Trichoderma-based fertilizer enhances quality of Elymus breviaristatus silage via microbial and metabolic modulation

Elymus breviaristatus is an important alpine forage, there is limited information regarding its potential use as silage and how fertilizer treatments affect the ensiling process in this forage crop. Here, we investigated how organic fertilizer (M), nitrogen-phosphorus-potassium fertilizer (NPK), and Trichoderma harzianum fertilizer (B) affect E. breviaristatus silage quality (30 days and 60 days ensiling) via microbiome and metabolome analyses. Before ensiling, plant height and chlorophyll content increased by 29.93% and 39.72%, respectively, in the B group. After 60 days of ensiling, the M group had reduced crude protein and elevated butyric acid, the NPK group had higher ammonia nitrogen and butyric acid, and the B group had increased crude protein and lactic acid. These quality shifts correlated with microbial and metabolic changes. In the M group, alpha-linolenic acid metabolism was downregulated and Alternaria enriched, while the NPK group had enhanced flavone biosynthesis and a reduced level of Lactiplantibacillus. The B group had enhanced glycine, serine, and threonine metabolism, and displayed the most complex microbial networks along with increased levels of Lactiplantibacillus and Aspergillus. Overall, these results demonstrate that Trichoderma-based fertilization enhances silage quality by promoting accumulation of beneficial microbes and increasing flux through specific metabolic pathways, potentially offering a sustainable strategy for alpine forage improvement.