Engineering the composting microbiome with a synthetic microbial community to accelerate lignocellulose degradation...

Bioaugmentation with synthetic microbial communities (SynComs) presents a promising engineering strategy to overcome the bottleneck of lignocellulose recalcitrance in organic waste valorization. However, the mechanisms by which SynComs modulate indigenous microbial networks and steer metabolic fluxes remain elusive. Here, we deconstruct these mechanisms by investigating the impact of a rationally designed five-member bacterial-fungal SynCom on the co-composting of cattle manure and mulberry branches. Through an integrated multi-omics approach, we reveal that SynCom inoculation acts as a potent ecological engineer, accelerating the process by significantly elevating pile temperatures and shortening the maturation period by accelerating entry into the maturation phase by approximately 7 days. Compared with the control, the SynCom treatment enhanced the overall degradation rates of lignin, cellulose, and hemicellulose by 19.3 %, 7.9 %, and 12.0 %, respectively, and boosted humus content by 34.4 %. Metagenomics revealed that the SynCom profoundly restructured the native microbiome, enriching for key functional genera such as Thermobifida and Actinomadura. This engineered community possessed an enhanced genetic toolkit, with a significantly increased abundance of crucial carbohydrate-active enzymes (CAZymes), including cellulases (GH5, GH12), hemicellulases (CE1, CE3), and lignin-modifying auxiliary activity enzymes (AA1, AA6). Untargeted metabolomics further identified a distinct metabolic footprint in the SynCom treatment, characterized by the enrichment of key humification precursors like protocatechuic acid and sinapic acid. Integrated Procrustes and correlation analyses confirmed a tight coupling between the engineered microbiome, its functional gene repertoire and metabolic output. This study deciphers the multi-layered mechanism by which a designed SynCom enhances biowaste valorization and provides a mechanistic blueprint for engineering microbial consortia for advanced biotechnology applications in sustainable agriculture.