Environmental DNA最新文献

{"title":"Application of Environmental DNA-Based Assessment for Upstream–Downstream Comparison of River Macroinvertebrates in a Metal-Contaminated River","authors":"Noriko Uchida,&nbsp;Yuichi Iwasaki,&nbsp;Ryoichi Kuranishi,&nbsp;Natsuko Ito Kondo","doi":"10.1002/edn3.70200","DOIUrl":"https://doi.org/10.1002/edn3.70200","url":null,"abstract":"<p>Environmental DNA (eDNA) is a powerful tool for biological monitoring that may overcome limitations of conventional macroinvertebrate surveys in running waters. However, the ability of eDNA to detect macroinvertebrate community changes immediately downstream of a perturbation, particularly in upstream–downstream comparisons, has not been adequately explored. To address this, we compared eDNA-based assessments with macroinvertebrate surveys in a river receiving inflow from a metal-contaminated tributary. Results from both eDNA-based assessment and benthic macroinvertebrate collection revealed distinctly lower richness of taxa and zero-radius operational taxonomic units (ZOTUs) at the metal-contaminated tributary site compared to other study sites. Results from the collection of macroinvertebrates indicated that most richness and abundance metrics were significantly reduced at three metal-contaminated sites located 150–1350 m downstream from the inflow of the tributary, compared with an upstream reference site. In contrast, the eDNA-based assessment revealed similar ZOTU richness at the reference site and the three contaminated sites. Although statistically not significant because sample sizes were small, eDNA-based nonmetric multidimensional scaling (NMDS) revealed some separation between the reference site and two downstream sites. However, no separation was apparent between the reference site and the site immediately downstream. This result suggested that eDNA at a site 150 m downstream from the inflow was likely affected by downstream drift of eDNA from the upstream reference area. That drift complicated the assessment of the community a short distance from the perturbation. The site separation detected by eDNA-based assessment was promising, but the ZOTUs that contributed to the separation were mainly from dipteran taxa rather than from metal-sensitive mayflies, which were significantly lower in abundance at the downstream, contaminated sites. Developing reliable local DNA barcoding information, particularly for these mayflies, may help overcome the limitations of making evaluations over relatively small spatial scales, such as upstream–downstream comparisons.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70200","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145272188","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":"Sample-To-Sample Variability Impacts eDNA Quantification, With Implications for Estimating Species Abundance","authors":"Meghan B. Parsley,&nbsp;Jesse L. Brunner,&nbsp;Erica J. Crespi,&nbsp;Tracy A. G. Rittenhouse,&nbsp;Caren S. Goldberg","doi":"10.1002/edn3.70195","DOIUrl":"https://doi.org/10.1002/edn3.70195","url":null,"abstract":"<p>Environmental DNA (eDNA) is increasingly used to infer species abundance, but uncertainty remains about how well individual water samples reflect system-wide eDNA concentrations. Currently, high levels of variation in estimated eDNA concentration among samples, even under similar conditions, limit the utility of eDNA estimates of abundance, especially in conservation and management scenarios. To investigate the sources and magnitude of variation in eDNA estimates, we analyzed eDNA from replicate water samples taken from mesocosms housing <i>Lithobates sylvaticus</i> tadpoles. We partitioned the variance of observed eDNA concentrations between biological replicates (distinct water samples) and technical replicates. We further tested whether stochastic variation in extraction efficiency (e.g., silica-column DNA binding and elution) introduced variance using internal control DNA. We then trialed modifications of sampling methods that could be applied to improve precision, including increased water volume, spatially pooled subsamples, and modified filtration. The observed variance in eDNA concentrations was substantial, ~75% of which was attributable to variation among replicate samples from the same mesocosm and &lt; 5% related to technical replicates; extraction-related variance was negligible. Sampling modifications, like increasing sample volume and taking combined samples of multiple scoops, improved precision, while others highlighted potential trade-offs between precision and accuracy. Our results suggest that sample-to-sample variation, even from seemingly homogeneous, controlled environments, can be substantial even under highly controlled conditions. This inherent variability imposes limits on the precision of abundance estimates derived from eDNA and underscores the importance of replication and protocol optimization in study design.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70195","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145272132","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":"Performance of eDNA Filtration Methods for Monitoring Fish Diversity in a Hyper-Tidal Estuary","authors":"Jake M. Jackman,&nbsp;Naiara Guimarães Sales,&nbsp;Chiara Benvenuto,&nbsp;Andrea Drewitt,&nbsp;Andrew Wolfenden,&nbsp;Peter E. Robins,&nbsp;Ilaria Coscia,&nbsp;Allan D. McDevitt","doi":"10.1002/edn3.70206","DOIUrl":"https://doi.org/10.1002/edn3.70206","url":null,"abstract":"<p>Environmental DNA (eDNA)-based monitoring has become an established and efficient method for surveying biodiversity in aquatic systems. However, there is a need to compare and standardize sampling methods across different ecosystem types, particularly complex ecosystems such as estuaries, where unique challenges exist for monitoring fish populations due to fluctuating environmental factors. Here, we compare species richness obtained from eDNA metabarcoding data using four different eDNA filtration methods: three manual filtration methods with different pore sizes (0.45, 1.2, and 5 μm) and a newly established passive method, the metaprobe. The study was applied across a salinity gradient in a hyper-tidal estuarine ecosystem. Overall, 44 fish species were detected across the four methods used. The 0.45 μm filter recovered the highest richness (39 species), then the metaprobe method (35), followed by the 1.2 μm (34) and 5 μm (33) filters. Filter performance between salinity gradients revealed that the 0.45 μm and the 1.2 μm methods recovered the highest species richness across all sampled zones. The 0.45 μm also had the most consistent detection probabilities using representative species from each zone. While the 0.45 μm method appeared to be the optimal method, each of the methods can be considered a viable and comparable option for biomonitoring in dynamic ecosystems such as estuaries and rivers. In particular, the passive metaprobe (used in a freshwater system for the first time here) performed well in comparison to the manual filtering methods despite a short deployment time. This study provides critical insights for optimizing fish diversity assessments using eDNA metabarcoding in estuarine ecosystems, providing a valuable framework for future monitoring efforts in similar systems worldwide.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70206","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145272133","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":"μCeta: A Set of Cetacean-Specific Primers for Environmental DNA Metabarcoding With Minimal Amplification of Non-Target Vertebrates","authors":"Masayuki Ushio,&nbsp;Sachie Ozawa,&nbsp;Shin-ichiro Oka,&nbsp;Tetsuya Sado,&nbsp;Robinson O. Kisero,&nbsp;Lindsay Porter,&nbsp;Eszter Matrai,&nbsp;Masaki Miya","doi":"10.1002/edn3.70193","DOIUrl":"https://doi.org/10.1002/edn3.70193","url":null,"abstract":"<p>Biodiversity monitoring is crucial for understanding ecosystem dynamics and species distributions, particularly in the context of anthropogenic impacts and climate change. Cetaceans, as key indicator species of marine ecosystems, face increasing threats from human activities, highlighting the need for effective, non-invasive monitoring methods. In the present study, we developed novel Cetacea-specific primer sets to enhance the detection efficiency of cetacean species through environmental DNA (eDNA) metabarcoding, while minimizing the amplification of non-target vertebrates, such as fish and humans. We retrieved mitochondrial genomes of 71 cetacean species from a public database and designed 20 candidate primer sets, which were assessed in silico for their specificity and capacity to differentiate cetacean sequences. Four primer sets with the best in silico performance were selected for empirical validation using DNA from tissue samples and eDNA from seawater collected from aquarium pools and Hong Kong coastal waters. All four primer sets effectively amplified cetacean DNA from tissue samples. However, in the aquarium pool tests, three primer sets failed to accurately identify one or more cetacean species due to a lack of interspecific variation within the amplified region. From these, we selected one primer set targeting a 267 bp region of the mitochondrial 12S rRNA gene, named μCeta, and applied it to water samples collected from Hong Kong coastal waters, where the iconic Indo-Pacific humpback dolphin (<i>Sousa chinensis</i>) was observed. μCeta successfully detected <i>S. chinensis</i> eDNA while avoiding amplification of non-target species such as fish or humans. Our results demonstrate that μCeta is a reliable tool for cetacean eDNA detection in Hong Kong waters, contributing to cetacean conservation and enhancing our understanding of marine biodiversity.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70193","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145271835","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":"Deciphering Landscape-Scale Plant Cover and Biodiversity From Soil eDNA","authors":"Tim Goodall,&nbsp;Robert I. Griffiths,&nbsp;Hyun S. Gweon,&nbsp;Lisa Norton,&nbsp;Susheel Bhanu Busi,&nbsp;Daniel S. Read","doi":"10.1002/edn3.70191","DOIUrl":"https://doi.org/10.1002/edn3.70191","url":null,"abstract":"<p>Biodiversity surveys are critical for detecting environmental change; however, undertaking them at scale and capturing all available diversity through observation is challenging and costly. This study evaluated the potential of soil-extracted eDNA to describe plant communities and compared these findings to traditional, observation-based field surveys. We analyzed 789 soil samples using high-throughput amplicon sequencing and compared DNA-based diversity metrics, indicator taxa, predicted vegetation class, and plant cover in a comparison with co-located field survey data. The results indicated that taxonomically aggregated (genus) eDNA-derived data, while showing slightly reduced Shannon's diversity scores, yielded remarkably similar overall richness and composition estimates. However, the DNA indicator taxa and predictive power for vegetation community classification were also lower overall than those recorded by the field survey. In many cases, plant cover could be inferred from amplicon abundance data with some accuracy despite widely differing scales of sampling—0.25 g crumb of soil versus a 1 m² quadrat. Overall, results from eDNA demonstrated lower sensitivity but were broadly in accordance with traditional surveys, with our findings revealing comparable taxonomic resolution at the genus level. We demonstrate the potential and limitations of a simple molecular method to inform landscape-scale plant biodiversity surveys, a vital tool in the monitoring of land use and environmental change.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70191","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145224313","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":"Significant Improvement of Environmental DNA Assay by Targeting Retrotransposon Sequences Characteristic to Anguilla Eels","authors":"Itsuki T. Hirayama,&nbsp;Yuta Kunimasa,&nbsp;Aya Takeuchi,&nbsp;Toshifumi Minamoto","doi":"10.1002/edn3.70197","DOIUrl":"https://doi.org/10.1002/edn3.70197","url":null,"abstract":"<p>Environmental DNA (eDNA) analysis faces challenges regarding sensitivity and quantification accuracy, particularly in areas with low target species densities or during seasons when eDNA release decreases. Multi-copy markers such as mitochondrial genomic DNA and ribosomal DNA (rDNA) have been widely used in eDNA analysis to address this issue. However, the copy number of the DNA markers per cell remains a potential bottleneck for eDNA sensitivity. In this study, we aimed to increase the sensitivity of eDNA assays by using retrotransposons, which are abundant in the genome, as novel target markers. We developed an assay targeting UnaSINE1, a short interspersed nucleotide element (SINE) characteristic of <i>Anguilla</i> eels, and compared its sensitivity and accuracy with that of an established mitochondrial 16S rRNA marker. Our results demonstrated that UnaSINE1 was detected at over 100 times the copy number of the mitochondrial marker in both genomic and eDNA samples. In the river surveys, the 16S marker was positive in 32 of the 81 samples, whereas the UnaSINE1 marker was positive in 62 samples, indicating that the use of the SINE marker remarkably reduced false negatives. Furthermore, both biological and technical replicates exhibited improved positive consistency and reduced variability in quantification, leading to more robust presence/absence determination and quantitative results. Utilizing retrotransposon sequences as markers requires additional effort for sequence acquisition and organization and may limit taxonomic resolution to the genus level. However, this approach significantly improves sensitivity without increasing the labor or cost of sampling and PCR analysis, making it highly practical for eDNA studies.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70197","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145224307","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":"Non-Invasive Monitoring of Tetracapsuloides bryosalmonae by eDNA: Influencing Environmental Parameters","authors":"Moritz Stelzer,&nbsp;Gary Delalay,&nbsp;Nico Christener,&nbsp;Jonas Steiner,&nbsp;Heike Schmidt-Posthaus","doi":"10.1002/edn3.70177","DOIUrl":"https://doi.org/10.1002/edn3.70177","url":null,"abstract":"<p><i>Tetracapsuloides bryosalmonae,</i> the causative agent of Proliferative Kidney Disease (PKD), affects salmonid populations in the northern hemisphere. In Switzerland, PKD monitoring to date has been conducted irregularly using invasive sampling. However, non-invasive detection protocols based on environmental DNA (eDNA) have been established, and there is still a lack of knowledge about environmental parameters that may influence detection. In this study, we evaluated which sampling period would be best for eDNA-based monitoring of <i>T. bryosalmonae</i> and which environmental parameters might influence the outcome by regularly sampling water from six Swiss rivers over an entire year and testing for presence of <i>T. bryosalmonae</i> DNA by droplet digital PCR (ddPCR). The <i>T. bryosalmonae</i> infection status of bryozoans from all investigated rivers was also assessed. Water temperature, precipitation, and air temperature were examined as environmental parameters. We found <i>T. bryosalmonae</i> DNA in all rivers by ddPCR. Positive results were almost exclusively retrieved between late spring and early autumn (mid-April until end of October). 98.3% of <i>T. bryosalmonae</i> positive water samples were collected when average daily water temperatures were above 8°C, and 71.9% of the positive samples when average daily water temperatures were above 14°C. Occupancy modeling corroborated the influence of water and air temperature on detecting <i>T. bryosalmonae</i> eDNA. Precipitation caused early clogging of filters in some cases and reduced detection by reducing sample volumes, suggesting when sampling for eDNA should be avoided. Finally, recommendations for a future eDNA-based monitoring of <i>T. bryosalmonae</i> are provided.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70177","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145224314","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":"Hydrolytic Enzymes' Fingerprints in Surface and Deep-Sea Prokaryotic Communities in the Ross Sea: A Metagenomic Approach","authors":"Rita Varchetta,&nbsp;Elisa Banchi,&nbsp;Federica Cerino,&nbsp;Vincenzo Manna,&nbsp;Alessandro Vezzi,&nbsp;Fabio De Pascale,&nbsp;Donata Canu,&nbsp;Mauro Celussi","doi":"10.1002/edn3.70198","DOIUrl":"https://doi.org/10.1002/edn3.70198","url":null,"abstract":"<p>The Ross Sea is characterized by a significant export of particulate organic carbon, with up to 50% of surface primary production being transferred to deep water layers. On their way to the ocean's interior, these particles undergo a remineralization process mainly carried out by prokaryotic communities through a complex set of hydrolytic enzymes. In this study, we used a metagenomic approach to explore the genetic repertoire of free-living and total prokaryotic communities at surface and in deep water masses of the Ross Sea. We focused on genes involved in the production of hydrolytic enzymes, including carbohydrate-active enzymes (CAZymes), proteases, and lipases. Our analysis revealed that the genetic profile of prokaryotes reflects different strategies for optimizing the degradation of organic substrates, adapting to variations in the quantity and quality of particulate organic matter along the water column, and at different locations. These results suggested that Ross Sea surface communities were strongly influenced by the dynamics of phytoplankton at different sampling sites, exhibiting greater variability in their enzymatic repertoire in respect to bottom communities. Deep-sea microbes, on the other hand, rely on a broader and more diverse set of enzymes compared to surface communities, being more adapted to a particle-bound lifestyle and playing a critical role in the remineralization of complex polysaccharides, such as algal cell wall components.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70198","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145146887","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":"Dead or Alive? Challenges in Discriminating Dietary From Host-Associated Community via RNA and DNA Metabarcoding in a Filter Feeder","authors":"Isabelle Junk,&nbsp;Lina Frank,&nbsp;Nina Marschel,&nbsp;Henrik Krehenwinkel","doi":"10.1002/edn3.70188","DOIUrl":"https://doi.org/10.1002/edn3.70188","url":null,"abstract":"<p>Environmental DNA metabarcoding has found application in a range of research areas by simplifying the collection of high-quality field data in a cost-efficient way. In biodiversity studies, environmental DNA metabarcoding of filter feeders like mussels and sponges has recently gained attention. Due to their continuous filtering activity, they accumulate a high amount of genetic signatures from their environment in their tissue. However, it can be difficult to separate genetic signatures of ingested dietary taxa from endobiotic ones originating from parasites or commensals living within the host. This issue parallels a broader problem in environmental DNA-based biodiversity studies: the inability to differentiate between DNA derived from living and dead organisms. A recent attempt to address this problem is using environmental RNA metabarcoding, which is believed to specifically represent the live and active community of an ecosystem. Therefore, we tested whether endobionts, as metabolically active organisms, can be distinguished from dietary taxa, as the presumed dead community, in a parallel RNA and DNA metabarcoding approach. We targeted nuclear 18S rDNA and rRNA to amplify mussel-associated communities (dietary and endobiotic taxa) in samples of <i>Dreissena polymorpha</i> and <i>Mytilus edulis</i>. Our results do not reveal any presence/absence or abundance pattern in the RNA and DNA library that could be used to distinguish dietary from endobiotic signatures. However, we found that over 40% of all genetic signatures were detected by RNA only and that those accounted for &lt; 4% of the total reads. This study thus demonstrates the outstanding sensitivity of RNA metabarcoding in comparison to DNA metabarcoding and suggests that using (environmental) RNA may be a way of capturing a larger proportion of the biodiversity in a given ecosystem.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70188","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145146753","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":"eDNA Metabarcoding to Monitor Fish Communities in a Large River Floodplain","authors":"Louis Astorg,&nbsp;Roxanne Giguère-Tremblay,&nbsp;Christine Martineau,&nbsp;Gilbert Cabana,&nbsp;François Guillemette,&nbsp;Vincent Maire,&nbsp;Marco A. Rodríguez,&nbsp;Vincent Fugère","doi":"10.1002/edn3.70182","DOIUrl":"https://doi.org/10.1002/edn3.70182","url":null,"abstract":"<p>Freshwater ecosystems are highly biodiverse and provide essential services that support both ecosystem health and economic sustainability. Despite their ecological significance, these ecosystems are disproportionately affected by the global biodiversity crisis. Large river floodplains constitute a fundamental component of freshwater ecosystems, sustaining fish biodiversity, growth, and reproduction. Yet, these floodplains face mounting threats from anthropogenic pressures, including physical modifications and land conversion for agriculture. In this context, there is an urgent need for scalable biomonitoring methods to more effectively assess floodplain ecosystems, which present methodological challenges due to their heterogeneous and dynamic nature. Traditional fish monitoring methods, however, are often invasive, costly, and resource-intensive. In contrast, environmental DNA (eDNA) metabarcoding presents a noninvasive, cost-effective, and scalable alternative. This study compares eDNA metabarcoding and electrofishing for fish community biomonitoring in the floodplain of Lake St. Pierre, the largest floodplain habitat along the St. Lawrence River. We assessed the effectiveness of these methods in monitoring fish community diversity and composition, as well as the influence of floodplain sectors and a gradient of land use from natural wetlands to annual (row) crops. eDNA metabarcoding detected a broader range of species than electrofishing, while both methods consistently identified abundant species. The two methods yielded uncorrelated diversity indices and distinct community compositions. Fish eDNA community composition was strongly associated with floodplain sectors, whereas land use within these sectors had a weaker influence on community diversity and composition. Our findings highlight eDNA metabarcoding as a valuable tool for characterizing broad patterns of fish communities in floodplain ecosystems. This method provides an additional tool to traditional methods for monitoring and conserving threatened floodplain habitats. However, careful consideration of study scale is essential to ensure effective conservation outcomes in these hydrologically dynamic environments.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 5","pages":""},"PeriodicalIF":6.2,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70182","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145146537","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}