Fungi power: Unlocking an underground network’s ability to address environmental challenges

About 500 million years ago, a fungus became intertwined with one of Earth’s first plants. It was the beginning of a massive, intricate underground network crucial to the survival of almost all plants and trees. 

A team of Stanford researchers is working to harness these powerful, but delicate fungi to address challenges such as climate mitigation and food security. Their project, funded by the Stanford Woods Institute for the Environment, draws on ecology, bioengineering, and plant biology to develop an open-access toolkit for identifying and manipulating fungal and plant genes that underpin key ecosystem functions. Practitioners worldwide could use this toolkit to help build shared knowledge of fungi and plants. The resulting knowledge could one day help scientists engineer fungi-plant symbiosis to store large amounts of carbon underground and break down toxins, such as plastics and pesticides, among other advances.

“I think of this project as having some peril and some promise,” said co-principal investigator Kabir Peay, an associate professor of biology and Earth system science at the Stanford Doerr School of Sustainability. “Modifying mycorrhizae genomes could open the way for novel solutions to environmental problems, but there are important questions to answer before we can do that safely.” 

The fungi, called mycorrhizae, burrow deep into soil to find nitrogen and phosphorus. In a life-sustaining symbiotic exchange with their plant and tree hosts, they swap these nutrients for carbon. Research has shown that some species of mycorrhizae are highly proficient at storing carbon away, improving plant responses to stress, and helping plants adapt to particular environments.

Peay and his fellow researchers are studying how global environmental changes, such as increased heat stress, are affecting the survival of mycorrhizae in order to inform their conservation, and potentially engineer them to supercharge the valuable services they provide.

Engineering mycorrhizae is uncharted territory. Unlike fruit flies and a small mustard plant called Arabidopsis thaliana, two types of organisms that have been commonly used in genetic studies, mycorrhizae are notoriously hard to work with. They aren’t what biologists call model organisms, which are easy to grow and have broad applications to genetic studies in humans and other life forms. 

“We don't know necessarily how to get DNA in to fungi, then isolate them to ensure the DNA encode something that will meaningfully change behavior,” said project co-principal investigator Jenn Brophy, an assistant professor of bioengineering, which is a shared department in the Stanford School of Engineering and Stanford School of Medicine. “Scientists haven’t worked with these organisms very much, so there’s a lot to do, but that makes this space really exciting.”

Brophy and her fellow researchers are working to create synthetic genetic circuits tailored to precisely “reprogram” how certain fungi species interact with other organisms. Peay and his team are aiming to inform the approach with new knowledge about mycorrhizal symbioses, such as how the diversity of fungi contributes to the conditions that plants are able to adapt to, and projections about which plants and fungi are most vulnerable to climate change. 

The researchers are exploring the use of bacteria to introduce genetic tools to fungi and trees. Depending on how the technology develops, they might also explore using an immune system-derived gene editing tool called Clustered Regularly Interspaced Short Palindromic Repeats or CRISPR. Either way, the team is committed to ensuring these tools are secure, safe, sustainable, and governed in cooperation with the people who steward the land where they will be deployed.

Read more about CRISPR

"One of the reasons I was drawn to Stanford is because I want to be able to make meaningful technologies that can better people's lives and the health of our planet,” said project collaborator Anna Johnson, a graduate student in the Brophy and Peay labs. “I’ve had a long-term interest in preserving biodiversity as a means to improve agriculture. I saw this project as an opportunity to build tools on a molecular scale that will aid on an ecological scale.”

If the research team is successful in engineering mycorrhizae, it could more clearly reveal the molecular signaling that mediates communication between trees and fungi. It could also help us better understand trees’ needs and lay the groundwork for protecting and representing trees and fungi under the law.

"In a future where we want to incorporate more legal rights for nature, we're going to need much better ways to measure and understand what forests need,” said project collaborator Rolando Perez, a former Stanford bioengineering graduate student who introduced Peay to Brophy and helped conceive the project. Perez views genetic tools as complimentary to Traditional Ecological Knowledge passed down over centuries through Indigenous Peoples’ observations of natural systems as kin. "Modern science is showing us what Indigenous communities have long known: we are a part of nature, and competition isn't the only way of life.”

Peay is also director of the Earth Systems Program at the Stanford Doerr School of Sustainability.