A multi-organism interaction system under soil acidification drives root rot aggravation in Torreya

Soil acidification driven by human activities has emerged as a key factor aggravating plant root diseases; however, the underlying interaction-based pathogenic mechanisms remain unclear. Here, using the economically and ecologically important gymnosperm Torreya grandis as a model, we integrated multi-omics analyses of rhizosphere biota with soil physicochemical profiling to identify factors associated with root rot. We found that cross-kingdom interactions under soil acidification, rather than pathogen abundance alone, contribute substantially to disease aggravation. Soil acidification induced structural imbalances in the rhizosphere biota, characterized by a cross-kingdom interaction network comprising pathogenic Fusarium, fungal Lectera, bacterial Acidothermus, and phytophagous Hemipyxis. Synthetic community experiments further confirmed that the multi-organism interaction system formed by these biotic factors disrupted plant-soil defense functions, and thereby aggravated the severity of root rot. Collectively, these findings reveal that acidification-conditioned cross-kingdom interactions can substantially aggravate root rot, providing insights for managing soil-borne diseases and restoring degraded agroforestry ecosystems.