Deciphering defense system modulating bacteria-mobile genetic elements symbiosis in microbial aggregates under...

Bacterial defense systems are under strong evolutionary pressures to defend against mobile genetic elements (MGEs), yet their distribution in microbial aggregates in engineered systems remains largely unexplored. Herein, we investigated the bacterial defensome and MGEs within activated sludge flocs (AS) and membrane-attached biofilm (MF) in a full-scale membrane bioreactor. Similar distribution pattern of bacterial defense systems (63 types) was observed in prokaryotic genome in AS and MF, including RM system (∼40 %), Cas system (∼18 %) and TA-Abi system (∼28 %), exhibiting a dependency on the genome size and bacterial taxonomy in microbial aggregates under elevated hydraulic stress (MF). In contrast to plasmid and provirus, which carried defense systems (22 types) similar to their associated hosts, virome (61 %) carried novel defense systems (40 types) absent in their associated hosts. With 54 % of which involved in MGEs geneflow network, 69 % of high quality bacterial genome bins were associated with horizontal gene transfer (HGT), facilitating the exchange of mobile core functional genes. This potentially conferred competitive advantages to hosts through habitat-specific payload genes related to biotic defense, antibiotic resistance, and nitrogen metabolism. The longer growth cycle and varied defense gene density suggested the potential defense redundancy and trade-off of metabolic expense and immunity in bacterial host-MGE symbionts. Furthermore, enhanced cooperative network modules of cross-feeding and defense were observed in the MF, potentially helped the symbiotic microbial communities in coping with hostile conditions under elevated hydraulic stress. These findings shed light on the dynamics of bacterial defense systems in host-MGE coevolution and provide new perspectives of microbial aggregates manipulation for ecological and engineering application.