Cover crops legacy modulates soybean rhizosphere microbiome across phenological stages

Agricultural development and productivity under sustainable practices depend on plant-soil-microorganism interactions in the rhizosphere, a central interface in environmental microbiology and microbial ecology. Although the influence of soybean phenological stages on the rhizosphere microbiome has been reported, studies addressing the legacy effects of off-season cover crops on microbial dynamics throughout soybean development remain scarce. We conducted a greenhouse experiment to evaluate the structure, diversity, composition, and network connections of bacterial and fungal communities in the soybean rhizosphere at different plant stages (V4, R1, and R5) under the influence of off-season cover crops, including a grass species (Ruzigrass), a legume (Sunn hemp), their combination (Mix), and a no-cover treatment (Fallow), using high-throughput sequencing. We found that differentiation in bacterial and fungal community structure in the soybean rhizosphere across plant development is modulated by the legacy effect of cover crops during the no-tillage off-season. Specific microbial groups were highlighted, including the bacterial phyla Pseudomonadota, Bacteroidota, and Actinomycetota, which showed differential relative abundance among soybean growth stages under cover crop treatments, as well as symbiotic arbuscular mycorrhizal fungal genera, such as Gigaspora , Dominikia , Paraglomus , and Glomus , which were more abundant during reproductive stages in the soybean rhizosphere. In addition, we observed variations in ecological interactions within bacterial and fungal networks according to the legacy effect of each cover crop, with greater network complexity under the Ruzigrass and Mix treatments. These results demonstrate that cover crop legacy is a key factor shaping microbial dynamics in the soybean rhizosphere, with implications for sustainable crop management.