Biochar and Cover Crop Integration Enhances Soil Fungal Community Structure and Ecosystem Services in a Perennial Orchard System

Sustainable management of perennial orchard soils is critically dependent on strategies that enhance soil fungal diversity and ecosystem services, given their central role in nutrient cycling, soil health, and long-term agricultural productivity. This study evaluated the interactive effects of biochar amendments and cover crop diversification on soil fungal community composition, diversity, and ecosystem service delivery in a mature Japanese apricot (Prunus mume) orchard. Two years of field treatments integrating rice husk biochar (Brh) or bamboo biochar (Bb), individually and in combination with mixed cover crops—bahiagrass (Bg) and white clover (Wc)—were implemented. Amplicon sequencing targeting the ITS region revealed that the Brh + Bg + Wc combination markedly increased the abundance of Mortierellaceae and overall fungal diversity compared to single amendments or control soils. Linear discriminant analysis identified distinct enrichment patterns: Brh + Bg + Wc favored beneficial saprotrophic taxa, while unmanaged controls were enriched in Didymellaceae and Nectriaceae. Although arbuscular mycorrhizal fungal (AMF) community diversity did not show statistically significant changes, trends indicated potential enhancement under combined amendment treatments. Pearson correlation and heatmap analyses demonstrated strong positive associations between key fungal families and soil biochemical traits, including enzyme activities linked to nutrient cycling. The results indicate that the integration of rice husk biochar with diverse cover cropping strategies synergistically promotes soil fungal resilience and functions critical for sustainable orchard management and environmental health. This research advances the understanding of how tailored amendment strategies can optimize ecosystem service delivery in perennial agroecosystems, informing soil management policies aimed at enhancing both productivity and long-term soil health.