Spatiotemporal Profiling of the Pathogen Complex Causing Common Bean Root Rot in China

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Root rot, a globally devastating disease of common bean (Phaseolus vulgaris L.), remains a major constraint on bean production across China. Despite its agricultural impact, the pathogen complex associated with this disease has been poorly characterized in most provinces. To address this critical knowledge gap, we conducted nationwide surveys during 2016–2018, systematically sampling 1–10 symptomatic plants from each of 121 (2016) and 170 (2018) field sites across 17 provinces in China’s major vegetable production regions. Isolates obtained from symptomatic root tissues underwent morphological screening, followed by molecular identification using partial sequences of EF1-α for Fusarium species and ITS regions for other genera. Pathogenicity of representative isolates was subsequently confirmed through controlled greenhouse assays. This integrated approach revealed fourteen fungal and oomycete genera, with Fusarium (predominantly F. oxysporum and F. solani) and Rhizoctonia (R. solani) emerging as the most prevalent pathogens. Notably, pathogen composition exhibited significant regional variation and underwent temporal shifts across developmental stages. Additionally, F. oxysporum, F. solani, and R. solani demonstrated significant interspecies associations with frequent co-occurrence in bean root rot systems. Collectively, this first comprehensive characterization of China’s common bean root rot complex not only clarifies spatial–temporal pathogen dynamics but also provides actionable insights for developing region- and growth stage-specific management strategies, particularly through targeted control of dominant pathogens during key infection windows.