DOI: 10.5061/dryad.ffbg79d4j
title: Data from: Bottom trawling and multi-marker eDNA metabarcoding surveys reveal highly diverse vertebrate and crustacean communities: A case study in an urbanized subtropical estuary

description: Estuarine habitats serve as critical feeding and nursery grounds for many
 aquatic species and support fisheries. However, monitoring these complex
 ecosystems using conventional trawling methods is destructive, costly, and
 labour-intensive. This study compared trawling and a multi-marker
 environmental DNA (eDNA) metabarcoding approach to monitor marine
 vertebrate and crustacean communities in an estuarine environment in
 subtropical Hong Kong. We analysed 16 bottom trawl samples and the eDNA
 from 32 two-litre water samples using primer sets specific to fishes and
 mammals (MiFish-U, 12S-V5, and Berry-Fish) and decapod crustaceans
 (MiDeca). We found that the eDNA approach detected more pelagic and
 demersal fishes (237 vs. 106 in trawling) and elasmobranchs (6 vs. 3) than
 trawling. The eDNA approach was also more effective than trawling in
 detecting threatened vertebrates (16 vs. 4), including the Indo-Pacific
 Finless Porpoise and the critically endangered Large Yellow Croaker. Among
 the detected fish at species-level, 70 species were detected by both
 approaches, 32 species were detected by trawling only, and 142 species
 were detected by the eDNA approach only. Regarding crustaceans, the eDNA
 approach detected slightly fewer decapods (61 vs. 77) and stomatopods (5
 vs. 8) than trawl surveys. However, the eDNA approach could be enhanced
 through the development of suitable decapod-specific primers and the
 expansion of the local reference database. In addition, multivariate
 analyses of the eDNA data revealed spatial patterns of fish and crustacean
 assemblages that might associate with sediment loading, oxygen and
 nutrient levels. Furthermore, there was a positive correlation between
 eDNA read counts and trawl catch, but their correlation coefficient was
 low. We conclude that eDNA metabarcoding can provide high-resolution
 detection of species, composition, and unravel community-environment
 relationships in estuarine ecosystems. Overall, integrating the
 non-destructive eDNA approach can complement the conventional trawling
 method for better-informed sustainable fishery management and
 conservation.
description: We utilized the 12S-V5 (Riaz et al., 2011), MiFish-U (Miya et al., 2015),
 and Berry-Fish (Berry et al., 2017) primers to target fish and marine
 mammals, along with the MiDeca primer set for decapod crustaceans (Komai
 et al., 2019). This dataset comprises raw Illumina data from four eDNA
 assays conducted on 32 water samples collected from southern Hong Kong
 waters, specifically from the Central Inner (CI), Central Outer (CO),
 Southern (S), and Southwestern (SW) regions (see the map in
 "list_data.xlsx" or the published paper). The raw Illumina
 paired-end reads were demultiplexed and trimmed of primers using Cutadapt
 v4.4. The dataset consists solely of clean Illumina reads, including 64
 fastq files each for MiFish-U, 12S-V5, Berry-Fish, and MiDeca (details in
 "list_data.xlsx"). For further information on downstream
 analysis, please refer to the article titled "Bottom Trawling and
 Multi-Marker eDNA Metabarcoding Surveys Reveal Highly Diverse Vertebrate
 and Crustacean Communities: A Case Study in an Urbanized Subtropical
 Estuary," published in *Environmental DNA*. Ip JCH, Loke H-X, Yiu
 Sam King F, Zhao M, Li Y, Lin Y, How C-M, Mo J, Yan M, Cheng J, et al.
 2024. Bottom Trawling and Multi-Marker eDNA Metabarcoding Surveys Reveal
 Highly Diverse Vertebrate and Crustacean Communities: A Case Study in an
 Urbanized Subtropical Estuary. Environmental DNA
 6:e70031. [https://doi.org/10.1002/edn3.70031](https://doi.org/10.1002/edn3.70031)