Using eDNA metabarcoding to establish targets for freshwater fish composition following river restoration

Ito, Gen; Yamauchi, Hiroshi; Shigeyoshi, Miwa; Ashino, Kousuke; Yonashiro, Chie; Asami, Maki; Goto, Yuko; Duda, Jeffrey J.; Yamanaka, Hiroki

doi:10.1016/j.gecco.2023.e02448

Cited by 3 publications

(1 citation statement)

References 35 publications

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“…In recent years, however, environmental DNA (eDNA: DNA released by macroorganisms into the environment) metabarcoding techniques have increasingly been used in freshwater aquatic environments for biodiversity monitoring and biological surveys of the presence of fishes or other animals (reviewed by [31,32]). This is also true in Japan where studies have recently been conducted on the diversity and distribution of fishes in estuarine or coastal waters [33][34][35][36], in specific rivers or regions [37,38], or to document seasonal changes in species composition [39]. Specific species have also been studied for different life stages, such as salmonids [40,41] and the Japanese eel (Anguilla japonica) [6,34,[42][43][44][45].…”

Section: Introductionmentioning

confidence: 99%

Environmental DNA Characterization of the Fish Species Composition in the Mukawa River and Adjacent Habitats

Ahn,

Miller

2024

Fishes

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The diverse freshwater fish fauna of the Japanese archipelago is distributed among four main island landmasses, which include Hokkaido in the north, with many diadromous species. One relatively well-preserved river drainage along the southern coast of Central Hokkaido is the Mukawa River. Fish fauna surveys in the Mukawa River were mostly in downstream areas and the fish diversity is not well-documented among the upper, lower river, and coastal environments. Fish communities in the river, estuary, and sea were sampled using eDNA analysis to evaluate upstream and downstream species detections, and tidal and spatial detection variation near the river mouth. The number of species was higher at the river mouth and nearshore sites compared to the river and offshore. Fish detections reflected life history categories (freshwater resident, diadromous, brackish, or marine) and the environments. Similarity analysis showed that fish species compositions were divided into (1) upstream and midstream, (2) downstream and river mouth, (3) adjacent shore, and (4) offshore. Salmonid, cyprinid, loach, and sculpin species were detected in the river, compared to a mixture of species downstream and along the coast. This rapid assessment type study demonstrated that eDNA survey methodology would be effective for multiple river comparative surveys, seasonality studies, or evaluating possible effects of cross-river weirs or dams.

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Section: Introductionmentioning

confidence: 99%

Environmental DNA Characterization of the Fish Species Composition in the Mukawa River and Adjacent Habitats

Ahn,

Miller

2024

Fishes

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eDNA monitoring detects new outbreak wave of corallivorous seastar (Acanthaster cf. solaris) at Lizard Island, Great Barrier Reef

Uthicke,

Doyle,

Gomez Cabrera

et al. 2024

Coral Reefs

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Crown-of-thorns seastar (CoTS, Acanthaster cf. solaris) outbreaks remain a significant cause of coral loss on the Great Barrier Reef (GBR) and across the West-Pacific Ocean. Previous outbreaks on the GBR have only been discovered once fully established, which constrains opportunities for effective control. Early detection of outbreaks would provide an important opportunity for early intervention and increase understanding of outbreak cause(s). Here, we assess the utility of environmental DNA (eDNA) monitoring to detect the initiation of a population outbreak at Lizard Island over five years (2019–2023), compared with density estimates obtained using Scooter-Assisted Large Area Diver-based (SALAD) surveys. At each of the five eDNA sampling sites, 30 replicate samples were collected annually and analysed with CoTS-specific primer sets and digital droplet PCR. Both methods detected distinct increases in CoTS densities from 2020/21 onwards, indicating the start of a new population outbreak. A large part of the observed variation in eDNA (expressed as the percentage of positive samples) was explained by changes in recorded CoTS density, confirming that eDNA data provide a quantitative estimate for adult CoTS abundance. SALAD surveys and eDNA are new and complementary monitoring methods that facilitate early detection of CoTS outbreaks, which will enable more effective management intervention.

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Fish communities and diversity in river ecosystems on the Qinghai-Tibet Plateau revealed by environmental DNA (eDNA) method

Gao,

Qu,

Ren

et al. 2023

Ecological Indicators

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Using eDNA metabarcoding to establish targets for freshwater fish composition following river restoration

Cited by 3 publications

References 35 publications

Environmental DNA Characterization of the Fish Species Composition in the Mukawa River and Adjacent Habitats

Environmental DNA Characterization of the Fish Species Composition in the Mukawa River and Adjacent Habitats

eDNA monitoring detects new outbreak wave of corallivorous seastar (Acanthaster cf. solaris) at Lizard Island, Great Barrier Reef

Fish communities and diversity in river ecosystems on the Qinghai-Tibet Plateau revealed by environmental DNA (eDNA) method

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