Environmental DNA最新文献

{"title":"eDNA Metabarcoding Applications Across Italian Marine Coastal Ecosystems: An Overview","authors":"Alice Tagliabue,&nbsp;Giulia Furfaro,&nbsp;Andrea Galimberti,&nbsp;Antonia Bruno,&nbsp;Lorenzo Zane,&nbsp;Alberto Pallavicini,&nbsp;Stefano Piraino","doi":"10.1002/edn3.70075","DOIUrl":"https://doi.org/10.1002/edn3.70075","url":null,"abstract":"<p>Climate emergency and other anthropogenic pressures urgently call for technological and methodological advances to enhance our ability to protect marine habitats and their ecosystem services. In recent years, environmental DNA (eDNA) metabarcoding has emerged as a powerful tool to achieve an integrative assessment of the environmental health status, through a broad, relatively rapid, and cost-effective taxonomic monitoring of biodiversity at different spatial scales. Here we provide a time-based overview of the applications of the eDNA metabarcoding methodology carried out across diverse Italian marine and coastal habitats, with an <i>in-depth</i> scrutiny of the commonly adopted operative procedures, from sampling to sequencing. The lack of standardization and low replicability in space/time arose as major issues of several monitoring campaigns, preventing appropriate cross-comparability of previous studies. Given the wide potential of eDNA metabarcoding surveys along the Italian coastline, this review aims to boost a wider application of eDNA metabarcoding for biodiversity inventories and to avoid major methodological weaknesses that could compromise the long-term value and broad spatial scope of future monitoring plans.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70075","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564894","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":"Overwintering Fish Community in Ice-Covered Environments in Hokkaido, Japan, Inferred From Environmental DNA","authors":"Tatsuya Kawakami,&nbsp;Makoto Ozaki,&nbsp;Aya Yamazaki,&nbsp;Daiki Nomura,&nbsp;Akihide Kasai","doi":"10.1002/edn3.70068","DOIUrl":"https://doi.org/10.1002/edn3.70068","url":null,"abstract":"<p>The overwintering ecology of fish in the seasonal ice zones (SIZs) remains largely unexplored owing to methodological limitations. Environmental DNA (eDNA) can reveal the distribution and diversity of fish species in various aquatic environments, thereby offering a possible solution to the methodological limitations of SIZ studies. Therefore, we aimed to detect the overwintering fish community in the ice-covered Saroma-ko Lagoon, located on the Okhotsk Sea coast of Hokkaido, and its inflow, using eDNA metabarcoding. eDNA extracted from under-ice seawater collected from the lagoon yielded 28 fish taxa, predominantly <i>Clupea pallasii</i> based on the relative DNA read abundance. Dissimilarity analysis suggested short-term temporal variations in eDNA composition in under-ice seawater, even at the same site. Nineteen fish taxa, predominantly <i>Tribolodon brandtii</i> and <i>T. hakonensis</i>, were detected in the eDNA extracted from under-ice river water. The high dissimilarity between eDNA results from under-ice seawater and river water suggested segregation of the overwintering community between the lagoon and river. Fish eDNA detected in meltwater from sea ice was assigned to five taxa, suggesting the entrainment of particulate matter containing fish eDNA during ice growth. The true species richness estimated based on eDNA results and discrepancies with historical reports suggest that sampling efforts need to be optimized for ice-covered environments to promote more comprehensive species detection. This study demonstrated the usefulness of using fish eDNA metabarcoding to study the ecology of overwintering fish under ice. Clarifying eDNA shedding patterns, persistence, and dispersal in under-ice environments would improve the reliability of this technique and expand its use in SIZs.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70068","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143554628","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":"Comparing the Fate of eDNA by Particle Sizes and Molecule Lengths in Recirculating Streams","authors":"Pedro F. P. Brandão-Dias,&nbsp;Elise Snyder,&nbsp;Jennifer L. Tank,&nbsp;Ursula H. Mahl,&nbsp;Brett Peters,&nbsp;Arial J. Shogren,&nbsp;Diogo Bolster,&nbsp;Gary A. Lamberti,&nbsp;Kyle Bibby,&nbsp;Scott P. Egan","doi":"10.1002/edn3.70066","DOIUrl":"https://doi.org/10.1002/edn3.70066","url":null,"abstract":"<p>The detection of environmental DNA (eDNA) has revolutionized aquatic species monitoring, yet interpreting eDNA data remains challenging due to gaps in our understanding of eDNA ecology (i.e., origin, state, transport, and fate) and variability in how eDNA methods are applied across the literature. A crucial aspect of the complexity of eDNA ecology is that eDNA is a heterogeneous mix of components that vary in size and other properties, thereby influencing interactions with the environment in diverse ways. In this study, we explore the interplay between three eDNA particle sizes (the physical dimension of eDNA-containing particles) and two molecule lengths (DNA size in base pairs) in flowing water systems. Specifically, we elucidated the mechanisms governing the removal of different eDNA components using a set of 24 recirculating mesocosms where we varied light and substrate conditions. Consistent with previous observations, our findings revealed substantial differences in the mechanisms of eDNA removal between small and large eDNA particles. In mesocosms with biofilm-colonized substrate, we found higher removal rates for smaller particles, but larger eDNA particles were removed more quickly in presence of any substrate. Importantly, we also found that biofilm removes longer eDNA molecules faster, shedding light on a probable mechanism underlying the longstanding association between eDNA removal and the presence of biofilm. Despite the association between biofilm colonization and faster removal of longer molecules, the two eDNA molecule sizes we analyzed (86 and 387 base pairs) exhibited somewhat consistent behavior. In combination, our observations highlight that particle size is an important predictor of eDNA fate, and that eDNA fate shows few differences across varying molecule lengths. Furthermore, our work suggests that conclusions regarding eDNA ecology from studies utilizing short DNA markers are applicable to metabarcoding applications, which typically use longer marker lengths.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70066","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143554230","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 Framework to Unify the Relationship Between Numerical Abundance, Biomass, and Environmental DNA","authors":"Matthew C. Yates,&nbsp;Taylor M. Wilcox,&nbsp;Shannon Kay,&nbsp;Pedro Peres-Neto,&nbsp;Daniel D. Heath","doi":"10.1002/edn3.70073","DOIUrl":"https://doi.org/10.1002/edn3.70073","url":null,"abstract":"<p>Does environmental DNA (eDNA) concentration correlate with numerical abundance (<i>N</i>) or biomass in aquatic organisms? We hypothesize that eDNA can be adjusted to simultaneously reflect both. Building on frameworks developed from the Metabolic Theory of Ecology, we derive two equations to adjust eDNA data to simultaneously reflect both <i>N</i> and biomass using population size structure data and allometric scaling coefficients. We also demonstrate that these equations share model parameters, necessitating the joint estimation of regressions between adjusted eDNA, <i>N</i>, and biomass. Furthermore, our framework can be extended to model how other variables (temperature, taxa, diet, trophic level, etc.) might impact relationships between eDNA, <i>N</i>, and biomass in natural ecosystems. We applied our framework to data from two previously published studies correlating eDNA to Brook Trout (<i>Salvelinus fontinalis</i>) <i>N</i> and biomass. In both case studies, point estimates of the scaling coefficient (<i>b</i>) reflected allometric processes (<i>b</i> = 0.51 and 0.37 for Case Study 1 and 2, respectively), with credible intervals indicating that b likely differed from zero (i.e., eDNA scales with <i>N</i>) and one (i.e., eDNA scales with biomass). Directly estimating the value of b improved estimates of <i>N</i> and biomass relative to assuming b equals 0, which particularly affected the capacity to estimate biomass. However, models assuming eDNA production scaled with biomass (i.e., <i>b</i> = 1) were largely similar to estimating <i>b</i>, implying that assuming eDNA scales linearly with biomass might be a sufficient approximation for some systems. Nevertheless, the framework demonstrates that correlating eDNA directly with either <i>N</i> or biomass (as is commonly done in many studies) inherently necessitates an adjustment to infer the other metric if populations exhibit size structure variation. Collectively, we demonstrate that quantitative eDNA data is unlikely to correspond exactly to either population <i>N</i> or biomass but can be adjusted to simultaneously reflect both.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70073","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143530337","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":"Invasive Crayfish: Drivers or Passengers of Degradation in Freshwater Ecosystems?","authors":"Jelle A. Dercksen,&nbsp;Maarten J. J. Schrama,&nbsp;Kevin K. Beentjes,&nbsp;Bob N. Bastiaans,&nbsp;Rody Blom,&nbsp;André van Roon,&nbsp;Peter W. Lindenburg,&nbsp;Krijn B. Trimbos","doi":"10.1002/edn3.70062","DOIUrl":"https://doi.org/10.1002/edn3.70062","url":null,"abstract":"<p>Invasive species, such as the freshwater crayfish <i>Procambarus clarkii</i>, reportedly negatively influence the abundance of various aquatic species. Moreover, these invaders are increasingly linked to ecological degradation of aquatic ecosystems, as invaded habitats show increased levels of turbidity, nitrogen, and organic matter concentration. <i>P. clarkii</i> has, among other impacts, been associated with eutrophication in invaded habitats. However, observations suggest that the presence of <i>P. clarkii</i> is often not accompanied by ecosystem degradation, raising the question of whether they are drivers of degradation or function as passive passengers, with the degradation being caused by other stressors. To investigate these contrasting hypotheses, we conducted a full factorial experiment in 24 mesocosms with <i>P. clarkii</i> and nutrient pollution (specifically N, P, and K), a ubiquitous stressor in aquatic ecosystems. Here, we assessed the effects on community compositions of morphologically identified macrophytes and chironomids, as well as the compositions of bacteria, phytoplankton, and diatoms identified using environmental DNA (eDNA) metabarcoding. Nutrient pollution induced significant shifts in macrophyte biomass and in the composition of the bacterial, diatom, and phytoplankton communities. All microbial communities exposed to nutrient pollution initially diverged from the control, after which the bacterial and phytoplankton communities converged back to the control in the final weeks. In contrast, we found only marginal effects of <i>P. clarkii</i>, rendering it unlikely as a significant short- to medium-term driver of the tested biodiversity. As microbial communities respond quickly to changes in the environmental conditions, these results signify that the mesocosms used in the study were relatively stable in spite of the presence of <i>P. clarkii</i>. The crayfish density and timeframe studied may be leveraged as threshold values in the design and execution of freshwater management strategies that aim to avert potential negative impacts of <i>P. clarkii</i> on ecosystem structure. Ultimately, the importance of nutrient pollution is reinforced as a driver of environmental change in aquatic ecosystems.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70062","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143530338","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":"Evaluation of Environmental DNA as a Surveillance Tool for Invasive House Mice (Mus musculus)","authors":"Antoinette J. Piaggio,&nbsp;Stacie J. Robinson,&nbsp;Aaron B. Shiels,&nbsp;Daniel R. Taylor,&nbsp;Danika R. Spock,&nbsp;Meagan Allira,&nbsp;Megan Serr,&nbsp;Caroline M. Klein,&nbsp;John Godwin,&nbsp;James C. Russell,&nbsp;Shaun Wilkinson,&nbsp;Nick D. Holmes,&nbsp;David J. Will,&nbsp;Neil J. Gemmell","doi":"10.1002/edn3.70069","DOIUrl":"https://doi.org/10.1002/edn3.70069","url":null,"abstract":"<p>Increasing the success of invasive species management depends on the development, testing, and deployment of new tools. Environmental DNA (eDNA) is an effective tool for monitoring invasive species that can help identify presence/absence, geographical boundaries of invasion, risk pathways, and population connectivity. In particular, understanding the sensitivity of eDNA detection rates to target species density allows calibration of sampling rates. In this study, we take a lab-validated eDNA assay for <i>Mus musculus</i> (house mouse) and test its detection rates at different populations densities for wild-caught, free-ranging <i>M. musculus</i> in a controlled laboratory and an outdoor mesocosm. The goal was to understand both eDNA accumulation after <i>M. musculus</i> is introduced and the persistence of the accumulated eDNA signal in the environment after animals were removed. We found that eDNA signal was detectable within 1 h of a single mouse being introduced and that the signal was detectable for months after in the controlled environment but largely undetectable after 4 days in an outdoor mesocosm. We suggest sampling strategies for post-eradication deployment of eDNA and highlight other uses for this assay, which are important to the deployment of this tool for invasive <i>M. musculus</i> management.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70069","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143438819","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":"Optimizing eDNA Metabarcoding Techniques for Assessing Arthropod Communities in Tree-Related Microhabitats","authors":"Mohammad Jamil Shuvo,&nbsp;Tasmina Tabassum,&nbsp;Gernot Segelbacher","doi":"10.1002/edn3.70064","DOIUrl":"https://doi.org/10.1002/edn3.70064","url":null,"abstract":"<p>Understanding the diversity and ecological roles of arthropods within tree-related microhabitats (TreMs) is crucial for forest ecosystem conservation and management. In our study, we aimed to identify the most effective environmental DNA (eDNA) metabarcoding approach for capturing ecologically important arthropod species primarily inhabiting the near-ground-level TreMs. We evaluated the use of COI and 16S primers for eDNA metabarcoding and compared direct and indirect eDNA sampling methods, including lying deadwood sediment sampling (LDS), standing deadwood sediment sampling (SDS), soil sampling (SS), and tree surface roller sampling (TSRS). Our results indicated significant biases and challenges, particularly in primer selection, with COI outperforming 16S in taxonomic resolution for most arthropod taxa. Our TSRS method effectively captured 408 OTUs at the species level, with the highest number of ecologically significant arthropods associated with TreMs compared to other approaches. Direct sampling from sediments revealed a higher abundance of fungi than arthropods, impacting diversity estimates. We also observed habitat-specific preferences among arthropods, with certain sampling methods capturing distinct taxa. Our findings underscore the importance of carefully selecting sampling methods and validating primers in eDNA metabarcoding studies and provide insights into the complexity of arthropod communities in TreMs. Optimized methods will advance monitoring techniques for forest ecosystems and inform conservation efforts to preserve arthropod diversity in TreMs.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70064","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143396877","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":"Investigating Fine-Scale Breeding Habitat Use by Amphibians in a Continuous Wetland Using Environmental DNA","authors":"Julie Morgane Guenat,&nbsp;Antoine Gander,&nbsp;Luca Fumagalli,&nbsp;Guillaume Lavanchy","doi":"10.1002/edn3.70063","DOIUrl":"https://doi.org/10.1002/edn3.70063","url":null,"abstract":"<p>Designing effective conservation plans to protect species from extinction requires a comprehensive understanding of their ecology. Conventional methods used to investigate habitat use are time-consuming, and the detectability of cryptic species is often insufficient. Environmental DNA (eDNA)-based approaches provide a complementary tool to traditional monitoring methods for ecosystem monitoring and assessment. Nevertheless, to our knowledge, such methods have rarely been applied to investigate habitat use at a fine scale in a continuous wetland environment. Here, we used an eDNA metabarcoding approach to characterize the breeding habitat use of local amphibian species in a wet meadow expanse along the southern shore of Lake Neuchâtel, Switzerland. We retrieved DNA from six out of the seven species expected to be present. We tested the influence of six abiotic environmental variables on overall species assemblages and individual species occurrences. We showed that the main factor structuring species assemblages was water temperature and that the distribution of three amphibian species was associated with several environmental variables. Our results indicate that the eDNA detection approaches are promising tools to study species' ecology at a small scale in continuous wetland habitats.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70063","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143111686","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 Sampling Systems for Salmon Ecosystem Monitoring","authors":"Christoph M. Deeg,&nbsp;Robert G. Saunders,&nbsp;Christopher Tam,&nbsp;Karia Kaukinen,&nbsp;Shaorong Li,&nbsp;Arthur L. Bass,&nbsp;Uu-a-thluk Fisheries,&nbsp;Kristina M. Miller","doi":"10.1002/edn3.70059","DOIUrl":"https://doi.org/10.1002/edn3.70059","url":null,"abstract":"<p>Environmental DNA (eDNA) is transforming the way aquatic ecosystems are monitored and managed by scientists, resource managers, ENGOs, First Nations communities, and citizen scientists alike. However, available sampling systems currently don't allow for combined high filtration volumes, rapid sample collection, and preservation in the field, thus far hindering broad scale eDNA studies in the ocean specifically for small and medium scale organizations. To overcome these challenges, several modular water sampling systems that utilize hollow-membrane (HM) filtration cartridges were developed by RKS laboratories and tested by the Fisheries and Oceans, Canada, Molecular Genetics Laboratory. Compared to Sterivex filters, an industry standard for eDNA filtration, the HM filtration cartridges allowed for a six-fold increase in filtration volume and threefold increase in filtration speed. The field sampling systems, which combine pumps, a programmable controller, an air pump, an ozone generator, and up to eight filters at once, enabled efficient direct eDNA filtration from diverse aquatic environments, from creeks to the open ocean. To evaluate ease of deployment, we present the results of a 3 day workshop where technical staff of an Indigenous resource management organization, without any prior knowledge in eDNA sampling, were trained and performed independent eDNA sample collection. The samples were analyzed by metabarcoding and qPCR to reveal the distributions of salmon and other species co-occurring in salmon ecosystems, from large ephemeral predators, to the planktonic prey of salmon, even including their pathogens. In this example study, we further observed a substantial shift in community composition in the vicinity of aquaculture facilities where marine species associated with aquaculture feed were detected in freshwater at high relative abundance. This study demonstrates how these sampling systems provide an efficient entry point for small and medium scale organizations to utilize eDNA to fulfill their research and monitoring objectives.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70059","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143111570","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":"Fish eDNA Composition Along a Gradient of Freshwater eDNA in an Estuarine Bay","authors":"Shota Homma,&nbsp;Shinya Hosokawa,&nbsp;Takashi Komuro","doi":"10.1002/edn3.70061","DOIUrl":"https://doi.org/10.1002/edn3.70061","url":null,"abstract":"<p>Metabarcoding of environmental DNA (eDNA) is becoming practically applied to fish monitoring and conservation surveys in estuaries. However, estuarine bays may be an unsuitable zone to use eDNA metabarcoding because they are affected by eDNA originating from upstream rivers. In this study, the transition of eDNA composition from river to bay was examined to investigate the influence of freshwater sources on the eDNA composition of the downstream bay. Samples were collected in a bay spanning around 1 km and an upstream river under high and low tide within 1 day in November and in January. The samples were analyzed by using eDNA metabarcoding for fish species and species-specific quantitative analysis for the freshwater fish <i>Cyprinus carpio</i>. Our findings reveal that the eDNA of freshwater fishes was drastically diluted in the model estuarine bay. As a result, the relative-read-based composition clearly changed from riverine to marine environments, and the freshwater inflow had little effect on the relative-read-based composition at those sites. However, eDNA from freshwater fishes was widely detected in the bay by species-specific and metabarcoding analysis, suggesting that fresh water may have a more significant impact when focusing on presence/absence-based composition. Our study also found that the transition zone for the concentration of freshwater eDNA fluctuated spatiotemporally with tides, indicating that the degree of influence from the river varies with tide. Therefore, prior measurement of the distribution of freshwater fish eDNA at low tide would help to conservatively determine better sampling sites and design more reliable sampling in estuaries.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70061","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143120477","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}