Fungal community composition and diversity across soil depths under different cover crop treatments

Authors: Muturi, Ephantus; Dunlap, Christopher; Ramirez, Jose; PERRY, WILLIAM - Illinois State University; HELLER, NICHOLAS - Illinois State University; RHYKERD, ROBERT - Illinois State University

Submitted to: The Journal of Fungi
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/28/2026
Publication Date: 1/31/2026
Citation: Muturi, E.J., Dunlap, C.A., Ramirez, J.L., Perry, W.L., Heller, N., Rhykerd, R.L. 2026. Fungal community composition and diversity across soil depths under different cover crop treatments. The Journal of Fungi. https://doi.org/10.3390/jof12020100.
DOI: https://doi.org/10.3390/jof12020100

Interpretive Summary: Soil fungi are crucial to the health of agricultural ecosystems. Some fungi promote plant growth by suppressing plant diseases and producing growth-promoting compounds, while others reduce crop yield by causing devastating plant diseases. Knowing how these fungal communities change across different soil depths is essential for understanding how to harness microbial properties to improve soil health in agricultural systems. This study investigated the influence of soil depth on soil fungal communities in agricultural soils under four cover crop treatments. These included cereal rye (CRYE), wild pennycress, a mixture of pea, crimson clover, radish, and oat (PCRO), and a winter fallow reference. Soils from plots with CRYE and PCRO had low abundance of Fusarium, a genus containing some devastating plant pathogens, and different fungal communities relative to the winter fallow plots. Fungal communities found in the deeper soil layer (10-20 cm depth) were significantly different from those found in the topsoil layer (0-4 cm). Fungi that are responsible for the breakdown of dead plants and animals decreased with increasing soil depth while those that live in mutually beneficial relationships with plants increased with increasing soil depth. Some fungi that cause economically important crop diseases were more abundant in the topsoil layer. These findings demonstrate that different fungal groups are adapted to different soil layers and cover crop treatments and can inform development of new strategies to enhance soil health in agricultural ecosystems.

Technical Abstract: Fungi are a critical component of microbial biomass in agricultural soils, but their distribution across soil depths under different cover crops remains poorly understood. We used high throughput sequencing of fungal ITS1 amplicons to characterize fungal communities across four soils depths (0-2, 2-4, 4-10, and 10-20 cm) in experimental field plots under four cover crop treatments: winter fallow reference (REF), cereal rye (CRYE), wild pennycress (WPEN), and a mixture of pea, crimson clover, radish, and oat (PCRO). There was no significant interaction between soil depth and cover crop treatment on both alpha diversity and beta diversity. CRYE and PCRO cover crops had low abundance of Fusarium, a genus including many important plant pathogens, and different fungal community composition relative to REF. Fungal diversity was significantly higher at 4-10 cm compared to 0-2 cm depth, but fungal richness was not affected by soil depth. Fungal community composition differed significantly between 0-4 and 10-20 cm soil depths. The relative abundance of Mortierella and unclassified Basidiomycota increased with increasing soil depth while that of Calvatia, Cryptococcus, Fusarium, and Idriella decreased with increasing soil depth. Most fungal taxa were assigned to more than one guild, but the few taxa that were classified as strict saprophytes decreased with increasing soil depth while those classified as strict symbionts increased with increasing soil depth. These differences were associated with low pH and high content of OM, K, S, P, Zn, and Mg in the topsoil layer compared to the deeper soil layer. The findings may inform the development of targeted soil management practices to promote beneficial fungi, but additional studies covering multiple study sites and sampling dates are needed for clarity.