Predicting trawl catches using environmental DNA

ICES Journal of Marine Science, Journal Year: 2024, Volume and Issue: 81(8), P. 1536 - 1548

Published: Aug. 7, 2024

Abstract Quantifying the biomass, or number of individuals, diversity, and distribution marine species is a critical aspect understanding managing ecosystems. In recent years, there has been growing interest in using environmental DNA (eDNA) for ecosystem management biodiversity assessment. However, main challenge hindering eDNA applicability inability to infer absolute abundances from multispecies analysis (eDNA metabarcoding). this study, we demonstrate way forward by estimating abundance commercially important fish Norwegian fjord joint Bayesian statistical model traditional trawl-catch data molecular derived eDNA. Using model, accurately predict out-of-sample trawl catches alone. Moreover, our provides empirical estimates key processes linking concentration population estimated observations, including catchability, shedding, degradation, dilution, transport, recovery rate, isolation efficiency. These processes, amplification efficiencies correcting Polymerase Chain Reaction (PCR) bias, are species-specific enable translation metabarcoding into abundances. findings have broad implications use conservation efforts.

Language: Английский

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Possible monitoring of mesophotic scleractinian corals using an underwater mini-ROV to sample coral eDNA

Royal Society Open Science, Journal Year: 2024, Volume and Issue: 11(2)

Published: Feb. 1, 2024

Mesophotic coral ecosystems (MCEs) are light-dependent tropical or subtropical communities occurring at depths of 30–150 m. Broader surveys MCEs needed to better understand stony corals, the keystone species coral-reef ecosystems. While have been studied by professional SCUBA divers and with deep-sea robots, comprehensive required. An eDNA metabarcoding method has recently used survey scleractinian corals in shallow reefs. We tested whether might be more comprehensively surveyed collecting seawater samples using an underwater mini-remote operated vehicle (mini-ROV). Seawater was collected 1–2 m above reef tops 20–80 24 sites six locations around Zamami Islands (Okinawa, Japan). Water were then subjected coral-specific amplification. Metabarcoding analyses amplicons showed that except for one site, from approximately 0.5 l sufficient identify genera. The proportion Acropora higher reefs upper ridges slopes, while Porites increased mesophotic . Although further technical improvements required, this study suggests it may possible monitor generic level mini-ROVs.

Language: Английский

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Validation of Environmental DNA for Estimating Proportional and Absolute Biomass

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(5)

Published: Sept. 1, 2024

ABSTRACT Environmental DNA (eDNA) has significant potential to improve the efficiency of biological sampling and detect species that pose challenges for traditional methods. However, a key obstacle in utilizing eDNA data ecosystem management is uncertainty surrounding ability estimate abundance or biomass multiple simultaneously. In this study, we use experimental trials with known biomasses explore feasibility (1) estimating proportions from metabarcoding (2) absolute concentrations by scaling single obtained qPCR. The focal study were three gadid fishes are components marine ecosystems Alaska vary their distribution habitat use: Walleye pollock ( Gadus chalcogrammus ), Pacific cod macrocephalus Arctic Boreogadus saida ). After designing gadid‐specific primers accounting PCR biases data, found corrected read closely approximated true species. Furthermore, strong positive relationships between concentration using quantitative combined estimates derived These findings suggest it possible accurately quantify compositions metrics gadids real‐world scenarios. work provides framework developing analytical approaches can be applied other utility eDNA.

Language: Английский

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The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data

Metabarcoding and Metagenomics, Journal Year: 2024, Volume and Issue: 8

Published: Dec. 30, 2024

Environmental DNA (eDNA) and RNA (eRNA) metabarcoding has become a popular tool for assessing biodiversity from environmental samples, but inconsistent documentation of methods, data metadata makes results difficult to reproduce synthesise. A working group scientists have collaborated produce set minimum reporting guidelines the constituent steps workflows, physical layout laboratories through archiving. We emphasise how suite should adhere findable, accessible, interoperable reproducible (FAIR) standards, thereby providing context evaluating understanding study results. An overview considerations each workflow step is presented then summarised in checklist that can accompany published or report. Ensuring workflows are transparent documented critical research allow more efficient uptake into management decision-making.

Language: Английский

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DNA metabarcoding captures temporal and vertical dynamics of mesozooplankton communities

ICES Journal of Marine Science, Journal Year: 2025, Volume and Issue: 82(2)

Published: Jan. 20, 2025

Abstract In this study, we evaluated how well DNA metabarcoding of environmental samples captures changes in marine mesozooplankton community composition to optimize the use sequencing data for studying seasonal dynamics. Although is increasingly used monitor distribution communities, there a lack standardized methods, and it remains uncertain what extent reflects patterns dynamics observed by other methods. Zooplankton net were collected every second week throughout 2017 northern Salish Sea, British Columbia. We compared two genetic markers (18S targeting eukaryotes cytochrome oxidase I invertebrates) with microscopic assessments zooplankton collected. also transformation using relative abundance, presence/absence, eDNA-index, affects linearity between morphological Despite low taxonomic agreement microscopy, found most biomass dominating genera be represented. Using generally good congruence cycles microscopy DNA, that discrete water analyzed can provide information on vertical distributions genera. conclude presenting guidelines future studies aim study

Language: Английский

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Basin-wide morphology and metabarcoding-based comparison of ichthyoplankton diversity and community structure in the Gulf of Mexico

Progress In Oceanography, Journal Year: 2025, Volume and Issue: unknown, P. 103482 - 103482

Published: April 1, 2025

Language: Английский

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Observation Bias in Metabarcoding

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

Published: May 15, 2025

ABSTRACT DNA metabarcoding is subject to observation bias associated with PCR and sequencing, which can result in observed read proportions differing from actual species the extract. Here, we amplify sequence a mock community of known composition containing marine fishes cetaceans using four different primer sets variety conditions. We first compare observations two expected based on total genomic target mitochondrial template DNA. find that calibrating concentration most appropriate as it isolates amplification bias; calibration results be attributed both ratios then model remaining approximately 60% explained by inherent species‐specific characteristics. These include primer‐template mismatches, amplicon fragment length, GC content, vary somewhat across Taq polymerases. Finally, investigate how protocols influence regardless changing strongly templates mismatches. Our findings suggest pairs without mismatches targeting narrow taxonomic group yield more repeatable accurate estimates species' true, underlying proportions. identify key factors should considered when designing studies aim apply data quantitatively.

Language: Английский

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First national survey of terrestrial biodiversity using airborne eDNA

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: June 2, 2025

Near real-time data across taxa are necessary for quantifying biodiversity at regional to continental scales and evaluating conservation measures. Yet, standardized methods globally distributed infrastructure still lacking. In this study, we conducted the first national survey of terrestrial using a metabarcoding approach on airborne environmental DNA collected by ambient air quality monitoring network. Our goal was perform multi-taxonomic assessment scale, compare detections with those another large-scale (citizen sciences) estimate tentative minimum eDNA transportation distance. We identified over 1,100 taxa, including vertebrates, invertebrates, protists, fungi plants covering wide range life history traits ecological niches. Citizen science were complementary, better mapping less charismatic difficult spot demonstrating its potential align global goals. Airborne signals relatively local (< 80 km), likely due deposition larger particles from shorter distances limited wind near ground level. Overall, our results show that molecular protocols integrated into existing networks can provide standardized, low field cost, broad scalability.

Language: Английский

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Quantifying impacts of an environmental intervention using environmental DNA

Ecological Applications, Journal Year: 2023, Volume and Issue: 33(8)

Published: Aug. 29, 2023

Abstract Environmental laws around the world require some version of an environmental‐impact assessment surrounding construction projects and other discrete instances human development. Information requirements for these assessments vary by jurisdiction, but nearly all analysis biological elements ecosystems. Amplicon‐sequencing—also called metabarcoding—of environmental DNA (eDNA) has made it possible to sample amplify genetic material many species present in those environments, providing a tractable, powerful, increasingly common way doing development projects. Here, we analyze 18‐month time series water samples taken before, during, after two culvert removals salmonid‐bearing freshwater stream. We also sampled multiple control streams develop robust background expectation against which evaluate impact this intervention treatment generate calibrated, quantitative metabarcoding data from amplifying 12s MiFish mtDNA locus complementary species‐specific PCR yield multispecies estimates absolute eDNA concentrations across time, creeks, sampling stations. then use linear mixed effects model reveal patterns over estimate removal on salmonids creek. focus our four salmonid species: cutthroat trout ( Oncorhynchus clarkii ), coho salmon kisutch rainbow mykiss sockeye nerka ). find that one creek seemed have no while second had large fish passage. The itself only transient during events. In context billions dollars court‐mandated road replacements taking place Washington State, USA, results suggest replacement can be conducted with minimal key management concern. Furthermore, methods effective efficient approach monitoring hundreds culverts prioritize are required replaced. More broadly, demonstrate rigorous, method reporting using is widely applicable environments worldwide.

Language: Английский

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Towards quantitative DNA Metabarcoding: A method to overcome PCR amplification bias

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 5, 2023

Abstract Metabarcoding analyses have recently undergone significant development due to the power of this technique in biodiversity monitoring. However, it is still difficult draw accurate quantitative conclusions about ecosystems studied, mainly because biases inherent environmental DNA or introduced during experimental process. These alter relationship between amount observed and biomass number individuals species detected. Two metabarcoding been measured: ratio total target concentrations, PCR amplification bias. A method for their correction proposed. All tests were performed on mock alpine plant communities using marker Sper01 , which expected low bias its highly conserved priming sites. Our approach combines standard techniques (qPCR digital droplet PCR) with a realistic stochastic model dynamics that accounts saturation. The was used estimate efficiencies each infer true proportions from read relative frequencies. corrections are easy implement can be applied previously generated data. This work demonstrates importance two considered an open door data, although many other remain considered.

Language: Английский

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