The Underground Revolution

A conversation with microbiologist Colin Averill

At what point did fungi and soil biomes become a specific area of interest for you?

Colin Averill: I first learned how forests and ecosystems can buffer our planet against climate change during my undergraduate studies, about 15 years ago. However, even then it was well known that the biggest gaps and open questions in forest ecology were all below ground. How do roots work? What is actually happening in soil? How does incredible soil biodiversity affect all of this? Through those learnings, I became convinced I needed to spend my efforts understanding how all the biodiversity in soil actually affects how entire forests work—and for me, mycorrhizal fungi were an obvious place to start. Beyond that, I really just hoped that a better scientific understanding of forest microbiology could someday lead to real climate solutions.

In your recent TED Talk, you emphasize the importance of looking “deep underground” to better understand diverse microscopic fungal networks, and how they combine with tree roots to form symbiotic partnerships with the environment. Can you briefly explain how this relationship works? 

Nearly all plants on earth form a root biological partnership, or what scientists call a “symbiosis” with mycorrhizal fungi. These fungi colonize the roots of plants and help plants access growth-limiting soil resources like water or nutrients. In exchange, plants share photosynthetic sugars with the fungus. These sugars are the direct result of plants converting CO2 in the air into carbohydrate nutrition, powered by the sun. It’s a trade whereby carbon that the plant acquires above ground is exchanged for soil resources the fungus acquires below ground.

While this general trade is a defining feature of mycorrhizal fungi, there are hundreds of thousands of species of these fungi. Each species engages in the trade slightly differently. Each fungal species specializes in a slightly different set of soil resources or perhaps accesses them in a slightly different way. Understanding the diversity of mycorrhizal species and strategies is really important to understand how they ultimately affect the capacity of the forest to remove carbon from the atmosphere

Could you explain how DNA has played a significant role in discovering how these systems work?

For a long time, it was really difficult to know which particular mycorrhizal fungal species were present in a forest. Scientists had to collect and then examine roots under a microscope. A small group of people could only tell which species was which based on deep experience and training. DNA sequencing has changed all of this. We can now take a simple sample of roots and soil in the forest, extract the DNA, and “sequence” a very specific region of fungal DNA that serves as a name tag, or barcode, that tells us which species a particular fungus is. By studying the variety of these fungal barcode DNA sequences in a sample, we can understand which mycorrhizal fungi are present much more quickly and easily.

How much of a game-changer is this work in terms of climate, and also in terms of food production? You have previously pointed out, for example, how fragile our existing agricultural monocultures are, and how “leaning into” biodiversity below ground might reverse the reductionist processes.

We have spent centuries manipulating plant genetics to massively increase plant productivity in forestry and agriculture. The plant microbiome is like an extension of the plant genome, but a part we have not really manipulated at all. I don’t think anyone knows the full potential of plant microbiome engineering and rewilding, but I also don’t think it is unreasonable to imagine it could have as much impact as all of plant genetics has had to date. I think a revolution is beginning in biotechnology.

Traditionally, biotech has focused on identifying single species and strains, simplifying systems, and then scaling them. What our science suggests is that there is also opportunity in biodiversity and biocomplexity. That there are some outcomes that you can’t achieve by simplifying a system. That you need a more complex system to realize these outcomes, and that these complex systems can be more resilient.

For example, biodiversity can make a system more likely to survive an extreme stress event like a pathogen outbreak. A biodiverse system reduces the probability of disease outbreaks since no single species is hyper-abundant. Furthermore, in a biodiverse system, losing a single species to disease, just one piece of the system, is less of a problem, as there are many others that can step in and compensate. Because we’re just starting to go down the road of managing the microbiome, there is an opportunity to avoid the reductionist single species fork, and instead, begin designing systems to both accommodate and take advantage of biodiverse communities of microorganisms.

Does this process have the potential to be accelerated or scaled up, or would that create some of the same problems as monocultural production? And what longer-term scenarios do you think could happen?

We think there are incredible opportunities for scale in managed landscapes. We’re beginning this process in forestry systems, by introducing wild communities of fungi to trees at the time of tree planting. This can be really important, as we know many traditional forestry practices decimate native fungal biodiversity. These interventions have real potential to change the fungal biodiversity that lives in a managed forest landscape, and also change how that landscape works for the better.

I really believe this kind of framework has the potential to be generalized for every managed landscape on earth. There is a huge movement towards regenerative agriculture. For example, asking how our food production landscapes can also serve as bird-and-bee habitats, which in turn can build sustainable agriculture landscapes. Here we’re posing the same question, but asking how we can have our managed food and forest landscapes act as reservoirs of below-ground biodiversity, and in the process, build more sustainable and regenerative food and forest agricultural practices.

Could you elaborate on the parallels you’ve talked about before between our own human biomes, i.e. gut bacteria, and soil or plant biomes?

The human body is a microbial ecosystem. Each of us houses an incredibly biodiverse community of bacteria within our gut, which has profound implications for our health. We call this collection of microorganisms the human microbiome. Losing key aspects of bacterial biodiversity from your microbiome can lead to serious medical conditions. Yet, at the same time microbiome transplants—essentially ecosystem restoration but for your body’s microbiome—can treat many of these conditions. The recent discovery of how the body’s microbial ecosystem affects nearly all aspects of human health is a breakthrough in our understanding and treatment of human health and disease. Perhaps even more profound, this discovery forces us to rethink at a fundamental level what a human is.

Humans aren’t alone in hosting a microbiome. Every plant species on earth houses an incredibly biodiverse community of fungi and bacteria within plant leaves, seeds, and roots. And while we find fungi in both plants and people, fungi seem to play a much bigger role in the forest microbiome. There is actually evidence that when plants first made the evolutionary transition from living in water to living on land, they evolved a symbiosis (i.e. a biological partnership) with soil fungi before they even evolved roots. Many tree species cannot establish themselves in the wild at all if these key symbiotic fungal partners are missing. These billions of species of bacteria and fungi are the plant microbiome, the forest microbiome, and the ecosystem microbiome.

Your work is very much centered around combating climate change, including your startup, Funga, which recently raised $4M in seed funding to lead the first carbon removal project powered by fungal microbiome restoration. Do you consider yourself a climate activist?

I absolutely consider myself a climate activist. I want to see real, meaningful climate action in my lifetime. My entire career has been focused on understanding and mitigating climate change, through one of the most powerful climate-regulating systems on earth—the global land surface. We each have our different strengths, and I try to lean into my own. Climate action is a huge motivator behind why I do the science I do. Funga felt like something I had to do. I had to take advantage of market mechanisms to scale these scientific discoveries at the speed necessary to meaningfully address both the climate and biodiversity crises.

Is there sometimes a tension between climate activism and science? For example, the recent sacking of Rose Abramoff from the Climate Change Science Institute for her activism work, an event that you publicly spoke out about.

There certainly seems to be a tension, which I don’t think needs to be present. Science is fundamentally a disruptive process. Science is people discovering and re-imagining how the world works in a foundational way. In climate science, those discoveries have been made, replicated, well-communicated, and accepted. We know the earth is in very real danger, we know why, and we know what we need to do to avoid the worst outcomes. Yet you walk into a climate science conference and everyone feels so complacent. You begin to wonder if science is enough. Our house is on fire. We’re not acting like it. People like Dr. Abramoff realize that the data don’t speak for themselves. If they did, we wouldn’t have to write scientific literature, we’d just post the numbers. Yet sometimes that literature still isn’t loud enough. I see Dr. Abramoff's and Dr. Kalmus’ actions as fundamentally part of the scientific process. Academic literature isn’t the only way to communicate important scientific findings. The science is extremely clear, the dangers are imminent, and we need action urgently. If our papers aren’t communicating this well enough, then we need to find ways to communicate the science better. We need to be louder.


Colin Averill is a speaker at The___Dream, our 2023 festival taking place from June 2-5 in Sintra, Portugal. As a senior scientist at ETH Zürich’s Crowther Lab, Averill studies the microbiome of the forest and how it’s linked to the emergent ecosystem function. He investigates how microbial diversity determines which trees grow in the forest, how they capture carbon, and how forest ecology offers clues to forecasting climate change. Moreover, he examines the ecology of mycorrhizal fungi—a type of fungi that forms a symbiosis with the roots of the majority of plants on the planet. He is a co-founder of SPUN (Society for the Protection of Underground Networks), a non-profit organization dedicated to documenting and protecting mycorrhizal fungal life; and a co-founder of Funga, a startup that harnesses the power of fungal networks to improve the health and resilience of forests.

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