Similarities and Differences in Fish Community Composition Accessed by Electrofishing, Gill Netting, Seining, Trawling, and Water eDNA Metabarcoding in Temperate Reservoirs

Abstract

It is difficult to understand the composition and diversity of biological communities in complex and heterogeneous environments using traditional sampling methods. Recently, developments in environmental DNA metabarcoding have emerged as a powerful, non-invasive method for comprehensive community characterization and biodiversity monitoring in different types of aquatic ecosystems. In this study, water eDNA targeting fish (wf-eDNA) and four traditional fish sampling methods (electrofishing, gill netting, seining, trawling) were compared to evaluate the reliability and efficiency of wf-eDNA (vertebrate mitochondrial 12S ribosomal RNA (rRNA) as an alternative approach to assess the diversity and composition of freshwater fish communities. The results of wf-eDNA showed a consistency between the traditional sampling methods regarding species detection. However, some fish species detected using wf-eDNA assay were not detected using traditional sampling methods and vice versa. Comparison of wf-eDNA and traditional sampling methods revealed spatial homogeneity in fish community composition in all reservoirs. Ordination analysis showed that the wf-eDNA approach covers all traditional sampling methods and occupies an intermediate position. In addition, based on the Shannon diversity index, we found that in one reservoir the wf-eDNA method yielded similar fish community diversity to traditional sampling methods. However, in other reservoirs, the calculated Shannon diversity index of the wf-eDNA method was significantly higher than traditional sampling methods. In general, significant positive correlations were found between the wf-eDNA method and almost all traditional sampling methods. We conclude that wf-eDNA seems to be a reliable and complementary approach for biomonitoring and ecosystem management of freshwater ichthyofauna.

Spatial fish distribution in autumn in a shallow mesotrophic lake, assessed by hydroacoustic surveys, trawling, and beach seining

“…Gillnets can be used to compare the species composition and relative density of fish in different water bodies, but in view of the restricted migration times of fish, which influence the probability of being caught (Prchalová et al, 2010), gillnets are not a suitable method for investigating diurnal patterns in fish distribution. As a combination of several techniques is often required to obtain a true picture of the fish community (Golpour et al, 2022; Kubečka et al, 2009), the intercalibration of different sampling techniques should not be disregarded in the future.…”

Combining eDNA metabarcoding and conventional method in rapid screening of fish diversity in Maros-Pangkep Global Geopark, South Sulawesi, Indonesia

“…It is such a way to compare the effectiveness of eDNA to the conventional practice of identifying fish. Some studies have also compared the effectiveness of eDNA in identifying fish diversity against gillnetting (Golpour et al 2022;Li et al 2023). The gillnet was deployed at exactly the same point where the water was taken.…”

“…It is important to note that traditional methods may still have advantages in certain occasions which could basically complement the weakness of eDNA. For instance, a study comparing eDNA and traditional sampling methods observed that some species such as Pseudorasbora parva, Carassius carassius and Lota lota were only detected using traditional sampling gears, while eDNA unsuccessfully detected the presence of these fishes (Golpour et al 2022). Another study reported that some fish species have been detected using gill nets but not with eDNA, including rare and invasive fishes such as non-native species like…”

“…eDNA as a non-destructive method has widely been used in fish biodiversity surveys, demonstrating its effectiveness in detecting and monitoring fish in freshwater ecosystems He et al 2022;Shen et al 2022). Several studies revealed that eDNA outperforms established conventional methods in detecting both rare and common freshwater fish species, yet gill net could still offer more insights when combined with eDNA to obtain a complete overview of species composition (Piggott et al 2021;Golpour et al 2022). Thus, this study aims to use eDNA in combination with gill net to rapidly screen fish diversity in several rivers in the Maros-Pangkep Global Geopark in an attempt to examine a potential mean of monitoring aquatic biota in the area.…”

eDNA metabarcoding as a means to track distributions of different fish species in a protected area

“…Development of environmental DNA (eDNA) methods and the related bioinformatics analyses has provided researchers with the ability to explore the biodiversity of aquatic communities via eDNA metabarcoding or to detect individual species via quantitative PCR (qPCR) (Cantera et al., 2022; Lacoursière‐Roussel et al., 2016; Laporte et al., 2021; Pilliod et al., 2013; Yang et al., 2021). These approaches, especially eDNA metabarcoding—the sequencing and characterization of all DNA of a given taxonomic group in an environmental sample—are now routinely applied in biodiversity and ecological studies across all types of ecosystems (Boivin‐Delisle et al., 2021; Closek et al., 2019; Czeglédi et al., 2021; Evans et al., 2016; Gamage et al., 2020; García Machado et al., 2022; Golpour et al., 2022; Harper et al., 2019; Hashemzadeh Segherloo, Tabatabaei, Abdolahi‐Mousavi, et al., 2022; McColl‐Gausden et al., 2021; Mena et al., 2021; Newton et al., 2023; Ritter et al., 2022; Roger et al., 2022; Sales et al., 2020; Yonezawa et al., 2020; Zhang et al., 2023). Among its advantages, eDNA is very sensitive, nondestructive, and noninvasive compared to conventional methods.…”