Plant Functional Type Composition, Rather Than Species Diversity, Shapes Soil Microbial Functional Diversity and Redundancy

Abstract

Cover crops (CCs) are widely used to improve soil health, but their species-specific effects on microbial functional diversity and redundancy remain poorly understood. We evaluated how monocultures of field pea (Pisum sativum), forage radish (Raphanus sativus), and cereal rye (Secale cereale), as well as a three-species mixture (3spp) and a five-species mixture (5spp), influence rhizosphere bacterial and fungal communities in a field experiment. Amplicon sequencing and predictive functional profiling were used to assess microbial diversity, composition, functional potential, and functional redundancy (FR). Microbial alpha diversity showed little change across treatments, but community composition and predicted functional profiles were strongly influenced by CC identity. The 3spp rhizobiome showed the highest bacterial FR, broad metabolic capacity, and greater network connectivity, suggesting increased functional stability of all treatments. In contrast, the 5spp rhizobiome showed reduced bacterial FR and more widespread functional depletion, likely due to imbalances in plant functional types. Monocultures showed species-specific patterns, with rye supporting functionally efficient communities and radish promoting more competitive interactions and reduced functional diversity. Fungal communities responded differently from bacterial communities. While fungal taxonomic shifts were limited, they showed stronger compositional differences among treatments and more stable functional profiles. Notably, fungal FR was highest in the 5spp rhizobiome. Overall, these findings highlight that balanced plant functional composition, rather than greater species richness alone, is important for shaping rhizosphere microbial function and redundancy. Balanced mixtures promoted higher bacterial redundancy, while more diverse but functionally imbalanced mixtures did not consistently enhance microbial function. ImportanceThe benefits of using CCs in agricultural settings are mostly influenced by microbial communities, including nutrient cycling, organic matter turnover, and resilience to disturbance. However, CC mixtures are often promoted on the assumption that more species provide greater soil benefits. This work challenges that assumption by showing that the functional identity and balance of CC species may matter more than the number of species alone. This distinction is important for farmers, land managers, and researchers because CC seed mixes can be costly, and poorly balanced mixtures may fail to deliver intended microbial benefits. Understanding which plant combinations support functionally stable microbial communities can improve CC recommendations and help design agricultural systems that maintain soil processes under changing environmental conditions.