Playing Nice with Fungi: Using Crops to Build Healthy Soil

Soils have a PR problem. Think about it: Does dirt excite you? Are you energized by earth? For many of us, soil is just the musty medium our trees, flowers and food grow from. Perhaps you’ve been advised to rub dirt on a skinned knee (I did this once and received a nasty soil-borne infection, no joke).

In reality, soils are integral components of terrestrial ecosystems, supporting the highest biodiversity on Earth — billions of microorganisms can inhabit a single handful of dirt — and delivering vital services such as water filtration, decomposition and greenhouse-gas storage. For thousands of years, humans have cultivated soils to grow food, fuel and fiber. Agricultural soils provide sustenance and economic value and represent our shared human heritage.

However, soils are a non-renewable resource and can be easily degraded by exhaustive agricultural practices and poor soil management, which, in turn, deplete the most essential component of soil quality: soil organic carbon (SOC). Soil organic carbon strengthens the soil’s physical structure, which prevents erosion and allows water and nutrients to flow. Losses of SOC threaten economic and environmental sustainability, as well as food security. If SOC is so important, how can we keep it in the ground to protect our food systems?

My interest in this question came shortly after I began working on farms in 2012. My mentor, Henry, worked diligently to help exhausted soils recover from intense cultivation, planting, weeding and harvesting. Admittedly, I struggled to visualize life below ground beyond worms and centipedes, even after I began managing a farm on my own. Then one day, I looked under a microscope at dyed plant roots at the Chicago Botanic Garden. I was intrigued to see roots covered in branching, translucent creatures called arbuscular mycorrhizal fungi. These fungi colonize roots using spindly, delicate-looking filaments called hyphae, which weave between cells and deposit glossy nutrient-filled orbs called vesicles. Unlike many fungus species, these creatures do not produce mushrooms, so evidence of their existence is can only be determined under the microscope lens.

Left: Branching arbuscular mycorrhizal fungi hyphae (in blue) colonizing a dyed plant root. Right: Vesicles left on plant root by arbuscular mycorrhizal fungi.

I had always associated fungi with decomposition and death. So, I was surprised to learn that arbuscular mycorrhizal fungi are actually beneficial to plants, providing water and nutrients as well as bolstering defense to disease and environmental stressors. In fact, these fungi are known to associate with 70 to 90 percent of land plants.

The vast majority of Earth’s soil carbon comes from the symbiosis between plants and these fungi: plants absorb carbon dioxide during photosynthesis, which is then fed to the fungi. The fungi then store the carbon in soils where it builds over time, improving soil quality and reducing carbon emissions, which helps plants grow and mitigate climate change. For these reasons, arbuscular mycorrhizal fungi are considered ‘soil quality indicators.’

Some organizations are developing crops that might restore soil quality. The Land Institute, (Salina, KS), for instance, developed a perennial alternative to wheat called Kernza™, which has shown to ‘build soil health’ by storing SOC in deep, extensive root systems. However, we don’t know much about Kernza’s interactions with beneficial soil organisms, like arbuscular mycorrhizal fungi, and whether these fungi will work well enough with Kernza to ‘build soil health.’

soil health ecology
A Kernza plot in the field site in Mettawa, IL

To investigate, my team converted an abandoned field about 40 miles north of Chicago into a long-term agroecology experiment. We applied six different cropping strategies, or treatments, to the soil to test whether certain crops affect soil quality. Throughout the growing season, I measured biological and physiochemical indicators of soil quality, such as fungal abundance and SOC levels, within each treatment’s plot. For example, I was able to test whether wheat stores more carbon than Kernza. These measurements set the standard for future research into soil ecology.

Kernza, seed heads prior to harvest, 2019.

During the first year of growth, none of the six treatments appeared to store more or less SOC than the others. This is not shocking, as SOC can take years to collect. I was pretty disappointed, but I reminded myself that, while not exactly exciting, all the results are important for long-term studies.

soil health experiment graph
Figure 1: Average % root colonization of six crops by arbuscular mycorrhizal fungi (AMF). These beneficial fungi are responsible for soil carbon storage and recognized as soil quality indicators.

But when I looked at the roots under the microscope, I saw change: I was surprised to see significant differences in the abundance of arbuscular mycorrhizal fungi inhabiting the roots of our six treatments (Fig. 1). Not only that, but arbuscular mycorrhizal fungi were more abundant on Kernza roots than all other treatments. In other words, while our treatments were not yet showing different rates of carbon storage, they were already colonized by the creatures that ultimately drive the creation of SOC.

These results suggest that certain crops may affect the abundance of beneficial soil organisms. Our findings could have broader implications for SOC management in agroecosystems. In other words, farmers may opt for planting crops that ‘play nice’ with soil organisms responsible for carbon storage, because this will not only improve future soil health, but also lead to greater economic returns and ensure food security. Many questions still remain, though: Do these fungi prefer a certain type of root? How long until we see carbon storage differ among our treatments? Are there different species of arbuscular mycorrhizal fungi at play in our field?

Prior to this study, I saw the soil in our experimental plots as somewhat lifeless and inert. But now, I am beginning to see how the diversity of life below ground may play a significant role in our food systems. I am just scratching the surface.

soil health

Lucas Chamberlain investigates strategies to improve ‘soil health’ in agroecosystems to address the ecological and socio-economic effects of climate change. Through farming and research, Chamberlain seeks to optimize strategic soil management to ensure agricultural sustainability and food security and to dismantle environmental racism. Currently, he is an MS student at Northwestern University, a research assistant at the Chicago Botanic Garden, and a volunteer at the Shedd Aquarium