Impact of Residual Glutaraldehyde-Didecyldimethylammonium Bromide on Fermentation Performance and Microbial Community in Ectopic Fermentation System

Ectopic fermentation systems (EFSs) are widely applied to treat livestock manure, yet residual disinfectants transferred from production areas into the manure collection system may compromise their performance, and the consequences of such continuous low-dose input remain unclear. Here, we aimed to determine whether long-term input of the widely used disinfectant glutaraldehyde–didecyldimethylammonium bromide (GD) impairs EFS operation, and to identify the changes in microbial communities and organic matter underlying these effects. Pig manure slurry containing 20 mg/kg GD was supplied continuously, and physicochemical parameters, enzyme activities, microbial communities, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and three-dimensional excitation–emission matrix (3D-EEM) spectra were monitored throughout the fermentation period. GD significantly reduced total nitrogen accumulation (p < 0.05) and suppressed lignocellulose-degrading enzyme activities during the late fermentation stage. Microbial richness declined significantly (Chao index, p < 0.05), accompanied by enrichment of thermotolerant taxa such as Thermobifida and Bacillus, while soluble microbial by-products decreased markedly. Unexpectedly, MGEs including intI1, intI2 and Tn916/1545 were less abundant under GD exposure, likely reflecting the overall inhibition of microbial growth. These findings demonstrate that GD residues exert cumulative adverse effects on EFS performance, and highlight the need to coordinate on-farm disinfection with downstream manure treatment.