Environmental DNA (eDNA) as a tool for assessing fish biomass: A review of approaches and future considerations for resource surveys

Environmental DNA, Journal Year: 2021, Volume and Issue: 4(1), P. 9 - 33

Published: Feb. 25, 2021

Abstract Environmental DNA (eDNA) has revolutionized our ability to identify the presence and distributions of terrestrial aquatic organisms. Recent evidence suggests concentration eDNA could also provide a rapid, cost‐effective indicator abundance and/or biomass for fisheries stock assessments. Globally, resources are under immense pressure, their sustainable harvest requires accurate information on sizes fished stocks. However, in many cases required remains elusive because reliance imprecise or costly fishery‐dependent independent data. Here, we review literature describing relationships between concentrations fish biomass, as well key influencing factors, precursor determining broader utility monitoring populations. We reviewed 63 studies published 2012 2020 found 90% identified positive focal species. Key biotic factors included taxon examined body size, distribution, reproduction, migration. abiotic mostly comprised hydrological processes affecting dispersal persistence eDNA, especially water flow temperature, although collection methods were influential. The cumulative influence these different likely explains substantial variability observed concentrations, both within among studies. Nevertheless, there is considerable support using an ancillary tool assessing population across discrete spatio‐temporal scales, following preliminary investigations determine species‐ context‐specific abundance/biomass relationship. Advantages relative other approaches include reduced costs, increased efficiencies, nonlethal sampling.

Language: Английский

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Environmental DNA illuminates the dark diversity of sharks

Science Advances, Journal Year: 2018, Volume and Issue: 4(5)

Published: May 2, 2018

Environmental DNA reveals unsuspected shark diversity and calls for monitoring protection of residual populations.

Language: Английский

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The choice of universal primers and the characteristics of the species mixture determine when DNA metabarcoding can be quantitative

Molecular Ecology, Journal Year: 2018, Volume and Issue: 28(2), P. 407 - 419

Published: June 25, 2018

Abstract DNA metabarcoding is a technique used to survey biodiversity in many ecological settings, but there are doubts about whether it can provide quantitative results, that is, the proportions of each species mixture as opposed list. While several experimental studies report similar number fail do so. Here, we rationale understand under what circumstances be quantitative. In essence, simulate S with defined initial abundance distribution. simulated PCR , increases its concentration following certain amplification efficiency. The final will reflect one when efficiency for all species; otherwise, and concentrations would poorly related. Although known factors modulate efficiency, focused on primer–template mismatches, arguably most important one. We 15 common primers pairs targeting mitochondrial COI region mitogenomes ca . 1,200 insect species. results showed some produced circumstances, whereas other failed conclusion, depending primer pair characteristics analysed (i.e., high richness, low evenness), estimate relative abundances different

Language: Английский

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Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding

PLoS ONE, Journal Year: 2017, Volume and Issue: 12(4), P. e0176343 - e0176343

Published: April 25, 2017

Molecular analysis of environmental DNA (eDNA) can be used to assess vertebrate biodiversity in aquatic systems, but limited work has applied eDNA technologies marine waters. Further, there is understanding the spatial distribution Here, we use an metabarcoding approach target and amplify a hypervariable region mitochondrial 12S rRNA gene characterize communities at 10 oceanographic stations spanning 45 km within Monterey Bay National Marine Sanctuary (MBNMS). In this study, collected three biological replicates small volume water samples (1 L) 2 depths each stations. We amplified fish using universal primer set. obtained 5,644,299 high quality Illumina sequence reads from samples. The were annotated lowest taxonomic assignment bioinformatics pipeline. survey identified, rank, 7 families, 3 subfamilies, genera, 72 species vertebrates study sites. These 92 distinct taxa come 33 unique families. observed significantly different community composition between sampling (0 m 20/40 deep) across all located on continental shelf (<200 bottom depth) versus deeper waters canyons (>200 depth). All 1 family identified known occur MBNMS. informs implementation for biomonitoring.

Language: Английский

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Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity

Conservation Biology, Journal Year: 2018, Volume and Issue: 33(1), P. 196 - 205

Published: July 13, 2018

Abstract Monitoring communities of fish is important for the management and sustainability fisheries marine ecosystems. Baited remote underwater video systems (BRUVs) are among most effective nondestructive techniques sampling bony fishes elasmobranchs (sharks, rays, skates). However, BRUVs sample visually conspicuous biota; hence, some taxa undersampled or not recorded at all. We compared diversity characterized using with detected via environmental DNA (eDNA) metabarcoding. sampled seawater captured imagery 48 locales that included reef seagrass beds inside outside a reserve (Jurien Bay in Western Australia). Eighty‐two genera from 13 orders were detected, community described eDNA combined yielded >30% more generic richness than when either method was used alone. Rather detecting homogenous genetic signature, assemblages mirrored BRUVs’ spatial explicitness; differentiation between clear despite relatively small geographical scale study site (∼35 km 2 ). Taxa by one approach, due to limitations biases intrinsic method, often other. Therefore, concert provides holistic view vertebrate across habitats. Both methods noninvasive, which enhances their potential widespread implementation surveillance

Language: Английский

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eDNA metabarcoding survey reveals fine‐scale coral reef community variation across a remote, tropical island ecosystem

Molecular Ecology, Journal Year: 2020, Volume and Issue: 29(6), P. 1069 - 1086

Published: Feb. 11, 2020

Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies from environmental samples, can detect diverse array of marine species filtered seawater samples. There is growing potential to integrate eDNA alongside existing monitoring methods in order establish or improve the assessment diversity. Remote island reefs are increasingly vulnerable climate-related threats and as such there pressing need cost-effective whole-ecosystem surveying baseline biodiversity, study assemblage changes ultimately develop sustainable management plans. We investigated utility metabarcoding high-resolution, multitrophic biomonitoring tool at Cocos (Keeling) Islands, Australia (CKI)-a remote tropical coral reef atoll situated within eastern Indian Ocean. Metabarcoding assays targeting mitochondrial 16S rRNA CO1 genes, well 18S nuclear gene, were applied 252 surface samples collected 42 sites 140 km2 area. Our successfully detected wide range bony fish elasmobranchs (244 taxa), crustaceans (88), molluscs (37) echinoderms (7). Assemblage composition varied significantly between sites, reflecting habitat partitioning across ecosystem demonstrating localisation signals, despite extensive tidal oceanic movements. In addition, we document putative new occurrence records 46 taxa compare efficiency our approach visual survey techniques CKI. demonstrates multimarker capturing biodiversity an entire sets important ongoing management.

Language: Английский

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The sceptical optimist: challenges and perspectives for the application of environmental DNA in marine fisheries

Fish and Fisheries, Journal Year: 2018, Volume and Issue: 19(5), P. 751 - 768

Published: April 6, 2018

Abstract Application of environmental DNA (e ) analysis has attracted the attention researchers, advisors and managers living marine resources biodiversity. The apparent simplicity cost‐effectiveness e make it highly attractive as species distributions can be revealed from water samples. Further, species‐specific analyses indicate that concentrations correlate with biomass abundance, suggesting possibility for quantitative applications estimating abundance specific organisms in ecosystems, such stock assessment. However, path detecting occurrence an organism to estimates is long indirect, not least concentration depends on several physical, chemical biological factors which influence its production, persistence transport ecosystems. Here, we provide overview basic principles relation potential fisheries application. We describe fundamental processes governing generation, breakdown summarize current uncertainties about these processes. five major challenges application assessment, where there immediate need knowledge building systems, point weaknesses compared established monitoring methods. emerging interest management recent technological advances, could improve efficiency. advise precaution against exaggerating present scope monitoring, but also argue informed insights into strengths limitations, become integrated tool assessment management.

Language: Английский

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Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus)

Ecology and Evolution, Journal Year: 2018, Volume and Issue: 8(12), P. 6330 - 6341

Published: May 29, 2018

Environmental DNA (eDNA) analysis is a rapid, cost-effective, non-invasive biodiversity monitoring tool which utilises left behind in the environment by organisms for species detection. The method used as species-specific survey rare or invasive across broad range of ecosystems. Recently, eDNA and "metabarcoding" have been combined to describe whole communities rather than focusing on single target species. However, whether metabarcoding sensitive targeted approaches detection remains be evaluated. great crested newt Triturus cristatus flagship pond international conservation concern first UK routinely monitored using eDNA. We evaluate has comparable sensitivity real-time quantitative PCR (qPCR) T. Extracted samples (N = 532) were screened qPCR analysed all vertebrate high-throughput sequencing technology. With threshold 1 12 positive replicates, newts detected 50% ponds. Detection decreased 32% when was increased 4 replicates. metabarcoding, 34% ponds without threshold, 28% (0.028%) applied. Therefore, provided greater but with no equivalent stringent threshold. proportion sequences each sample positively associated number replicates (qPCR score) suggesting may indicative concentration. holds enormous potential holistic assessment routine freshwater monitoring. advocate this community approach guide management conservation, whereby entire can initially surveyed best inform use funding time surveys.

Language: Английский

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Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary

PLoS ONE, Journal Year: 2017, Volume and Issue: 12(4), P. e0175186 - e0175186

Published: April 12, 2017

The difficulty of censusing marine animal populations hampers effective ocean management. Analyzing water for DNA traces shed by organisms may aid assessment. Here we tested aquatic environmental (eDNA) as an indicator fish presence in the lower Hudson River estuary. A checklist local and their relative abundance was prepared compiling 12 traditional surveys conducted between 1988-2015. To improve eDNA identification success, 31 specimens representing 18 species were sequenced two mitochondrial gene regions, boosting coverage 12S target sequence to 80% taxa. We collected 76 one-liter shoreline surface samples at contrasting estuary locations over six months beginning January 2016. amplified with vertebrate-specific primers. Bioinformatic analysis DNA, using a reference library GenBank our newly generated sequences, detected most (81%) locally abundant or common relatively few (23%) uncommon taxa, corresponded seasonal habitat preference determined surveys. Approximately 2% reads commonly consumed that are rare absent waters, consistent wastewater input. Freshwater rarely despite inflow. These results support further exploration suggest will facilitate fine-scale geographic temporal mapping low cost.

Language: Английский

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Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool?

Genes, Journal Year: 2019, Volume and Issue: 10(3), P. 192 - 192

Published: March 1, 2019

Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations contribute to effective conservation management. However, collecting samples can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way sample material non-invasively without requiring visual observation. While eDNA has been trialed extensively as biodiversity biosecurity monitoring tool strong taxonomic focus, it yet fully explored means for obtaining population information. Here, we review current research that employs approaches the study populations. We outline challenges facing eDNA-based methodologies, suggest avenues future developments. advocate further optimizations, this emergent field holds great potential part genetics toolkit.

Language: Английский

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