Tan Yixiao, Yu Pingfeng, Yu Zhuodong, Xuan Fan, Zhu Liang
College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310085, China.
College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310085, China; Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan 314100, China.
Water Res. 2025 Jan 1;268(Pt A):122590. doi: 10.1016/j.watres.2024.122590. Epub 2024 Oct 9.
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.
细菌防御系统面临着抵御移动遗传元件（MGEs）的强大进化压力，但其在工程系统中微生物聚集体中的分布仍 largely 未被探索。在此，我们研究了全尺寸膜生物反应器中活性污泥絮体（AS）和膜附着生物膜（MF）内的细菌防御组和 MGEs。在 AS 和 MF 的原核基因组中观察到细菌防御系统（63 种类型）的相似分布模式，包括 RM 系统（约 40%）、Cas 系统（约 18%）和 TA-Abi 系统（约 28%），在升高的水力应力（MF）下，微生物聚集体中表现出对基因组大小和细菌分类学的依赖性。与携带与其相关宿主相似的防御系统（22 种类型）的质粒和前病毒不同，病毒群落（61%）携带其相关宿主中不存在的新型防御系统（40 种类型）。其中 54%参与 MGEs 基因流动网络，69%的高质量细菌基因组 bins 与水平基因转移（HGT）相关，促进了移动核心功能基因的交换。这可能通过与生物防御、抗生素抗性和氮代谢相关的栖息地特异性有效载荷基因赋予宿主竞争优势。较长的生长周期和不同的防御基因密度表明细菌宿主-MGE 共生体中潜在的防御冗余以及代谢消耗和免疫的权衡。此外，在 MF 中观察到交叉喂养和防御的增强合作网络模块，可能有助于共生微生物群落在升高的水力应力下应对恶劣条件。这些发现揭示了宿主-MGE 共同进化中细菌防御系统的动态，并为生态和工程应用中的微生物聚集体操纵提供了新的视角。
