic AMF, which put biomass into soil, than from rhizophilic AMF, which put it into roots. Earth system models currently ignore this and assume a constant exchange rate.

Functional diversity of plants and microbes

I developed the AMF functional type framework during my graduate work (Weber et al. 2019), now widely used by other groups to interpret plant–AMF interactions — and recently validated and converted into a numerical index by other researchers, which makes it far easier to put into models. Using it, I tested how nitrogen deposition, altered precipitation, and plant invasion disrupt native shrub–AMF relationships and reduce fungal biomass (Weber et al. 2019; Phillips et al. 2019).

At SPRUCE, bog plants sort neatly by root traits and mycorrhizal type: narrow-rooted ericoid shrubs, thick-rooted ectomycorrhizal trees, and non-mycorrhizal herbs (Weber & Iversen 2023). Narrower roots turn over faster, so I predicted shrubs would increase root production most under warming — which is what I found (Weber et al. 2026). Working with Earth system modelers, that knowledge improved the accuracy of the E3SM Land Model at SPRUCE (Wang et al. 2026).

I also lead the Functional Mycorrhizae Working Group, currently setting out what land managers need in order to bring mycorrhizal fungi into plans for soil carbon sequestration, agroecosystems, and restoration.

How can competition among symbiotic microbes raise bioenergy yields through more efficient nutrient uptake? Plants get more phosphorus from diverse AMF communities at lower carbon cost — but is that functional complementarity among fungi, or a plant physiological response to fungi competing for its carbon? The answer changes how the gain could be managed. I will test this in switchgrass in EcoFABs across fifteen compositions of five Glomeraceae species, arranged as a diallel, with imaging, RNA-seq for nutrient transporter expression, and metabolomics. Submitting to the DOE JGI Community Science Program New Investigator call.

Plant–microbe interactions in bioenergy systems

Miscanthus has far deeper and thicker roots than other bioenergy crops, and process-based models couldn't handle them. So I built the capacity to model plant–microbe interactions and microbial decomposition down to 100 cm with Deep FUN-BioCROP (Weber et al., in prep.).

I'm now leading a study of miscanthus and AMF across West Virginia sites carrying legacies of coal-mining disturbance and fertilization, mentoring Emily Protain (PhD student, WVU) on a dissertation chapter. Those data will constrain how AMF biomass relates to soil carbon sequestration and miscanthus nutrient uptake in the model. In summer 2026 I supervised Stella Rhodes (CABBI RISE intern) on how microbial biomass and the phosphorus-sensitivity of nitrogen fixation vary across the same sites.

Do AMF recruit beneficial microbes that maintain bioenergy crop production under drought? Co-PI on a pending USDA AFRI Microbiomes proposal on the tripartite interaction between miscanthus, AMF, and plant-growth-promoting microbes. We'll test how drought tolerance varies with microbial assemblage in the greenhouse, identify the mechanism, validate in the field, and encode it in Deep FUN-BioCROP with distinct process rates per functional group.

Carbon and nutrient cycling

In a series of doctoral experiments I traced resource exchange between pasture plants and AMF with radioisotopes. Given a choice between two fungal partners, plants acquired more nutrients from the one with the lower carbon cost (Weber et al. 2024). That pattern holds as diversity increases: plants receive more phosphorus from diverse AMF communities, at a lower rate of carbon exchanged (Weber et al. 2025, with an invited commentary). Higher AMF diversity should also mean greater AMF biomass through reduced niche overlap — which implies we could manage ecosystems for more production, nutrient uptake, and soil carbon.

How does the size of the mycorrhizal biomass pool influence resource cycling? Mycorrhizal fungi are entering global models only as modifiers of uptake efficiency per unit plant mass, so size-dependent effects of the fungal pool are ignored entirely. I will request soils from the NEON Biorepository for AMF-dominant sites, estimate biomass with NLFAs and microscopy, sequence marker genes for diversity, and constrain the biomass–nutrient uptake relationship against NEON nutrient budgets.

Across these three threads I'm asking one question at three scales: what does a plant get back for the carbon it spends on its fungal partners, and what governs that return? Mesocosms where gene expression and metabolites can be measured properly; field manipulations in bioenergy systems; continental-scale sampling for the large patterns.

If you work on related questions, or you're a prospective student, I'd like to hear from you.