Comparison of environmental DNA metabarcoding and bottom trawling for detecting seasonal fish communities and habitat preference in a highly disturbed estuary

Jiang, Peiwen; Zhang, Shuai; Xu, Shannan; Xiong, Pengli; Chen, Zuozhi; Li, Min

doi:10.1016/j.ecolind.2022.109754

Cited by 27 publications

(7 citation statements)

References 93 publications

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“…Detection of those taxa and a slime eel indicate that MiFish primers (Miya et al., 2015) amplify a region conserved across many gnathostomes. We show that prominent species, of high interest to conservation efforts (including whales and bottlenose dolphins; e.g., Currey et al., 2009; Zhang et al., 2023) can be detected with eDNA in Te Wāhipounamu (Figure S6), and reassuringly we observed bottlenose dolphins during field work.…”

Section: Discussionsupporting

confidence: 75%

Comparison of traditional and molecular surveys of fish biodiversity in southern Te Wāhipounamu/Fiordland (Aotearoa/New Zealand)

Czechowski,

de Lange,

Heldsinger

et al. 2024

Environmental DNA

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Effective management of biodiversity requires regular surveillance of multiple species. Analysis of environmental DNA (eDNA) by metabarcoding holds promise to achieve this relatively easily. However, taxonomy‐focused eDNA surveys need suitable molecular reference data, which are often lacking, particularly at the species level and for remote locations. To evaluate the comparability of environmental DNA surveys and traditional surveys in a real‐life case study in a marine area of high conservation value, we conducted a biodiversity survey of the fish in remote and pristine Te Wāhipounamu/Fiordland (Aotearoa/New Zealand), incorporating multiple data sources. We compared eDNA‐derived species identifications against Baited Remote Underwater Video (BRUV) data collected at the same time and locations as eDNA. We also cross‐referenced both eDNA and BRUV data against literature and the Ocean Biodiversity Information System (OBIS), with literature and OBIS data representing a summary of multiple traditional surveying approaches. In total, we found 116 fish species in our study area. Environmental DNA detected 43 species; however, only three of those species overlap with species known from the literature, OBIS, or our BRUV analyses. A total of 61 fish species were known from the region from the literature, while OBIS listed 28 species, and our BRUV analyses picked up 26 species. BRUV data coincided more strongly than eDNA data with literature and OBIS data. Twenty of the 26 species detected by BRUV were known from literature and OBIS. We argue that limitated DNA reference databases are the main cause of this discrepancy, and our results indicate that eDNA of rare and endangered species can be detected if matching reference data were available. Environmental DNA analyses can only identify species present among reference data and with relaxed taxonomic assignment parameters may converge on relatives of detected species if the actually existing species themselves are missing among reference data. However, the high number of species detected by our eDNA analyses confirms that eDNA could be a powerful tool for biodiversity surveys if suitable investments in local reference databases were made.

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Section: Discussionsupporting

confidence: 75%

Comparison of traditional and molecular surveys of fish biodiversity in southern Te Wāhipounamu/Fiordland (Aotearoa/New Zealand)

Czechowski,

de Lange,

Heldsinger

et al. 2024

Environmental DNA

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“…After sample arrival, they were maintained at 23 • C in a recirculating system of 50 L aquaria filled with aerated seawater. An acclimation temperature of 23 • C was selected because it is probably appropriate for both species, considering that it falls into a cope of normal temperatures fluctuation (3.0-26.7 • C and 16.9-29.9 • C) (Table 1) in natural habitat for both species, and fish assemblage or spawning event occur when this ambient water temperature arrives (e.g., O. rebecca assembles in Zhongshan coastal waters when the temperature is 24.7 • C [28] and O. lacepedii spawns in Tianjin coastal water when the temperature is 21.5-25.5 • C [29]). The eel gobies were fed with small live shrimp Penaeus vannamei twice a day and acclimated for two weeks before experiments to allow the fish to recover from the adverse effects of transportation.…”

Section: Sample Collectionmentioning

confidence: 99%

Comparative Transcriptome Analyses Provide New Insights into the Evolution of Divergent Thermal Resistance in Two Eel Gobies

Liu,

Liu

et al. 2023

CIMB

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Adaptation to thermal conditions in tidal mudflats always involves tolerating frequent fluctuations and often extreme environmental temperatures. Regulation of gene expression plays a fundamental role in the evolution of these thermal adaptations. To identify the key gene regulatory networks associated with the thermal adaptation, we investigated the capability of cold tolerance, as well as the transcriptomic changes under cold stress in two mudflat inhabitants (Odontamblyopus lacepedii and O. rebecca) with contrasting latitude affinity. Our results revealed a remarkable divergent capacity of cold tolerance (CTmin: 0.61 °C vs. 9.57 °C) between the two gobies. Analysis of transcriptomic changes under cold stress unveiled 193 differentially expressed genes exhibiting similar expression profiles across all tissues and species, including several classic metabolic and circadian rhythm molecules such as ACOD and CIART that may represent the core cold response machinery in eel gobies. Meanwhile, some genes show a unique expression spectrum in the more cold-tolerant O. lacepedii suggesting their roles in the enhanced cold tolerance and hence the extreme thermal adaptations. In addition, a weighted gene co-expression network analysis (WGCNA) revealed a subset of metabolic hub genes including MYH11 and LIPT2 showing distinct down-regulation in O. lacepedii when exposed to cold stress which highlights the role of reduced energy consumption in the enhanced cold tolerance of eel gobies. These findings not only provide new insights into how mudflat teleosts could cope with cold stress and their potential evolutionary strategies for adapting to their thermal environment, but also have important implications for sound management and conservation of their fishery resources in a scenario of global climate warming in the marine realm.

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“…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%

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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Comparison of environmental DNA metabarcoding and bottom trawling for detecting seasonal fish communities and habitat preference in a highly disturbed estuary

Cited by 27 publications

References 93 publications

Comparison of traditional and molecular surveys of fish biodiversity in southern Te Wāhipounamu/Fiordland (Aotearoa/New Zealand)

Comparison of traditional and molecular surveys of fish biodiversity in southern Te Wāhipounamu/Fiordland (Aotearoa/New Zealand)

Comparative Transcriptome Analyses Provide New Insights into the Evolution of Divergent Thermal Resistance in Two Eel Gobies

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

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