World Soil Day is held annually on December 5^th as a way to foster awareness for soil conservation. This year’s theme for World Soil Day is “Caring for Soils: Measure, Monitor, Manage.” One of the best ways to manage soils is to treat them as a living ecosystem. Soil is very much alive! Recent research suggests that soil is the most biodiverse habitat on the planet, harboring around 59% of all the species on Earth (Anthony et al., 2023). It is home to animals that burrow underground, such as salamanders and chipmunks, harbors thousands of invertebrate species that are vital to the food web, like nematodes, springtails, and mites, and contains millions of bacterial and fungal species.

In HF&G’s soil ecology lab, a large focus of our research is on these species of fungi and bacteria and how they contribute to soil health. Even though these organisms are from two separate domains of life, they do similar things in soil, like decomposition and associate with plant roots, which can help promote growth. We know that diverse communities of bacteria and fungi are imperative for nutrient rich soil. Thus, studying these organisms in tandem is important when the overall goal is to understand soil health.

It can be challenging to study soil bacteria and fungi for a number of reasons, but mostly because we can’t see them. Bacteria are microscopic and, thus, we need the aid of microscopes to visualize them. For fungi, even though mushrooms and other sporocarps are visible when they are fruiting, most of a fungus’s life is spent belowground as hyphae. Hyphae are filamentous (or thread-like) structures with an average size of only 4-6 micrometers in diameter. Because these organisms 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 bacteria and fungi while still in the soil and not separated from it. Thankfully, we have DNA sequencing!

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 specific group of soil organisms that we are interested in. And, finally, we determine the taxonomic identity of the organisms in the soil sample using DNA sequencing.

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). Once we have the millions of DNA sequences, we then group them together based on their DNA sequence similarity. DNA sequences 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 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 taxa (or species) of fungi 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, we are beginning to understand that the bacteria and fungi belowground are not only very diverse, but also are highly variable across space. Even in depths that span just a few centimeters or moving a meter away from a rotting tree, the fungal and bacterial taxa in the soil can change dramatically. There is an effort to understand not only what drives these dramatic changes, but also what factors can erode this inherent variability. Of primary concern for our forests are the effects of pollution, climate change, and invasive pests and diseases. If these cause widespread changes to soil structure or nutrient content in our forests, could this in turn lead to less spatial variability of fungi and bacteria?

At HF&G, we are researching some of these very questions (see Burke et al. 2019, for example) and certainly appreciate how with every step we take in the forest, we could be walking onto an entirely new community of organisms beneath our feet. I can think of no better way to celebrate World Soil Day 2024 than to appreciate the incredible life harbored in this ecosystem.