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Application of environmental DNA metabarcoding to identify fish community characteristics in subtropical river systems
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  • Sai Wang,
  • Dong-Hai Wu,
  • En-Ni Wu,
  • Nan-Lin Chen,
  • Shi-Di Fan,
  • Tuan-Tuan Wang,
  • Zhong-Bing Chen,
  • Yong-Duo Song,
  • Yang Zhang,
  • Zhuo-Luo a,
  • Lei Xiang,
  • Yu-Xi Yang,
  • Rong-Mei Zi
Sai Wang
Hainan University
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Dong-Hai Wu
Hainan University
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En-Ni Wu
Hainan University
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Nan-Lin Chen
Hainan University
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Shi-Di Fan
Hainan University
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Tuan-Tuan Wang
Hainan University

Corresponding Author:[email protected]

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Zhong-Bing Chen
Czech University of Life Sciences Prague
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Yong-Duo Song
Hainan University
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Yang Zhang
Shenzhen Guanghuiyuan Environment Water Co., Ltd.
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Zhuo-Luo a
China Water Resources Pearl River Planning Surveying & Designing Co., Ltd.
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Lei Xiang
Jinan University
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Yu-Xi Yang
Hainan University
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Rong-Mei Zi
Hainan University
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Abstract

Fish play vital roles in river ecosystems; however, traditional investigations of fish usually cause certain ecological damage. Extracting DNA from aquatic environments and identifying DNA sequences offers an alternative, non-invasive approach for detecting fish species. In this study, environmental DNA (eDNA), coupled with PCR and next-generation sequencing, and electrofishing were used to compare their effects in identifying fish community characteristics. In three subtropical rivers of southern China, fish specimens and eDNA in water were collected from headwaters to estuaries. Both eDNA OTU richness and individual abundance (including number and biomass) could group 38 sampling sites into eight spatial zones with significant differences in local fish community composition. Compared with the order-/family-level grouping, the genus-/species-level grouping could more accurately recognize the differences between upstream zones I − III, midstream zones IV − V, and downstream zones VI – VIII. From headwaters to estuary, two environmental gradients significantly influenced the longitudinal distribution of fish species, including the first gradient composed of habitat and physical water parameters and the second gradient composed of chemical water parameters. The high regression coefficient of alpha diversity between eDNA and electrofishing methods as well as the accurate recognition of dominant, alien, and biomarker species at each spatial zone indicated that eDNA could characterize fish community attributes at a similar level of traditional approach. Generally, our results demonstrated that eDNA metabarcoding can be used as an effective tool in revealing fish composition and diversity, which is important for using the eDNA technique in aquatic field monitoring.
04 Aug 2023Submitted to Ecology and Evolution
04 Aug 2023Submission Checks Completed
04 Aug 2023Assigned to Editor
21 Aug 2023Reviewer(s) Assigned
29 Oct 2023Review(s) Completed, Editorial Evaluation Pending
30 Oct 2023Editorial Decision: Revise Minor
05 Nov 20231st Revision Received
16 Nov 2023Submission Checks Completed
16 Nov 2023Assigned to Editor
16 Nov 2023Review(s) Completed, Editorial Evaluation Pending
05 Feb 20242nd Revision Received
06 Feb 2024Submission Checks Completed
06 Feb 2024Assigned to Editor
06 Feb 2024Review(s) Completed, Editorial Evaluation Pending
17 Feb 20243rd Revision Received
20 Feb 2024Assigned to Editor
20 Feb 2024Submission Checks Completed
20 Feb 2024Review(s) Completed, Editorial Evaluation Pending
29 Feb 2024Submission Checks Completed
29 Feb 2024Assigned to Editor
29 Feb 2024Review(s) Completed, Editorial Evaluation Pending