RNA viromes from terrestrial sites across China expand environmental viral diversity (original) (raw)

Data availability

The sequence reads generated in this study are available at the NCBI Sequence Read Archive (SRA) database under BioProject accession PRJNA716119. All viral sequences generated in this study have been deposited in GenBank under accession numbers (https://www.ncbi.nlm.nih.gov/nuccore?term=716119%5BBioProject%5D) MW784004-MW784109, MW896840-MW897324, MZ218144-MZ218759, MZ556337-MZ556592, MZ678955-MZ680357, ON049747-ON050964, ON161767-ON164489. All other data are available in the paper or in the supplementary materials. The CheckV database used for viral genome quality and completeness estimation can be accessed via https://bitbucket.org/berkeleylab/checkv. The Conserved Domain Database (CDD) used for ORF annotation can be accessed via https://www.ncbi.nlm.nih.gov/cdd/. The UniRef30_2021_03 database used in HHblits analysis can be accessed via http://wwwuser.gwdg.de/~compbiol/uniclust/2021_03/. The SILVA database used for rRNA removal can be accessed via https://www.arb-silva.de/. Source data are provided with this paper.

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Acknowledgements

We thank D.-X. Wang, K. Li, W.-B. Zhao, X.-N. Diao, A.-J. Gong, Y.-L. Zhang, J.-B. Wang, H. Luo, D.-A. Zhang, Y.-Q. Zhao and M.-Li for their contributions to sample collection, and X.-Q. Luo, R.-X. Hu, M.-Z. Liu, J. Liu, Y. Jiang, J.-J. Guo, J.-J. Wang and P. Lu for assisting with PCR confirmations. This study was supported by the National Natural Science Foundation of China (grant nos. 32130002, 31930001, 32041004, 81861138003 and 81672057 to Y.-Z.Z) and the National Key R&D Program of China (2016YFC1201900 to Y.-Z.Z). E.C.H was supported by an ARC Australian Laureate Fellowship (FL170100022).

Author information

Author notes

  1. These authors contributed equally Yan-Mei Chen, Sabrina Sadiq.

Authors and Affiliations

  1. Shanghai Public Health Clinical Center, Shanghai Key Laboratory of Organ Transplantation of Zhongshan Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
    Yan-Mei Chen, Wen Wang, Edward C. Holmes & Yong-Zhen Zhang
  2. Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
    Sabrina Sadiq, Michelle Wille & Edward C. Holmes
  3. Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
    Jun-Hua Tian
  4. College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China
    Xiao Chen
  5. Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang, China
    Xian-Dan Lin
  6. Yancheng Center for Disease Control and Prevention, Yancheng, Jiangsu, China
    Jin-Jin Shen & Feng Li
  7. Jiangsu Yancheng Wetland National Nature Reserve of Rare Birds, Yangcheng, Jiangsu, China
    Hao Chen
  8. Henan Center for Disease Control and Prevention, Zhengzhou, Henan, China
    Zong-Yu Hao
  9. Professional Committee of Native Aquatic Organisms and Water Ecosystem of China Fisheries Association, Beijing, China
    Zhuo-Cheng Zhou
  10. Jiyuan People’s Hospital, Jiyuan, Henan, China
    Jun Wu
  11. Neixiang Center for Disease Control and Prevention, Nanyang, Henan, China
    Hong-Wei Wang
  12. College of Ocean and Earth Science, Xiamen University, Xiamen, Fujian, China
    Wei-Di Yang
  13. Yili Prefecture Center for Disease Control and Prevention, Yili, China
    Qi-Yi Xu
  14. Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
    Wen Wang & Wen-Hua Gao

Authors

  1. Yan-Mei Chen
  2. Sabrina Sadiq
  3. Jun-Hua Tian
  4. Xiao Chen
  5. Xian-Dan Lin
  6. Jin-Jin Shen
  7. Hao Chen
  8. Zong-Yu Hao
  9. Michelle Wille
  10. Zhuo-Cheng Zhou
  11. Jun Wu
  12. Feng Li
  13. Hong-Wei Wang
  14. Wei-Di Yang
  15. Qi-Yi Xu
  16. Wen Wang
  17. Wen-Hua Gao
  18. Edward C. Holmes
  19. Yong-Zhen Zhang

Contributions

Y.-Z.Z. conceived and designed the study. Y.-M.C., J.-H.T., X.C., X.-D.L., J.-J.S., H.C., Z.-Y.H., W.-D.Y., Z.-C.Z., J.W., F.L., H.-W.W. and Q.-Y.X. performed sample collection and geographic information recording. S.S., Y.-M.C., M.W. and E.C.H. analysed the data. Y.-M.C., W.-H.G. and W.W. performed the experiments. S.S., Y.-M.C., E.C.H. and Y.-Z.Z. wrote the paper with input from all authors. Y.-Z.Z. led the study.

Corresponding author

Correspondence toYong-Zhen Zhang.

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Competing interests

The authors declare no competing interests.

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Extended data

Extended Data Fig. 1

Environments and Chinese provinces sampled in this study.

Extended Data Fig. 2 Viral composition of each library.

Relative proportions were determined by the number of reads corresponding to contigs with viral hits to each viral clade as a proportion of total viral reads in each of 442 biologically independent samples (analysis performed using DIAMOND BLASTX).

Source data

Extended Data Fig. 3 Ecological factors significantly associated with viral abundance in environmental viruses.

(A) Model-averaged effect sizes of ecological metadata for 265 biologically independent samples on viral abundance with confidence intervals of 95% and factors significant in the best subset selected model (p < 0.05, in orange) do not overlap the central line and are denoted with an asterisk (*) (identical to Fig. 6a). Boxplots represent abundance values plotted against (B) environment, (C) location, (D) total phosphorus, (E) total potassium, (F) available phosphorus, (G) available potassium, (H) organic content, (I) eukaryote species abundance, and (J) eukaryote species richness. For all boxplots, the horizontal box lines in the boxplots represent the first quartile, the median, and the third quartile. Whiskers denote the range of points within the first quartile − 1.5× the interquartile range and the third quartile + 1.5× the interquartile range.

Extended Data Fig. 4 Ecological factors significantly associated with viral abundance in animal-associated viruses.

(A) Model-averaged effect sizes of ecological metadata for 265 biologically independent samples on viral abundance with confidence intervals of 95% and factors significant in the best subset selected model (p < 0.05, in orange) do not overlap the central line and are denoted with an asterisk (*) (identical to Fig. 7a), along with the abundance values plotted against (B) location, (C) organic content, and (D) eukaryote species abundance. For all boxplots, the horizontal box lines in the boxplots represent the first quartile, the median, and the third quartile. Whiskers denote the range of points within the first quartile − 1.5× the interquartile range and the third quartile + 1.5× the interquartile range.

Extended Data Fig. 5 Ecological factors significantly associated with Shannon diversity in environmental viruses.

(A) Model-averaged effect sizes of ecological metadata for 265 biologically independent samples on Shannon diversity with confidence intervals of 95% and factors significant in the best subset selected model (p < 0.05, in orange) do not overlap the central line and are denoted with an asterisk (*) (identical to Fig. 6c). Boxplots represent Shannon diversity values plotted against (B) environment, (C) location, (D) pH, (E) total nitrogen, (F) total potassium, (G) available nitrogen, (H) organic content, and (I) eukaryote species richness. For all boxplots, the horizontal box lines in the boxplots represent the first quartile, the median, and the third quartile. Whiskers denote the range of points within the first quartile − 1.5× the interquartile range and the third quartile + 1.5× the interquartile range.

Extended Data Fig. 6 Ecological factors significantly associated with true diversity in environmental viruses.

(A) Model-averaged effect sizes of ecological metadata for 265 biologically independent samples on true diversity with confidence intervals of 95% and factors significant in the best subset selected model (p < 0.05, in orange) do not overlap the central line and are denoted with an asterisk (*) (identical to Fig. 6d), along with the true diversity values plotted against (B) environment, (C) location, (D) pH, (E) total nitrogen, (F) total potassium, (G) available nitrogen, (H) organic content, (I) eukaryote species richness, and (J) eukaryote species true diversity. For all boxplots, the horizontal box lines in the boxplots represent the first quartile, the median, and the third quartile. Whiskers denote the range of points within the first quartile − 1.5× the interquartile range and the third quartile + 1.5× the interquartile range.

Extended Data Fig. 7 Ecological factors significantly associated with Shannon diversity in animal-associated viruses.

(A) Model-averaged effect sizes of ecological metadata for 265 biologically independent samples on Shannon diversity with confidence intervals of 95% and factors significant in the best subset selected model (p < 0.05, in orange) do not overlap the central line and are denoted with an asterisk (*) (identical to Fig. 7c), along with the Shannon diversity values plotted against (B) environment. For all boxplots, the horizontal box lines in the boxplots represent the first quartile, the median, and the third quartile. Whiskers denote the range of points within the first quartile − 1.5× the interquartile range and the third quartile + 1.5× the interquartile range.

Extended Data Fig. 8 Ecological factors significantly associated with true diversity in animal-associated viruses.

(A) Model-averaged effect sizes of ecological metadata for 265 biologically independent samples on true diversity with confidence intervals of 95% and factors significant in the best subset selected model (p < 0.05, in orange) do not overlap the central line and are denoted with an asterisk (*) (identical to Fig. 7d), along with the true diversity values plotted against (B) environment. For all boxplots, the horizontal box lines in the boxplots represent the first quartile, the median, and the third quartile. Whiskers denote the range of points within the first quartile − 1.5× the interquartile range and the third quartile + 1.5× the interquartile range.

Extended Data Fig. 9 Ecological factors significantly associated with viral richness in environmental viruses.

(A) Model-averaged effect sizes of ecological metadata for 265 biologically independent samples on viral richness with confidence intervals of 95% and factors significant in the best subset selected model (p < 0.05, in orange) do not overlap the central line and are denoted with an asterisk (*) (identical to Fig. 6b). Boxplots represent richness values plotted against (B) environment, (C) location, (D) pH, (E) total phosphorus, (F) available nitrogen, (G) organic content, (H) eukaryote species richness, (I) eukaryote species Shannon diversity, and (J) eukaryote species true diversity. For all boxplots, the horizontal box lines in the boxplots represent the first quartile, the median, and the third quartile. Whiskers denote the range of points within the first quartile − 1.5× the interquartile range and the third quartile + 1.5× the interquartile range.

Extended Data Fig. 10 Ecological factors significantly associated with viral richness in animal-associated viruses.

(A) Model-averaged effect sizes of ecological metadata for 265 biologically independent samples on viral richness with confidence intervals of 95% and factors significant in the best subset selected model (p < 0.05, in orange) do not overlap the central line and are denoted with an asterisk (*) (identical to Fig. 7b), along with the richness values plotted against (B) environment, (C) location, (D) pH, (E) total phosphorus, (F) organic content, (G) eukaryote species richness, and (H) eukaryote species true diversity. For all boxplots, the horizontal box lines in the boxplots represent the first quartile, the median, and the third quartile. Whiskers denote the range of points within the first quartile − 1.5× the interquartile range and the third quartile + 1.5× the interquartile range.

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Chen, YM., Sadiq, S., Tian, JH. et al. RNA viromes from terrestrial sites across China expand environmental viral diversity.Nat Microbiol 7, 1312–1323 (2022). https://doi.org/10.1038/s41564-022-01180-2

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