Technology Readiness Level of biodiversity monitoring with molecular methods – where are we on the road to routine implementation?

Metabarcoding and Metagenomics, Год журнала: 2025, Номер 9

Опубликована: Янв. 30, 2025

Human activities are causing rapid biodiversity loss across ecosystems, affecting human well-being and crucial ecosystem services. Traditional monitoring tools cannot keep up with the increasing demands of due to their limited spatial or temporal coverage, high costs, lack taxonomic expertise. Thus, implementation novel molecular methods such as environmental DNA (eDNA) metabarcoding, necessary. Molecular offer significant benefits for assessment: sensitivity accuracy, non-invasive sampling, broad range cost time efficiency. However, diverse methodological approaches lead poor comparability between studies surveys, highlighting need standardised assessments. We used Technology Readiness Level (TRL) framework evaluate maturity methods, providing a structured assessment readiness routine use. In systematic literature review, 420 articles fulfilling study criteria were assessed both individual method categories ranked according TRL scale. The findings revealed growing number studies, particularly in aquatic environments, most validating technologies on small scale but lacking large-scale system demonstrations. Aquatic eDNA-based targeting fish showed overall higher technology compared other sample types taxa applications into highest predominantly freshwater studies. Key barriers broader include international standards, better quantitative estimates comprehensive reference libraries. National cooperation is establishing common ensuring reliable comparable results expediting use monitoring. Recent efforts towards standardisation encouraging, further coordinated actions necessary global acceptance these methods.

Язык: Английский

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Marine invasive alien species in Europe: 9 years after the IAS Regulation

Frontiers in Marine Science, Год журнала: 2023, Номер 10

Опубликована: Окт. 11, 2023

Biological invasions, resulting from human activities, exert substantial impacts on ecosystems worldwide. This review focuses marine invasive alien species (IAS) in Europe, examining the current state, proposing strategies to address problem, and offering recommendations for enhanced management. Effective management of biological invasions relies accessible, accurate data inform decision-making. Information systems such as European Alien Species Network (EASIN), Aquatic Non-Indigenous Cryptogenic (AquaNIS), World Register Introduced Marine (WriMS) provide comprehensive databases IAS, but their sustainability requires long-term maintenance, continuous updates, support. Most countries lack specific monitoring programs standardization improvement methods are needed. Port plays a vital role early detection new arrivals, recent advancements molecular techniques show promise effective IAS monitoring. Risk screening tools commonly employed rank taxa based invasiveness potential regions, variations protocols can yield inconsistent results. impact assessments highlight resource competition, novel habitat creation, predation primary mechanisms negative biodiversity, while creation habitats represents key mechanism positive impacts. Preventing introductions is critical, measures ballast water treatment implemented reduce likelihood introductions. However, understanding introduction pathways remains uncertain many IAS. Eradication control efforts have limited success, emphasizing need biosecurity measures. Climate change, especially ocean warming, intensify native ecosystems. In climate change hotspots, some tropical aliens may, however, compensate loss thermally sensitive natives with similar traits. Therefore, it imperative consider interactions between developing conservation strategies. Enhancing Europe entails i) securing adequate funding, ii) expanding list Union Concern adequately cover iii) learning successful practices, iv) sustaining information systems, v) improving warning innovative technologies, vi) enhancing prediction models, vii) conducting integrated mapping cumulative impacts, considering benefits ecosystem functioning services.

Язык: Английский

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Advective Transport Drives Environmental DNA Dispersal in an Estuary

Environmental Science & Technology, Год журнала: 2025, Номер unknown

Опубликована: Апрель 11, 2025

Environmental DNA (eDNA) is increasingly used for species detection and biodiversity monitoring in estuary marine environments. The dynamic nature of these environments affects eDNA distribution relative to its source organisms, complicating the interpretation observations challenging field sampling design. Here, an fate transport model, built on ocean model with Lagrangian particle tracking, provided a spatiotemporal estimate rapidly diluted shed by rare targets environment before sampling. Based predicted densities, over 70% preselected stations detected target eDNA. Despite potential variations strength patchy distributions, explained approximately 40% observed variation abundance; comparison, concentration was uncorrelated straight-line distance from or simplified oceanographic model. Our study revealed extent advective shaping abundance demonstrated utility models tracking integrating degradation, transport, dilution processes; thus, it suggests broader applications enhance understanding signals dispersal optimize strategies other estuarine

Язык: Английский

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Abundance estimation with DNA metabarcoding – recent advancements for terrestrial arthropods

Metabarcoding and Metagenomics, Год журнала: 2023, Номер 7

Опубликована: Ноя. 23, 2023

Biodiversity is declining at alarming rates worldwide and large-scale monitoring urgently needed to understand changes their drivers. While classical taxonomic identification of species time labour intensive, the combination with DNA-based methods could upscale activities achieve larger spatial coverage increased sampling effort. However, challenges remain for when number individuals per and/or biomass estimates are required. Several methodological advancements exist improve potential DNA metabarcoding abundance analysis, which however need further evaluation. Here, we discuss laboratory, as well some bioinformatic adjustments workflows regarding estimation from arthropod community samples. Our review includes pre-laboratory processing such specimen photography, laboratory use spike-in an internal standard like correction factors. We conclude that photography coupled currently promises greatest estimates, but approaches spike-ins factors promising pursue further.

Язык: Английский

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Centering accessibility, increasing capacity, and fostering innovation in the development of international eDNA standards

Metabarcoding and Metagenomics, Год журнала: 2024, Номер 8

Опубликована: Сен. 24, 2024

Environmental DNA (eDNA) includes a set of rapidly emerging technologies that have the potential to support environmental monitoring and biodiversity conservation through novel, non-invasive, cost-effective democratic methods tools. Meanwhile, eDNA researchers are developing international standards for technologies, data outputs. For be accessible, useful appropriate, we must ensure any developed include broad conception users from around world, diversity ecological contexts locations and, most importantly, realistic outlook on research capacities infrastructure. In this article, assemble perspectives standardisation diverse global group experts Africa, South America Pacific Islands. The authors article collaborated by answering discussing open-ended questions aimed at eliciting hopes, concerns experiences regarding standards. result is emergent themes generative consensus highlight need creation adaptable standards, development regional capacity, increased sensitising sovereignty viewing as capacity-building activity.

Язык: Английский

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Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoring

Metabarcoding and Metagenomics, Год журнала: 2025, Номер 9

Опубликована: Янв. 10, 2025

DNA metabarcoding of benthic diatoms has been successfully applied for biomonitoring at the national scale and can now be considered technically ready routine application. However, protocols methods still vary between within countries, limiting their transferability comparability results. In order to overcome this, use diatom requires knowledge sources variability introduced by different steps procedure. Here, we examine how elements procedures contribute European laboratories. A set four experiments were performed focusing on extraction PCR amplification evaluate reproducibility laboratories currently scientific community. Under guidance a reference laboratory, 17 participants from 14 countries in parallel, using same fixed protocol own choice protocol. Experiments each participant standardised biofilm samples (river, lake mock community) investigate potential systematic random errors. Our results revealed successful amongst labs highly similar consistent ecological assessment outcome obtained regardless used participant. We propose an “all one but prove them all” strategy, suggesting that distinct community, as long consistency is proven following minimum standard requirements.

Язык: Английский

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A novel ddPCR™ assay for eDNA detection and quantification of Greater Amberjack Seriola dumerilli and three congeners in US waters: challenges and application to fisheries independent surveys

PeerJ, Год журнала: 2025, Номер 13, С. e18778 - e18778

Опубликована: Янв. 27, 2025

Four Seriola species support recreational and commercial fisheries along the U.S. Atlantic Ocean Gulf of Mexico, with S. dumerili Mexico stock being overfished for over three decades. The study presented here is part a fisheries-independent project initiated to determine an absolute abundance dumerili, expand biological knowledge develop novel tools management. Environmental DNA (eDNA) aimed at detection quantification target are starting emerge in marine surveys. Key progressing field Droplet Digital™ PCR (ddPCR™), highly sensitive technique advanced multiplexing direct capabilities that can provide scientists improved interpretation eDNA data. We developed validated tetraplex ddPCR™ assay able detect distinguish between fasciata, rivoliana, zonata from seawater samples. In order groundtruth data, explore its capacity estimates, we compared detections quantifications data inferred multiple camera (ROV, S-BRUV, chevron trap) acoustic (VPS array) gears deployed during research gear-calibration cruise. demonstrated contamination controls best practice protocols, it viable conduct as survey sampling was completed less time than (15 min vs 2 h). Both detected presence rivoliana both sites all days, but not fasciata zonata. concentration higher line patterns obtained gears. highest correlation (r = 0.97) measures gear deployments ROV. Incorporating surveys would require additional days sea could improve precision fish abundance. be valuable complement geographic areas or seasons poor visibility conditions, where may present cannot confidently identified level. high ROV collected adds growing number studies demonstrating potential indicator assessments. Time-series carefully designed survey, estimates relative abundance, used index assessment. To achieve this, investment into follow-up increased sample sizes spatial temporal replication necessary allow year-to-year comparisons validate robustness observed.

Язык: Английский

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Navigating uncertainty in environmental DNA detection of a nuisance marine macroalga

PLoS ONE, Год журнала: 2025, Номер 20(2), С. e0318414 - e0318414

Опубликована: Фев. 4, 2025

Early detection of nuisance species is crucial for managing threatened ecosystems and preventing widespread establishment. Environmental DNA (eDNA) data can increase the sensitivity biomonitoring programs, often at minimal cost effort. However, eDNA analyses are prone to errors that complicate their use in management frameworks. To address this, studies must consider imperfect detections estimate error rates. Detecting low abundances with uncertainty vital successful containment eradication. We developed a novel assay detect marine macroalga across its colonization front using surface seawater samples from Papahānaumokuākea Marine National Monument (PMNM), one world’s largest reserves. Chondria tumulosa cryptogenic red alga invasive traits, forming dense mats overgrow coral reefs smother native flora fauna PMNM. verified site-occupancy modeling quantitative polymerase chain reaction (qPCR) data, calibrated visual estimates benthic cover C . ranged < 1% 95%. Results were subsequently validated high-throughput sequencing amplified negative control samples. Overall, probability detecting occupied sites was least 92% when multiple qPCR replicates positive. False-positive rates 3% or less false-negative 11% less. The proved effective routine monitoring shallow (less than 10 m), even abundance below 1%. Successful implementation tools conservation decision-making requires balancing uncertainties both molecular methods. Our results demonstrated assay’s high , we outline steps infer ecological presence-absence data. This reliable, cost-effective tool enhances low-abundance species, supports timely interventions.

Язык: Английский

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Translating eDNA data into conservation action: Partnerships to support imperiled amphibians in coastal California wetlands

Conservation Science and Practice, Год журнала: 2025, Номер unknown

Опубликована: Фев. 3, 2025

Abstract Environmental DNA (eDNA) detections of imperiled species have the potential to inform conservation action, but this requires acceptance new technologies by decision‐makers. Here we describe how engaging stakeholders into a collaborative process led successful translation eDNA findings outcomes. We characterized distribution three federally listed pond‐breeding amphibians across nearly 200 wetlands in coastal California using both traditional field surveys and sampling; latter had greater detection rates overall. Regulatory agency staff gained trust rigor effectiveness data joining through development recommendations for adoption methods. Extensive outreach local community within range highly endangered Santa Cruz long‐toed salamander resulted invitations sample previously unsurveyed on private property breeding sites. Conservation organizations resource management agencies were integrated our core team from start, ultimately shaped wetland actions, siting wetlands, land acquisition priorities informed generated. Thus, project serves as model actionable science directly affecting conservation.

Язык: 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, Год журнала: 2025, Номер 13(2)

Опубликована: Фев. 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.

Язык: Английский

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