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Viral metagenome reveals microbial hosts and the associated antibiotic resistome on microplastics

Nature Water volume 2, pages 553–565 (2024)Cite this article

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Abstract

Microplastics provide a unique niche for viruses, promoting viral interactions with hosts and accelerating the rapid ‘horizontal’ spread of antibiotic resistance genes (ARGs). Currently, however, there is a lack of knowledge concerning the main drivers for viral distribution on microplastics and on the resulting patterns of viral biogeographic distributions and the spread of the associated ARGs. Here we performed metagenomic and virus enrichment-based viromic sequencings on both polyethylene and polypropylene microplastics along a river. Experimental results show that Proteobacteria, Firmicutes, Actinobacteria and Cyanobacteria were the potential hosts of viruses on microplastics, but only approximately 4.1% of viral variations were associated with a bacterial community. Notably, two shared ARGs and six metal resistance genes were identified in both viral and their host bacterial genomes, indicating the occurrence of horizontal gene transfer between viruses and bacteria. Furthermore, microplastics introduce more distinctive elements to viral ecology, fostering viral diversification and virus–host linkage while refraining from an escalated level of horizontal gene transfer of ARGs in contrast to natural matrixes. Our study provides comprehensive profiles of viral communities, virus-related ARGs and their driving factors on microplastics, highlighting how these anthropogenic niches provide unique interfaces that comprise highly defined viral ecological features in the environment.

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Fig. 1: Diversity and composition of viral communities.
Fig. 2: Relative abundance of bacterial and viral-encoded resistance genes.
Fig. 3: MRG and taxonomic dynamics of bacterial and viral communities.
Fig. 4: Viral–host interaction structure.
Fig. 5: Comparisons of viral community composition, richness and evenness in natural particles and microplastics.

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Data availability

The raw sequencing reads of bacterial and viral communities have been deposited into the NCBI Sequence Read Archive (SRA) under the accession number PRJNA1104113 and PRJNA1104403 (https://www.ncbi.nlm.nih.gov/sra). The other data generated in this study are provided in the main text or Supplementary Information.

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Acknowledgements

Y.-G.Z.’s lab members were supported financially by the National Natural Science Foundation of China (42021005, 22193061, 21922608), Key Collaborative Research Program of the Alliance of International Science Organizations (ANSO-CR-KP-2020-03, ANSO-PA-2020-18) and Chinese Academy of Sciences (ZDBS-LY-DQC027).

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Author notes

  1. These authors contributed equally: Ruilong Li, Xin-Li An.

Authors and Affiliations

  1. Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China

    Ruilong Li, Xin-Li An, Jian-Qiang Su & Yong-Guan Zhu

  2. College of Light Industry and Food Engineering, Guangxi University, Nanning, China

    Ruilong Li & Yijin Wang

  3. School of Water, Energy and Environment, Cranfield University, Cranfield, UK

    Zhugen Yang

  4. The School of Engineering, The University of Glasgow, Glasgow, UK

    Jonathan Cooper

  5. State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China

    Yong-Guan Zhu

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  1. Ruilong Li
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Contributions

R.L. designed the experiments and contributed to data analysis and the writing of the paper. X.-L.A. performed viral DNA extraction, sequencing and identification and the writing of the paper. Y.W. contributed to the creation of the final figures and the writing of the paper. Z.Y. contributed to the writing of the paper and discussion of results. J.-Q.S. contributed to the writing of the paper. J.C. contributed to the discussion of results. Y.-G.Z. conceived the idea of the study and contributed to the writing of the paper. All authors contributed to the review and editing of the paper.

Corresponding author

Correspondence to Yong-Guan Zhu.

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Nature Water thanks Bin Ma and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Tables 1 and 2 and Figs. 1–20.

Supplementary Data 1

Pathogenic bacteria.

Supplementary Data 2

Host–virus pairs.

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Li, R., An, XL., Wang, Y. et al. Viral metagenome reveals microbial hosts and the associated antibiotic resistome on microplastics. Nat Water 2, 553–565 (2024). https://doi.org/10.1038/s44221-024-00249-y

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