The Relationship Between Cover Crop Species and Soil Fungal Communities in Irrigated Vineyards in the Okanagan Valley, Canada

Many techniques adopted by annual crop growers, addressing challenges such as disease, are not viable for perennial systems. Groundcover vegetation can be employed as a natural method for increasing soil health and perennial plant performance; however, cover crop species may differ in the plant–soil feedback effects that modulate the rhizosphere. To investigate the relationship between cover crop identity and soil microbial composition and to determine potential impacts of cover crop species on pathogen occurrence in perennial systems, we characterized the fungal communities in soil sampled from nine cover crop species used for under-vine groundcover at three separate Okanagan vineyards. Soil characteristics, particularly available phosphorus levels, varied significantly among sites, with SuRDC at 39.9 ppm, Covert at 140.1 ppm, and Kalala at 276.2 ppm. Of 1876 fungal species, SuRDC showed lower richness and diversity. A random forest model classified samples by site with 98.4% accuracy (p < 0.001), but cover crop classification was minimal (2.4% accuracy). Phacelia had significantly lower variance in Shannon’s (p = 2.35×10−7) and Simpson’s diversity (p = 3.59×10−12). Crescendo ladino clover had simpler fungal networks than buckwheat, with a negative correlation between fungal species count and co-occurrence affinity across cover crops (p < 0.001). We found that within sites, soil fungal communities did not vary greatly in composition and measures of community structure, regardless of cover crop identity. Nectriaceae were abundant across all samples, suggesting that cover crops may recruit certain fungal pathogens. Soil fungal communities were distinct across sites, indicating that site-specific conditions may play a larger role in shaping soil fungal communities in BC vineyards than cover crop–microbe interactions and that cover crops do not have consistent short-term (<1 year) effects on soil fungi across sites. Altogether, this research encourages careful consideration of both groundcover species and site-specific conditions when using cover crops in perennial agriculture.