Streamlining large-scale oceanic biomonitoring using passive eDNA samplers integrated into vessel's continuous pump underway seawater systems

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 946, P. 174354 - 174354

Published: June 30, 2024

Passive samplers are enabling the scaling of environmental DNA (eDNA) biomonitoring in our oceans, by circumventing time-consuming process water filtration. Designing a novel passive sampler that does not require extensive sample handling time and can be connected to ocean-going vessels without impeding normal underway activities has potential rapidly upscale global efforts onboard world's oceanic fleet. Here, we demonstrate utility an artificial sponge continuous pump seawater system as means enable biomonitoring. We compared performance this sampling protocol with standard filtration at six locations during research voyage from New Zealand Antarctica early 2023. Eukaryote metabarcoding mitochondrial COI gene revealed no significant difference phylogenetic α-diversity between methods both delineated progressive reduction number Zero-Radius Operational Taxonomic Units (ZOTUs) increased latitudes. While comparable trends geographical community compositions, distinct clusters were identified for each location. Additionally, greater variability replicates was observed samplers, resulting estimated level replication needed recover 90 % biodiversity. Furthermore, traditional failed detect three phyla extrapolation analysis larger ZOTUs all locations. Our results eDNA highlight areas where emerging technology could improved, thereby large-scale offshore marine leveraging fleet interfering activities.

Language: Английский

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eDNA Sampling Systems for Salmon Ecosystem Monitoring

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(1)

Published: Jan. 1, 2025

ABSTRACT Environmental DNA (eDNA) is transforming the way aquatic ecosystems are monitored and managed by scientists, resource managers, ENGOs, First Nations communities, citizen scientists alike. However, available sampling systems currently don't allow for combined high filtration volumes, rapid sample collection, preservation in field, thus far hindering broad scale eDNA studies ocean specifically small medium organizations. To overcome these challenges, several modular water that utilize hollow‐membrane (HM) cartridges were developed RKS laboratories tested Fisheries Oceans, Canada, Molecular Genetics Laboratory. Compared to Sterivex filters, an industry standard filtration, HM allowed a six‐fold increase volume threefold speed. The field systems, which combine pumps, programmable controller, air pump, ozone generator, up eight filters at once, enabled efficient direct from diverse environments, creeks open ocean. evaluate ease of deployment, we present results 3 day workshop where technical staff Indigenous management organization, without any prior knowledge sampling, trained performed independent collection. samples analyzed metabarcoding qPCR reveal distributions salmon other species co‐occurring ecosystems, large ephemeral predators, planktonic prey salmon, even including their pathogens. In this example study, further observed substantial shift community composition vicinity aquaculture facilities marine associated with feed detected freshwater relative abundance. This study demonstrates how provide entry point organizations fulfill research monitoring objectives.

Language: Английский

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Eukaryotic biodiversity of sub-ice water in the marginal ice zone of the European Arctic: A multi-marker eDNA metabarcoding survey

The Science of The Total Environment, Journal Year: 2025, Volume and Issue: 968, P. 178840 - 178840

Published: Feb. 21, 2025

The effects of climate change, including warming waters, loss sea ice habitat and the resulting changes in primary production, are inducing shifts marine communities across Arctic Ocean. marginal zone (MIZ) is a highly dynamic ecosystem transition between pack open ocean. It for wide range organisms, sympagic pelagic taxa, all which affected by changing physical dynamics MIZ. Here we use multi-marker (18S rRNA V1-2 COI Leray-XT) approach to investigate eukaryotic biodiversity upper water column this understudied habitat. Environmental DNA (eDNA) was sequenced from seawater samples collected directly beneath at depth 5 m, sourced floes representing different regimes. To explore abiotic factors influencing under-ice diversity, combined satellite-derived environmental data with simultaneous situ hydrographic measurements. Our analysis identified metazoans, along producers typical region, as well substantial uncharacterised diversity. Alpha diversity indices were higher immediately below ice, community composition differed depths floe stations. We show that properties meltwater stratification ocean, concentration distance edge, significantly shape composition. These findings highlight effectiveness eDNA metabarcoding monitoring sub-ice enhance our understanding

Language: Английский

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Metazoan Diversity and Its Drivers: An eDNA Survey in the Pacific Gateway of a Changing Arctic Ocean

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(2)

Published: March 1, 2025

ABSTRACT Climate change drives species to adapt or undergo range shifts survive. The Arctic Ocean, experiencing more drastic environmental changes than any other ocean, has two primary inflow regions that facilitate these shifts: the wide, deep Atlantic Gateway and narrow, shallow Pacific Gateway. Environmental DNA (eDNA) surveys have proven be effective in characterizing community composition understanding its ecological drivers. We conducted first COI marker‐based eDNA survey analyzed seawater samples from various geographic regions, depths, water masses across Bering Strait, Chukchi Sea, South Beaufort Sea. Metazoan taxa 15 different phyla indicator for were identified. characterized a highly diverse neritic fauna Strait aligning with known locations of benthic hotspots. On slope we observed transitions copepod‐dominated epipelagic waters cnidarian‐ sponge‐dominated deeper areas. Alpha diversity peaked near seabed coastlines was highest within warmest Alaskan Coastal Water mass. linked metazoan communities variables, being associated higher temperatures fluorescence, majority them lower salinities. This included mostly Pseudocalanus copepod verongiid sponges. While rising might enhance alpha diversity, anticipate this will primarily due influx warmer fresher masses. Several taxa, including bivalve Macoma calcarea seastar Leptasterias arctica , as well jellyfish Chrysaora melanaster Triconia borealis colder, saltier likely negatively impacted by ongoing change. Our study successfully rapidly changing Ocean.

Language: Английский

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Water Volume, Biological and PCR Replicates Influence the Characterization of Deep‐Sea Pelagic Fish Communities

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(2)

Published: March 1, 2025

ABSTRACT The pelagic deep sea is challenging to investigate due logistical constraints regarding access and collection of samples; however, environmental DNA (eDNA) can potentially revolutionize our understanding this ecosystem. Although recent advancements are being made eDNA technology autonomous underwater vehicles, no investigation has been performed assess the impact different experimental designs using gear found on many research vessels (i.e., CTD mounted with Niskin bottles). Here, we investigated effects sampled water volume, biological PCR replicates in characterizing deep‐sea biodiversity at level species exact sequence variants (ESVs, representing intraspecific variation). Samples were collected a nighttime depth 450 m northern Gulf Mexico bottles, targeted fish community MiFish primer (12S rRNA). Our results show that 1 L insufficient characterize communities. 5 10 treatments detected similar structure combination number relative occurrence) numbers per replicate; treatment higher total species, more ESVs, when considering ESVs. We five detect up 80% each treatments, near saturation point. also had an important role ESV detection, which implies increasing if volume limited. suggest future studies collect least L, or field replicates, 5–10 adequately eDNA, resource limitations. study provides guidance for potential route expand global scale.

Language: Английский

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Monitoring Atlantic Salmon (Salmo salar) Smolt Migration in a Large River System Using Environmental DNA

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(2)

Published: March 1, 2025

ABSTRACT Effective monitoring strategies are key for aquatic species conservation, but traditional methods often require significant resources, especially in large systems. The emergence of quantitative environmental DNA (eDNA) is a promising alternative. Yet, few studies have evaluated the possibility quantifying Atlantic salmon abundance with eDNA when individuals at low and occur river In this study, we tested efficacy to monitor quantify daily variation smolt counts during their downstream migration system smolts. During 2021 2022 migrations, trap nets were used conduct census smolts Romaine Puyjalon rivers (Québec, Canada) while samples collected over transect perpendicular riverbank. Using real‐time qPCR, showed that discharge‐corrected concentrations positively correlated both years. addition, found controlling temperature precipitation improved model transferability between years, showing importance considering correlates using quantification. Finally, on same day, not 1 or 2 days prior, highlighting capacity track fluctuations abundance. Our results underscore potential systems hydrology conditions documented.

Language: Английский

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Contrasting the contributions of 12S eDNA metabarcoding, visual surveys and anaesthetic collections to the historical regional diversity of cryptobenthic and conspicuous fish

Journal of Fish Biology, Journal Year: 2025, Volume and Issue: unknown

Published: April 19, 2025

Abstract Taxonomic gaps in community biodiversity assessments are now commonly addressed by combining traditional monitoring methods and environmental DNA (eDNA) metabarcoding, widely recognized for having the ability to uncover rare cryptic diversity. However, only a few studies have assessed efficacy of this novel technique detecting cryptobenthic fishes tested limitations incomplete genetic reference availability historically neglected component fish communities. Our goals were (i) compare conspicuous detections 12S eDNA visual surveys anaesthetic collections, (ii) emerging regional diversity patterns against long‐term historical record Gulf California. Despite adding new local references 36 fishes, metabarcoding detected seven taxa. Visual provided similar results, highlighting collections as primary source, with 57 recovered. Conspicuous had an equal highly complementary contribution surveys. When contemporary from all methods, we recovered 43% 16% relative records. The spatial structure differed expectations showing no differences richness nor composition between Northern Central study highlights that their structuring driven distinct factors compared fishes.

Language: Английский

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eDNA metabarcoding shows highly diverse but distinct shallow, mid-water, and deep-water eukaryotic communities within a marine biodiversity hotspot

PeerJ, Journal Year: 2025, Volume and Issue: 13, P. e19249 - e19249

Published: April 22, 2025

As the impact of human activities continues to move beyond shallow coastal waters into deeper ocean layers, it is fundamental describe how diverse and distinct eukaryotic assemblages from deep layers are compared ecosystems. Environmental DNA (eDNA) metabarcoding has emerged as a molecular tool that can overcome many logistical barriers in exploring remote areas. We analyzed water samples (<30 m) collected via SCUBA diving adjacent (mid-water 30–150 m, deep-water >200 obtained with Niskin samplers within 16 locations recognized hotspot marine biodiversity (Gulf California, Mexico). sequenced an eDNA library targeting fragment COI gene eukaryotes. demonstrated diversity operational taxonomic units (OTUs) did not peak at regions mid-water benthic pelagic had similar levels sites, but detected significant vertical zonation between habitats. Our results suggest refugia hypothesis, which posits environments protect during environmental changes, enabling species survive repopulate shallower regions, supported for most taxa only applies about third (34.9%) 5,495 OTUs identified were shared layers. In comparison, rest exclusive either (30.8%) or zones (34.28%). The observation communities rich quite supports extending spatial management conservation tools habitats include fraction unique phylogenetic functional diversity.

Language: Английский

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Environmental DNA recovers fish composition turnover of the coral reefs of West Indian Ocean islands

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(5)

Published: May 1, 2024

Islands have been used as model systems to study ecological and evolutionary processes, they provide an ideal set-up for validating new biodiversity monitoring methods. The application of environmental DNA metabarcoding marine requires understanding the spatial scale eDNA signal, which is best tested in island systems. Here, we investigated variation Actinopterygii Elasmobranchii species composition recovered from along a gradient distance-to-reef four five French Scattered Western Indian Ocean. We collected surface water samples at increasing distance reefs (0 m, 250 500 750 m). protocol based on 'teleo' primers target reef fishes classified taxa according their habitat types (benthic or pelagic). effect β diversity using generalised linear mixed models estimated species-specific effects model-based approach community data. Environmental analyses distinct fish compositions across inventoried islands variations gradient. analysis

Language: Английский

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Polar AUV Challenges and Applications: A Review

Drones, Journal Year: 2024, Volume and Issue: 8(8), P. 413 - 413

Published: Aug. 22, 2024

This study presents a comprehensive review of the development and progression autonomous underwater vehicles (AUVs) in polar regions, aiming to synthesize past experiences provide guidance for future advancements applications. We extensively explore history notable AUV deployments worldwide, identifying addressing key technological challenges these face. These include advanced navigation techniques, strategic path planning, efficient obstacle avoidance, robust communication, stable energy supply, reliable launch recovery, thorough risk analysis. Furthermore, this categorizes typical capabilities applications AUVs contexts, such as under-ice mapping measurement, water sampling, ecological investigation, seafloor mapping, surveillance networking. also briefly highlight existing research gaps potential evolving field.

Language: Английский

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