Abstract
Microorganisms secrete extracellular vesicles (EVs) that transport bioactive molecules, including proteins and metabolites. While their functions are well studied in model microbes, their ecological contributions to natural ecosystems remain largely unexplored. Here we performed an integrative study investigating the role of environmental EVs in shaping microbial community assembly in the Xinglinwan Reservoir. By combining genome-scale metabolic models and multi-omics of field EVs, we found that EVs mediated metabolite exchanges mainly through carrying amino acids, disaccharides, carbohydrate-active enzymes (CAZymes) and signals. EVs can facilitate the growth of amino acid auxotrophic strains. Moreover, EVs act as an external reservoir of functional traits, potentially reinforcing stochastic assembly processes and conferring functional redundancy to the ecosystem. Collectively, our integrative data demonstrate that EV-mediated metabolic exchange is an auxiliary mechanism supplementing classical nutrient transport in aquatic environments. EVs emerge here as a significant, distinct vector in biogeochemical cycling, offering a critical layer for resolving complex natural microbial interactions.
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Data availability
All the metagenomic sequencing data has been uploaded and is publicly available in the BIG Submission at https://ngdc.cncb.ac.cn/gsa/browse/CRA027247. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the iProX partner repository (accession: PXD065377). Full mass spectrometry metabolomic data were deposited to MetaboLights (MTBLS12874). Source data are provided with this paper.
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Acknowledgements
This work was supported by National Natural Science Foundation of China (42177362) and National Basic Science Data Center ‘Environment Health DataBase’ (number NBSDC-DB-21). We thank Y. Tao and N. Xue from Institute of Microbiology, Chinese Academy of Sciences, for providing the auxotrophic E. coli strains. We thank Z. Guo and Y. Duan for their help in sampling and data analysis.
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X.X. conducted the experiments, generated and analysed the data and wrote the paper. M.W. wrote the paper. A.U.O. and L.-T.Z. helped with the data analysis. F.L. and Y.G. provided the suggestions for computational adjustments. X.L., Z.S. and M.Z. contributed to extract EV experiments. Q.H. wrote the paper and got the funding.
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Xu, X., Obeten, A.U., Zhu, LT. et al. Extracellular vesicle-mediated metabolic exchange shapes the seasonal assembly of aquatic bacterial communities.
Nat Water (2026). https://doi.org/10.1038/s44221-026-00605-0
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DOI: https://doi.org/10.1038/s44221-026-00605-0
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