A comparison of seasonal composition and structure of fish community between environmental DNA technology and gillnetting in the Pearl River Estuary, China

Li, Zhuoying; Jiang, Peiwen; Wang, Longxin; Liu, Li; Li, Min; Zou, Keshu

doi:10.1016/j.ecolind.2023.109915

Cited by 13 publications

(6 citation statements)

References 96 publications

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“…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.…”

Section: Conventional Methods Of Catching Fishmentioning

confidence: 99%

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

AMBENG,

IQRAM,

LITAAY

et al. 2024

Biodiversitas

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Abstract. Ambeng, Iqram M, Litaay M, Hasyim Z, Moka WJC, Tinungki GM. 2024. Combining eDNA metabarcoding and conventional method in rapid screening of fish diversity in Maros-Pangkep Global Geopark, South Sulawesi, Indonesia. Biodiversitas 25: 819-828. A newly designated geopark by UNESCO, Maros-Pangkep Global Geopark, South Sulawesi, Indonesia owns great geodiversity, exceptional cultural heritage, and high biodiversity. However, the global biodiversity crisis that has hit the earth might also occur in Maros-Pangkep river systems, potentially threatening endemic freshwater fish and all other biota. It has been reported that there is high pressure on the environment along the watershed in the Maros-Pangkep rivers, including a high sedimentation rate downstream, which is linked to extreme erosion upstream and could eventually affect fish populations such as endemic ones. This should prompt a call for the authorities to build a strategy for monitoring and documenting aquatic biota such as fish to preserve biodiversity. Environmental DNA (eDNA) could be considered a method for monitoring fish species based on the DNA traces they shed in the water. Hence, this study aims to use eDNA to survey fish biodiversity in several rivers in the Maros-Pangkep Global Geopark and compare the result against the traditional gillnet method. The results showed that using two methods, 29 fish species in 19 families and 15 orders were obtained from the three rivers. Despite the majority of detected species, 25 species, as the result of using eDNA, 4 species were only detected using a traditional method which eDNA failed to identify. Among those species, several endemic and non-native species were successfully identified by either one or both methods. This could eventually be a suggestion for responsible authorities in biodiversity conservation to combine both approaches to monitor and conserve local biodiversity.

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Section: Conventional Methods Of Catching Fishmentioning

confidence: 99%

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

AMBENG,

IQRAM,

LITAAY

et al. 2024

Biodiversitas

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“…Species lists obtained from the pipeline have yet to be verified; each species on the list was checked against originally aligned sequences by the NCBI Basic Local Alignment Search Tool [67]. Thereafter, only ZOTUs with a number of reads > 0.05% (i.e., ≥16 reads) were used for future analyses [6,23,44]. Any species that failed to meet these requirements were excluded from the fish list, as failure indicates a highly suspicious sign of contamination.…”

Section: Bioinformatic Analysismentioning

confidence: 99%

“…Spearman's correlation was applied to find the correlations between environmental factors and fish communities for each season [73]. The Mantel tests combined with Spearman correlation matrices were performed using the 'linkET' package (manteltest function) in R software to determine the correlations between environmental factors and fish community composition [23,74]. To compare the fish species detected by eDNA in this study with those identified in previous studies in the Seto Inland Sea and other coastal areas, a comprehensive checklist of the fish species found in the Seto Inland Sea was compiled.…”

Section: Multivariate Analysismentioning

confidence: 99%

“…Fish spcies detect by eDNA on Ikuchijima vs previous studies. References [7,8,14,15,23,44,53,100] are cited in the supplementary materials.…”

Section: Supplementary Materialsmentioning

confidence: 99%

“…For example, seasonal changes in physical and biogeochemical factors, such as temperature and salinity, as well as nutrient loadings can significantly impact the abundance and composition of fish communities [20,21]. During the rainy season, high freshwater discharge can modify environmental conditions, leading to seasonal fluctuations in temperature, salinity, and nutrient loadings [22][23][24]. Variations in nutrient loadings influence the production and biomass of phytoplankton, impacting competition for resources and predator-prey dynamics [24][25][26].…”

Section: Introductionmentioning

confidence: 99%

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Evaluation of the Effects of Environmental Factors on Seasonal Variations in Fish Diversity on a Coastal Island in Western Japan

Nhat,

Saito,

Hamada

et al. 2024

Environments

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Coastal habitats are crucial for supporting ecological processes and serve as vital ecosystems for diverse fish species, providing essential functions such as feeding, nursery provision, and reproductive habitats. Fish communities are ecologically important components of coastal ecosystems and are affected by multiple environmental factors. Despite their importance, determining the effects of environmental factors on seasonal variations in fish species diversity and community dynamics remains a challenge. The advent of environmental DNA (eDNA) technology, an environmentally conscious approach, has resulted in considerable advancements in recent years and has been progressively adopted for marine fish population monitoring. Here, we used environmental DNA metabarcoding to study seasonal variations in fish community structure on a coastal island, and we assessed the effects of environmental factors in structuring these communities. Our findings revealed a rich diversity of 72 fish species across 40 families and 23 orders in the seawater surrounding an island of the Seto Inland Sea (SIS), Western Japan. Notably, the composition of fish communities varied significantly between seasons, with seawater temperature, salinity, and dissolved inorganic phosphorus (DIP) concentration identified as important factors correlated with fish communities’ structures. In conclusion, our study provides useful information of fish diversity, and we suggest that eDNA is a valuable technique for monitoring fish diversity in coastal areas. These findings are crucial for ecological studies and the environmental monitoring of oceanic coastal environments.

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Bottom Trawling and Multi‐Marker eDNA Metabarcoding Surveys Reveal Highly Diverse Vertebrate and Crustacean Communities: A Case Study in an Urbanized Subtropical Estuary

Ip,

Loke,

Yiu

et al. 2024

Environmental DNA

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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 labor‐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 analyzed 16 bottom trawl samples and the eDNA from 32 two‐liter 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 be associated 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.

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A comparison of seasonal composition and structure of fish community between environmental DNA technology and gillnetting in the Pearl River Estuary, China

Cited by 13 publications

References 96 publications

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

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

Evaluation of the Effects of Environmental Factors on Seasonal Variations in Fish Diversity on a Coastal Island in Western Japan

Bottom Trawling and Multi‐Marker eDNA Metabarcoding Surveys Reveal Highly Diverse Vertebrate and Crustacean Communities: A Case Study in an Urbanized Subtropical Estuary

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