Page 165 - 《水产学报》2026年第04期

4 期 水 产 学 报 50 卷

A comparison of fish diversity results based on eDNA metabarcoding and
trawl net: a case study of the southern coastal waters of Zhejiang Province

1
3
2
2
2
CHEN Zhi , JIANG Rijin , LU Zhanhui , ZHANG Yazhou , LIU Shanshan ,
2
GAO Tianxiang , LI Pengfei 2*
(1. Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, Sanya 572022, China;
2. Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China;
3. BGI Research, Shenzhen 518083, China)
Abstract: To compare the similarities and differences in fish diversity between eDNA metabarcoding and trawl net, this study,
taking the southern coastal waters of Zhejiang Province as a case area, analyzed the fish composition, species dominance, and
community diversity index of the two survey methods using bioinformatics, traditional morphological identification, non-met-
ric multidimensional scaling analysis, significance test of differences and linear regression analysis. The results are as follows:
① A considerable number (19.92%) of non-indigenous fish OTUs (e.g., freshwater fish, deep-sea fish, tropical coral reef fish)
were detected in the high-throughput sequencing results; although the sampling water layer (surface, mid-depth, bottom) did not
affect the number of fish OTUs detected by eDNA (P≥0.073), it did influence the composition of fish OTUs (stress=0.138,
R=0.117, P=0.001); increasing sampling density (number of replicates, number of water layers) significantly increased the num-
-3
ber of fish OTUs (P≤1.1×10 ); a significant proportion (24.402%) of fish OTUs in this area were in a low annotation state, and
some fish sequences exhibited interspecific identity or intraspecific variation. ② The number of fish species detected by eDNA
was much higher than that by trawl net (152 species vs. 75 species), and there was a significant linear correlation between the
2
two survey methods (P=0.049 7, r Pearson =0.381, R =0.153). ③ When all fish species were analyzed, the two survey methods
showed a significant difference in species dominance (P=0.034); for many shared fish species and dominant/keystone domin-
ant species, such as Engraulis japonicus and Nibea albiflora, the species dominance differed by 1-2 orders of magnitude
between the two survey methods. ④ Among the 12 frequently occurring fish species, only Harpadon nehereus and Ctenotryp-
auchen chinensis showed a linear correlation between sequence abundance and individual counts/weight, while the r Pearson val-
ues in the fitted models for the remaining species were low or even negative. ⑤ The community diversity index measured by
the two survey methods differed considerably, and their linear correlation was also very low (P≥0.087). This study demon-
strates that: ① eDNA has considerable uncertainty. ② Except for some indicators, species, or stations, it is difficult to model
and predict the corresponding values of one survey method based on the results of the other. ③ The two survey methods can-
not replace each other but rather have a complementary and cross-validating relationship. This study provides a basis for under-
standing the advantages and disadvantages of eDNA metabarcoding and for the rational use of different survey methods.
Key words: fish diversity; eDNA; metabarcoding; trawl net; the southern coastal waters of Zhejiang Province

Corresponding author: LI Pengfei. E-mail: pengfei5116@163.com
Funding projects: National Key R & D Program of China (2024YFD2400401)

https://www.china-fishery.cn 中国水产学会主办 sponsored by China Society of Fisheries
16