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

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-metric 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 number of fish OTUs (P≤1.1×10^-3); 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 two survey methods (P=0.049 7, r_Pearson=0.381, R²=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 dominant 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 Ctenotrypauchen chinensis showed a linear correlation between sequence abundance and individual counts/weight, while the r_Pearson values 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 demonstrates 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 cannot replace each other but rather have a complementary and cross-validating relationship. This study provides a basis for understanding the advantages and disadvantages of eDNA metabarcoding and for the rational use of different survey methods.