Development of species‐specific multiplex real‐time PCR assays for tracing the small pelagic fishes of North Pacific with environmental DNA

Wong, Marty Kwok‐Shing; Nobata, Shigenori; Ito, Shin‐ichi; Hyodo, Susumu

doi:10.1002/edn3.275

Cited by 4 publications

(6 citation statements)

References 52 publications

(55 reference statements)

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“…Extracted genomic DNA was used, instead of a gBlock, to establish the LOD and LOQ. As in some of the other recent studies [marine pelagic fish species in Wong et al (2022) and Esox lucius in Karlsson et al (2022)] which used genomic DNA for the LOD and LOQ calculations, we assumed no interference during PCR from the rest of the species’ genome, other genetic material or potential co‐extracted inhibitory compounds. The mesocosm experiments, as well as sites where A. cryptocallus had been captured previously and which served as positive controls, allowed further validation of the methodology.…”

Section: Discussionmentioning

confidence: 99%

Environmental DNA survey to detect an endemic cryptic fish, Anablepsoides cryptocallus, in tropical freshwater streams

Baudry

Mauvisseau

Arqué

et al. 2023

Aquatic Conservation

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Martinique island is a biodiversity hotspot in the Lesser Antilles that harbours many endemic species. One of these, Anablepsoides cryptocallus, also known as ‘Poisson gale’, is the only endemic freshwater fish of Martinique and a species with a poorly understood distribution range. In this study, an environmental DNA (eDNA) detection protocol was developed, validated, and optimized, targeting a short fragment (125 bp) of the A. cryptocallus COI mitochondrial gene, to investigate the presence of this species in Martinique. Fifty‐seven sites spread over 43 permanent rivers and two wetlands were sampled using both eDNA and conventional fishing (dip net capture). Presence was confirmed in 27 sites using eDNA detection, and in nine sites by dip net fishing. eDNA‐based detection of A. cryptocallus was effective and less time‐consuming than conventional fishing, making it a relevant tool for future studies throughout the island. Even though A. cryptocallus was found to be present in a significant number of sites, many sites previously known for this species were found to be negative, highlighting the need for continuous monitoring. There is now an urgent need to propose protection status for this endemic species to preserve its preferential habitats, as these are being increasingly threatened by human activities that are leading to habitat loss and fragmentation.

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Section: Discussionmentioning

confidence: 99%

Environmental DNA survey to detect an endemic cryptic fish, Anablepsoides cryptocallus, in tropical freshwater streams

Baudry

Mauvisseau

Arqué

et al. 2023

Aquatic Conservation

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show abstract

“…It is important to note that data for benthic species should be the most accurate due to their sedentary nature. On the other hand, while this method still presents challenges in accurately quantifying species abundance (Wong et al, 2022), it proves valuable for detecting a diverse set of species in our study area, including cryptobenthic species. Aglieri et al (2020) showed that eDNA monitoring may go beyond the identification of taxonomic entities and be applied to ecological studies of functional diversity, providing more robust results than sampling with fishing nets or baited underwater video.…”

Section: Discussionmentioning

confidence: 99%

Non‐extractive fish diversity assessment in Mediterranean rhodolith beds

Cabrito,

Maynou,

Simide

et al. 2024

Aquatic Conservation

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Rhodolith beds, recognized as biodiversity hotspots with high ecological and conservation importance, face local anthropic pressures, including trawl fishing. However, monitoring the diversity associated with this sensitive biogenic habitat in the deep waters of the Mediterranean Sea is challenging. Traditional monitoring methods, such as experimental trawling and trammel nets, are extractive and have sampling limitations in providing comprehensive diversity inventories. In this work, we explore three alternative techniques (still video cameras, environmental DNA [eDNA] and bioacoustics) to monitor fish assemblages associated with rhodolith beds in the Menorca Channel at 45–80 m depth. Ten sites were surveyed with eDNA, and 66 fish taxa were identified, including endangered sharks and cryptic species. The molecular operational taxonomic units (MOTUs) richness varied significantly according to habitat heterogeneity, being higher in homogeneous bottoms, and to exposure to trawling, with higher richness in non‐exposed areas. Bioacoustics, though limited by a reduced library of fish sounds, detected differences in sound richness between habitat types, and the highest abundance of sounds was recorded in the areas with the greatest small‐scale habitat heterogeneity. Underwater video revealed limitations in species detection but proved effective for characterizing small‐scale habitat types and heterogeneity. In summary, each technique provides valuable information at different spatial scales and levels of detail. To assess the feasibility of these techniques for long‐term monitoring, we explored their capabilities and limitations in terms of costs, survey logistics and data output.

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“…Quantitative multiplex PCR (e.g. Wong et al, 2022) can measure eDNA for several target species, small species, and even cryptic species, but is limited for quantitative assessment (e.g., Shelton et al, 2023). Diversity, evenness and dominance can also be influenced by other factors such as food availability or contamination, independently or synergistically with deoxygenation (Rozenzweig and Abramsky, 1993;Levin and Gage, 1998;Pilo et al, 2015).…”

Section: Ecosystem Indicatorsmentioning

confidence: 99%

Reviews and syntheses: Biological Indicators of Oxygen Stress in Water Breathing Animals

Roman,

Altieri,

Breitburg

et al. 2024

Preprint

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Abstract. Anthropogenic warming and nutrient over-enrichment of our oceans have resulted in significant, and often catastrophic, reductions in dissolved oxygen (deoxygenation). Stress on water-breathing animals from this deoxygenation has been shown to occur at all levels of biological organization: cellular; organ; individual; species; population; community; and ecosystem. Most climate forecasts predict increases in ocean deoxygenation, thus it is essential to develop reliable biological indicators of oxygen stress that can be used by regional and global oxygen monitoring efforts to detect and assess the impacts of deoxygenation on ocean life. This review focuses on indicators of low-oxygen stress that are manifest at different levels of biological organization and at a variety of spatial and temporal scales. We compare particular attributes of these indicators to the dissolved oxygen threshold of response, time-scales of response, sensitive life stages and taxa, and the ability to scale the response to oxygen stress across levels of organization. Where there is available evidence, we discuss the interactions of other biological and abiotic stressors on the biological indicators of oxygen stress. We address the utility, confounding effects, and implementation of the biological indicators of oxygen stress for both research and societal applications. Our hope is that further refinement and dissemination of these oxygen stress indicators will provide more direct support for environmental managers, fisheries and mariculture scientists, conservation professionals, and policy makers to confront the challenges of ocean deoxygenation. An improved understanding of the sensitivity of different ocean species, communities and ecosystems to low oxygen stress will empower efforts to design monitoring programs, assess ecosystem health, develop management guidelines, track conditions, and detect low-oxygen events.

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Development of species‐specific multiplex real‐time PCR assays for tracing the small pelagic fishes of North Pacific with environmental DNA

Cited by 4 publications

References 52 publications

Environmental DNA survey to detect an endemic cryptic fish, Anablepsoides cryptocallus, in tropical freshwater streams

Environmental DNA survey to detect an endemic cryptic fish, Anablepsoides cryptocallus, in tropical freshwater streams

Non‐extractive fish diversity assessment in Mediterranean rhodolith beds

Reviews and syntheses: Biological Indicators of Oxygen Stress in Water Breathing Animals

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