Environmental DNA最新文献

{"title":"Passive Gauze-Based eDNA Sampler Proves Efficient and Cost-Effective in the Marine Environment","authors":"Molly M. Kressler,&nbsp;Lucy Whitelegg,&nbsp;Benedict Tutt-Leppard,&nbsp;Andrew Matthews,&nbsp;Dave Hudson,&nbsp;Richard B. Sherley","doi":"10.1002/edn3.70256","DOIUrl":"https://doi.org/10.1002/edn3.70256","url":null,"abstract":"<p>While environmental DNA (eDNA) is an increasingly valuable tool for marine biodiversity monitoring, the high cost of conventional eDNA sampling methods may limit long-term or large-scale applications. Here, we present the first empirical comparison of the metaprobe 2.0, a low-cost, passive eDNA sampler, against an industry standard Sterivex filtration method using dip-collected 1-L water samples (“water bottles”). Although the metaprobe has been used in a limited number of prior studies—primarily in comparison to traditional net-based sampling—its adoption remains limited, and this is the first study to benchmark its performance directly against a widely used eDNA sampling methodology. Across 14 joint deployments, we assessed detection and quantification of eDNA of two elasmobranch and two teleost species. While Sterivex filters outperformed metaprobes in detecting copies of DNA, metaprobes showed comparable detection performance within biologically significant margins and exhibited a lower variance among sampling replicates. Our study is the next step in the upscaling of this passive sampler and establishes a workflow for integrating metaprobes into biodiversity and species monitoring in marine ecology. We outline the methodological deviations from a “traditional” Sterivex filter eDNA workflow and identify how metaprobes might widen the accessibility of eDNA monitoring in the future through their simple yet effective sampling, filtering, and preservation protocols.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70256","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147563479","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":"Genomics-Based Approaches to Ant Monitoring in Land Management: Validation of COI Metabarcoding Primers","authors":"Allyson Malpartida,&nbsp;Maxine P. Piggott,&nbsp;Sam Banks,&nbsp;Andrew Harford,&nbsp;Kate Montgomery,&nbsp;Mieke van der Heyde,&nbsp;Paul Nevill,&nbsp;Alan N. Andersen","doi":"10.1002/edn3.70245","DOIUrl":"https://doi.org/10.1002/edn3.70245","url":null,"abstract":"<p>Ants (Hymenoptera: Formicidae) are globally dominant invertebrates and widely used as bioindicators of ecosystem change. However, their application in biomonitoring is constrained by the time required to process samples and the need for ever diminishing taxonomic expertise. DNA metabarcoding potentially offers an alternative approach, but validated ant-specific assays essential for accurate assessment of ant diversity are lacking. In this study, using a hierarchical framework aligned with recommended validation guidelines, we assessed primer performance in silico, in vitro and in situ to identify assays that maximize detection while minimizing bias for detecting ant species in Australian tropical savanna. In silico analyses involved evaluating 14 COI primer sets, including three newly designed ant-specific primers (AntF1, AntR1 and EPTDr2n_Ant) and 17 general invertebrate primers previously validated for terrestrial arthropods, against a custom reference database of 19 Australian ant genera with PrimerMiner. AntF1/AntR1, fwhF2/EPTDr2n_Ant and fwhF2/fwhR2n had the lowest penalty scores. In vitro metabarcoding of mock communities recovered 68% and 70% of genera with AntF1/AntR1 and fwhF2/fwhR2n, respectively, but only 0.05% for fwhF2/EPTDr2n_Ant. Spike-in assays revealed strong inhibitory effects of primer-template mismatches and soil environmental matrix on amplification efficiency. In situ comparisons of five surface soil eDNA samples recovered a subset of genera previously detected from far more extensive pitfall-trapping, with the ant-specific AntF1/AntR1 outperforming the general invertebrate primer fwhF2/fwhR2n for genus-level detection. We recommend AntF1/AntR1 as the primary assay for ant biomonitoring in Australia (and likely elsewhere in the world), suitable for both soil eDNA surveys and specimen metabarcoding, and fwhF2/fwhR2n for specimen metabarcoding. This study provides the first targeted validation of metabarcoding primers specifically for ants in Australia, providing a robust foundation for incorporating eDNA approaches into ant biomonitoring in land management.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70245","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147569868","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":"Genomics-Based Approaches to Ant Monitoring in Land Management: Validation of COI Metabarcoding Primers","authors":"Allyson Malpartida,&nbsp;Maxine P. Piggott,&nbsp;Sam Banks,&nbsp;Andrew Harford,&nbsp;Kate Montgomery,&nbsp;Mieke van der Heyde,&nbsp;Paul Nevill,&nbsp;Alan N. Andersen","doi":"10.1002/edn3.70245","DOIUrl":"https://doi.org/10.1002/edn3.70245","url":null,"abstract":"<p>Ants (Hymenoptera: Formicidae) are globally dominant invertebrates and widely used as bioindicators of ecosystem change. However, their application in biomonitoring is constrained by the time required to process samples and the need for ever diminishing taxonomic expertise. DNA metabarcoding potentially offers an alternative approach, but validated ant-specific assays essential for accurate assessment of ant diversity are lacking. In this study, using a hierarchical framework aligned with recommended validation guidelines, we assessed primer performance in silico, in vitro and in situ to identify assays that maximize detection while minimizing bias for detecting ant species in Australian tropical savanna. In silico analyses involved evaluating 14 COI primer sets, including three newly designed ant-specific primers (AntF1, AntR1 and EPTDr2n_Ant) and 17 general invertebrate primers previously validated for terrestrial arthropods, against a custom reference database of 19 Australian ant genera with PrimerMiner. AntF1/AntR1, fwhF2/EPTDr2n_Ant and fwhF2/fwhR2n had the lowest penalty scores. In vitro metabarcoding of mock communities recovered 68% and 70% of genera with AntF1/AntR1 and fwhF2/fwhR2n, respectively, but only 0.05% for fwhF2/EPTDr2n_Ant. Spike-in assays revealed strong inhibitory effects of primer-template mismatches and soil environmental matrix on amplification efficiency. In situ comparisons of five surface soil eDNA samples recovered a subset of genera previously detected from far more extensive pitfall-trapping, with the ant-specific AntF1/AntR1 outperforming the general invertebrate primer fwhF2/fwhR2n for genus-level detection. We recommend AntF1/AntR1 as the primary assay for ant biomonitoring in Australia (and likely elsewhere in the world), suitable for both soil eDNA surveys and specimen metabarcoding, and fwhF2/fwhR2n for specimen metabarcoding. This study provides the first targeted validation of metabarcoding primers specifically for ants in Australia, providing a robust foundation for incorporating eDNA approaches into ant biomonitoring in land management.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70245","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147570058","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":"Comparison of Environmental DNA Metabarcoding and Trawl Data Highlights Gear Selectivity of Marine Demersal Fish Surveys on the Faroese Plateau","authors":"I. Salter,&nbsp;M. Brandner,&nbsp;A. Djurhuus,&nbsp;K. Præbel,&nbsp;O. Wangensteen","doi":"10.1002/edn3.70253","DOIUrl":"https://doi.org/10.1002/edn3.70253","url":null,"abstract":"<p>Environmental DNA (eDNA) has emerged as a promising tool for studying fish dynamics in aquatic environments. However, the quantitative capabilities of eDNA metabarcoding, especially in marine systems, remain contentious due to limited comparative studies. This study presents a comparison between a standardized trawl survey and eDNA metabarcoding (12S) in demersal fishing grounds around the Faroe Islands. Data were collected at 26 sites distributed across six regions. A total of 31 fish species were detected from trawls. Inclusion of Molecular Operational Taxonomic Units increased survey taxa richness by 151% to 47, with 21 species shared between methods, 11 unique to trawling, and 15 unique to eDNA. Unique trawl detections were linked to low biomass species (rarity) and technical limitations in species differentiation (e.g., <i>Sebastes</i> spp.). Unique eDNA detections were associated with rarity, size, gear-behavioral traits, and pelagic species. For taxa detected by both methods, total reads were positively correlated with trawl biomass over the survey area (<i>r</i> = 0.85, <i>q</i> &lt; 0.001), but not by site or region. Accounting for stochastic amplification in technical replicates improved the survey-wide eDNA-biomass correlation (<i>r</i> = 0.91, <i>q</i> &lt; 0.001). Regional distribution of sandeel eDNA agreed with stomach contents of <i>Gadus morhua</i>, providing information on its spatial distribution otherwise missed by trawling. Overall, eDNA metabarcoding identified small species under-sampled by trawl gear, thus enhancing species richness when methods were combined. The study also highlighted the potential for eDNA to describe the spatial distribution of sandeel, a keystone species in the Faroese marine ecosystem, and generated reliable quantitative estimates of species rank biomass. However, the study highlights limitations of both eDNA and trawling that are problematic in marine systems: (i) detection of low biomass species, (ii) variability over small spatial scales, and some limitations specific to eDNA: (iii) vertical mixing of eDNA signals from pelagic and demersal habitats.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70253","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147569526","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":"Comparison of Environmental DNA Metabarcoding and Trawl Data Highlights Gear Selectivity of Marine Demersal Fish Surveys on the Faroese Plateau","authors":"I. Salter,&nbsp;M. Brandner,&nbsp;A. Djurhuus,&nbsp;K. Præbel,&nbsp;O. Wangensteen","doi":"10.1002/edn3.70253","DOIUrl":"https://doi.org/10.1002/edn3.70253","url":null,"abstract":"<p>Environmental DNA (eDNA) has emerged as a promising tool for studying fish dynamics in aquatic environments. However, the quantitative capabilities of eDNA metabarcoding, especially in marine systems, remain contentious due to limited comparative studies. This study presents a comparison between a standardized trawl survey and eDNA metabarcoding (12S) in demersal fishing grounds around the Faroe Islands. Data were collected at 26 sites distributed across six regions. A total of 31 fish species were detected from trawls. Inclusion of Molecular Operational Taxonomic Units increased survey taxa richness by 151% to 47, with 21 species shared between methods, 11 unique to trawling, and 15 unique to eDNA. Unique trawl detections were linked to low biomass species (rarity) and technical limitations in species differentiation (e.g., <i>Sebastes</i> spp.). Unique eDNA detections were associated with rarity, size, gear-behavioral traits, and pelagic species. For taxa detected by both methods, total reads were positively correlated with trawl biomass over the survey area (<i>r</i> = 0.85, <i>q</i> &lt; 0.001), but not by site or region. Accounting for stochastic amplification in technical replicates improved the survey-wide eDNA-biomass correlation (<i>r</i> = 0.91, <i>q</i> &lt; 0.001). Regional distribution of sandeel eDNA agreed with stomach contents of <i>Gadus morhua</i>, providing information on its spatial distribution otherwise missed by trawling. Overall, eDNA metabarcoding identified small species under-sampled by trawl gear, thus enhancing species richness when methods were combined. The study also highlighted the potential for eDNA to describe the spatial distribution of sandeel, a keystone species in the Faroese marine ecosystem, and generated reliable quantitative estimates of species rank biomass. However, the study highlights limitations of both eDNA and trawling that are problematic in marine systems: (i) detection of low biomass species, (ii) variability over small spatial scales, and some limitations specific to eDNA: (iii) vertical mixing of eDNA signals from pelagic and demersal habitats.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 2","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70253","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147569529","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":"Correction to “Tunneling Dung Beetle Effects on Soil Microbial Communities and Nutrient Cycling in Pasturelands: Implications for Soil Carbon Dynamics”","authors":"","doi":"10.1002/edn3.70257","DOIUrl":"https://doi.org/10.1002/edn3.70257","url":null,"abstract":"<p>Lipton, S., R. S. Meyer, K. M. Scow, A. L. Simons, and S. M. Philpott. 2025. “Tunneling Dung Beetle Effects on Soil Microbial Communities and Nutrient Cycling in Pasturelands: Implications for Soil Carbon Dynamics.” <i>Environmental DNA</i> 7, no. 6: e70228. https://doi.org/10.1002/edn3.70228.</p><p>Corrected version of Figure 1</p><p>We apologize for this error.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70257","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147653240","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 Environmental DNA Variability and Species Detections Through Passive and Active Sampling Across Time: A Case Study From a Hyper-Diverse Coastal System","authors":"Daniel Estévez-Barcia,&nbsp;Jannes Landschoff,&nbsp;Sophie von der Heyden","doi":"10.1002/edn3.70258","DOIUrl":"https://doi.org/10.1002/edn3.70258","url":null,"abstract":"<p>The conservation of biodiversity is fundamental for the persistence of ecosystems, particularly under climate change. The South African marine environment is characterized by high levels of biodiversity as well as endemism, but species distribution patterns are generally not well characterized. Environmental DNA (eDNA) metabarcoding is a promising tool to help plug the biodiversity information gap, but evidence from previous studies has shown highly variable eDNA signals, even at small temporal–spatial scales (&lt; 300 m, 24 h). Passive samplers, deployed over several hours may circumvent some of the challenges of high eDNA variation by accumulating DNA over time. Using multiple markers (mtDNA 12S rRNA, mtDNA COI), we test both active (using Sterivex) and passive sampling (gauze filled metaprobe) in the detection of kelp forest-associated biodiversity, focussing on fishes and invertebrates. We conducted our experiment across different time periods (6, 12, 24 h) and hypothesized that metaprobes at 24 h would harbor the greatest species richness. We detected 33 ESVs, assigned to 18 different fish families, with 12S rRNA, where active sampling retrieved a larger proportion of diversity (94% vs. 64%, <i>p</i> &lt; 0.001). For COI, we detected 1481 ESVs assigned to 17 different phyla, 99 families, and 55 species, with passive sampling detecting more ESVs (82% vs. 67%, <i>p</i> &lt; 0.001). COI metabarcoding detected an additional four families of fishes, highlighting the importance of multi-marker approaches. For passive sampling only, there was a trend of significant accumulation of numbers of reads and ESVs over time. We found that active samples were more consistent across all statistics: variation in the number of reads, ESVs, and taxa retrieved, which was less in active than passive replicates. Overall, we highlight the need for region-specific approaches and careful project planning before implementing eDNA metabarcoding as a biomonitoring tool.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70258","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147320953","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 Gradients and Ecological Processes Are Main Drivers of Eukaryotic Diversity in the Eastern Red Sea","authors":"Carlos Angulo-Preckler,&nbsp;Sofia Frappi,&nbsp;Elisa Laiolo,&nbsp;Kah Kheng Lim,&nbsp;Diego E. Rivera Rosas,&nbsp;Christopher A. Hempel,&nbsp;Larissa Frühe,&nbsp;Anastasiia Martynova,&nbsp;Alexandra Steckbauer,&nbsp;Taiba Alamoudi,&nbsp;Shannon G. Klein,&nbsp;Vincent A. Pieribone,&nbsp;Mohammad A. Qurban,&nbsp;Susana Agusti,&nbsp;Carlos M. Duarte","doi":"10.1002/edn3.70254","DOIUrl":"https://doi.org/10.1002/edn3.70254","url":null,"abstract":"<p>Microeukaryotes, including protists, microalgae, and small fungi, are fundamental components of marine ecosystems, driving energy transfer, nutrient cycling, and primary production. Despite their ecological significance, they remain understudied due to their small size and taxonomic complexity. Here, we present a comprehensive assessment of eukaryotic diversity across the entire water column of the Eastern Red Sea, integrating surface to deep-sea layers along a latitudinal gradient. Environmental DNA metabarcoding of bottle-net hauls from 266 samples across 128 stations spanning the eastern Red Sea revealed 4298 MOTUs from 40 phyla, with a substantial fraction lacking reliable taxonomic assignments. While traditional diversity indices showed little variation across regions or depths, multivariate analyses revealed pronounced community turnover along the latitudinal gradient and subtler vertical structuring. Temperature, dissolved oxygen, and turbidity emerged as significant correlates of β-diversity, with the remainder likely reflecting unmeasured drivers. Despite a large core of MOTUs shared across epipelagic, mesopelagic, and bathypelagic layers, ecological groups displayed depth-specific abundance patterns, and co-occurrence networks identified phototrophic and microbial hubs with a southward shift toward stronger benthic–pelagic coupling. Notably, we observed a latitudinal transition from fungal- and algal-dominated communities in the north to more complex microbial–benthic–vertebrate networks in the south. Our results indicate that Red Sea eukaryote communities are shaped by both abiotic gradients and biological interactions, and that water column-integrated sampling reduces depth bias and captures biodiversity patterns overlooked by single-depth surveys. This work provides a regional baseline for biodiversity monitoring and conservation in a rapidly changing tropical sea.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70254","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147320781","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":"BirT: A Novel Primer Pair for Avian Environmental DNA Metabarcoding","authors":"Bettina Thalinger,&nbsp;Rachel Empey,&nbsp;Megan Cowperthwaite,&nbsp;Katerina Coveny,&nbsp;Dirk Steinke","doi":"10.1002/edn3.70255","DOIUrl":"https://doi.org/10.1002/edn3.70255","url":null,"abstract":"<p>Environmental DNA (eDNA) metabarcoding is widely used to detect animals from environmental samples and on the brink of being implemented into routine species monitoring. Surprisingly, birds are among the taxonomic groups which have received comparably little attention in eDNA research regarding primer optimization—particularly reducing the amplification of non-target taxa, the availability of appropriate reference sequence databases for the targeted fragments, and the evaluation of different filter types for their capability to detect avian eDNA from water samples. Here, we present a novel primer pair (BirT) for metabarcoding avian eDNA. We optimized specificity and fragment length with regard to taxonomic resolution and available sequencing platforms. Additionally, we evaluated the availability of 12S rRNA gene reference sequences for birds and filled database gaps by generating novel barcodes. Finally, we tested the applicability of the BirT primer pair using field-collected eDNA samples obtained with three different filter types and compared the eDNA metabarcoding results to visual observations uploaded to eBird (www.eBird.org). Our results confirm the suitability of the BirT primer pair for avian eDNA metabarcoding with no amplification of key non-target groups and improved taxonomic resolution. Albeit there are still substantial gaps in the 12S reference sequence database, the analysis of bird eDNA from water samples resulted in species-level taxonomic resolution for 91% of the detected taxa. All tested filters delivered similar results for total read numbers per sample (mean: 623,990 ± 331,236 SD) and species detected per sample (mean: 5.0 ± 2.0 SD). Ninety-five percent of the bird detections were highly plausible based on eBird data collected at the time of eDNA sampling and 64% were directly confirmed by visual observations. Most detected species were closely associated with aquatic habitats confirming the suitability of water samples for the detection of waterfowl and species inhabiting similar ecological niches via eDNA.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70255","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146211366","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 Comparison of DNA Metabarcoding Cloacal Swabs and Stomach Contents for Shark Diet Reconstruction","authors":"Savannah J. Ryburn,&nbsp;Eldridge Wisely,&nbsp;Jeffrey D. Plumlee,&nbsp;Creed C. Branham,&nbsp;F. Joel Fodrie,&nbsp;John F. Bruno","doi":"10.1002/edn3.70247","DOIUrl":"https://doi.org/10.1002/edn3.70247","url":null,"abstract":"<p>Metabarcoding fecal matter is increasingly common in dietary studies across a variety of taxa. This approach assumes that enough prey DNA remains detectable in the fecal DNA (fDNA) as the prey DNA becomes degraded while passing through the digestive tract. However, as prey DNA is degraded during digestion, diet reconstruction based on metabarcoding of fDNA could become incomplete, i.e., species for which DNA was highly degraded would not be detected. The purpose of this study was to test the use of cloacal swabs and metabarcoding fDNA for shark diet reconstruction. To do this, both stomach contents and cloacal swabs were collected from the same individual sharks and metabarcoded using two previously published primer sets targeting teleost fishes and crustaceans. Samples were collected from four coastal species of sharks in a temperate estuary: bonnethead (<i>Sphyrna tiburo; n</i> = 10), blacknose (<i>Carcharhinus acronotus; n</i> = 4), blacktip (<i>C. limbatus; n</i> = 4), and Atlantic sharpnose (<i>Rhizoprionodon terraenovae; n</i> = 5). We determined how well the fDNA represented the corresponding prey DNA from the stomach contents (stDNA) and found no statistical difference in taxonomic richness or diversity when comparing the two sample types. Our results indicate that the less invasive, non-lethal method of DNA metabarcoding cloacal swabs provided higher taxonomic resolution than more common methods for studying trophic ecology (i.e., morphological stomach contents identification and trophic biomarkers such as stable isotope analysis) with no statistical difference in overall diet description between the two sample types.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70247","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146217378","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}