Combined Use of eDNA Metabarcoding and Bottom Trawling for the Assessment of Fish Biodiversity in the Zhoushan Sea

Abstract

With the increase in fishing intensity and the intensification of marine pollution, the fishery resources in the Zhoushan Sea are seriously degraded, and the difficulty of censusing fish diversity hampers effective management in marine fishes. Environmental DNA metabarcoding and bottom trawl methods were used to determine the ability of the methods to distinguish fish assemblages in the Zhoushan Sea. The species composition and diversity of the Zhoushan Sea were assessed via high-throughput sequencing analysis of eDNA coupled with bottom trawl fishery survey data, after which the two methods were compared. eDNA screening identified 38.2% more fish species than bottom trawls. Combining these two methods, 33 orders, 65 families, and 130 species of fishes were identified. Perciformes and Clupeiformes, the most abundant orders in the catch, represented 31.5 and 10.0% of the total fish abundance, respectively. The results of ANOSIM and redundancy analyses indicated that the fish community structure varied significantly between summer and winter, however depth and temperature being the main environmental factors influencing fish distribution. The biodiversity index was higher in summer than in winter. Thus, our work provides more detailed seasonal data on biodiversity in the Zhoushan Sea, which is essential for the long-term management and conservation of coastal biodiversity. Compared with traditional survey methods, eDNA determination is highly sensitive, accurate, cost-efficient, and suitable for fish diversity studies in relevant sea areas. Although this approach cannot completely replace traditional methods, our findings demonstrate that it provides a reliable complementary method for assessing fish diversity in marine ecosystems.

Novel assay for endangered Hong Kong grouper (Epinephelus akaara) to assess eDNA shedding, decay, and population status

“…Previous studies had detected E. akaara eDNA throughout its distribution range with eDNA metabarcoding, including East China Sea, Yellow Sea and the Sea of Japan (Ahn et al, 2020; Kenji et al, 2022; Kim, 2020; Lin et al, 2022). However, no eDNA metabarcoding study in the South China Sea ever recorded the presence of E. akaara , especially in Guangdong Province of China where E. akaara fishery was once prevalent (Cheang et al, 2020; Liu & Sadovy De Mitcheson, 2009; Zhang et al, 2024; Zhou et al, 2022; Chung et al, 2024). Hence, we suggest E. akaara in Hong Kong and South China Sea region as a whole could be currently suffering the worst population devastation compared to other populations across its distribution range.…”

“…akaara, especially in Guangdong Province of China where E. akaara fishery was once prevalent (Cheang et al, 2020;Liu & Sadovy De Mitcheson, 2009;Zhang et al, 2024;Zhou et al, 2022;Chung et al, 2024). Hence, we suggest E. akaara in Hong Kong and South China Sea region as a whole could be currently suffering the worst population devastation compared to other populations across its distribution range.…”

An automated workflow to assess completeness and curate GenBank for environmental DNA metabarcoding: The marine fish assemblage as case study

“…Studies using marine water eDNA metabarcoding to assess fish diversity based on 12S rRNA perform taxonomic assignment in a variety of ways. Some authors assign taxonomy by directly querying GenBank (e.g., Lamy et al, 2021; Sato et al, 2021; Zhou et al, 2022), which might result in erroneous assignments due to the presence of problematic records (Li et al, 2018). Others rely on filtered versions of GenBank containing only the target barcode of the sequences from the species of interest.…”

“…However, because eDNA extracted from water samples contains traces of many abundant organisms other than fish, the use of COI metazoan universal primers results in over-amplification of non-target taxa (Collins et al, 2019;Fraija-Fernández et al, 2020), and fish-specific primers have been developed, mostly based on the 12S rRNA gene, such as those amplifying the teleo (Valentini et al, 2016) or MiFish (Miya et al, 2015) regions Studies using marine water eDNA metabarcoding to assess fish diversity based on 12S rRNA perform taxonomic assignment in a variety of ways. Some authors assign taxonomy by directly querying GenBank (e.g., Lamy et al, 2021;Sato et al, 2021;Zhou et al, 2022), which might result in erroneous assignments due to the presence of problematic records (Li et al, 2018). Others rely on filtered versions of GenBank containing only the target barcode of the sequences from the species of interest.…”

An automated workflow to assess completeness and curate GenBank for eDNA metabarcoding: the marine fish assemblage as case study

“…Some authors assign taxonomy by directly querying GenBank (e.g. Lamy, Pitz et al (2021); Sato, Inoue et al (2021); Zhou, Fan et al (2022)). Others rely on filtered versions of GenBank containing only the target barcode of the sequences from the species of interest.…”