Cover crops as a strategy for root rot management in common beans: effects on crop performance and root microbial dynamics in a Cerrado soil

Abstract

No-till farming is a key restoration technique that helps preserve soil health and productivity without expanding cultivated areas. Here, we investigate the influence of different cover crops on the performance and root microbial diversity of common beans in a Brazilian Cerrado soil. The study was conducted for five years on a commercial farm, with six treatments and three replicates. Treatments were evaluated yearly for yield and dry root rot severity (Fusarium spp.). Rhizospheric soil samples were analyzed for microbiome diversity using metataxonomics in the last year of the experiment. Oat and sunn hemp consistently performed better for severity, while a mix of cover crops, oat and palisade grass resulted in higher yields than fallow. Diversity metrics did not vary between treatments for both bacterial and fungal communities. Streptomyces was prominent in oat and sunn hemp, while Fusarium dominated the fungal community across treatments with a relative abundance of >35%. Characteristics prediction highlighted significant bacterial functions and fungal traits, with palisade grass showing distinct methanol oxidation and oat exhibiting diverse fungal endophytes, saprotrophs, and organic matter decomposers that may compete against Fusarium spp. Network analysis revealed variable co-occurrence patterns, with Fusarium spp. exhibiting different associations depending on the treatment. The network analysis also highlighted competing fungal genera that may guide biocontrol strategies. Mix, oat, and pearl millet were the cover crops favoring the highest number of genera negatively correlated with Fusarium spp. in the common bean rhizosphere. Future studies should explore the long-term effects and temporal dynamics of the common bean root microbiome.