Anaerobic digestion (AD) is widely used to treat livestock manure that harbors diverse pollutants (resistance genes (ARGs), metal/biocide resistance genes (MBRGs), integron-integrase genes, human pathogens and pathogen virulence factors (VFs)). However, the interplays of these pollutants and the effects of substrate complexity on pollutants in AD are elusive. This study investigated the dynamics of these pollutants and bacterial communities during AD of swine manure, by metatranscriptomic sequencing and amplicon sequencing of 16 S rRNA and 16 S rRNA gene. The pollutant profiles and bacterial communities differed across AD processes, nevertheless with consistent dominance of ARGs of multi-drugs, tetracycline, aminoglycoside and rifamycin, MBRGs of multi-biocides, multi-metals, copper and arsenic, the integron-integrase gene intI1, potential pathogens of Escherichia coli, Streptococcus gallolyticus and Clostridium perfringens, VFs involved in pathogen adherence, and bacterial phyla of Firmicutes, Bacteroidetes and Proteobacteria. Reduced substrate complexity (replacing a part of swine manure, a complex substrate, with a simple substrate, apple waste or fructose) decreased the prevalence and stochastic turnover of ARGs and MBRGs. Network analyses revealed decreased interplays among pollutants under reduced substrate complexity. Our findings provide a mechanical understanding of diverse pollutants dynamics during AD, and reveal the importance of substrate complexity in controlling prevalence and interplays of pollutants.

厌氧消化（AD）广泛用于处理含有多种污染物（抗性基因（ARGs）、金属/杀菌剂抗性基因（MBRGs）、整合子整合酶基因、人类病原体和病原体毒力因子（VFs））的牲畜粪便。然而，这些污染物的相互作用以及底物复杂性对 AD 污染物的影响是难以捉摸的。本研究通过 16 S rRNA 和 16 S rRNA 基因的宏转录组测序和扩增子测序，调查了猪粪 AD 期间这些污染物和细菌群落的动态。污染物谱和细菌群落在 AD 过程中有所不同，但多药、四环素、氨基糖苷和利福霉素的 ARGs、多杀菌剂的 MBRGs、多金属、铜和砷、整合子整合酶基因始终占主导地位intI1 、大肠杆菌、溶食性链球菌和产气荚膜梭菌的潜在病原体、参与病原体粘附的 VF 以及厚壁菌门、拟杆菌门和变形菌门的细菌门。降低基质复杂性（用简单基质、苹果废料或果糖代替部分猪粪、复杂基质）降低了 ARG 和 MBRG 的流行率和随机周转率。网络分析显示，在降低底物复杂性的情况下，污染物之间的相互作用减少。我们的研究结果提供了对 AD 期间各种污染物动态的机械理解，并揭示了底物复杂性在控制污染物的流行和相互作用中的重要性。