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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A National Scale “BioBlitz” Using Citizen Science and eDNA Metabarcoding for Monitoring Coastal Marine Fish

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

Published: March 28, 2022

Marine biodiversity is threatened by human activities. To understand the changes happening in aquatic ecosystems and to inform management, detailed, synoptic monitoring of across large spatial extents needed. Such challenging due time, cost, specialized skills that this typically requires. In an unprecedented study, we combined citizen science with eDNA metabarcoding map coastal fish at a national scale. We engaged 360 scientists collect filtered seawater samples from 100 sites Denmark over two seasons (1 p.m. on September 29th 2019 May 10th 2020), sampling nearly exact same time all sites, obtained overview largely unaffected temporal variation. This would have been logistically impossible for involved without help volunteers. high return rate 94% samples, total richness 52 species, representing approximately 80% Danish species 25% marine species. retrieved distribution patterns matching known occurrence both invasive, endangered, cryptic detected seasonal variation accordance phenology. Dissimilarity community compositions increased distance between sites. Importantly, comparing our data National Fish Atlas (the latter compiled century observations) found positive correlation values congruent pattern compositions. These findings support use eDNA-based detect biodiversity, approach readily scalable other countries, or even regional global scales. argue future large-scale biomonitoring will benefit using emerging technology, such be important data-driven management conservation.

Language: Английский

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

Frontiers in Marine Science, Journal Year: 2023, Volume and Issue: 10

Published: Oct. 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.

Language: Английский

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Tide impacts the dispersion of eDNA from nearshore net pens in a dynamic high‐latitude marine environment

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

Published: March 1, 2024

Abstract Environmental DNA (eDNA) is increasingly used to detect animals in aquatic habitats, but uncertainty remains about the relationship between present location of an animal relative eDNA detections. In marine environments, physical characteristics—such as tides and currents—can influence distribution eDNA. this study, we make use hatchery net pens containing >46 million juvenile chum salmon ( Oncorhynchus keta ) nearshore Southeast Alaska test for dispersion effects tide. Initially, collected filtered surface water every 80 m along a 2 km transect attenuation over distance during incoming outgoing on single day. The following year, sampled at three depths (0 m, 5 10 m) 500 same well perpendicular transect, understand by depth additional directions. Chum was quantified using species‐specific qPCR. We found that samples showed consistent signal decreasing across R = 0.665), with majority detections within 1.5 pens. Tide had significant effect, resulting higher concentrations throughout tide steeper decline 0.759). Depth affected concentration, amount increasing depth. This study addresses one critical knowledge gaps applying fisheries management providing empirical evidence demonstrating most are likely from nearby individuals either currently or recently present. Yet even close proximity, strength fluctuates depends environmental variables given sampling event.

Language: Английский

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A vision for global eDNA-based monitoring in a changing world

Cell, Journal Year: 2024, Volume and Issue: 187(17), P. 4444 - 4448

Published: May 15, 2024

Language: Английский

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Accumulation and diversity of airborne, eukaryotic environmental DNA

Environmental DNA, Journal Year: 2022, Volume and Issue: 4(6), P. 1323 - 1339

Published: July 18, 2022

Abstract Environmental DNA (eDNA) metabarcoding is increasingly being implemented as a non‐invasive and efficient approach for biodiversity research monitoring across ecosystems. However, accurate detection of species with eDNA requires robust experimental designs analysis carries risk contamination at every step the fieldwork laboratory processes. Several studies focus on rigorous procedures processing sequencing data, but surprisingly, little investigates process background input in field. For example, airborne from localities outside study area could potentially contaminate samples. Here, we use an setup to diversity accumulation eukaryotic exposed surfaces At two different natural locations, coastal marine site terrestrial grassland site, placed open containers each filled 0.5 liters water, which was then sampled eight successive time points after exposure surroundings. We found detected richness samples, reached its maximum end experiment, 24 h exposure. This result consistent both sites markers (COI eukaryotes 12S vertebrates). While many were contaminants commonly studies, also several other taxa. Most notable metazoan such birds, fish, insects, likely originating transport eDNA. that increasing number PCR cycles tended have positive impact unfiltered reads negative bioinformatic filtering. Our results add sparse evidence can be transported by air, wide implications calls increased implementation field control

Language: Английский

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Opportunities and inherent limits of using environmental DNA for population genetics

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(5), P. 1048 - 1064

Published: Aug. 9, 2023

Abstract Molecular techniques using DNA retrieved from community or environmental samples, in particular (eDNA), are becoming increasingly popular for detecting individual species, assessing biodiversity, and quantifying ecological indices. More recently, eDNA has also been proposed as a template population genetics, several studies have already tested the feasibility of this approach, mostly looking at vertebrate species. Their results along with general opportunities offered by these types “community‐based” such possibility to target multiple species same time, generated great enthusiasm expectations genetics. However, not every aspect genetics can be addressed eDNA‐based data some inherent limitations may challenge its conclusions. Here, we firstly review state current knowledge samples Then, focusing on eDNA, summarize but detail four main use population‐level inferences, namely, (1) difficulty retrieve species‐specific dataset, (2) potential lack correlation between observed true allelic frequencies, (3) loss information multi‐locus genotyping linkage loci, (4) uncertainty about individuals contributing sampled pool (e.g., number, life‐stage, sex). Some might overcome development new technologies models that account specificities eDNA. Others, however, inherent, their effect inferences must thoroughly evaluated. The gaining insights into genetic diversity structure is appealing scientists, conservation managers, other practitioners. Yet, avoid false incorrect it imperative known considered alongside advantages.

Language: Английский

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Deep‐sea sponge derived environmental DNA analysis reveals demersal fish biodiversity of a remote Arctic ecosystem

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(6), P. 1405 - 1417

Published: Aug. 18, 2023

Abstract The deep‐sea is vast, remote, and largely underexplored. However, methodological advances in environmental DNA (eDNA) surveys could aid the exploration efforts, such as using sponges natural eDNA filters for studying fish biodiversity. In this study, we analyzed from 116 sponge tissue samples compared these to 18 water visual obtained on an Arctic seamount. Across survey methods, revealed approximately 30% of species presumed inhabit area 11 were detected via derived alone. These included commercially important Greenland halibut Atlantic mackerel. Fish detection was highly variable across samples. Highest rates found with low microbial activity those class Hexactinellida. different methods also alternate communities, highlighted by only one overlap between Therefore, conclude that can be a useful tool surveying demersal communities it synergises improving overall biodiversity assessments. Datasets form comprehensive baselines seamounts, which turn inform marine management conservation practices regions where are undertaken.

Language: Английский

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Environmental DNA metabarcoding of pan trap water to monitor arthropod‐plant interactions

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

Published: March 1, 2024

Abstract Globally, the diversity of arthropods and plants upon which they rely are under increasing pressure due to a combination biotic abiotic anthropogenic stressors. Unfortunately, conventional survey methods used monitor ecosystems often challenging conduct on large scales. Pan traps commonly pollinator method environmental DNA (eDNA) metabarcoding pan trap water may offer high‐throughput alternative aid in detection both plant resources on. Here, we examined if eDNA can be identify species from water, investigated effect different extraction methods. We then compared identified by with observation‐based floral surveys also assessed contribution airborne (plant not carried arthropods) using marble reduce putative false positives dataset. Arthropod was only detected 17% samples there minimal overlap between results morphological identifications. In contrast, for plants, 64 taxa, 53 were unique dataset, no differences two kits. able significantly final dataset traps. This study demonstrates that detect highlights potential applied investigations arthropod‐plant interactions.

Language: Английский

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Tidal effect on environmental DNA communities in Arctic estuarine and marine ecosystems

Frontiers in Marine Science, Journal Year: 2024, Volume and Issue: 11

Published: June 13, 2024

Introduction Arctic marine ecosystems are changing rapidly, largely due to the observed accelerated warming that is associated with ongoing climate change. Environmental DNA (eDNA) combined metabarcoding has great potential for large-scale biomonitoring of communities. However, important limitations remain, such as understanding complexity and drivers spatio-temporal variation in eDNA distribution. Methods In this study, we investigated effect tidal dynamics on aquatic metazoan (vertebrates invertebrates) results from nearshore estuarine ports Churchill (Manitoba) Milne Inlet (Nunavut), respectively. We collected sequenced 54 water samples per port at low, middle high tide across three days, well two depths (surface, bottom), using four universal primer pairs (two primers COI gene 18S rRNA gene). Results a significant transition community structure low tide, whereas was more stable tides. The differed between surface bottom waters both ecosystems. biodiversity pattern within column significantly different Finally, short-term temporal communities systems. Discussion Altogether, our highlight dynamic nature derived coastal This variability should be accounted sampling design ensure robust characterization long-term time series, particularly environments where effects depth important.

Language: Английский

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