Environmental DNA最新文献

{"title":"Optimizing Environmental DNA Metabarcoding of Archived Suspended Particulate Matter for River Biodiversity Monitoring","authors":"Robin Schütz,&nbsp;Keiichi Fukaya,&nbsp;Arne J. Beermann,&nbsp;Cecilia Díaz,&nbsp;Ann-Christin Lenz,&nbsp;Till-Hendrik Macher,&nbsp;Jan Koschorreck,&nbsp;Florian Leese","doi":"10.1002/edn3.70130","DOIUrl":"https://doi.org/10.1002/edn3.70130","url":null,"abstract":"<p>Environmental DNA (eDNA) metabarcoding has become a prominent method in aquatic biodiversity research and monitoring. A widely underexplored sample type is suspended particulate matter (SPM), composed of small organic and inorganic particles that contain eDNA. SPM is typically collected with sedimentation boxes, for instance by the German Environmental Specimen Bank for chemical monitoring of rivers. Its standardized collection and storage make SPM a potentially ideal source for eDNA time series analysis, linking environmental pressures and responses. This study evaluated key steps in the laboratory workflow allowing for the implementation of SPM in biodiversity research and monitoring. After validating an in-house extraction protocol, we extracted eDNA from three 12-year-old SPM samples representing three river sites. To quantify replicate variation in species detection, each sample was processed with three subsamples, four extraction replicates per subsample, and four PCR replicates per extraction replicate (48 replicates per SPM sample). Additionally, mechanically ground samples were investigated to test for decreased inter-sample variation. Our analysis revealed extensive, and plausible taxa lists for fish and aquatic invertebrates with significant differences between the sites. Within sites, we found high stochasticity in species detection of all replicates with the highest similarity between PCR replicates. In agreement with this, a Bayesian occupancy model demonstrated that species detection probability decreases in the PCR, while replicates earlier in the workflow were more effective in increasing species richness detection compared to PCR replicates or further increasing sequencing depth. Generally, 4–8 replicates were sufficient to recover 50% of all species, which contributed over 90% of the reads. Based on our results, we recommend at least eight replicates for biodiversity assessments using SPM. These should include at least one subsample or extraction replicate to maximize species richness. Our study supports the future use of SPM samples in biodiversity monitoring and provides a framework for assessing other eDNA matrices for robust species detection.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70130","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144520079","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":"SmartScreen-AIS: A High-Throughput qPCR Chip for Nationwide Surveillance of Aquatic Invasive Species","authors":"John A. Kronenberger,&nbsp;Taylor M. Wilcox,&nbsp;Michael K. Schwartz","doi":"10.1002/edn3.70144","DOIUrl":"https://doi.org/10.1002/edn3.70144","url":null,"abstract":"<p>Effective wildlife conservation requires frequent and widespread data on species occurrence. With the maturation of eDNA-based monitoring—now widely recognized as sensitive, cost effective, and legally defensible—nationally coordinated eDNA strategies are beginning to take shape. Such ambitious initiatives will require eDNA analytics with the throughput and sensitivity required for surveillance of many protected, pathogenic, and invasive species across broad geographic scales. Here, we help meet this need with SmartScreen-AIS: a high-throughput qPCR (HT-qPCR) chip with 46 assays targeting aquatic invasive species of widespread concern. SmartScreen-AIS was validated for use throughout the continental United States and can be subdivided into smaller chip formats as desired for use in specific regions or biomes. Assay performance in HT-qPCR was strong relative to conventional qPCR, with slightly lower specificity in some cases (due to pre-amplification) but significantly higher sensitivity. Contamination was rare, PCR inhibition was minimal to nonexistent, and demonstration at three military installations detected eDNA from all species on the chip that were known to be present and one species that was previously undocumented. Cost savings will depend on the number of assays used and samples tested, but in this study we estimate that eDNA analyses were 75% cheaper using HT-qPCR than they would be with our conventional qPCR protocol. To facilitate use, we provide appendices with assay details, bench protocols, a script for processing results, and an online app with state-level assay specificity information. SmartScreen-AIS has the potential to advance early detection of invasive species in the United States, and we hope our HT-qPCR workflow inspires chip development and use globally.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70144","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144482344","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":"Automating the Curation of DNA Barcode Databases for Vascular Plants","authors":"Andreas Kolter,&nbsp;Paul Hebert","doi":"10.1002/edn3.70125","DOIUrl":"https://doi.org/10.1002/edn3.70125","url":null,"abstract":"<p>Comprehensive, curated, and current DNA barcode reference databases are essential for both the identification of single specimens and for the interpretation of metabarcoding data. In the case of plants, nuclear (ITS) and plastid (rbcL, matK) markers are commonly used together. Because the plastid regions are segments of protein-coding genes, their alignment and analysis are usually straightforward. By contrast, the assembly and validation of ITS records is considerably more difficult for two reasons: the prevalence of indels and intraindividual sequence variation. This complexity has provoked the development of several workflows to support the curation of reference databases for the internal transcribed spacer (ITS) region for plant barcoding. However, the pipelines used to create these databases lack functionalities which are essential to ensure a solid post-analytical validation. This paper presents a new workflow to address these shortcomings, with the goal of enhancing the reliability and accuracy of plant barcoding studies. We furthermore demonstrate that clustering of reference databases results in a substantial drop in the fraction of queries that gain a correct species-level assignment. By contrast, setting an acceptance threshold for identifications, based on the distance between query and match, leads to a meaningful reduction of error rates in incomplete reference databases.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70125","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144492670","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":"Drivers of Insect Diversity and Community Turnover in Protected Tropical Deciduous Forests of Mexico","authors":"Pilar Benites,&nbsp;Antonio García-Bautista,&nbsp;Natalia Bautista-Briseño,&nbsp;Flavio E. Zárate-Hernández,&nbsp;Ek del-Val,&nbsp;Antonio Hernández-López,&nbsp;Enrique Ramírez-García,&nbsp;Diana P. Zavala-de la Rosa,&nbsp;Alfried P. Vogler,&nbsp;Alejandro Zaldívar-Riverón","doi":"10.1002/edn3.70143","DOIUrl":"https://doi.org/10.1002/edn3.70143","url":null,"abstract":"<p>Tropical deciduous forests (TDFs) are among the world's most biodiverse yet endangered ecosystems. In the Neotropics, TDFs have experienced substantial range reductions due to land use changes, with profound implications for their insect diversity, much of which remains unknown. Here we conducted extensive Malaise trap sampling and metabarcoding of whole insect communities to investigate the influence of seasonality, anthropogenic disturbance, and habitat physical parameters on insect taxonomic diversity and community structure in two protected TDFs on the Pacific coast of Mexico, at Chamela (Jalisco) and Huatulco (Oaxaca), located approximately 1000 km apart. We recorded high insect species diversity, with 4626 and 3672 MOTUs identified at Chamela and Huatulco, respectively, of which only 18.5% were shared between the two regions. Nonmetric multidimensional scaling (NMDS), fourth-corner model, and zeta diversity analyses revealed a complex, multi-factorial community turnover driven by seasonal fluctuations and varying disturbance levels. Species turnover also was partially explained by the distance between sites and specific forest features (total deadwood volume, tree diversity, canopy coverage), suggesting that habitat heterogeneity shapes local insect diversity and community turnover. Our findings highlight the unexpectedly high local and regional turnover in insect communities in Neotropical TDFs, underscoring the importance of conservation of each remaining forest reserve and their semi-disturbed surroundings.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70143","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144308900","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":"Distinct Community Compositions of Prokaryotes, Eukaryotes, and Fishes Revealed Through Environmental DNA Analysis at Different Salinities Around Ishigaki Island, Okinawa, Japan","authors":"Kohei Hamamoto,&nbsp;Miyuki Nishijima,&nbsp;Kodai Gibu,&nbsp;Atsushi Suzuki,&nbsp;Jinya Yamazaki,&nbsp;Keita Koeda,&nbsp;Nobuyuki Aoki,&nbsp;Akira Iguchi","doi":"10.1002/edn3.70115","DOIUrl":"https://doi.org/10.1002/edn3.70115","url":null,"abstract":"<p>Environmental DNA metabarcoding has proven effective for local biodiversity assessment with relatively low sampling effort and cost. However, it is still necessary to evaluate whether it can capture changing community composition along with environmental parameters such as salinity. Salinity is a fundamental abiotic feature that defines suitable habitats for many creatures, mainly due to osmotic considerations. We comprehensively investigated environmental DNA collected from two environments with different salinities, oligohaline (greater than salinity 0.5) and limnetic (less than salinity 0.5), using metabarcoding at different taxonomic levels: 16S prokaryotic universal metabarcoding, 18S eukaryotic universal metabarcoding, and MiFish fish-specific metabarcoding. These results showed that shared and unique genera in each salinity displayed different patterns at all taxonomic levels. An nMDS plot revealed that community composition is clearly segregated between salinity groups based on 16S analysis, but overlaps slightly when based on MiFish results. This may reflect osmotic tolerance, as fish communities change gradually, whereas bacterial communities change dramatically with sharp thresholds. PERMANOVA showed that these two salinity groups have significantly different community compositions at 16S, 18S, and MiFish levels. We further estimated taxa that differed in abundance in each salinity. Our results revealed that saltwater indicator bacteria such as <i>Planococcaceae</i> and <i>Woeseiaceae</i> were significantly more abundant in oligohaline sites, demonstrating that metabarcoding is capable of detecting halophilic bacteria, even though differences in salinity are relatively small. Several potentially harmful taxa, that is, fish-borne fluke, <i>Haplorchis taichui</i>, or toxic bloom-forming dinoflagellates, <i>Karlodinium</i>, were detected in limnetic and oligohaline sites, respectively. Considering Ishigaki Island's great biodiversity and in view of public health, further monitoring utilizing eDNA metabarcoding is necessary.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70115","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144300389","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":"Tropical Rainfall and eDNA Washout Impact Estimations of Amazonian Biodiversity Patterns From Environmental Samples","authors":"Céline Condachou,&nbsp;Opale Coutant,&nbsp;Antoine Fouquet,&nbsp;Alice Valentini,&nbsp;Sébastien Brosse,&nbsp;Jérôme Murienne","doi":"10.1002/edn3.70141","DOIUrl":"https://doi.org/10.1002/edn3.70141","url":null,"abstract":"<p>Environmental DNA (eDNA) has been extensively used to facilitate the characterization of both terrestrial and aquatic communities. However, implementing temporal biodiversity monitoring remains a major challenge requiring a better understanding of how seasonal variations in biological and ecological factors influence eDNA detection. Focusing on a French Guiana river, our research investigates the impact of tropical rainfall on ecological patterns of aquatic and terrestrial communities using eDNA samples. We collected water eDNA samples during the dry and rainy seasons to detect fish, mammals, and amphibians. Between seasons, gamma diversity was stable for fish but increased in the rainy season for mammals and amphibians. This shift is explained by the transport of eDNA from terrestrial to aquatic systems through rainfall (eDNA washout) and by the increase of activity during the rainy season for amphibians. In terms of beta diversity, we found species homogenization between sites, affecting both terrestrial and aquatic taxa during the rainy season. This is driven by the increase in water discharge and decrease in water temperature, leading to eDNA drift over longer distances. We recommend sampling eDNA during the dry season for local community inventories and during the rainy season for regional species monitoring, particularly to maximize terrestrial species detection.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70141","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144300449","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 (eDNA) Quantitative Polymerase Chain Reaction-Based Assays for Surveying 125 Taxa of Importance to North America","authors":"Valerie S. Langlois,&nbsp;Mark Louie D. Lopez,&nbsp;Michael J. Allison,&nbsp;Jacob J. Imbery,&nbsp;Julie Couillard,&nbsp;Neha Acharya-Patel,&nbsp;Lauren C. Bergman,&nbsp;Matthew T. Bonderud,&nbsp;Marie-Pier Brochu,&nbsp;Marie-Lee Castonguay,&nbsp;Lauren Coombe,&nbsp;Anna H. Dema,&nbsp;Emma T. Groenwold,&nbsp;Hajeong Lee,&nbsp;Isabel G. Ma,&nbsp;Yilin Ren,&nbsp;Graeme K. Knowles,&nbsp;Fidji Sandré,&nbsp;Tuan Anh To,&nbsp;René L. Warren,&nbsp;Cecilia L. Yang,&nbsp;Inanc Birol,&nbsp;Caren C. Helbing","doi":"10.1002/edn3.70139","DOIUrl":"https://doi.org/10.1002/edn3.70139","url":null,"abstract":"<p>Timely and accurate assessment of the presence of at-risk or invasive species is critical for effective responses to climate change and human impacts. For example, at-risk species are often difficult to find, while invasive species are often well established before their infiltration is detected using conventional surveying methods. However, all organisms release genetic material such as DNA into their surroundings, leaving traces of themselves that can be detected using environmental DNA (eDNA) methods. These approaches are powerful tools in the conservation toolbox, as they are transforming how risk assessments and the evaluation of mitigation and remediation effectiveness are done. Despite this, poorly performing tools hinder broad adoption of eDNA-based detection methods, due in part to their associated high false negatives and false positives that can impair effective management decision-making. iTrackDNA is a multi-year, large-scale applied research project that is addressing these concerns with researchers and end users from various sectors across North America. It is building end-user capacity through innovative, accessible, socially responsible genomics-based analytical eDNA tools for effective decision-making by publishing 125 quantitative real-time polymerase chain reaction (qPCR) primer/probe sets designed to detect key invertebrates, fish, amphibians, birds, reptiles, and mammals in coastal and inland ecosystems important to North America, with an emphasis on Canada. These 125 assays were designed to meet or exceed the new Canadian Standards Association (CSA) consensus-based and multi-stakeholder national standards for eDNA (CSA W214:21 and CSA W219:23). Herein, we describe how we applied eDNA assay design and validation approaches across a wide range of animal taxa to achieve compliance.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70139","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144264545","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":"Comprehensive Sequencing of Environmental RNA From Japanese Medaka at Various Size Fractions and Comparison With Skin Swab RNA","authors":"Kyoshiro Hiki,&nbsp;Toshiaki S. Jo","doi":"10.1002/edn3.70137","DOIUrl":"https://doi.org/10.1002/edn3.70137","url":null,"abstract":"<p>Environmental RNA (eRNA) is emerging as a non-invasive tool for assessing the molecular status and physiological responses of macro-organisms, but key information on its origin and particle sizes remains unclear. In this study, we aimed to determine the optimal filter pore size range for eRNA analysis and evaluate the contribution of skin and mucus to eRNA profiles. We performed comprehensive RNA-sequencing of eRNA (&gt; 13 Gb/sample) collected from tank water containing Japanese medaka (<i>Oryzias latipes</i>), using sequential filtration through filters with pore sizes of 10, 3, and 0.4 μm. Fish skin and mucus RNA was collected using a cotton swab, then sequenced, and compared with eRNA. Our results showed that the 3–10 μm fraction contained the lowest relative abundance of microbial RNA, the highest amount of medaka eRNA, and the largest number of detected medaka genes (5398 genes), while the 0.4–3 μm fraction had the fewest (972 genes). Only a small number of genes (42 genes) were unique to the 0.4–3 μm fraction. These findings suggest that a 3 μm filter is optimal for eRNA analysis, as it allows for larger filtration volumes while maintaining the relative abundance of macro-organism eRNA. Furthermore, 81% of the genes detected in eRNA overlapped with skin swab, indicating skin and mucus are major sources of fish eRNA.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70137","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144244180","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":"Geographic Genetic Divergence in Tychoplanktonic Taxa Dominating Diatom Communities in Marine Biofilms","authors":"Raphaëlle Barry-Martinet,&nbsp;Thomas Pollet,&nbsp;Fabienne Fay,&nbsp;Alina Tunin-Ley,&nbsp;Jean Turquet,&nbsp;Jean-François Ghiglione,&nbsp;Cédric Garnier,&nbsp;Aurélie Portas,&nbsp;Gaëtan Burgaud,&nbsp;Frédéric Rimet,&nbsp;Jean-François Briand","doi":"10.1002/edn3.70116","DOIUrl":"https://doi.org/10.1002/edn3.70116","url":null,"abstract":"<p>Diatoms constitute the main photosynthetic group in marine biofilms throughout the world's oceans, in particular, on plastic debris, which has become a major problem in the marine environment. However, they remain largely unexplored in this context compared to prokaryotes. Here, we aim to understand the dynamics of diatom communities in the plastisphere at different levels: how taxa are selected from the planktonic community and how communities are structured over time and at large spatial scales. Biofilms were collected from PVC (polyvinyl chloride) panels immersed (i) for 1 year in two NW Mediterranean sites, a mesotrophic one (Toulon Bay) and an oligotrophic one (Banyuls Bay), and (ii) for 1 month in Toulon Bay and two other eutrophic sites (Lorient in South Brittany in the Atlantic Ocean and Reunion Island in the Indian Ocean). Plastispheres were analyzed using both microscopic and molecular approaches, focusing on the relationship between diatoms and other microorganisms in biofilms. Light microscopy revealed spatio-temporal differences in cell abundance and biovolume. Metabarcoding, targeting the rbcL gene for diversity and composition, revealed that the richness of diatom species was already maximal in the early stages of biofilm formation, and beta-diversity showed a clear temporal evolution in the Mediterranean Sea. Including prokaryotic and fungal communities, we described microorganism interactions within biofilms throughout the colonization process of the plastisphere. In addition, environmental parameters on a large geographical scale were shown to be stronger drivers in structuring diatom communities, considering both planktonic and biofilm lifestyles. A core biofilm community represented by a few abundant species was observed across sites. The occurrence of tychoplanktonic taxa emphasizes the specificity of diatoms among other microorganisms in biofilms. Finally, the complete absence of common genetic variants among Lorient, Reunion Island, and Toulon suggests that dispersal by marine currents over a large geographical scale has led to adaptation processes.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70116","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144244178","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":"Decaying Uncertainties: Exploring the Role of Decay Rate Variability in Marine eDNA Dispersal Using Lagrangian Transport Modeling","authors":"Mohamed Yosri Zanni,&nbsp;Verena M. Trenkel,&nbsp;Robin Faillettaz","doi":"10.1002/edn3.70140","DOIUrl":"https://doi.org/10.1002/edn3.70140","url":null,"abstract":"<p>Environmental DNA (eDNA) has emerged as a powerful tool for fisheries management and biodiversity monitoring, offering novel insights into marine ecosystems. However, linking eDNA concentrations to species abundance remains a significant challenge. Limited understanding of the biotic and abiotic factors influencing eDNA production, decay, and transport in marine environments continues to hinder its broader application. This study aims to address these gaps by modeling eDNA decay and transport dynamics using a Lagrangian particle tracking model, the Connectivity Modeling System. Specifically, we (1) fitted and implemented five temperature-dependent decay rate relationships and (2) simulated eDNA transport accounting for temperature-dependent decay rate variability. We modeled eDNA dispersal at three contrasting locations in the Bay of Biscay, Northeast Atlantic, over a full year under the five decay rate scenarios. For eDNA transport, current velocity was the most important factor, followed by the decay rate relationship, while the converse effects were found for eDNA dispersion and lifetime. Temperature was found to have the least impact on transport variability. On average, eDNA persisted between 5 and 30 h, with transport distances varying between 0.3 km and 39.1 km, depending on location, month, decay rate, and depth. Our results emphasize the need for precise decay rate estimates, tailored to species-specific and encountered temperature conditions, to enhance the power of eDNA-based monitoring.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70140","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144244181","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}