Environmental DNA最新文献

{"title":"Exploring Multifunctional Microbial Genes From the Rhizosphere of Allium ampeloprasum Under Different Fertilization Systems","authors":"Oluwaseun Emmanuel Shittu,&nbsp;Ben Jesuorsemwen Enagbonma,&nbsp;Olubukola Oluranti Babalola","doi":"10.1002/edn3.70275","DOIUrl":"10.1002/edn3.70275","url":null,"abstract":"<p>The diversity and environmental degradation caused by overreliance on chemical fertilizers in crop production have facilitated the development of alternatives to ensure agricultural sustainability. Previous studies have examined how fertilization affects functional genes in microorganisms in the root zones of cereals and legumes. However, the impact of fertilization on the functional genes of the vegetable rhizosphere remains underexplored. Therefore, this study aimed to identify the multifunctional genes associated with the <i>A. ampeloprasum</i> rhizosphere that are influenced by chemical fertilizers and biofertilizers. We extracted whole DNA from the soil samples of the <i>A. ampeloprasum</i> rhizosphere amended with chemical fertilizers and a biofertilizer. The mined DNA samples were analyzed through shotgun metagenomics sequencing to obtain functional genes of agricultural importance. Our findings revealed taxonomic groups with 43 functional genes with plant growth-promoting traits associated with fixing atmospheric nitrogen, solubilizing phosphate, producing phytohormones, and others. A greater prevalence of these genes was observed in the plot treated with biofertilizer (G2), with 22 genes compared with 11 genes found within the plot treated with synthetic fertilizer (G1) and 10 genes in the bulk soil plot (G3). Our microbiome analysis at the class taxonomic level revealed the prevalence of Actinomycetes, Alphaproteobacteria, and Acidimicrobiia. Our α diversity analysis results demonstrated that, compared with G1 and G3, G2 presented greater within-sample functional gene diversity. Compared with those of the other samples, β diversity analyses revealed partial differences in the microbial functional gene composition in the biofertilizer-treated soil (G2). These results indicate that biofertilizer application maintains a stable, functionally diverse microbial gene pool associated with stress tolerance, nutrient solubilization, and nutrient cycling, thereby supporting sustainable agriculture. This, however, highlights the potential of biofertilizers as sustainable soil amendments that can preserve microbial functional diversity without disrupting community diversity.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70275","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147668540","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 Great Microbiome Extraction Anomaly: How Extraction Bias Distorts Microbial Community Profiles","authors":"Daniel J. Browne","doi":"10.1002/edn3.70276","DOIUrl":"10.1002/edn3.70276","url":null,"abstract":"<p>Research on the human microbiome has become one of the most frequently published and highly cited areas in science. In parallel, environmental DNA (eDNA) and RNA (eRNA) microbiome studies have expanded rapidly, often using similar technical workflows. Numerous studies optimizing these workflows have demonstrated that nucleic acid purification can significantly influence bacterial metagenomic outcomes. Although this issue is widely acknowledged and efforts are often made to ensure workflow consistency, such protocol standardization may obscure a deeper problem. Specifically, even when protocols are consistent, the resulting data is unlikely to reflect the true microbial community. This systemic bias, herein described as <i>The Great Microbiome Extraction Anomaly</i>, refers to the widespread distortion of observed microbial community composition caused by variation in nucleic acid extraction efficiencies across microbial nucleic acid states, species biology, and specimen composition. The term draws inspiration from <i>The Great Plate Count Anomaly</i>, a long-recognized discrepancy between observable and cultivable microbial diversity. <i>The Great Microbiome Extraction Anomaly</i> presents a parallel methodological challenge which, like the original, will likely require novel technological innovation to resolve, as to date, no current protocol has achieved truly unbiased microbial DNA recovery. Currently, this limitation can only be addressed with carefully considered analytical controls that enable transparent reporting of microbial DNA recovery biases. However, the rate of control use in microbiome research remains very low. This review examines the evidence for nucleic acid state, microbe biology, and specimen-specific nucleic acid extraction efficiency biases specifically within eDNA and eRNA microbiome workflows, while citing evidence of extraction bias from human microbiome and molecular diagnostic research to demonstrate the broader constraints underlying differential microbial nucleic acid recovery. In addition, this review evaluates the extent to which controls are implemented in microbiome research, outlines explicit examples of analytical controls that are essential for inclusion in microbiome research, and argues that implementing these robust analytical control strategies, especially the use of positive controls, is essential to detect and mitigate the biases of <i>The Great Microbiome Extraction Anomaly</i>.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70276","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147668239","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":"Design, Validation, and Implementation Considerations for Species-Targeted Environmental RNA Assays to Detect Presence and Physiological State","authors":"Mark Louie D. Lopez,&nbsp;Amy Migneault,&nbsp;Sarah L. Trilesky,&nbsp;Emma M. Field,&nbsp;Marin P. Crane,&nbsp;Vanessa C. Thompson,&nbsp;Caren C. Helbing","doi":"10.1002/edn3.70272","DOIUrl":"10.1002/edn3.70272","url":null,"abstract":"<p>Environmental RNA (eRNA) is emerging as a promising tool for detecting species presence and/or physiological condition in biodiversity monitoring, ecotoxicology, and conservation. However, compared to environmental DNA (eDNA), optimization of eRNA analysis protocols is relatively undeveloped, and consensus among researchers is limited. While eRNA assay design and implementation have many commonalities with eDNA assays, there are additional key considerations needed for specific and sensitive eRNA assays while mitigating false positives and negatives. We critically examine these in the current perspective for targeted real-time polymerase chain reaction (qPCR). Selection of RNA targets should be guided by the specific objectives of the eRNA assay and should account for genomic DNA (gDNA) removal and RNA-to-cDNA conversion before qPCR analysis. This includes consideration of RNA type and origin; if the measured RNA is acting as a physiological indicator reflecting organismal health, stress, or demographic patterns; if the RNA is acting as an indicator of presence; or if the RNA is a normalizer for the physiological indicators. Primer–probe design should, when possible, span exon–exon junctions to minimize gDNA amplification. If that is not possible, minus reverse transcriptase (RT–) reactions are required for every sample. Rigorous assay validation begins with in silico screens against target and non-target taxa transcript sequences, followed by in vitro testing using cDNA generated from RNA and gDNA extracts from voucher specimens. Benchmarking sensitivity performance through measures such as limit of detection (LOD), limit of quantification (LOQ), and amplification efficiency strengthens assay confidence. Field validation of eRNA assays using environmental samples where target species are present and absent and/or in a desired physiological state (e.g., exposed to contaminants) helps estimate false-positive and false-negative rates. We critically examine current eRNA practices and provide guidance and suggestions for robust eRNA assay design and implementation.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70272","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147668321","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 Metabarcoding Read Numbers Reveal Consistent Patterns of Microhabitat Use Among Fish Species Within Multiple Lakes and Tidal Creeks","authors":"Logan Chandler,&nbsp;Stephanie Burnette,&nbsp;Naomi Heilen,&nbsp;James Skelton","doi":"10.1002/edn3.70269","DOIUrl":"10.1002/edn3.70269","url":null,"abstract":"<p>Environmental DNA (eDNA) metabarcoding has emerged as a powerful tool for biodiversity assessments in aquatic ecosystems, yet its utility to resolve fine-scale spatial patterns of community structure within well-connected habitats remains unclear. We investigated whether eDNA metabarcoding can detect microhabitat-specific community structure by comparing fish assemblages across distinct zones within two ecosystem types: littoral, pelagic, and benthic zones in freshwater reservoirs, and inlets versus main channels in oligohaline tidal creeks. We collected 80 water samples across eight sites in the Virginia Peninsula region in Virginia USA and used mitochondrial 12S metabarcoding (MiFish-U) to characterize fish communities. While per-sample species richness did not differ significantly among microhabitats, multivariate analyses revealed distinct compositional differences that aligned with known species ecology. In lakes, microhabitat identity explained 12.9% of compositional variation (PERMANOVA <i>R</i>²), with <i>Lepomis macrochirus</i> strongly associated with littoral zones and <i>Dorosoma cepedianum</i> with benthic-pelagic areas. Tidal creek systems showed even stronger microhabitat structuring (18.9% of variation), with <i>Fundulus heteroclitus</i> serving as a clear indicator of inlet habitats while species including <i>Brevoortia tyrannus</i> and <i>Morone americana</i> characterized main channels. These findings demonstrate that eDNA maintains sufficient spatial fidelity to capture ecologically meaningful community patterns at scales of tens of meters, despite hydrodynamic mixing processes. Comparative analysis showed that analysis of read numbers identified species-habitat relationships missed by analysis of presence-absence data alone. Metabarcoding of eDNA is valuable for habitat-specific conservation monitoring and restoration assessment even within well-mixed aquatic habitats, opening new avenues for high-resolution biodiversity monitoring.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70269","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147667928","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":"Applying Environmental DNA Metabarcoding to Calculate an Index of Biotic Integrity for Freshwater Fish","authors":"Amanda N. Curtis,&nbsp;Lynsey R. Harper,&nbsp;Mark A. Davis,&nbsp;Eric R. Larson","doi":"10.1002/edn3.70251","DOIUrl":"https://doi.org/10.1002/edn3.70251","url":null,"abstract":"<p>Multi-metric indices like the Index of Biotic Integrity (IBI) are important biomonitoring tools for Clean Water Act compliance in the USA. Environmental DNA (eDNA) metabarcoding could complement IBIs by increasing detection sensitivity for rare taxa while also reducing monitoring costs. To date, there is a lack of studies that have examined the efficacy of using eDNA metabarcoding to calculate IBIs in the USA. Here, we used eDNA metabarcoding to calculate a fish-based IBI for streams and rivers of the Tennessee River Basin in northern Alabama, USA. We collected water samples from 50 stream and river sites across a gradient of land use intensity, extracted eDNA from these samples, and sequenced the eDNA using vertebrate-specific primers. We compared our eDNA-IBI to a previous fish-IBI implemented by the state of Alabama using conventional sampling, as well as predicted biological condition of these streams from the US Environmental Protection Agency (EPA) based on benthic macroinvertebrates. We found a significant, positive relationship between the eDNA-IBI and fish-IBI, as well as shared relationships to a measure of in-stream habitat quality, but a weaker, non-significant positive relationship to predicted biological condition from benthic macroinvertebrates. Notably, the former was recovered despite eDNA-IBI sampling being conducted 9 years after the conventional fish sampling at slightly different locations (although distance did not explain variation), the fish-IBI having used greater sampling effort throughout the year (including spring and autumn rather than only summer sampling), and a lack of reference DNA sequences that prevented eDNA detection for some species detected by conventional fish sampling. Our study provides a baseline for how an eDNA-IBI may work relative to multi-metric indices calculated from conventional sampling, which can be improved through future directions identified and discussed in our paper.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70251","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147615211","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":"DNA Retention in Sea Lamprey Digestive Tracts: Insights From Controlled Feeding Experiments","authors":"Conor O'Kane,&nbsp;Nicholas S. Johnson,&nbsp;Kim T. Scribner,&nbsp;Jeannette Kanefsky,&nbsp;Weiming Li,&nbsp;Tyler Bruning,&nbsp;John D. Robinson","doi":"10.1002/edn3.70268","DOIUrl":"https://doi.org/10.1002/edn3.70268","url":null,"abstract":"<p>The sea lamprey (<i>Petromyzon marinus</i>), a non-native species in the Laurentian Great Lakes, has significantly impacted native fish communities and commercial fisheries, requiring population suppression efforts. While traditional control methods such as lampricides and barriers have reduced sea lamprey population abundance, questions remain regarding sea lamprey dietary composition given the focus of current damage assessments on economically and ecologically important host species. Recent advances in molecular technology offer promising methods of sea lamprey dietary assessment. Specifically, DNA metabarcoding enables species-specific identification of taxonomically diverse prey items from gut and fecal samples, and has proven effective in many taxa, including hematophagous species such as Arctic lamprey (<i>Lethenteron camtschaticum</i>) and sea lamprey. However, studies on DNA retention within digestive tracts are limited, particularly given the potential effects of environmental and dietary factors among hematophagous species. We used controlled feeding experiments to understand the effects these factors may have on DNA retention and host detectability within sea lamprey digestive tracts. Additionally, we evaluated the utility of metabarcoding for identifying multiple host species from consecutive feedings. Results indicate that host DNA can be detected up to 30 days post-feeding, with detection probability decreasing with increasing time following feeding. Temperature effects were dependent upon fasting periods, and host-switching trials indicated multiple previous host species could be detected from a single lamprey. Findings provide valuable insights for refining dietary analysis protocols for wild-caught sea lamprey within native and introduced ranges.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70268","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147615210","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":"DNA Retention in Sea Lamprey Digestive Tracts: Insights From Controlled Feeding Experiments","authors":"Conor O'Kane,&nbsp;Nicholas S. Johnson,&nbsp;Kim T. Scribner,&nbsp;Jeannette Kanefsky,&nbsp;Weiming Li,&nbsp;Tyler Bruning,&nbsp;John D. Robinson","doi":"10.1002/edn3.70268","DOIUrl":"https://doi.org/10.1002/edn3.70268","url":null,"abstract":"<p>The sea lamprey (<i>Petromyzon marinus</i>), a non-native species in the Laurentian Great Lakes, has significantly impacted native fish communities and commercial fisheries, requiring population suppression efforts. While traditional control methods such as lampricides and barriers have reduced sea lamprey population abundance, questions remain regarding sea lamprey dietary composition given the focus of current damage assessments on economically and ecologically important host species. Recent advances in molecular technology offer promising methods of sea lamprey dietary assessment. Specifically, DNA metabarcoding enables species-specific identification of taxonomically diverse prey items from gut and fecal samples, and has proven effective in many taxa, including hematophagous species such as Arctic lamprey (<i>Lethenteron camtschaticum</i>) and sea lamprey. However, studies on DNA retention within digestive tracts are limited, particularly given the potential effects of environmental and dietary factors among hematophagous species. We used controlled feeding experiments to understand the effects these factors may have on DNA retention and host detectability within sea lamprey digestive tracts. Additionally, we evaluated the utility of metabarcoding for identifying multiple host species from consecutive feedings. Results indicate that host DNA can be detected up to 30 days post-feeding, with detection probability decreasing with increasing time following feeding. Temperature effects were dependent upon fasting periods, and host-switching trials indicated multiple previous host species could be detected from a single lamprey. Findings provide valuable insights for refining dietary analysis protocols for wild-caught sea lamprey within native and introduced ranges.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70268","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147615212","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":"Applying Environmental DNA Metabarcoding to Calculate an Index of Biotic Integrity for Freshwater Fish","authors":"Amanda N. Curtis,&nbsp;Lynsey R. Harper,&nbsp;Mark A. Davis,&nbsp;Eric R. Larson","doi":"10.1002/edn3.70251","DOIUrl":"https://doi.org/10.1002/edn3.70251","url":null,"abstract":"<p>Multi-metric indices like the Index of Biotic Integrity (IBI) are important biomonitoring tools for Clean Water Act compliance in the USA. Environmental DNA (eDNA) metabarcoding could complement IBIs by increasing detection sensitivity for rare taxa while also reducing monitoring costs. To date, there is a lack of studies that have examined the efficacy of using eDNA metabarcoding to calculate IBIs in the USA. Here, we used eDNA metabarcoding to calculate a fish-based IBI for streams and rivers of the Tennessee River Basin in northern Alabama, USA. We collected water samples from 50 stream and river sites across a gradient of land use intensity, extracted eDNA from these samples, and sequenced the eDNA using vertebrate-specific primers. We compared our eDNA-IBI to a previous fish-IBI implemented by the state of Alabama using conventional sampling, as well as predicted biological condition of these streams from the US Environmental Protection Agency (EPA) based on benthic macroinvertebrates. We found a significant, positive relationship between the eDNA-IBI and fish-IBI, as well as shared relationships to a measure of in-stream habitat quality, but a weaker, non-significant positive relationship to predicted biological condition from benthic macroinvertebrates. Notably, the former was recovered despite eDNA-IBI sampling being conducted 9 years after the conventional fish sampling at slightly different locations (although distance did not explain variation), the fish-IBI having used greater sampling effort throughout the year (including spring and autumn rather than only summer sampling), and a lack of reference DNA sequences that prevented eDNA detection for some species detected by conventional fish sampling. Our study provides a baseline for how an eDNA-IBI may work relative to multi-metric indices calculated from conventional sampling, which can be improved through future directions identified and discussed in our paper.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70251","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147615409","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":"Integrating Environmental DNA Into Early Detection Efforts for an Invasive Terrestrial Beetle","authors":"Kathleen E. Kyle,&nbsp;Michael C. Allen,&nbsp;Mario Hernandez,&nbsp;Anthony R. Vastano,&nbsp;Anne L. Nielsen,&nbsp;Keith Weiser,&nbsp;Shannon Dickey,&nbsp;Julie L. Lockwood","doi":"10.1002/edn3.70262","DOIUrl":"10.1002/edn3.70262","url":null,"abstract":"<p>The economic cost of invasive species continues to rise as more species are introduced globally every year. One of the most effective ways to reduce these costs is to implement robust early detection and rapid response (EDRR) programs, in which invasive populations are detected at low enough abundances that control efforts are effective and cost-efficient. Environmental DNA (eDNA) surveys have become increasingly common in aquatic invasive species EDRR programs, but they have not been explored for use in terrestrial ecosystem invasions. Here, we investigate the deployment of eDNA surveys to detect invasive coconut rhinoceros beetles (<i>Oryctes rhinoceros</i>; CRB) on the island of Oʻahu, Hawaiʻi, USA. CRB impose substantial economic and cultural impacts across Pacific Island nations and territories, with the potential to spread globally. We designed a sensitive, species-specific molecular assay targeting a 64-bp segment of the COI region. We tested four field sampling methods at CRB-positive sites, with roller and mulch-rinse samples successfully capturing CRB eDNA. We estimated these two methods had per-sample detection probabilities of 0.47 and 0.54, respectively, in sites with known CRB presence. We then evaluated how these methods performed at low- or unknown-CRB-abundance sites. The overall per-sample probability of detection dropped to 0.09 and 0.06 for the roller and mulch methods, respectively, due to low eDNA concentrations in samples. Finally, we compared eDNA detection probability with co-located pheromone-baited traps to assess the performance of eDNA against a standard early-detection protocol. We found that roller eDNA sampling exhibited twice the per-sample detection probability of traps, with mulch sampling showing comparable patterns, though with greater uncertainty. Our results indicate that eDNA surveys for CRB can be a feasible and useful addition to EDRR programs in Hawaiʻi, and perhaps other sites where CRB are likely to be introduced.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70262","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147579855","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":"Contaminant-Driven Modulation of Environmental DNA and RNA in Aquatic Systems","authors":"Marie-Lee Castonguay,&nbsp;Tuan Anh To,&nbsp;Fidji Sandré,&nbsp;Léo Sillon,&nbsp;Guillaume Côté,&nbsp;Valerie S. Langlois","doi":"10.1002/edn3.70266","DOIUrl":"https://doi.org/10.1002/edn3.70266","url":null,"abstract":"<p>Metals and microplastics rank among the most concerning contaminants in aquatic environments due to their persistence, ubiquity, and impacts on ecosystem stability and living organisms' health. The use of environmental DNA and environmental RNA (also called eDNA and eRNA) for biomonitoring has been suggested to assess the effects of these contaminants on aquatic species distribution, behavior, and/or health. However, understanding the impact of contaminants directly on the ecology of environmental nucleic acids (eNAs) could lead to a better interpretation of the data during monitoring surveys in polluted environments. In this study, we assessed the influence of lead (Pb) and polyethylene (PE) microbeads on both eDNA and eRNA production and persistence in juvenile landlocked salmons (<i>Salmo salar</i>) and American eels (<i>Anguilla rostrata</i>) through a series of controlled laboratory experiments. Data show no effect of Pb on eNA production following an exposure of 48 h at a concentration of 0.1 mg/L. The persistence was not affected either by this metal. On the other hand, exposure of fish individuals to 1 mg/L of PE microbeads led to increased eRNA levels during the production phase, which may be associated with an upregulation of genes associated with a generalized stressing event. Microplastics also led to a slower degradation of eNA molecules, allowing a longer persistence of the genetic material in aquatic ecosystems. Further investigations are needed to fully understand the direct and indirect interactions between contaminants and environmental nucleic acids. Thus, this would allow a better interpretation of the data during monitoring surveys, especially in contaminated environments.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70266","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147567466","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}