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Introduction
Corn rust (Puccinia spp.), a globally widespread fungal disease, primarily includes southern rust (caused by Puccinia polysora) and common rust (caused by Puccinia sorghi). Southern rust, prevalent in tropical and subtropical regions, is characterized by small, round, red–orange uredinia that proliferate rapidly under high-temperature and high-humidity conditions. In contrast, common rust, found in temperate areas, features larger, brown to cinnamon-brown uredinia that infect corn plants at lower temperatures [1, 2–3]. Rust infections reduce corn's photosynthetic capacity by 18% and water use efficiency by 28%, impairing grain development and significantly lowering yield [4, 5]. However, while the impact of rust diseases on corn grain yield has been extensively studied [6], the mechanisms underlying their effects on silage quality remain poorly understood.
Plant diseases can alter the chemical properties of raw materials, including water-soluble carbohydrates, cellulose, and lignin content, and reshape microbial community structures, particularly through the production of fungal mycotoxins. These alterations influence silage fermentation characteristics and nutritional composition [7, 8, 9–10]. Eberl [11] reported that rust infection reduces photosynthetic activity but does not necessarily lower carbohydrate levels, indicating that plants may adapt to pathogen stress through metabolic adjustments. Similarly, Luo [12] found that rust-infected Zostera marina maintains physiological balance under adverse conditions by increasing levels of photosynthetic pigments and water-soluble carbohydrate content, suggesting that plants regulate carbohydrates as a defense mechanism. Additionally, Hassani [13] reported that the infestation of Puccinia spp. in corn can convert photosynthates, such as glucose and fructose, into products specific to the fungus, allowing it to thrive under high pH conditions during ensiling. While existing studies have focused on microbial succession and changes in fermentation quality during corn silage production, there remains a significant gap in systematic research regarding the effects of field diseases—particularly rust stress—on microbial community structure, functional metabolic potential, and toxin degradation mechanisms throughout the corn silage process.
In recent years, metagenomic technology has emerged as a powerful tool for deciphering the structure and functional potential of complex microbial communities. It enables the comprehensive characterization of both cultivable and uncultivable microorganisms while simultaneously uncovering their functional genes and associated metabolic pathways that drive community dynamics. Based on this, corn plants from Gansu (common rust) and Hebei (southern rust) were selected to evaluate the impact...