Fish Diversity Monitored by Environmental DNA in the Yangtze River Mainstream
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Sites and Collection
2.2. DNA Extraction and PCR
2.3. Library Preparation and Sequencing
2.4. Bioinformatic Statistics and Fish Identification
2.5. Seasonal Difference Comparison
3. Results
3.1. Fish Resource Results by eDNA
3.2. Diversity of Fish Communities
3.3. Seasonal Variation Analysis
3.4. Relationship with Environmental Factors
4. Discussion
4.1. Fish Diversity in the Mainstream of the Yangtze River Based on eDNA
- (1)
- Insufficient sample collection: The fish activities in the Yangtze River mainstream are relatively large; in the present study, we only set 11 sampling points in the Yangtze River mainstream, which may have led to insufficient sampling. Ficetola et al. (2015) pointed out that replication, i.e., the number of water samples collected as opposed to the number of technical replicates run from a single sample, can be adjusted to compensate for false negatives [53]. Therefore, adding sampling points according to the study area would increase the possibility of detecting fish.
- (2)
- Less eDNA preservation: The amount of eDNA secreted by fish is related to itself; studies have shown that different species secrete DNA at different rates and quantities [54]. Moreover, the preservation of eDNA is also very important, as the long transportation after sampling, temperature, time and other factors will affect the preservation effect of the eDNA experiment. In addition, delayed extraction from the Sterivex filter may also result in less DNA being extracted. Thus, special attention should be paid to the preservation of samples, and timely filtration after sampling will reduce the degradation rate of eDNA.
- (3)
- Lack of local reference database information: This study did not establish a more accurate local reference database for fish in the Yangtze River mainstream, which may have reduced the number of native species identified. The effectiveness of eDNA depends on the quality of the reference sequence database and the classification parameters employed [55]. In future investigations and studies, we will consider establishing a local database. At the same time, the results of this survey will also serve as a reference for future surveys of fish in the Yangtze River mainstream.
- (4)
- Inapplicability of 12S primer to freshwater fish: The primers that we used may not be suitable for the identification of fish in the mainstream of the Yangtze River, which could explain the small number of identification results. Many studies have used other primers, such as the mitochondrial cytochrome c oxidase subunit I (COI) sequence and the 16S primer for the fish amplification [56]. In future studies, different primers can be designed to explore primers that are more suitable for Yangtze River fish. In the non-closed fishing season, fish body muscle tissue can be used for primer design, which will be our next research direction.
4.2. Seasonal Variation between Spring and Autumn
4.3. Relationship between Fish Assemblage and Environmental Factors
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Number | Station | Longitude | Latitude | Spring | Autumn | ||
---|---|---|---|---|---|---|---|
Sampling | Time | Sampling | Time | ||||
1 | Panzhihua | 101.70 | 26.56 | C19SE01 | 12 April 2019 | C19AE01 | 13 October 2019 |
2 | Yibin | 104.66 | 28.77 | C19SE02 | 14 April 2019 | C19AE02 | 15 October 2019 |
3 | Chongqing | 106.57 | 29.55 | C19AE03 | 15 October 2019 | ||
4 | Wanzhou | 108.43 | 30.76 | C19SE03 | 15 April 2019 | C19AE04 | 16 October 2019 |
5 | Badong | 110.34 | 31.05 | C19SE04 | 16 April 2019 | C19AE05 | 17 October 2019 |
6 | Yichang | 111.40 | 30.57 | C19SE05 | 17 April 2019 | C19AE06 | 18 October 2019 |
7 | Yuyang | 113.12 | 29.40 | C19SE06 | 17 April 2019 | C19AE07 | 18 October 2019 |
8 | Wuhan | 114.30 | 30.55 | C19SE07 | 18 April 2019 | C19AE08 | 19 October 2019 |
9 | Jiujiang | 116.03 | 29.75 | C19SE08 | 19 April 2019 | C19AE09 | 20 October 2019 |
10 | Datong | 117.74 | 30.86 | C19SE09 | 20 April 2019 | C19AE10 | 21 October 2019 |
11 | Nanjing | 118.75 | 32.12 | C19SE10 | 20 April 2019 | C19AE11 | 22 October 2019 |
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Jia, H.; Zhang, H.; Xian, W. Fish Diversity Monitored by Environmental DNA in the Yangtze River Mainstream. Fishes 2022, 7, 1. https://doi.org/10.3390/fishes7010001
Jia H, Zhang H, Xian W. Fish Diversity Monitored by Environmental DNA in the Yangtze River Mainstream. Fishes. 2022; 7(1):1. https://doi.org/10.3390/fishes7010001
Chicago/Turabian StyleJia, Hui, Hui Zhang, and Weiwei Xian. 2022. "Fish Diversity Monitored by Environmental DNA in the Yangtze River Mainstream" Fishes 7, no. 1: 1. https://doi.org/10.3390/fishes7010001