Effects of Sterilization Pretreatment and Microbial Inoculation on Physicochemical Characteristics and Fungal Community Structure in Aerobic Composting of Mushroom Residue and Livestock Manure

Aerobic co-composting of spent mushroom substrate (SMS) and cattle manure is a vital technology for agricultural waste recycling. However, high refractory lignocellulose content and low indigenous microbial activity usually hinder compost heating and maturation. Exogenous inoculation and raw material sterilization are common microbiome regulation strategies, while their divergent functional mechanisms and the contributions of native versus exogenous microbiota remain unclear. Herein, three treatments (control with intact indigenous microbiota, sterilization pretreatment, and 0.5% w/w fungal–bacterial inoculation) were established to explore their effects on composting performance and fungal community succession over 34 days. Compost stability and maturity were evaluated via thermophilic duration and germination index (GI), with fungal communities analyzed by ITS high-throughput sequencing. The results revealed that sterilization severely suppressed composting, causing delayed heating, a low peak temperature of 55.2 °C, inhibited lignocellulose degradation, and disordered fungal community structure with increased richness but decreased evenness due to random colonization by weak degraders. In contrast, microbial inoculation prominently improved composting efficiency, with a peak temperature of 67.5 °C, eight days of sustained high temperature, and a final GI of 89.67%. The degradation rates of cellulose, hemicellulose and lignin reached 68.32%, 72.15% and 35.28%, respectively. Inoculation directionally enriched core lignocellulose-degrading fungi (Chaetomium, Aspergillus fumigatus, Thermoascus) and maintained functional community balance. Core fungal genera dominated lignocellulose decomposition and humification driven by environmental factors. This study clarifies that indigenous microbiota underpin spontaneous composting, while targeted inoculation optimizes functional microbiota, and single sterilization impairs composting. It provides mechanistic guidance for efficient agricultural waste composting.