Compact and automated eDNA sampler for in situ monitoring of marine environments

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: March 30, 2023

Abstract Using environmental DNA (eDNA) to monitor biodiversity in aquatic environments is becoming an efficient and cost-effective alternative other methods such as visual acoustic identification. Until recently, eDNA sampling was accomplished primarily through manual methods; however, with technological advances, automated samplers are being developed make easier more accessible. This paper describes a new sampler capable of self-cleaning multi-sample capture preservation, all within single unit deployed by person. The first in-field test this took place the Bedford Basin, Nova Scotia, Canada alongside parallel samples taken using typical Niskin bottle collection post-collection filtration method. Both were able same microbial community counts representative sequences well correlated between R $$^{2}$$ 2 values ranging from 0.71–0.93. two returned top 10 families near identical relative abundance, demonstrating that composition common microbes Niskin. presented provides robust methods, amenable autonomous vehicle payload constraints, will facilitate persistent monitoring remote inaccessible sites.

Language: Английский

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Comparing eDNA and eRNA Sampling Methodologies From Pond Environments

Aquatic Conservation Marine and Freshwater Ecosystems, Journal Year: 2025, Volume and Issue: 35(2)

Published: Feb. 1, 2025

ABSTRACT Molecular traces are increasingly being applied to assess the presence of species and communities. Studies on environmental DNA (eDNA) have, a large extent, become common practice in detection, but less studies have compared biodiversity estimations with more temporary RNA (eRNA). This study compares metabarcoding results from pond water obtained both molecule types by sequencing V4 region 18S rRNA marker. Water was collected two depths, 20 80 cm, filtered sequentially through filter porosities, 0.45 0.22 μm. Each cut half before fixation either 96% ETOH or RNAlater. The showed no differences between fixatives for molecule. Overall, estimates eDNA significantly overperformed eRNA, likely due higher concentrations terrestrial sources. Comparisons depths variation only, increasing levels found at upper layer. Both pore sizes captured distinctive compositions taxa, where about 30% diversity uniquely identified second, finer filter. Taken together, these findings imply that choice molecular marker, depth size affects pond.

Language: Английский

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Navigating Methodological Trade‐Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Environmental DNA (eDNA) metabarcoding technologies promise significant advances in biodiversity monitoring, yet their application requires extensive optimisation and standardisation. Recent research demonstrated that increased sampling analytical efforts are needed to improve estimates, though fully optimising study designs is often hindered by resource constraints. Consequently, researchers must carefully navigate methodological trade-offs design effective eDNA monitoring studies. We conducted a water survey of vertebrates Mediterranean watershed identify key factors influencing species richness composition estimates. examined the impacts using high- versus low-capacity filtration capsules, varying levels biological technical replication, pooling PCR replicates before indexing. The primary sources variation identified were capsule capacity site replication across watershed. While within sites also improved effects comparatively smaller. Pooling indexing performed more poorly than analysing them independently. Methodological stronger on terrestrial aquatic species. Based these results, we recommend priority should be given high-capacity multiple sites. Site-level deserves lower priority, especially when filtering large volumes. crucial for detecting rare but balanced with eventually site-level replication. Avoiding important enhance sensitivity Overall, stress importance balancing choices constraints goals, emphasise need assessing different systems.

Language: Английский

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Assessing mesopelagic fish diversity and diel vertical migration with environmental DNA

Frontiers in Marine Science, Journal Year: 2023, Volume and Issue: 10

Published: Dec. 11, 2023

Mesopelagic fishes are an important component of the world’s oceans in terms their abundance, biomass, and ecosystem function. These contributors to biological carbon pump via feeding behaviors, whereby they facilitate transfer from shallow waters deep sea. Several species undertake diel vertical migration, shallower at night moving deeper during day. This process actively expedites downward flux carbon. However, budgets climate models require accurate information regarding depth distributions migration patterns these fishes, environmental DNA (eDNA) analyses can provide this information. Here, we utilize eDNA approaches, generating taxonomically-informative COI 12S reference barcodes for 80 mesopelagic which be used species-level identification sequences. Using these, along with a publicly available database, compare results analysis traditional net sampling, explore ability techniques detect samples collected Northwest Atlantic Slope Water. We found that often resulted different identifications, demonstrating would otherwise missed methods. In our samples, also detected more (12) shallowest category (0 - 100 m) than day (3). is consistent increased diversity due migration. Based on variability observed sample duplicates, suggest future studies incorporate larger volumes scaled-up sampling efforts. note potential applications addressing ecological questions related predator-prey relationships foraging hotspots, flow through ocean’s midwaters.

Language: Английский

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Decoding dissolved information: environmental DNA sequencing at global scale to monitor a changing ocean

Current Opinion in Biotechnology, Journal Year: 2023, Volume and Issue: 81, P. 102936 - 102936

Published: April 14, 2023

Language: Английский

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Autonomous eDNA collection using an uncrewed surface vessel over a 4200‐km transect of the eastern Pacific Ocean

Environmental DNA, Journal Year: 2023, Volume and Issue: 6(1)

Published: Aug. 29, 2023

Abstract The collection of environmental DNA (eDNA) samples is often laborious, costly, and logistically difficult to accomplish at high frequency in remote locations over large geographic areas. Here, we addressed those challenges by combining two robotic technologies: an uncrewed surface vessel (USV) fitted with automated eDNA sample device survey waters the eastern North Pacific Ocean from Alameda, CA Honolulu, HI. USV Surveyor SD 1200 (Saildrone) carrying Environmental Sample Processor (ESP) collected 2‐L water filtration followed RNAlater preservation regular intervals a 4200‐km, 29‐day transit. Sixty (52 field 8 controls) were acquired used estimate concentration specific genes assess eukaryotic diversity via targeted qPCR metabarcoding cytochrome oxidase subunit I (COI) gene, respectively. Comparisons control revealed important considerations for interpreting results. Samples stored ambient temperatures onboard length voyage had less total recoverable target gene concentrations compared same material immediately flash‐frozen after laboratory. In contrast, biodiversity COI was similar regardless age storage condition. affiliated 40 phyla found native during voyage. distribution dominance varied across different regions, some taxa spanning continuous stretches >2000 km, while others only detected single sample. This work highlights utility potential using USVs autonomous devices improve ocean exploration support large, basin‐scale, systematic surveys. Results this study also inform future technical samplers acquire store it prolonged periods under prevailing conditions.

Language: Английский

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Comparing eDNA metabarcoding and conventional pelagic netting to inform biodiversity monitoring in deep ocean environments

ICES Journal of Marine Science, Journal Year: 2023, Volume and Issue: 80(10), P. 2545 - 2562

Published: Nov. 9, 2023

Abstract The performance of environmental DNA (eDNA) metabarcoding has rarely been evaluated against conventional sampling methods in deep ocean mesopelagic environments. We assessed the biodiversity patterns generated with eDNA and two co-located methods, oblique midwater trawls vertical multinets, to compare regional sample-level diversity. then concordance ecological across water column habitats how markers level effort influenced inferred community. found characterized diversity well, detecting more taxa while identifying similar as samples. Within locations, detected than one replicate. While were within sample stations, fewer compared multinets. Our simulations show greater would improve methods. also observed that using taxonomic data from multiple most those Patterns Exact Sequence Variants stable suggesting they are powerful for change. is a valuable tool monitoring biological hotspots but some methodological adjustments recommended

Language: Английский

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Drop it all: extraction-free detection of targeted marine species through optimized direct droplet digital PCR

PeerJ, Journal Year: 2024, Volume and Issue: 12, P. e16969 - e16969

Published: Feb. 23, 2024

Molecular biomonitoring programs increasingly use environmental DNA (eDNA) for detecting targeted species such as marine non-indigenous (NIS) or endangered species. However, the current molecular detection workflow is cumbersome and time-demanding, thereby can hinder management efforts restrict “opportunity window” rapid responses. Here, we describe a direct droplet digital PCR (direct-ddPCR) approach to detect species-specific free-floating extra-cellular eDNA (free-eDNA) signals, i.e ., of without need filtration extraction, with seawater samples. This first proof-of-concept aquarium study was conducted three distinct species: Mediterranean fanworm Sabella spallanzanii , ascidian clubbed tunicate Styela clava brown bryozoan Bugula neritina evaluate detectability free-eDNA in seawater. The assessed by directly analysing water samples using an optimized ddPCR assay. results demonstrated consistent S. B. when these organisms were present high abundance. Once removed, signal exponentially declined, noting that persisted between 24–72 h. Results indicate organism biomass, specimen characteristics ( e.g stress viability), biological differences may influence detectability. represents step assessing feasibility direct-ddPCR technology Our provide information could aid development new technology, field systems, which allow automated continuous monitoring species, enabling point-of-need

Language: Английский

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Advances in environmental DNA monitoring: standardization, automation, and emerging technologies in aquatic ecosystems

Science China Life Sciences, Journal Year: 2024, Volume and Issue: 67(7), P. 1368 - 1384

Published: March 18, 2024

Language: Английский

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Applying environmental DNA approaches to inform marine biodiversity conservation: The case of the Ocean Twilight Zone

Marine Policy, Journal Year: 2024, Volume and Issue: 165, P. 106151 - 106151

Published: May 6, 2024

Effective governance of the global ocean under accelerating environmental and social changes depends on sufficient scientific knowledge that unravels complexity dynamic marine ecosystems. In case vast remote twilight zone (OTZ), management is particularly challenged by lack data. Traditional biodiversity monitoring methods are unable to scale efficiently or effectively address these gaps new technologies needed inform policy. Environmental DNA (eDNA) has quickly gained traction in recent years as an enabling technology for conservation will play a transformative role OTZ high seas general. Through comprehensive review science policy literature analysis existing data, we discuss importance OTZ, gaps, summarize developments eDNA research. We identify key components framework implications relevant Biodiversity Beyond National Jurisdiction (BBNJ) Agreement. show integrated science-policy approach based transdisciplinary research essential achieving sustainability 30×30 target conserving biodiversity.

Language: Английский

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