A comparison of biomonitoring methodologies for surf zone fish communities

PLoS ONE, Journal Year: 2023, Volume and Issue: 18(6), P. e0260903 - e0260903

Published: June 14, 2023

Surf zones are highly dynamic marine ecosystems that subject to increasing anthropogenic and climatic pressures, posing multiple challenges for biomonitoring. Traditional methods such as seines hook line surveys often labor intensive, taxonomically biased, can be physically hazardous. Emerging techniques, baited remote underwater video (BRUV) environmental DNA (eDNA) promising nondestructive tools assessing biodiversity in surf of sandy beaches. Here we compare the relative performance beach seines, BRUV, eDNA characterizing community composition bony (teleost) cartilaginous (elasmobranch) fishes at 18 open coast beaches southern California. Seine BRUV captured overlapping, but distinct fish communities with 50% (18/36) detected species shared. more frequently larger (e.g. sharks rays) while one most abundant species, barred surfperch ( Amphistichus argenteus ). In contrast, metabarcoding 88.9% (32/36) all observed seine plus 57 additional including 15 frequent zone habitats. On average, over 5 times than BRUVs 8 a given site. approaches also showed significantly higher sensitivity consistently 31 32 (96.9%) jointly across The four by BRUV/seines, not were only resolved taxonomic ranks Embiotocidae surfperches Sygnathidae pipefishes). co-detection between limited comparisons richness abundance estimates, highlighting challenge comparing biomonitoring approaches. Despite potential improvement, results overall demonstrate provide cost-effective tool long-term monitoring complements data from surveys, allowing comprehensive vertebrate diversity

Language: Английский

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Signal and noise in metabarcoding data

PLoS ONE, Journal Year: 2023, Volume and Issue: 18(5), P. e0285674 - e0285674

Published: May 11, 2023

Metabarcoding is a powerful molecular tool for simultaneously surveying hundreds to thousands of species from single sample, underpinning microbiome and environmental DNA (eDNA) methods. Deriving quantitative estimates underlying biological communities metabarcoding critical enhancing the utility such approaches health conservation. Recent work has demonstrated that correcting amplification biases in genetic data can yield template concentrations. However, major source uncertainty stems non-detections across technical PCR replicates where one replicate fails detect observed other replicates. Such are special case variability among data. While many sampling processes underlie variation data, understanding causes an important step distinguishing signal noise studies. Here, we use both simulated empirical 1) suggest how may arise 2) outline steps recognize uninformative practice, 3) identify conditions under which amplicon sequence reliably signals. We show with simulations that, given species, rate function concentration species-specific efficiency. Consequently, conclude datasets strongly affected by (1) deterministic during (2) stochastic amplicons sequencing-both model-but also (3) rare molecules prior PCR, remains frontier metabarcoding. Our results highlight importance estimating efficiencies critically evaluating patterns non-detection better distinguish inherent detections targets.

Language: Английский

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Marine Microbiota Responses to Shipping Scrubber Effluent Assessed at Community Structure and Function Endpoints

Environmental Toxicology and Chemistry, Journal Year: 2024, Volume and Issue: 43(5), P. 1012 - 1029

Published: Feb. 28, 2024

Abstract The use of novel high-throughput sequencing (HTS) technologies to examine the responses natural multidomain microbial communities scrubber effluent discharges marine environment is still limited. Thus, we applied metabarcoding targeting planktonic unicellular eukaryotic and prokaryotic fraction (phytoplankton, bacterioplankton, protozooplankton) in mesocosm experiments with from a polluted an unpolluted site. Furthermore, metagenomic analysis revealed changes taxonomic functional dominance after additions. results indicated clear shift such additions, which favored bacterial taxa known oil polycyclic aromatic hydrocarbons (PAHs) biodegradation capacities. These bacteria exhibited high connectedness eukaryotes employing variable trophic strategies, suggesting that environmentally relevant can influence community structure. Clusters Orthologous Genes associated pathways PAHs monocyclic hydrocarbon degradation increased numbers at treatments additions acutely. genes are express enzymes acting various substrates including PAHs. indications, combination abrupt decrease most abundant below limit detection—much faster than their half-lives—could point toward bacterioplankton-initiated rapid ultimate toxic contaminants effluent. implementation HTS could be valuable tool develop multilevel biodiversity indicators impacts on environment, lead improved impact assessment. Environ Toxicol Chem 2024;43:1012–1029. © 2024 Authors. Environmental Toxicology Chemistry published by Wiley Periodicals LLC behalf SETAC.

Language: Английский

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Advancing the environmental DNA and RNA toolkit for aquatic ecosystem monitoring and management

PeerJ, Journal Year: 2025, Volume and Issue: 13, P. e19119 - e19119

Published: March 18, 2025

The application of environmental DNA (eDNA) and RNA (eRNA) technologies to aquatic ecosystem monitoring management has increased rapidly in the last decade. These methods are providing many new exciting opportunities for enhanced biodiversity assessment, ecological health evaluation, species detection. This special issue PeerJ Life Environment brings together 20 innovative studies that collectively advance eDNA toolkit. Four key themes covered: (i) Methodological advancements, (ii) Ecological assessments biomonitoring, (iii) Species detection, (iv) Application management. cover a suite topics including; optimizing sample collection, developing species-specific assays, evaluating bioindicator species, assessing microbial activity, diverse freshwater marine habitats. Emerging applications, such as use genome skimming identify fish markers, showcase advancements this field. also highlight challenges, including need standardized protocols ethical considerations must be addressed before these tools can implemented or adopted decision making at national global scales. Together, contributions demonstrate transformative potential nucleic acids' advancing conservation By bridging methodological rigor with applied research, provide an important resource researchers, policymakers, practitioners committed sustainable stewardship.

Language: Английский

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Insights in Pharmaceutical Pollution: The Prospective Role of eDNA Metabarcoding

Toxics, Journal Year: 2023, Volume and Issue: 11(11), P. 903 - 903

Published: Nov. 5, 2023

Environmental pollution is a growing threat to natural ecosystems and one of the world’s most pressing concerns. The increasing worldwide use pharmaceuticals has elevated their status as significant emerging contaminants. Pharmaceuticals enter aquatic environments through multiple pathways related anthropogenic activity. Their high consumption, insufficient waste treatment, incapacity organisms completely metabolize them contribute accumulation in environments, posing all life forms. Various analytical methods have been used quantify pharmaceuticals. Biotechnology advancements based on next-generation sequencing (NGS) techniques, like eDNA metabarcoding, enabled development new for assessing monitoring ecotoxicological effects metabarcoding valuable biomonitoring tool pharmaceutical because it (a) provides an efficient method assess predict status, (b) identifies sources, (c) tracks changes levels over time, (d) assesses ecological impact pollution, (e) helps prioritize cleanup mitigation efforts, (f) offers insights into diversity composition microbial other bioindicator communities. This review highlights issue while emphasizing importance using modern NGS-based actions its environmental more consistently effectively.

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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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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Looking to the past to inform the future: What eDNA from herbarium specimens can tell us about plant–animal interactions

Applications in Plant Sciences, Journal Year: 2025, Volume and Issue: 13(2)

Published: Feb. 5, 2025

The importance of natural history collections in modern ecological and genetic research cannot be overstated. Herbarium specimens provide historical information that can used to investigate community ecology, phenology, population genetics. In this study, environmental DNA (eDNA) metabarcoding next-generation sequencing were test the efficacy detecting plant-animal interactions from herbarium specimen flowers. A modified eDNA isolation method standard Illumina protocols used. Animal was amplified using both cytochrome c oxidase subunit I (COI) 16S primers increase detection probability. relationship between age (0-69 years) target taxa read depth also investigated. We generated identified over 1.5 million sequences animal belonging 29 clades (families or orders). These methods enabled including birds, mammals, hymenopterans, lepidopterans, coleopterans, "intrafloral" communities. While overall yielded less identifiable compared fresh material, negligibly affected amount and/or non-target detected With careful consideration types data may obtained through sampling specimens, these could prove valuable future on interactions.

Language: Английский

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Monitoring of the Invasive Round Goby (Neogobius melanostomus) in an Estuarine Seascape Based on eDNA

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

Published: March 1, 2025

ABSTRACT In marine environments, nonindigenous species (NIS) are especially difficult to manage since they often first detected when fully established and near impossible eradicate. The development implementation of effective monitoring methods for NIS therefore crucial early detection valuable management. this study, we develop evaluate environmental DNA using quantitative digital PCR (dPCR) assess the presence euryhaline round goby ( Neogobius melanostomus ) in a seascape environment close Scandinavia's largest shipping port. We developed dPCR assay species, targeting region 12S gene, verified its specificity compared other locally common from gobiid family. Using captive live fish, also experimentally determined decaying rate N. water half‐life 9.8 h 15 ppt salinity 15°C. Finally, sampled 10 sites within 400 km 2 area eDNA, fyke nets, baited remote video validate accuracy samples predict abundance species. found that number copies extracted varied strongly at where were caught nets or on video, but average value four significantly correlated with an total catch each site. eDNA signals no fish by fishing video. These results show method is sensitive low abundance, enough replicates, it can be possible determine relative between sites.

Language: Английский

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Environmental DNA metabarcoding differentiates between micro‐habitats within the rocky intertidal

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(2)

Published: March 1, 2024

Abstract While the utility of environmental DNA (eDNA) metabarcoding surveys for biodiversity monitoring continues to be demonstrated, spatial and temporal variability eDNA, thus limits differentiability an eDNA signal, remains under‐characterized. In this study, we collected samples from distinct micro‐habitats (~40 m apart) in a rocky intertidal ecosystem over their exposure period tidal cycle. During period, transitioned being interconnected, physically isolated, interconnected again. Using well‐established eukaryotic (cytochrome oxidase subunit I) assay, detected 415 species across 28 phyla. Across variety univariate multivariate analyses, using exclusively taxonomically assigned data as well all amplicon sequence variants (ASVs), identified unique signals different sampled. This paralleled expected ecological gradients increased sites became more disconnected. Our results demonstrate that biomonitoring can differentiate only 40 apart, these differences reflect known ecology area, physical connectivity informs degree differentiation possible. These findings showcase potential power increase resolution marine data, aiding research, conservation, management efforts.

Language: Английский

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