The untargeted metabolites of field EVs from Xinglinwan Reservoir, Xiamen, China.

Microorganisms secrete extracellular vesicles (EVs) that transport bioactive molecules such as proteins, metabolites, and enzymes. While their functions are well studied in model microbes, their ecological contributions to natural ecosystems remain largely unexplored.To address this issue, we performed a year-long, integrative study investigating the role of environmental EVs in shaping microbial community assembly in the Xinglinwan Reservoir (XLR). By combining shotgun metagenomics, genome-scale metabolic modelling, and multi-omics of field EVs, we found that EVs mediated metabolite exchanges mainly through carrying signal molecules, amino acids, disaccharides, and CAZymes. These cargoes could be derived from the metabolisms within EVs or directly sourced from their donors, and were closely linked to the carbon cycle and nitrogen metabolism in aquatic environments. In addition, EVs increased the contribution of stochastic processes to the community assembly and improved the stability of the community by maintaining high functional redundancy. Our study demonstrates that EV-mediated metabolic exchanges are prevalent in aquatic communities and pivotal for shaping community assembly and driving biogeochemical cycles. These results clarify the ecological functions of EVs in natural habitats and provide new insights into manipulating microbial communities through controlling environmental EVs.