Environmental DNA最新文献

{"title":"Out in the Open: Investigating Passive Airborne eDNA Detection of Bats at Artificial Feeding Stations","authors":"Daniel E. Sanchez,&nbsp;Faith M. Walker,&nbsp;Savannah J. Marriott,&nbsp;Anna L. Riley,&nbsp;Sarah Stankavich,&nbsp;Amanda M. Adams,&nbsp;Donald Solick,&nbsp;Doug Bradley,&nbsp;Christian Newman","doi":"10.1002/edn3.70108","DOIUrl":"https://doi.org/10.1002/edn3.70108","url":null,"abstract":"<p>Environmental DNA (eDNA) is a valuable biomonitoring tool, but application in terrestrial settings remains challenging due to a lack of generalizable sampling approaches. With bat species needing urgent research attention, airborne eDNA may offer this generalizability, as current eDNA sampling for bats is mostly limited to conspicuous sources (e.g., guano). While previous studies detected bats from roosts and open-air sites using active air sampling, it remains uncertain whether bats can be readily detected from the open air using passive approaches. In central Texas, we used passive air sampling to determine if we could recover bat assemblages with metabarcoding and an imperiled focal species (tricolored bat, <i>Perimyotis subflavus</i>) with qPCR. Outside two cave locations, we positioned passive air samplers (two collection media per sampler; <i>n</i> = 24 media) near artificial prey patches, monitoring acoustically for bat activity and foraging. In the lab, we subjected the media to multiple eDNA extraction methods, direct DNA extraction, and two resuspension-concentration approaches (filtration and pelleting). Metabarcoding allowed the detection of two bat species within a single sample, while qPCR allowed detection of <i>P. subflavus</i> in two samples. Although the detections all came from direct extraction, pelleting substantially improved taxonomic recovery and sample success for vertebrates overall. Detection of bat eDNA from passive samplers establishes a lower bound possibility for open-air settings, and the low number of detections highlights the need for improved sampling strategies. We offer recommendations to enhance future efforts and introduce a qPCR assay for <i>P. subflavus</i> that can be used in a variety of eDNA contexts.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70108","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143925815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CRISPR-Based Environmental Biosurveillance Assisted via Artificial Intelligence Design of Guide-RNAs","authors":"Benjamín Durán-Vinet,&nbsp;Jo-Ann L. Stanton,&nbsp;Gert-Jan Jeunen,&nbsp;Ulla von Ammon,&nbsp;Jackson Treece,&nbsp;Xavier Pochon,&nbsp;Anastasija Zaiko,&nbsp;Neil J. Gemmell","doi":"10.1002/edn3.70105","DOIUrl":"https://doi.org/10.1002/edn3.70105","url":null,"abstract":"<p>Environmental biosecurity challenges are intensifying as climate change and human activities accelerate the spread of invasive species, disrupting ecosystem composition, function, and essential services. Environmental DNA (eDNA) has transformed traditional biosurveillance by detecting trace DNA fragments left by organisms in their surroundings, primarily by applying quantitative polymerase chain reaction (qPCR) methods. However, qPCR presents challenges, including limited portability, reliance on precise thermal cycling, and susceptibility to inhibitors. To address these challenges and enable field-deployable monitoring, isothermal amplification techniques such as recombinase polymerase amplification (RPA) paired with clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) have been proposed as promising alternatives. CRISPR-Cas technology also presents challenges, including searching and optimizing a guide RNA (gRNA) that is highly sensitive and has no off-target interactions for use as an effective environmental biosurveillance tool. We present here the development of SENTINEL (<b>S</b>mart <b>E</b>nvironmental <b>N</b>ucleic-acid <b>T</b>racking using <b>I</b>nference from <b>N</b>eural-networks for <b>E</b>arly-warning <b>L</b>ocalization) that harnesses the programmability, specificity and sensitivity of a one-pot RPA-CRISPR-Cas13a reaction by integrating an accessible and pre-trained neural network to accelerate assay design for rapid deployment. We challenged SENTINEL with waterborne eDNA from two marine sites invaded by species not native to New Zealand as proof-of-concept fluorescence-based tests: <i>Sabella spallanzanii</i> (Mediterranean fanworm) and <i>Undaria pinnatifida</i> (Wakame). Off-target effects were explored by challenging the SENTINEL assays on gDNA from a suite of co-occurring species. SENTINEL presented a robust, streamlined method incorporating the trained neural network, achieving a sensitivity down to 10 attomolar using recombinant DNA and down to ~0.34 copies/μL for eDNA samples with 1 h, costing 3.5 USD per sample. There was a 100% agreement between SENTINEL results and qPCR-based analysis of the eDNA samples. SENTINEL displayed no off-target activity when challenged against 23 gDNA samples from co-occurring species. Thus, our study showcases SENTINEL's potential as a robust platform for eDNA screening applications.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70105","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143925816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Time- and Cost-Effective eDNA Protocol to Survey Freshwater Mussels (Bivalvia: Unionida) in Tropical Rivers","authors":"Alexandra Zieritz,&nbsp;Tabitha Richmond,&nbsp;Florian Melzer,&nbsp;Khairul Adha A. Rahim,&nbsp;John-James Wilson,&nbsp;Hazeeqah Filzah binti Kassim,&nbsp;Hanna Hartikainen","doi":"10.1002/edn3.70099","DOIUrl":"https://doi.org/10.1002/edn3.70099","url":null,"abstract":"<p>Tropical freshwater mussels (Bivalvia: Unionida) are one of the most endangered groups of animals globally, but conservation is hindered by a lack of species distribution data. Traditional hand-sampling is time- and cost-intensive and not always possible, for example, because of the presence of crocodiles. Surveying freshwater mussel populations by environmental DNA (eDNA) could potentially rapidly increase data availability, but no published study and protocols targeted towards tropical freshwater mussels are available to date. We aimed to develop a reliable and cost-efficient eDNA protocol for surveying tropical freshwater mussels. We first developed and validated a qPCR primer-probe assay within the cytochrome <i>c</i> oxidase subunit 1 (COI) gene for <i>Rectidens sumatrensis</i>. We applied this assay in a controlled laboratory setting on eDNA collected from lake and river water, respectively, at two different <i>R. sumatrensis</i> densities in order to test a set of 18 different protocols for capturing, preserving, and extracting freshwater mussel eDNA. All protocols use equipment that is readily available and reusable. Our results revealed that samples stored in Longmire's buffer (at 4°C) yielded more mussel DNA than when stored in absolute ethanol (at −20°C), with &lt; 1% of ethanol- and 78% of buffer-preserved samples fulfilling the criteria for positive <i>R. sumatrensis</i> eDNA detection (i.e., amplifying above the limit of detection in at least four out of five qPCR replicates). Across buffer-preserved samples, eDNA detection and amplification success rates were higher and quantification cycle values were lower for eDNA captured without pre-filtration and with filter membrane pore sizes &gt; 0.45 μm, and eDNA extracted with the Qiagen DNeasy Blood &amp; Tissue Kit rather than the PowerSoil ProKit (albeit latter exhibiting fewer instances of amplification in negative controls). The assay detailed here was capable of detecting down to <i>R. sumatrensis</i> eDNA concentrations of 6.38 × 10⁻⁷ ng/μL and reflected the difference in stocking density.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70099","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143926011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Impact of Flow Velocity on Environmental DNA Detectability for the Application in River Systems","authors":"Jelle A. Dercksen,&nbsp;Jan Willem Foppen,&nbsp;Astrid Blom,&nbsp;Krijn B. Trimbos,&nbsp;Julia Gebert,&nbsp;Thom A. Bogaard,&nbsp;Laura Maria Stancanelli","doi":"10.1002/edn3.70111","DOIUrl":"https://doi.org/10.1002/edn3.70111","url":null,"abstract":"<p>Organisms perpetually release genetic material in their surroundings, referred to as environmental DNA (eDNA), which can be captured and subsequently analyzed to detect biodiversity across the tree of life. In lotic, dynamic environments, little is known about the specific factors that affect the concentration of eDNA between release by the host and its dissemination into the environment. This gap in knowledge introduces significant uncertainty when applying eDNA as a monitoring tool. Our objective is to provide insight on the factors that affect the eDNA concentrations in ecosystems representative of rivers and streams. To this end, we conducted a series of laboratory experiments in a rotating circular (annular) flume, which allows for extended degradation experiments under conditions of flow. Here, we show that flow velocity impacts the observed eDNA concentration over time. Our results suggest that flow-induced transport keeps eDNA in suspension, reducing eDNA removal from the water column, which increased the observed concentration of eDNA. We observed a temporary increase in eDNA concentration over the early phase of the flume experiment with the highest flow velocity. This increase in eDNA concentration seems to be due to a combination of low eDNA degradation rates and high shear stress, which fragment and subsequently homogenize eDNA particles over the water column. The results of our study show the importance of better understanding and assessing the detection probability of eDNA, both in controlled laboratory and larger-scale environmental conditions.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70111","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143919320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Capture—Incubate—Release: An Animal-Friendly Approach to Assess Local Aquatic Macroinvertebrate Species Diversity Through Environmental DNA Metabarcoding","authors":"Mandy Sander,&nbsp;Arne J. Beermann,&nbsp;Dominik Buchner,&nbsp;Martina Weiss,&nbsp;Marie-Thérése Werner,&nbsp;Florian Leese","doi":"10.1002/edn3.70112","DOIUrl":"https://doi.org/10.1002/edn3.70112","url":null,"abstract":"<p>Metabarcoding of environmental DNA (eDNA) from water samples has become an important tool for aquatic biodiversity assessment because it is minimally invasive, time-efficient, and generates comprehensive taxa lists. Nevertheless, species lists differ noticeably from those obtained via bulk metabarcoding of the local benthic community because of eDNA traces transported in the water column. However, it is important for several assessments to capture local biodiversity signals. Our goal was to test whether we can combine the advantages of both methods, that is, obtaining a local signal and being minimally invasive. Therefore, our developed method includes capturing local benthic invertebrates, incubating them in a water container for eDNA enrichment and analysis, and releasing them back to their habitat. We first quantified eDNA release over time for 10 invertebrate species in a laboratory setting using qPCR. We found that a 5-min incubation is sufficient to successfully detect 50% of the replicates for six of the 10 species. Three of the species showed a significant increase in eDNA molecules over time. However, the experiment showed a species-specific eDNA release pattern that was not directly linked to body sclerotization nor biomass. As a second experiment, we sampled bulk samples at three field sites and incubated the bulk samples for 0, 20, 40, and 80 min in containers filled with stream water to compare taxa lists obtained via metabarcoding of bulk and the enriched eDNA samples. Our results showed a much higher overlap between bulk and enriched eDNA metabarcoding (55%–60%) in comparison to reported overlaps between bulk and stream eDNA metabarcoding from other studies (often &lt; 20%). This overlap did not change with incubation time. Thus, our study demonstrates that it is possible to detect most locally occurring species via eDNA metabarcoding after shortly incubating them in water. Therefore, this approach has great potential for point-sample eDNA analysis of macroinvertebrates without compromising animal welfare.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70112","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143904894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Harnessing eDNA Metabarcoding to Monitor Species Diversity in Restoration Sites: Insights From Laikipia, Kenya","authors":"Cornelius Okello,&nbsp;Nina Wambiji,&nbsp;Susana W. Kihia,&nbsp;Nehemiah Ongeso,&nbsp;Samuel Mwakisha Mwamburi,&nbsp;Anthony Wandera,&nbsp;Marie-Estelle Demory,&nbsp;Margaret Awuor Owuor","doi":"10.1002/edn3.70110","DOIUrl":"https://doi.org/10.1002/edn3.70110","url":null,"abstract":"<p>Restoration of degraded arid and semi-arid lands (ASALs) dryland ecosystems gained traction globally with the enactment of the Bonn Challenge and UN Decade of Restoration. This has been domesticated in Kenya's context by The Forest and Landscape Restoration Implementation Plan (FOLAREP). However, effectively monitoring restored ecosystems is crucial but challenging because of data gaps and technical hurdles, highlighting the need for innovative approaches to assess and restore biodiversity. This study aimed to pilot soil environmental DNA (eDNA) metabarcoding to detect species compositions rapidly, evaluate population structures and abundances, and characterize taxonomic groups. The results from this study serve as a foundational step toward monitoring the impact of water bunds, a restoration approach on biodiversity conservation, in Lower Naibunga Community Conservancy in Laikipia County, Kenya. This study used 16S rDNA and rbCL metabarcoding to assess prokaryotic and plant diversity. Plant growth-promoting rhizobacteria species attributed to enhancing nutrient availability and improving plant resilience to abiotic stress were prevalent across all six sites: Lorubai (Site 1), Burtany (Site 2), Nkirashi (Site 3), Losopukia (Site 4), Munushoi (Site 5), and Loika (Site 6). Plant species attributed to drought tolerance and rangeland rehabilitation were also identified. The study demonstrates the potential of eDNA metabarcoding as an effective tool for monitoring nature-based solutions (NbS) interventions to enhance biodiversity and ecosystem restoration in ASALs.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70110","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143904992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental DNA Methods for Detection of Varroa destructor in Honey Bee (Apis mellifera) Hives","authors":"John M. K. Roberts,&nbsp;Richard J. Hall,&nbsp;Foyez Shams,&nbsp;Francisco Encinas-Viso,&nbsp;Florence Bravo,&nbsp;Jenn Soroka,&nbsp;Liz Milla,&nbsp;Natale Snape,&nbsp;Francesco Martoni,&nbsp;Antonette Walford,&nbsp;Dianne Gleeson,&nbsp;Alejandro Trujillo-González","doi":"10.1002/edn3.70109","DOIUrl":"https://doi.org/10.1002/edn3.70109","url":null,"abstract":"<p>The parasitic mite, <i>Varroa destructor</i>, is a worldwide problem for honey bees (<i>Apis mellifera</i>). The recent spread of this pest to Australia, which was one of the few varroa-free honey bee populations remaining, highlights the importance of effective biosecurity methods for managing incursions. Detection of varroa mite environmental DNA (eDNA) could be a valuable complementary tool to increase the sensitivity and cost-effectiveness of varroa surveillance as it spreads to new areas. Using a newly developed <i>V. destructor</i> quantitative PCR assay, we deployed eDNA testing on honey bee hives in New Zealand and Australia with a range of mite infestation levels. The detection sensitivity of eDNA methods using honey and hive surface swabs was comparable with a conventional alcohol wash method used by beekeepers, with the advantage of not harming bees. However, we observed greater variability in eDNA detection, particularly for hive entrance swabs, when estimated mite infestation levels were below 1%. Using varroa-free hives introduced from the Chatham Islands to Wellington, New Zealand, we were also able to show that <i>V. destructor</i> eDNA was detectable during the initial invasion of hives. Our data highlight the potential for incorporating eDNA methods into Australia's biosecurity surveillance programs to help limit the spread of varroa mites to new areas and detect future incursions.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70109","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143904893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabarcoding Versus Species-Specific Primers to Estimate Salmo trutta Biomass and Density in Mountain Streams","authors":"Alba M. Losa,&nbsp;Alejandra Goldenberg-Vilar,&nbsp;María Morán-Luis,&nbsp;David R. Vieites,&nbsp;Jose Barquín,&nbsp;Agustín P. Monteoliva","doi":"10.1002/edn3.70090","DOIUrl":"https://doi.org/10.1002/edn3.70090","url":null,"abstract":"<p>Environmental DNA (eDNA) is a cost-efficient, noninvasive method to monitor fish populations, but the quantitative aspect of this technique (e.g., estimating biomass or densities) remains underexplored. Few studies have established relationships between fish DNA concentration and biomass/density. Here, we investigate the relationship between eDNA concentration (copies per liter) and trout biomass and densities estimated by electrofishing in mountain streams of Picos de Europa National Park (Spain). We assessed eDNA effectiveness in inferring biomass/density using 18S rRNA (18S) and cytochrome c oxidase I (COI) metabarcoding, and quantitative PCR with a COI-specific <i>Salmo trutta</i> primer, each performed with different datasets from the same sampling points. Salmonidae eDNA concentration positively correlates with trout biomass and density. Both 18S and specific-COI markers showed a significant increase in DNA concentration as trout biomass and density rose in electrofishing surveys. However, general COI did not exhibit significant trout DNA concentration and biomass/density relationships, despite providing greater taxonomic resolution at the species level. Further analysis exploring eDNA concentration and biomass/densities across different trout size classes (fry, juvenile, and adult) revealed that juvenile trout biomass contributed the most to the observed eDNA concentration–biomass/density relationship. Our results suggest that DNA concentration estimated from metabarcoding, when using an appropriately selected primer, can reliably indicate trout biomass and density in these mountain streams where trout is the dominant species. Although quantitative PCR showed similar trends, it had lower explanatory power. This study highlights the importance of integrating a quantitative framework in metabarcoding for ecological monitoring and biodiversity assessments. Factors such as amplicon length, genetic region, marker specificity, or fish size class can influence the relationship between sequencing reads and electrofishing data. This methodology could aid the conservation and management of fish populations and other communities, though further research is needed to extend these results and assess eDNA detection reliability.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70090","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143852861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing the Relationship Between Sedimentary Microbial Community Structure and Pollutants in Stormwater Wetlands Using eDNA Metabarcoding","authors":"Anna S. Flynn,&nbsp;Kathryn L. Hassell,&nbsp;A. Mark Osborn,&nbsp;Vincent Pettigrove,&nbsp;Jeff Shimeta,&nbsp;Sara M. Long","doi":"10.1002/edn3.70096","DOIUrl":"https://doi.org/10.1002/edn3.70096","url":null,"abstract":"<p>Environmental pollution is regarded as one of the most substantial threats facing freshwater ecosystems. Two contaminant types in particular, metals and pesticides, represent both long-term and widespread hazards to aquatic environments. Contamination negatively affects the health of aquatic flora and fauna. Constructed wetlands are an important mitigation measure for managing stormwater in urban landscapes. Given that constructed wetlands are designed to capture and retain contaminants from stormwater in sediments, the resulting chemical profiles are largely representative of contamination in the surrounding local catchment and aquatic environments. Environmental DNA is expanding the field of aquatic monitoring, introducing the ability to assess biological profiles quickly and reliably, and expanding the knowledge of how contamination affects ecosystems down to a microbial level. Here, we used environmental DNA (eDNA) metabarcoding to characterize the sedimentary microbial profiles of nine urban stormwater wetlands and one rural wetland with low levels of contamination and assess the variation in community structures between sites as well as between the inlet and outlet within each site. We found significant variation in microbial communities between the rural (reference) wetland and stormwater wetlands, variation between some stormwater wetlands, and between over half of the inlets to outlets. The bacterial phyla Cyanobacteria and Proteobacteria were mostly driving this variation, along with Planctomycetota and Bacteroidota. We also found correlations between microbial community structure and chemical occurrences, particularly zinc and barium, with the latter not previously reported to be associated with microbial dynamics in freshwater environments. Our study validates the ability of eDNA metabarcoding to reliably evaluate sedimentary microbial profiles in stormwater wetlands and highlights its value in the assessment and prediction of contamination in these environments.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70096","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143840581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative Analysis of Environmental DNA Metabarcoding and Spectro-Fluorescence for Phytoplankton Community Assessments","authors":"Romana Salis,&nbsp;Lars-Anders Hansson","doi":"10.1002/edn3.70097","DOIUrl":"https://doi.org/10.1002/edn3.70097","url":null,"abstract":"<p>Quantifications of phytoplankton biomass and species composition are crucial for monitoring biodiversity and population dynamics in aquatic environments, and both direct microscopic counts and fluorescence-based methods have been widely used for monitoring. Recent advancements in DNA metabarcoding offer an alternative way of easily assessing diversity and species composition. However, a comprehensive comparison of the relative merits and limitations of DNA- and fluorescence-based methods is currently lacking. Here we compare phytoplankton community composition measured via fluorescence and DNA metabarcoding in an outdoor, replicated mesocosm experiment. We show that there is a positive correlation between fluorescence-measured biomass and DNA read and amplicon sequence variants (ASV) numbers for cyanobacteria, but either weak or no correlation for the other phytoplankton groups assessed (cryptophytes, chromophytes, and green algae). In addition, DNA metabarcoding was systematically better at detecting cryptophytes, which were rarely detected via fluorescence. Hence, while DNA metabarcoding may not provide reliable biomass estimates for the majority of phytoplankton groups, metabarcoding analysis offers higher taxonomic resolution and the capability to detect rare phytoplankton groups. Overall, our findings provide new insights into the strengths and limitations of each method and highlight the considerable potential and importance of including DNA barcoding in freshwater ecosystem assessment and biomonitoring programmes with a focus on biodiversity assessments.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70097","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143840653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}