Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(20), P. 5132 - 5164

Published: Aug. 16, 2022

Abstract Vast global declines of freshwater and marine fish diversity population abundance pose serious threats to both ecosystem sustainability human livelihoods. Environmental DNA (eDNA)‐based biomonitoring provides robust, efficient, cost‐effective assessment species occurrences trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks facilitate conservation fisheries management. However, the many technical considerations rapid developments underway eDNA arena can overwhelm researchers practitioners new field. Here, we systematically analysed 416 studies summarize research terms investigated targets, aims, study systems, reviewed applications, rationales, methodological considerations, limitations methods with an emphasis on research. We highlighted how technology may advance our knowledge behaviour, distributions, genetics, community structures, ecological interactions. also synthesized current several important concerns, including qualitative quantitative power has recover biodiversity abundance, spatial temporal representations respect its sources. To applications implementing techniques, recent literature was summarized generate guidelines effective sampling lentic, lotic, habitats. Finally, identified gaps limitations, pointed out newly emerging avenues eDNA. As optimization standardization improve, should revolutionize monitoring promote management that transcends geographic boundaries.

Language: Английский

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Artificial intelligence and automated monitoring for assisting conservation of marine ecosystems: A perspective

Frontiers in Marine Science, Journal Year: 2022, Volume and Issue: 9

Published: July 28, 2022

Conservation of marine ecosystems has been highlighted as a priority to ensure sustainable future. Effective management requires data collection over large spatio-temporal scales, readily accessible and integrated information from monitoring, tools support decision-making. However, there are many roadblocks achieving adequate timely on both the effectiveness, long-term success conservation efforts, including limited funding, inadequate sampling, processing bottlenecks. These factors can result in ineffective, or even detrimental, decisions already impacted ecosystems. An automated approach facilitated by artificial intelligence (AI) provides managers with toolkit that help alleviate number these issues reducing monitoring bottlenecks costs monitoring. Automating collection, transfer, access greater information, thereby facilitating effective management. Incorporating automation big availability into decision system user-friendly interface also enables adaptive We summarise current state techniques used science use examples other disciplines identify existing potentially transferable methods enable improve predictive modelling capabilities making. discuss emerging technologies likely be useful research computer associated continues develop become more accessible. Our perspective highlights potential AI analytics for supporting decision-making, but points important knowledge gaps multiple areas processes. challenges should prioritised move toward implementing informed understanding successful outcomes managers. conclude emphasis assisted several scientific may mean future is improved implementation automation.

Language: Английский

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Bivalve molluscs as bioindicators of multiple stressors in the marine environment: Recent advances

Continental Shelf Research, Journal Year: 2023, Volume and Issue: 264, P. 105056 - 105056

Published: June 19, 2023

Language: Английский

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Environmental DNA: The next chapter

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(11)

Published: April 16, 2024

Abstract Molecular tools are an indispensable part of ecology and biodiversity sciences implemented across all biomes. About a decade ago, the use implementation environmental DNA (eDNA) to detect signals extracted from samples opened new avenues research. Initial eDNA research focused on understanding population dynamics target species. Its scope thereafter broadened, uncovering previously unrecorded via metabarcoding in both well‐studied understudied ecosystems taxonomic groups. The application rapidly became established research, field by its own. Here, we revisit key expectations made land‐mark special issue Ecology 2012 frame development six areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour environment (6) reference database development. We pinpoint success eDNA, yet also discuss shortfalls not met, highlighting areas priority identify unexpected developments. In parallel, our retrospective couples screening peer‐reviewed literature with survey users including academics, end‐users commercial providers, which address focus efforts advance eDNA. With rapid ever‐increasing pace technical advances, future looks bright, successful applications best practices must become more interdisciplinary reach full potential. Our retrospect gives towards concretely moving forward.

Language: Английский

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Environmental DNA provides quantitative estimates of Pacific hake abundance and distribution in the open ocean

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2022, Volume and Issue: 289(1971)

Published: March 23, 2022

All species inevitably leave genetic traces in their environments, and the resulting environmental DNA (eDNA) reflects present a given habitat. It remains unclear whether eDNA signals can provide quantitative metrics of abundance on which human livelihoods or conservation successes depend. Here, we report results large ocean survey (spanning 86 000 km 2 to depths 500 m) understand distribution Pacific hake ( Merluccius productus ), target largest finfish fishery along west coast USA. We sampled parallel with traditional acoustic-trawl assess value surveys at scale relevant fisheries management. Despite local differences, two methods yield comparable information about broad-scale spatial abundance. Furthermore, find depth patterns closely correspond estimates for hake. demonstrate power efficacy sampling estimating move analysis data beyond sample-to-sample comparisons management scales. posit that are capable providing general applications will prove especially valuable data- resource-limited contexts.

Language: Английский

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Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary

PLoS ONE, Journal Year: 2022, Volume and Issue: 17(6), P. e0266720 - e0266720

Published: June 17, 2022

Metabarcoding of environmental DNA is increasingly used for biodiversity assessments in aquatic communities. The efficiency and outcome these efforts are dependent upon either de novo primer design or selecting an appropriate set from the dozens that have already been published. Unfortunately, there a lack studies directly compared efficacy different metabarcoding primers marine estuarine systems. Here we evaluate five commonly sets designed to amplify rRNA barcoding genes fishes compare their performance using water samples collected sites highly biodiverse Indian River Lagoon Florida. Three portion mitochondrial 12S gene (MiFish_12S, 171bp; Riaz_12S, 106 bp; Valentini_12S, 63 bp), one amplifies 219 bp 16S (Berry_16S), other 271 nuclear 18S (MacDonald_18S). vast majority reads (> 99%) generated assigned non-target (non-fish) taxa therefore this was omitted most analyses. Using conservative 99% similarity threshold species level assignments, detected comparable number (55 49, respectively) similarly high Shannon's diversity values Riaz_12S Berry_16S sets. Meanwhile, just 34 32 were MiFish_12S Valentini_12S sets, respectively. We able both bony cartilaginous four with (>99%) former. greatest elasmobranchs (six species) suggesting it may be suitable candidate detection sharks rays. Of total 76 fish identified across all datasets, combined three 85.5% (65 while combination 93.4% (71 species). These results highlight importance employing multiple as well target genomic regions. Moreover, our suggest widely adopted not best choice, rather found effective eDNA-based surveys system.

Language: Английский

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Environmental DNA Methods for Ecological Monitoring and Biodiversity Assessment in Estuaries

Estuaries and Coasts, Journal Year: 2022, Volume and Issue: 45(7), P. 2254 - 2273

Published: June 25, 2022

Abstract Environmental DNA (eDNA) detection methods can complement traditional biomonitoring to yield new ecological insights in aquatic systems. However, the conceptual and methodological frameworks for eDNA interpretation were developed primarily freshwater environments have not been well established estuaries marine that are by nature dynamic, turbid, hydrologically complex. context species life history critical successful application of methods, challenges associated with subject a symposium held at University California Davis on January 29, 2020 ( https://marinescience.ucdavis.edu/engagement/past-events/edna ). Here, we elaborate upon topics addressed evaluate monitoring biodiversity studies estuaries. We first provide concise overview science then examine San Francisco Estuary (SFE) as case study illustrate how programs regional guidance future potential applications. Additionally, offer recommendations enhancing communication between scientists natural resource managers, which is essential integrating into existing programs. Our intent create accessible those outside field eDNA, especially without oversimplifying or advantages these methods.

Language: Английский

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Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 23(2), P. 396 - 409

Published: Sept. 24, 2022

Environmental DNA (eDNA) metabarcoding is an effective method for studying fish communities but allows only estimation of relative species abundance (density/biomass). Here, we combine with the total eDNA amplified by our universal marker (teleo) using a quantitative (q)PCR approach to infer absolute species. We carried out 2850-km survey within Danube catchment spatial integrative sampling protocol coupled traditional electrofishing biomass and density estimation. Total concentrations were highly correlated. The correlation between per taxon specific was comparable strength when all sites pooled remained significant considered separately. Furthermore, nonlinear mixed model showed that richness underestimated amount teleo-DNA extracted from sample below threshold 0.65 × 10

Language: Английский

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Experimental assessment of downstream environmental DNA patterns under variable fish biomass and river discharge rates

Environmental DNA, Journal Year: 2022, Volume and Issue: 5(1), P. 102 - 116

Published: Oct. 26, 2022

Abstract The development of environmental DNA (eDNA) methods toward implementation as a cost‐effective, nonlethal tool for fish biomonitoring in lotic environments requires insights on the temporal and spatial distribution eDNA river systems. Yet, little is known how downstream dispersal affected by combination discharge source biomass effects. In this study, we aimed at unraveling effect source‐ system‐specific processes stream reach eDNA. We used longitudinal cage study two sections characterized significantly different rate, where invasive native species were introduced under contrasting treatments. Using droplet digital PCR (ddPCR) analyses, found that concentrations become strongly reduced 2 km from source, an strengthened with increasing coinciding dilution Higher rates resulted equal or even higher detection probabilities distance source. introduction high stock increase concentrations, well parallel stochasticity measurements. A peak ranging between 300 m confirms complexity plume‐shaped patterns. Our results showed interspecific variation emission suggest species‐specific differences persistence. This underlines impact both rate

Language: Английский

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Extracting abundance information from DNA‐based data

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 23(1), P. 174 - 189

Published: Aug. 20, 2022

The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to diet analysis and food-web reconstruction, the inference species interactions, modelling population dynamics distributions, biomonitoring environmental state change, false positives negatives. However, multiple sources bias noise in sampling processing combine inject error into sets. To understand how extract abundance information, it is useful distinguish two concepts. (i) Within-sample across-species quantification describes relative abundances one sample. (ii) Across-sample within-species each individual varies sample sample, such as over a time series, an gradient or different experimental treatments. First, we review literature on methods recover (by removing what call "species pipeline biases") "pipeline noise"). We argue that many ecological questions can be answered with just quantification, therefore demonstrate use "DNA spike-in" correct for information. also introduce model-based estimator used sets without physical spike-in approximate noise.

Language: Английский

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