National Mushroom Month: Studying the Fungi Under our Feet

By Sarah Carrino-Kyker

We are continuing to celebrate National Mushroom Month! Mushrooms and other sporocarps are great and certainly worth celebrating, but they are a short stage in the fungal life cycle. Much of a fungus’s life is spent below ground as hyphae. Hyphae are filamentous (or thread-like) structures with an average size of only 4-6 micrometers in diameter. Hyphae are very active below ground, including decomposing organic matter or taking up nutrients for plant partners. But, because they are so small and difficult to separate from soil, scientists have had to find ways to study fungi in situ. In other words, we have had to find ways to study fungi while still in the soil and not separated from it. Thankfully, we have DNA sequencing! For this week’s Science on Fridays with Holden, we want to tell you about how we use DNA sequencing at Holden to study the diversity of fungi below ground.

It might be hard to imagine getting DNA from a soil sample, but this is exactly what we do. We collect soil from our study site and then subject it to a DNA extraction. We don’t get DNA from the soil particles, of course, but we do get DNA from any organisms we collected along with the soil sample. From there, we use polymerase chain reaction (PCR) to isolate different groups of soil organisms that we are interested in, such as fungi. And, finally, we determine the taxonomic identity of the organisms in the soil sample using DNA sequencing.

Recent data suggest that there are between 11.7 and 13.2 million species of fungi worldwide (Wu et al. 2019). This is an incredible diversity that can be difficult to study given that only about 10% of fungal species will grow in culture. But, the current DNA sequencing technology, called high throughput sequencing, allows for millions of DNA molecules to be sequenced at the same time. For example, we collected soil samples from an old growth forest in Stebbins Gulch, and obtained over 8.9 million fungal DNA sequences (Burke et al. 2019). This high number of DNA sequences allows for a much better understanding of fungal diversity than with previous methods.

Once we have the millions of DNA sequences, we then group them together based on their percent similarity. Typically, DNA sequences that are 97% similar to one another are grouped together into what scientists called operational taxonomic units (OTUs); an OTU is a precise way of referring to different fungal groups, but for our purposes we can consider an OTU to be a fungal species. In the Stebbins Gulch samples, the 8.9 million DNA sequences grouped into 1129 OTUs. So, we can say that there over 1,100 different fungal taxa (or species) in just this one location in Stebbins Gulch. This is pretty incredible because the samples were collected within about 100 meters of one another! As we have expanded our DNA sequencing efforts at the arboretum, we are seeing more like 7,000 different fungal taxa in the 334 hectares of forest across Stebbins Gulch!

Thanks to high throughput sequencing, scientists are beginning to understand that the fungi below ground are very diverse and are highly variable. Even over just a few centimeters of soil, the fungal taxa can change dramatically and there is an effort to understand what drives these dramatic changes. Of primary concern for our forests are the effects of pollution, such as acid rain, climate change, and invasive pests and diseases on soil fungi since changes to fungal communities can affect nutrient availability and plant growth. We are studying some of these very drivers of fungal changes at Holden and researching what the high variability in fungal taxa means for forest health. So, the next time you are on a walk at HF&G, think about the incredible diversity below your feet and how with each step, you might be standing on top of a different fungal species.


Burke, D.J., Carrino-Kyker, S.R., & Burns, J.H. (2019) Is it climate or chemistry? Soil fungal communities respond to soil nutrients in a multi-year high-resolution analysis, Ecosphere, 10:10, e02896, DOI: 10.1002/ecs2.2896

Wu, B., Hussain, M., Zhang, W., Stadler, M., Liu, X., & Xiang, M. (2019) Current insights into fungal species diversity and perspective on naming the environmental DNA sequences of fungi, Mycology, 10:3, 127-140, DOI: 10.1080/21501203.2019.1614106