Stanford ecologists study how soil fungi respond to wildfire

In the wake of the 2017 North Bay fires, the golden hills of Santa Rosa, California, were unrecognizable. Smoky, seared and buried under ash, the landscape appeared desolate, save for some ghostly, blackened – but still alive – oak trees. For Stanford University graduate student, Gabriel Smith, whose family lives in Santa Rosa, the devastation was heartbreaking, but it also offered a unique scientific opportunity: a natural experiment on the effects of wildfires on the microbes that live in soil, which Smith studies in the form of fungi.

Oak and evergreen trees in Hood Mountain Regional Park and Preserve in Santa Rosa in August 2019. (Image credit: Gabriella Selva)

So, Smith and his mother spent his winter break collecting soil samples from burned areas near trees in Santa Rosa’s Trione-Annadel State Park and Hood Mountain Regional Park and Preserve. For comparison, they also gathered samples from unburned locations.

“I wanted to know how these ecosystems that, on the outside, looked so burned and so destroyed might have been affected at a level that is not so obvious – the soil fungi that I study,” said Smith, who is a member of the lab of Kabir Peay, an associate professor of biology in the School of Humanities and Sciences. Most people know soil fungi by their fruit – mushrooms – but there’s much more to these organisms, both physically and functionally. Working alongside plant roots and other microbes that live in the soil, soil fungi play important roles in their ecosystems, including helping trees grow and aiding in decomposition.

The research, which was published Dec. 9 in Molecular Ecology, focused on two ecosystems in these parks, oak woodland and mixed evergreen forest. As the researchers expected, analysis of dozens of soil samples established that, among the areas that had not burned, the ecosystems contained a different mix of soil fungi. The analysis also showed that, when comparing burned and unburned areas, the oak woodland soil fungal community was less altered by the fires than those in the evergreen forests. This aligns with the fact that oak woodlands depend on regular fire to thrive, whereas evergreen forests are less dependent on fire to survive. The researchers have continued this work by planting seedlings in some of the soil samples – those results will be detailed in a future paper. They are also hoping to find out more about the physiological mechanisms that could explain the responses of the fungi.

“There has been renewed interest in how climate change is influencing the frequency of fires and how that’s going to affect fire-mediated ecological processes in California going forward,” said Peay, who is senior author of the research. “So it’s important to have specific details about how changes in the fire regimes in California, and the West Coast in general, are going to be influencing ecosystems.”

Looking deeper

Oak woodlands benefit from fire to the extent that many parks, including Trione-Annadel, are treated with prescribed burns to keep their oaks healthy. Fire clears leaf litter and dead branches, creates improved conditions for some seeds, and controls insects and pathogens that might otherwise cause disease. Most importantly, fire can prevent other trees – such as those found in evergreen forests – from invading the oak forests. While mature evergreens can survive, and even benefit from, fires, encroaching seedlings may not.

To understand how the 2017 fires altered soil fungal communities in these two ecosystems, Smith and his mother dug up the top 10 centimeters of soil from 12 sites in Trione-Annadel and six at Hood Mountain, with guidance from the California Park Service. While Smith was home for break, the samples had to be temperature regulated.

“We ended up filling not only my parents’ fridge but also my grandmother’s fridge and my aunt’s fridge. We also rigged a top-loading chest freezer to keep the right temperature,” said Smith, who is lead author of the research. “There was a great deal of family support that went into this research.”

Back at the Stanford lab, Smith and Lucy Edy, a co-term student in earth systems who worked on this project as part of the Stanford Biology Summer Undergraduate Research Program, determined what fungi resided in each sample through DNA analysis. What he found suggests that how fungal communities respond to fire belowground mirrors how other parts of their ecosystems respond to fire above ground.

“There was a much greater difference between the burned and unburned points in evergreen forests than there was in the oak woodland communities,” said Smith. “We predicted there would be a difference between the two ecosystems, but the extent of that difference was actually more than we expected.”

It will take additional research to understand why this is the case, but the researchers hypothesize that part of the reason may be that the soil fungal community “resets” when it burns. This would mean that the soil fungi associated with the oaks have less time between fires to change from its reset form, and the evergreen soil fungi have longer, leading to the greater differences seen in the soil of burned and unburned evergreen forests.

The future forest

For much of the history of studying fungi, researchers had to depend on what they could see above ground, including mushrooms. But increased access to DNA sequencing has opened up the field, helping scientists detail the complex relationships between various soil microbes, plants and ecosystem functions. Still, many questions remain concerning the effects of microbial diversity in the soil – for example, the consequences of losing half the population of one microbe versus two-thirds or all of it, and the net impact of losing microbes that could cause disease in certain plants in addition to losing microbes that benefit those plants.

“As fire regimes increase in intensity and frequency with climate change, we must understand the ecological responses of these ecosystems in order to determine our necessary responses in relation to them,” said Edy, who is a co-author of the paper. “Fungal ecology is perhaps outside the realm of first consideration when people think about the impact of wildfire, but these below-ground microbial interactions fuel and sustain entire ecosystems.”

This project, born from terrible circumstances, will likely produce many more studies, like the seedling experiments, and further investigations into how the fungal communities in the oak woodlands withstand fire.

“This was not originally part of Gabriel’s PhD project. He had the foresight to recognize that this is not just something that was interesting on a personal level, but also that there’s nice intellectual potential here,” said Peay. “Works like this can advance our understanding of how the changes we see in the soil might then play a role in changing what future ecosystem types look like.”