Legacy effects of cover cropping and crop phase on soybean health and associated rhizosphere microbiome in corn-soybean rotation

Authors: Yin, Chuntao; Osborne, Shannon; Lehman, Richard

Submitted to: Environmental Microbiome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/9/2026
Publication Date: 5/2/2026
Citation: Yin, C., Osborne, S.L., Lehman, R.M. 2026. Legacy effects of cover cropping and crop phase on soybean health and associated rhizosphere microbiome in corn-soybean rotation. Environmental Microbiome. 21. Article 80. https://doi.org/10.1186/s40793-026-00899-3.
DOI: https://doi.org/10.1186/s40793-026-00899-3

Interpretive Summary: Proper use of cover crops offers numerous benefits to soil health across diverse cropping systems. However, knowledge remains limited regarding how cover crops affect soil and subsequent crop health, and plant root-associated microbes. This study evaluated the legacy effects of five years of cover cropping in a long-term corn-soybean rotation on soybean health and root microbiomes under soilborne pathogen pressure (Fusarium graminearum or soybean cyst nematode) in controlled conditions. Results showed that soils with a cover cropping history protected soybeans from F. graminearum infection but had minimal influence on soybean response to soybean cyst nematode. Microbial profiling revealed that both cropping practices and pathogen pressure shaped the structure and composition of microbial communities surrounding soybean roots. F. graminearum infection was the primary factor modulating these communities, contributing to enhanced soybean resistance to fungal root rot disease. Overall, these results point to opportunities for designing cropping systems and crop rotations that suppress plant pathogens and enhance crop health more efficiently and sustainably.

Technical Abstract: Crop diversification through crop rotation or cover cropping is an important strategy for managing soilborne diseases, yet its outcomes are often complex. This study evaluated the legacy effects of cover crops and crop phase on soybean root diseases and root-associated microbiome. Soybean plants were grown in soils collected from a corn-soybean rotation field experiment with and without cover crops, and then challenged with either Fusarium graminearum or soybean cyst nematode (SCN) in the growth chamber. Soils with a cover crop history significantly reduced F. graminearum-induced root rot, but had a limited impact on SCN, indicating divergent disease responses. Microbial profiling revealed that F. graminearum strongly reshaped bacterial communities, reducing Shannon diversity and enriching fast-growing copiotrophic taxa, including Bacteroidota genera (Pedobacter, Chitinophaga, Flavobacterium, and Mucilaginibacter) and Proteobacteria genera (Dyella, Pseudomonas, Rhizobium, and Paraburkholderia) regardless of cover crops. In contrast, SCN infection increased bacterial Shannon diversity in soybean-phase soils regardless of cover crops but decreased fungal Shannon diversity in soybean soils without cover crops, highlighting pathogen-specific microbial shifts. Cover cropping enhanced microbial heterogeneity under both pathogen pressures, enriching microbial taxa potentially involved in nutrient cycling (Chitinophaga and Mucilaginibacter), antagonism (Flavobacterium, Streptomyces, Pseudonocardia, and Nocardioides), and competitive interactions (Paraburkholderia). Correlation analyses further identified bacterial and fungal genera associated with soybean diseases, linking microbial composition with pathogen suppression. Overall, soilborne pathogens and cropping practices exert interconnected, pathogen- and crop-specific effects, with cover cropping offering a promising tool to enhance microbial-mediated disease resilience in soybean systems.