Using Optimal Environmental DNA Method to Improve the Fish Diversity Survey—From Laboratory to Aquatic Life Reserve

Abstract

Conserving aquatic ecosystems requires efficient tools to accurately assess the biodiversity of aquatic species. However, existing knowledge is insufficient in terms of the reliability and the comparability of methods measuring fish diversity. Environmental DNA (eDNA), as a promising method, was used to detect fish taxa in this study. We optimized the eDNA method in the laboratory, and applied the optimal eDNA method to survey fish diversity in a natural aquatic life reserve. We simulated necessary steps of the eDNA method in the lab to increase the confidence of the field survey. Specifically, we compared different eDNA sampling, extraction, and sequencing strategies for accurately capturing fish species of the target area. We found that 1L water samples were sufficient for sampling eDNA information of the majority taxa. The filtration was more effective than the centrifugal precipitation for the eDNA extraction. The cloning sequencing was better than the high-throughput sequencing. The field survey showed that the Shannon–Wiener diversity index of fish taxa was the highest in Huairou Reservoir. The diversity index also showed seasonal changes. The accuracy rate of detecting fish taxa was positively correlated with the eDNA concentration. This study provides a scientific reference for an application of the eDNA method in terms of surveying and estimating the biodiversity of aquatic species.

Maximizing sampling efficiency to detect differences in fish community composition using environmental DNA metabarcoding in subarctic fjords

“…Many studies have now confirmed the strengths of eDNA metabarcoding for local detection of species and, thus community composition inference (Hansen et al, 2018). Similarly to analogous studies (Cilleros et al, 2019; Fraija‐Fernández et al, 2020; Jeunen, Knapp, et al, 2019; Jo et al, 2019; Larson et al, 2022; Li et al, 2021; Turon et al, 2022), our eDNA metabarcoding study confirm that fish community composition and biodiversity patterns can be reliably estimated using this approach.…”

Application of E-Dna for Detection Faunal Diversity in a Lotic Habitat: A Review

“…These kits are less expensive, easy to use and have efficient PCR amplification and also they do not contain any harmful chemical. Hence, they are regarded as best option for extracting e-DNA (Li et al, 2021,). It is evidently known that in both lentic and lotic habitats sediments present in water interfere with the detection of e-DNA from water samples (Goldberg et al, 2011).…”

Fishing eDNA in One of the World’s Largest Rivers: A Case Study of Cross-Sectional and Depth Profile Sampling in the Yangtze

“…Increasing the sampling effort will increase the amount of biodiversity detected, and a threshold must be determined for an optimal sampling volume of eDNA . Up until now, sampling efforts of eDNA have profoundly varied between studies, ranging from 15 mL to 60 L, , which hinders the comparability of biodiversity estimates. A recent paper proposed adjusting the sampling effort to the size or volume of the aquatic ecosystems with a spatial-explicit river flow model .…”