Shifts in rhizosphere microbial cross-kingdom co-occurrence network underpin Fusarium solani-mediated root rot in tobacco

Fusarium solani –mediated tobacco root rot causes significant agricultural losses, yet the synergistic roles of multiple soil properties and non-pathogenic microbiota in disease outbreaks remain unclear. Based on analyses of 72 root and leaf samples from healthy and diseased tobacco plants across three major planting areas in Yunnan, China. The results showed that, in rhizosphere soil, although micronutrients explain 8%–11% of the variation in microbial community composition between healthy and diseased plants, exceeding the explanatory power of other soil properties, there was still a large amount of unexplained variance. This indicates that abiotic factor micronutrient played a certain role in regulating root rot, while biotic factors were still the dominant factor in the occurrence of the disease. Furthermore, machine learning identifies 14 bacterial, five fungal, and three protistan taxa (e.g., Mortierella and Gonostomum ) that are positively correlated with disease severity and form cooperative networks with Fusarium solani . Cross-kingdom co-occurrence networks in diseased tobacco show systematic reconstruction interactions increasing by 8%–27% (rhizosphere, 37% vs 29%; rhizoplane, 45% vs 18%) and bacterial–fungal interactions decreasing by 11%–21% (rhizosphere, 20% vs 31%; rhizoplane, 25% vs 26%). The impaired root nutrient uptake caused by root rot results in a significant surplus of available nutrients (NO 3 − -N, AP, AK, and DON) in diseased rhizosphere soil, increasing the risk of nutrient losses. A disease outbreak pattern is proposed in which a shift in cross-kingdom microbial cooperation and synergistic effects of soil properties disrupt rhizosphere homeostasis following pathogen infection, thereby triggering tobacco root rot. These findings indicate that multiple soil properties (including TK, Mn, Mg, Cu, and Zn) function as previously underappreciated regulators of cooperative interactions between microbial communities and pathogens and provide potential targets for the management of tobacco root rot. Changes in cross-kingdom microbial community interactions dominated by micronutrient aided tobacco root rot and reduced available nutrient absorption • Soil micronutrients enhance tobacco root rot severity at high pathogen abundance. • Micronutrients reshape cross-kingdom microbial interactions. • Fungal-fungal interactions increase in diseased rhizosphere and phyllosphere. • Machine learning identified non-pathogenic microbes aiding F_solani invasion.