Smut disease reduces not only the biomass yield of whole-crop silage maize (WCSM) but also its fermentation quality and nutritional value. The present study aimed to systematically evaluate the effects of smut disease on fermentation characteristics and protein degradation processes of WCSM and evaluate the efficacy of lactic acid bacteria (LAB) inoculation as a remediation strategy. The experiment consisted of three treatments: healthy maize (Healthy), smut-infected maize (Diseased), and smut-infected maize inoculated with LAB (DLAB), with five fermentation periods (3, 7, 15, 30, and 60 d). The diseased treatment exhibited higher levels of neutral detergent fiber (528 vs. 442 g/kg DM) and acid detergent fiber (320 vs. 265 g/kg DM) than the healthy treatment. Although protease activity declined over time in all treatments, overall protease activity remained higher in the diseased group than in the healthy and DLAB groups. Bacterial community composition in the DLAB treatment closely resembled that of the healthy group and showed a significant increase in Lactobacillus plantarum abundance (P < 0.01) compared to the diseased treatment, with negative correlations observed between L. plantarum and most protein degradation-related parameters. The diseased treatment accumulated a wide range of protein degradation-related metabolites. In contrast, the DLAB treatment achieved rapid pH reduction; effectively inhibited key proteases, such as aminopeptidase and carboxypeptidase; reduced accumulation of free amino acids and their derivatives, and increased the abundance of tricarboxylic acid cycle intermediates such as cis-aconitic anhydride, significantly, thereby enhancing microbial energy metabolism. Additionally, the DLAB treatment increased the levels of plant-derived metabolites with known antioxidant and anti-pathogenic properties, contributing to silage microecological stability and fermentation quality. In conclusion, DLAB treatment mitigated silage deterioration under smut disease stress through multi-level regulation of protein degradation and metabolic network reprogramming.
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