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From Mushrooms to Microbes: How Fungi Fine-Tune Orchard Health

A mushroom in a pecan orchard.

Commonly known as “Dead Man’s Foot,” Pisolithus tinctorius forms mycorrhizal associates with pecan tree roots, potentially benefiting pecan trees. (Photo by McKenzie Stock)

Harnessing the beneficial role of soil fungi is an important strategy to ensure the vitality of pecan agriculture for the future, and understanding the soil microbiome is key to a full-bodied picture of soil health. In the southwestern United States, both saprotrophic and mycorrhizal fungi can aid in the success of pecan trees.

The soil microbiome, a complex community of microorganisms including bacteria, fungi, and other microbes, is a hidden powerhouse beneath our feet. Among these microorganisms, fungi stand out for their remarkable symbiotic relationships with plants. An estimated 80 to 90 percent of terrestrial plant species, including pecan trees, associate with mycorrhizal fungi, forming mutually beneficial partnerships that are vital for nutrient acquisition, resilience to stress, and overall plant health (Smith & Read, 2008). The term mycorrhiza refers to fungi that form symbioses—or specific, long-term relationships—with plant roots. These fungi play multifaceted roles in the orchard ecosystem. They aid plants in water and nutrient uptake, offer protection from pathogens, and increase plant drought tolerance (Ortas, 2018). The mycelia, or thread-like structures of the fungus, extend throughout the soil, acting as an extension of the plant root system and increasing the root functional capacity. Plants without root hairs, such as pecan trees, are especially dependent on mycorrhizae, as these fungal partners take on many similar roles as root hairs (Smith & Read, 2008).

A big mushroom in comparison to two hiking boots.

Large mushrooms can be found in southwestern pecan orchards! As seen growing among the orchard’s cover crops, a mushroom from the Tricholomataceae family is nearly as large as a pair of boots. (Photo by McKenzie Stock)

Mycorrhizal fungi fall under two broad categories. Endomycorrhizal fungi colonize plant roots by entering root cortical cells, forming intricate associations within plant tissues. On the other hand, ectomycorrhizal fungi colonize plant roots without entering root cells, but rather they create a specialized structure around the root tip. Both types of mycorrhizal fungi play crucial roles in pecan agriculture, facilitating nutrient uptake and improving overall tree health.

In addition to mycorrhizal fungi, saprotrophic fungi are also important in pecan orchards. They act as decomposers which break down complex materials such as leaf litter or woodchips into soil organic matter which can be used by plants. The presence of mushrooms, the fruiting bodies of fungi, in pecan orchards can serve as evidence of the presence of mycorrhizal or saprotrophic fungi, indicating a healthy and dynamic soil microbiome.

Some research has been done on ectomycorrhizal fungi in Georgia, where researchers identified truffle (Tuber), which can be an edible delicacy, and Scleroderma fungi, many species of which are beneficial for plants and are found in commercial inoculants (Ge et al., 2017). Scleroderma and Pisolithus mushroom-forming fungi were also found in Laguna Comarca, Mexico (Sáenz-Hidalgo et al., 2023). These fungi have been shown to benefit plants and soil.

Two mushrooms growing together in a pecan orchard.

Some species of the Scleroderma genus are found in commercially-available inoculants aimed at improving plant and soil health. Species of this genus can also be found in pecan orchards. (Photo by McKenzie Stock)

Similar species were found in pecan orchards in the southwestern United States according to our study at New Mexico State University, indicating the presence of beneficial microbial partners for pecan trees. Along with grower help, we collected mushrooms to study their genetics and physical characteristics. We found a variety of mycorrhizal species, including Pisolithus tinctorius, various Scleroderma species, an Inocybe species, and Tuber lyonii (the pecan truffle). These fungi work together with plant roots to offer ecosystem services. P. tinctorius can survive high acidity, drought stress, high concentrations of heavy metals, and hot soil temperatures (Blaudez et al., 2000). Its many ecological functions suggest that it may aid in improving soil health for pecan orchard soils. Many species of Scleroderma are included in commercial mycorrhizal inoculants due to their assumed plant growth beneficial roles. Tuber species, or truffle fungi, are often used as a culinary delicacy and could be explored as another economically viable crop for pecan growers (Benucci et al., 2012). Saprotrophic mushrooms were noted most often in orchards which featured cover crops where there was ample plant material for them to break down into useful soil organic matter. Many saprotrophic species, like Parasola species and Chlorophyllum molybdites, aid in decomposing pecan plant litter, enriching soil with nutrients crucial for pecan trees and cover crops (Martina et al., 2018).

We found more mushrooms in orchards with cover crops than with bare soil, demonstrating that cover crops may enhance fungal communities, particularly for decomposer fungi. Since mycorrhizal fungi associate specifically with the pecan tree, we found that they were more likely to be located in closer proximity to the tree base.

At New Mexico State University, we are conducting research to better understand how orchard floor and soil management practices affect the soil microbiome. We will study the effects of bare soil, cover crops, compost, and commercial bacterial and mycorrhizal inoculants. From preliminary data, we can already see some differences in the soil microbiome based on management practices. For example, we found significant differences in fungal biodiversity between bare soil treatments and combination (cover crops + compost) treatments—fungal biodiversity was higher when soil cover included both cover crops and compost. These preliminary findings suggest that the way we manage orchard soils makes a difference in the microbial communities. These findings agree with other research, which reports that cover crops can increase the resources available for pecans (Rodriguez-Ramos et al., 2022).

While there is a temptation to get rid of fungi in pecan orchards due to the pathogenic nature of some species, many fungi offer important benefits for pecan trees! So, next time you are walking in your orchard and see a mushroom, maybe don’t get rid of it just yet. While some fungi cause diseases, none of the fungi found in our study are known as harmful pathogens. This research offers a practical guide to finding mushroom-forming fungi in pecan orchards in the Southwest, as well as an insight into the fungal communities in pecan soil. Free smartphone apps, such as iNaturalist, can help you identify the mushroom, or you can reach out to an expert if you’re curious to learn more.

Understanding and harnessing the beneficial interactions within the soil microbiome, including the symbiotic relationships between pecan trees and fungi, are essential for sustainable pecan agriculture. By fostering a diverse and resilient soil microbiome, farmers can enhance nutrient availability, improve water retention, and promote overall ecosystem health, ensuring the continued success of pecan agriculture for generations to come.

Information from this study is in the process of being submitted for peer-review publication.


We would like to acknowledge the New Mexico Department of Agriculture Specialty Crop Block Grant AM#21SCBPNM1027 and the Trees for the Future Grant, USDA NIFA 2022-51181-38332, for supporting our research.

Benucci, G. M. N., Bonito, G., Falini, L. B., & Bencivenga, M. (2012). Mycorrhization of Pecan trees (Carya illinoinensis) with commercial truffle species: Tuber aestivum Vittad. and Tuber borchii Vittad. Mycorrhiza, 22(5), 383–392.
Blaudez, D., Jacob, C., Turnau, K., Colpaert, J. V., Ahonen-Jonnarth, U., Finlay, R., Botton, B., & Chalot, M. (2000). Differential responses of ectomycorrhizal fungi to heavy metals in vitro. Mycological Research, 104(11), 1366–1371.
Ge, Z.-W., Brenneman, T., Bonito, G., & Smith, M. E. (2017). Soil pH and mineral nutrients strongly influence truffles and other ectomycorrhizal fungi associated with commercial pecans (Carya illinoinensis). Plant and Soil, 418(1–2), 493–505.
Ortas, I. (2018). Role of mycorrhizae on mineral nutrition of fruit trees. Acta Horticulturae, 1217, 271–284.
Rodriguez-Ramos, J. C., Scott, N., Marty, J., Kaiser, D., & Hale, L. (2022). Cover crops enhance resource availability for soil microorganisms in a pecan orchard. Agriculture, Ecosystems & Environment, 337, 108049.
Sáenz-Hidalgo, H. K., Jacobo-Cuellar, J. L., Zúñiga-Rodríguez, E., Avila-Quezada, G. D., Olalde-Portugal, V., Hashem, A., & Abd_Allah, E. F. (2023). Soil Structure and Ectomycorrhizal Root Colonization of Pecan Orchards in Northern Mexico. Journal of Fungi, 9(4), 440.
Smith, S. E., & Read, D. J. (2008). Mycorrhizal symbiosis (3rd ed). Academic Press.
Author Photo

McKenzie Stock

McKenzie Stock is a PhD student in Plant and Environmental Sciences at New Mexico State University. With a background and studying mushroom-forming fungi in pecan orchards across the southwestern United States during her Master’s program, McKenzie’s current research focuses on pecan orchard soil health, particularly the dynamics of fungal communities. She has presented her work at different venues, such as the Western Pecan Grower’s Association annual meetings and webinar series, the ISHS International Symposium on Walnut and Pecan in France, and more. McKenzie is deeply passionate about agricultural ecosystems and strives to bridge the gap between research and practical application by collaborating closely with growers. She is a member of Dr. Richard Heerema’s lab group and finds great joy in this collaborative research environment.