Environmental DNA最新文献

{"title":"ANEMONE Global's First eDNA-Based Assessment: Insights Toward a Standardized Global Monitoring Network","authors":"Imane Sioud,&nbsp;Yuki Minegishi,&nbsp;Tadashi Kajita,&nbsp;Yukinobu Isowa,&nbsp;Akifumi S. Tanabe,&nbsp;Hisashi Yamakawa,&nbsp;Oliver Berry,&nbsp;Mohammad Basyuni,&nbsp;Hong Leong Cheah,&nbsp;Bruce Deagle,&nbsp;Jean Fall,&nbsp;Kazi Ashan Habib,&nbsp;Shalika Kumbregama,&nbsp;Wanlada Klangnurak,&nbsp;Venus E. Leopardas,&nbsp;Ndeye Codou Mbaye,&nbsp;Nasreen Peer,&nbsp;Kannan Sivakumar,&nbsp;Itchika Sivaipram,&nbsp;Ulla Von Ammon,&nbsp;Alison Wee,&nbsp;Sau Pinn Woo,&nbsp;Michio Kondoh","doi":"10.1002/edn3.70252","DOIUrl":"https://doi.org/10.1002/edn3.70252","url":null,"abstract":"<p>Environmental DNA (eDNA) enables sensitive detection of species from environmental samples, particularly water. Large-scale, standardized monitoring of coastal fish communities remains challenging across diverse regions. The ANEMONE Global network was established to address this gap, expanding the workflow developed in Japan to a coordinated worldwide survey using standardized eDNA metabarcoding. Between June and November 2024, 12 countries, including several in Southeast Asia, collected surface water samples from beaches, rocky shores, estuaries, and near coastal protective structures using harmonized protocols for filtration, RNAlater preservation, and metadata recording. Daytime and nighttime sampling captured temporal variation in community composition. All samples were processed with the MiFish metabarcoding protocol, quantitative internal standards, and rigorous contamination controls. Analysis of 90 samples generated over 16.6 million high-quality reads, revealing more than 500 putative fish OTUs across diverse families, genera, and species. Species richness varied geographically, reflecting differences in fish fauna, and assemblages differed across the Atlantic, Indian, North Pacific, and South Pacific Oceans. Diel variation was most pronounced in the North Pacific, and diversity patterns reflected both habitat complexity and ocean basin, with waters adjacent to coastal protective structures and rocky shores supporting the highest diversity. These findings highlight how both habitat complexity and ocean basin geography shape coastal fish assemblages, offering insights for global marine biodiversity monitoring using eDNA. This survey demonstrates that a globally standardized eDNA workflow can generate comparable quality data across ecological and logistical contexts. By combining international collaboration, open data, and locally informed implementation, ANEMONE Global provides a framework for long-term, high-resolution monitoring of coastal biodiversity and sets the stage for expanding coverage to additional aquatic ecosystems worldwide.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70252","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146211355","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":"Improving Species Abundance Information From River eDNA Metabarcoding Data","authors":"Eva Cereghetti,&nbsp;Florian Altermatt,&nbsp;Luca Carraro","doi":"10.1002/edn3.70250","DOIUrl":"https://doi.org/10.1002/edn3.70250","url":null,"abstract":"<p>Accurate information on species abundances and their distribution in space is key to ecological research and essential for informed decision-making in environmental management. Environmental DNA (eDNA) allows community-wide detection of biodiversity, but its limited ability to estimate species abundance from metabarcoding outputs poses important challenges for its broader application. The eDNA Integrating Transport and Hydrology (eDITH) framework addresses some of these limitations by partly accounting for eDNA transport and decay dynamics in river networks and allows predicting the spatial distribution of taxa at high resolution. However, its capability for providing quantitative estimates of taxon abundances has so far not been empirically validated. Here, we utilized spatially replicated eDNA and kick-net samples collected in spring and summer at 25 sites along a 126 km² river catchment. We contrasted species-level relative abundances of insect communities obtained via eDNA metabarcoding read counts and via eDITH estimates with those obtained from the kick-net samples. We found that eDNA read counts of sampled locations did not correlate with the associated local kick-net (i.e., realized) insect abundance, but that the eDITH estimates did. However, results varied across insect orders and the improvements provided by eDITH were highly species-specific. Our findings corroborate the inadequacy of utilizing raw read counts for quantitative inference and pose forward the potential of the eDITH framework in circumventing some of the limitations of metabarcoding outputs. Together with other recently proposed correction approaches, this framework contributes to ongoing efforts to refine the interpretability of metabarcoding data. As the demand for quantitative biodiversity data continues to grow in both ecological research and environmental management, refining and validating sampling approaches remains a critical priority.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70250","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146216847","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 as a Tool for the Assessment of Coral (Anthozoa) Composition in the Chagos Archipelago","authors":"Boxian Wen,&nbsp;Rosalie Dowell,&nbsp;Margaux Steyaert,&nbsp;Catherine E. I. Head","doi":"10.1002/edn3.70235","DOIUrl":"https://doi.org/10.1002/edn3.70235","url":null,"abstract":"<p>Human-induced global warming has triggered a persistent decline in the health of marine ecosystems, particularly coral reefs, which are experiencing increasingly frequent and severe bleaching and mortality events. Refining cost-effective and precise monitoring tools, such as environmental DNA (eDNA) metabarcoding, is essential to supplement future coral reef monitoring programs, with ongoing efforts focused on improving methods, validating results, and understanding limitations. Although eDNA has been widely used in aquatic ecosystem studies, its application to corals (Anthozoa) remains underexplored. Here, we investigate the use of eDNA metabarcoding with molecular markers targeting the ITS2 region of Anthozoa for monitoring coral communities in a remote and relatively undisturbed atoll system. We integrate three mainstream taxonomic assignment approaches (IDTAXA, BLAST Top Hits, and BLAST LCA), retaining only consensus identifications across methods for downstream analyses. This conservative strategy ensures highly robust and reliable taxonomic resolution, with over 90% of the sequences classified within Anthozoa, encompassing 18 genera and 15 genera of hard corals (Scleractinia). A considerable overlap in coral identification is observed between eDNA and traditional benthic transect surveys, giving support to the ability of eDNA to identify the community composition of Anthozoan taxa. Importantly, cryptic genera, such as <i>Cycloseris</i>, <i>Cyphastrea</i>, <i>Merulina</i>, <i>Oxypora</i>, and <i>Turbinaria</i> were identified by the eDNA approach but not the traditional surveys. Conversely, genera such as <i>Alveopora</i>, <i>Astreopora</i>, <i>Caulastrea</i>, <i>Fungia</i>, <i>Galaxea</i>, <i>Halomitra</i>, <i>Herpolitha</i>, <i>Leptastrea</i>, <i>Platygyra</i>, <i>Plerogyra</i>, and <i>Stylophora</i> were identified by the traditional surveys but not the eDNA approach, likely due to primer bias, taxonomic resolution or incomplete reference databases, supporting the complementary use of both methods. We also observe that the eDNA metabarcoding may capture differences in coral community structure between our lagoonal and seaward reef habitat types and point to potential characteristic taxa. This study underscores the utility of eDNA metabarcoding as a noninvasive, cost-effective tool for coral biodiversity monitoring and provides insights into how to improve eDNA techniques for use as a coral biodiversity monitoring tool.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70235","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146139397","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":"Tracking the Phenology of Riverine Insect Communities Using Environmental DNA","authors":"Eva Cereghetti,&nbsp;Xhesida Ajvazi,&nbsp;Raphaël Bossart,&nbsp;François Keck,&nbsp;Andrea Patrignani,&nbsp;Nicolò Tartini,&nbsp;Florian Altermatt,&nbsp;Luca Carraro","doi":"10.1002/edn3.70249","DOIUrl":"https://doi.org/10.1002/edn3.70249","url":null,"abstract":"<p>Aquatic insects are iconic and ecologically highly relevant inhabitants of riverine ecosystems. They are also often the target of monitoring programs to assess the ecological status of these lotic habitats. Environmental DNA (eDNA) techniques have been widely and successfully implemented to investigate freshwater insects and other macroinvertebrates. Commonly, such monitoring is conducted at one or two timepoints per year, despite the known phenology of aquatic insects' life history strongly affecting species presence—or detection—and population dynamics through the seasons. Here, we assessed if and to which extent eDNA can capture the temporal changes of the orders Ephemeroptera (mayflies), Plecoptera (stoneflies), Trichoptera (caddisflies), and Diptera (true flies). We carried out eDNA sampling at roughly monthly intervals from April to October at 25 sites across a whole river catchment in the northeastern part of Switzerland. We found pronounced, cyclic phenological trends in all orders but Trichoptera: the communities diverged from spring to summer and then in fall gradually returned closer to the spring state. The four orders exhibited different predominance in gains or losses of species detection throughout this time interval. Lastly, we found that field replicates, despite showing a relatively high local stochasticity, were able to provide a more complete assessment of aquatic communities. Field replicates, when used as a proxy for the frequency of observation of a species through the seasons, yielded comparable temporal patterns to the ones extracted from the Global Biodiversity Information Facility (GBIF) for about 35% of the investigated species. Overall, our findings demonstrate that eDNA techniques can be used to reveal intra-annual dynamics of aquatic insects. Given the current necessity to assess and monitor the biodiversity status of ecosystems, we therefore show that eDNA methods are a viable option to obtain a deeper understanding of the structuring of freshwater communities over time.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70249","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146193376","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 Ground Surface Rolling Method for Detecting Environmental DNA of Terrestrial Animals","authors":"Manami Kakita,&nbsp;Yoshikazu Furuta,&nbsp;Hidenori Tanaka","doi":"10.1002/edn3.70248","DOIUrl":"https://doi.org/10.1002/edn3.70248","url":null,"abstract":"<p>Biodiversity monitoring is essential for conservation and ecosystem management, but current terrestrial survey methods, such as visual observation, trapping, and camera traps, are labor-intensive and time-consuming. Environmental DNA (eDNA) analysis offers a non-invasive alternative and is well-established in aquatic systems, yet terrestrial eDNA methods remain underdeveloped. Existing terrestrial approaches, such as water or soil sampling and air filtration, face limitations in target coverage, DNA persistence, and ease of deployment. Surface-swabbing techniques show promise but often lack scalability for frequent, multisite sampling. We aimed to develop and evaluate a simple, power-free, and scalable terrestrial eDNA collection method capable of sampling wide ground-surface areas for biodiversity monitoring. We designed the Koro-rin sampler, consisting of a rotating body with a single-use nonwoven fabric collector. This device collects surface-associated particles (soil, leaf litter, and fine debris) from diverse substrates without a power source. Over 14 months, we collected 90 ground-surface samples and 29 water samples from a drinking site within the same secondary forest in Japan. Samples were analyzed using MiBird and MiMammal metabarcoding, and results were compared with concurrent camera trap and seasonal observation data. Metabarcoding detected 53 bird and mammal taxa from ground and surface samples. Of these, 92% were also recorded by camera traps in front of the sampling areas, validating detection sensitivity. Seasonal patterns in eDNA detections matched the arrival timing of migratory birds observed visually. The method enabled high-frequency, wide area sampling with minimal labor. The Koro-rin sampler is a practical, sensitive, and time-resolved approach for terrestrial eDNA monitoring. Its portability and disposability make it suitable for large-scale, long-term surveys. Combined with aquatic eDNA monitoring, it enables integrated ecosystem assessments.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70248","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146154596","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":"Explainable Multimodal Machine Learning Using Combined Environmental DNA and Biogeographic Features for Ecosystem Biomonitoring","authors":"Joshua Chee Oon Koh","doi":"10.1002/edn3.70232","DOIUrl":"https://doi.org/10.1002/edn3.70232","url":null,"abstract":"<p>Machine learning (ML) has been proposed as a taxonomy-independent approach using environmental DNA (eDNA) for ecosystem biomonitoring. Representations of eDNA amplicons either as clustered sequences termed operational taxonomic units (OTUs) or unique sequences termed amplicon sequence variants (ASVs) are used as inputs in current ML practices with varied successes. The use of eDNA as sole input in ML inherently limits the potential of ML for ecosystem biomonitoring and prediction. Biogeographic data encompassing the physical, climate, and ecological observations provide a repository of potential informative features that can augment ML performance in combination with eDNA data. A multimodal ML workflow using combined eDNA and biogeographic features for ecosystem biomonitoring is introduced in this study. Differentially abundant ASVs were merged with biogeographic data and used as input in an automated ML approach. Using Switzerland's freshwater macroinvertebrate eDNA dataset collected across 163 biomonitoring sites and impact prediction as an example, the multimodal ML approach (83.3% accuracy) significantly outperformed ML using only ASVs (66.7% accuracy) or OTUs (64.6% accuracy). Shapley additive explanation of the best ML model revealed key biogeographic features and species/taxa impacting upon predictions. The proposed workflow can be readily adopted in existing bioinformatics/ML pipelines and will further advance the use of eDNA for ecosystem biomonitoring across large spatiotemporal scales.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70232","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146148268","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 Reflects Differences in Freshwater Habitat Use Between Two Pacific Salmonids at Fine Temporal Scales","authors":"Brock T. Burgess,&nbsp;Richard Chea,&nbsp;Kristen M. Westfall,&nbsp;Cathryn L. Abbott,&nbsp;Josephine C. Iacarella","doi":"10.1002/edn3.70231","DOIUrl":"https://doi.org/10.1002/edn3.70231","url":null,"abstract":"<p>Environmental DNA (eDNA) has emerged as a powerful tool to detect aquatic species, providing a non-invasive survey option for applications in freshwater fisheries, including delineating habitat use and informing stock management strategies. For species like salmonids with life stage-specific habitat requirements and timing, effective use of eDNA for species detection at fine spatial and temporal scales is contingent upon a robust understanding of eDNA detectability across all life stages. We conducted a 12-month eDNA survey in two Canadian rivers to describe temporal variation in eDNA concentrations of two anadromous fishes, Chinook (<i>Oncorhynchus tshawytscha</i>; Salmonidae) and coho salmon (<i>O. kisutch</i>), and relate this to important life history periods including spawning, egg incubation, fry emergence, rearing, and outmigration. We sampled downstream of known spawning grounds and found discharge-corrected eDNA concentrations were closely associated with known migratory patterns across species. For example, eDNA concentrations peaked during fall spawning for both species and followed similar monthly trends in summer. Sharp declines in eDNA were observed following spawning and concentrations remained low until spring when small spikes were detected as a result of fry emergence and rearing. We also found evidence of eDNA concentrations providing species detection at fine temporal scales in rivers, as a large hatchery release of Chinook was detected by eDNA only on the day of release and not on subsequent days. These results demonstrate eDNA as a temporally specific and effective detection tool across salmonid freshwater life stages and highlight the promise of eDNA for assessing major life history periods of Pacific salmon in freshwater. Overall, our work builds on the rapidly growing field of eDNA for applications to fish and fisheries and reinforces the promise of this technology for improving current management practices.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70231","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146148218","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":"Complete Mitochondrial Genomes Recovered From Environmental Metagenomics Samples Can Facilitate Non-Intrusive Population Genetic/Genomics Studies in the South American Sea Lion Otaria byronia","authors":"Juan Antonio Baeza,&nbsp;Angélica Colín,&nbsp;Maryam Dehghanian,&nbsp;Eduardo Castro-Nallar,&nbsp;Simon Berents","doi":"10.1002/edn3.70213","DOIUrl":"https://doi.org/10.1002/edn3.70213","url":null,"abstract":"<p>The abundance of many marine mammals is declining due to local, regional, and global climate stressors that characterize the Anthropocene. Long-term monitoring is crucial for understanding how these declining populations respond to further environmental stress, and developing non-invasive genetic sampling strategies is needed to guide their recovery effectively. The aim of this study was to test if complete mitochondrial genomes can be assembled from environmental DNA (eDNA) metagenomics scat samples taken non-invasively using the South American Sea Lion <i>Otaria byronia</i> as a model and examine if the retrieved mitochondrial genomes can facilitate non-intrusive population genetic studies. Complete mitochondrial genomes of <i>O. byronia</i> were assembled from each of a total of 30 eDNA samples with coverages greater than 40× using a “target-restricted-assembly” bioinformatics strategy. The AT-rich mitochondrial genomes contained 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. Mitochondrial gene order in <i>O. byronia</i> was identical to that reported for all other cofamilial species. An Analysis of Molecular Variance and pairwise Φ_ST tests using a 228 bp fragment of the CR demonstrated statistically significant genetic dissimilarity among the sampled population and others in the Pacific and Atlantic basin. This study demonstrates that complete mitochondrial genomes can be assembled from eDNA metagenomics scat samples, with which insights into metapopulation genetics can be achieved. Mitochondrial genomes assembled from eDNA metagenomics scat samples can support non-disruptive biomonitoring of this iconic marine mammal across its distribution.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70213","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146140175","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 Sediment and Water eDNA Metabarcoding for Monitoring Aquatic Biodiversity in a Plateau Lake","authors":"Xiu Feng,&nbsp;Xiaoling Wang,&nbsp;Ren Zhu,&nbsp;Yintao Jia,&nbsp;Xiaoyun Sui,&nbsp;Zhixian Qiao,&nbsp;Yifeng Chen","doi":"10.1002/edn3.70244","DOIUrl":"https://doi.org/10.1002/edn3.70244","url":null,"abstract":"<p>Environmental DNA (eDNA) metabarcoding is a powerful tool for monitoring aquatic biodiversity in extreme environments like the Qinghai–Tibet Plateau (QTP), where traditional methods face significant challenges. However, key knowledge gaps remain, particularly in selecting optimal sampling substrates for target taxonomic groups and understanding substrate-specific detection differences. Here, using eDNA metabarcoding with five primer sets (targeting mitochondrial, nuclear, and nucleoid sequences), we systematically compared biodiversity detection between sediment and water samples collected from five sites in the Dongjicuona Lake across the tree of life (encompassing archaea, bacteria, algae, fungi, plants, protozoa, invertebrates, fishes, birds, and mammals). The results showed that sediment eDNA exhibited significantly higher amplicon sequence variant (ASV) richness compared to water eDNA for most taxonomic groups. In contrast, the opposite pattern was observed for fishes, while no significant differences were observed for fungi and birds. Community composition differs significantly between sediment and water samples for most taxonomic groups, except for mammals. Across all taxonomic groups, 18.0% of ASVs were shared between sediments and water, with fishes showing the highest overlap (42.6%) and archaea the lowest (4.5%). Additionally, the percentages of ASVs contributing to major community dissimilarity (cumulatively accounting for 80%) ranged from 6.4% (invertebrates) to 17.4% (protozoa), with most taxa exhibiting distinct habitat preferences. These findings support water sampling as an effective method for monitoring fish diversity, while emphasizing the need for a multi-substrate approach to comprehensively monitor other taxonomic groups in plateau lakes.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70244","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146193622","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":"Consistent Species Richness Patterns but Not Richness Estimates Based on Both ASV and OTU Inference Methods on ITS2-Based Soil Fungal Communities","authors":"Julia Kyaschenko,&nbsp;Jeanette Tångrot,&nbsp;Anders Dahlberg,&nbsp;Björn D. Lindahl,&nbsp;Anna Rosling","doi":"10.1002/edn3.70246","DOIUrl":"https://doi.org/10.1002/edn3.70246","url":null,"abstract":"<p>Fungi play essential roles in key ecosystem functions and processes, yet they often occur in inconspicuous, species-rich, and complex communities that remain difficult to study. Studies of fungal communities based on DNA extracted from environmental samples commonly rely on clustering sequence reads into units of diversity, followed by taxonomic identification and, in some cases, linkage to ecological traits. In this study, we evaluated how two clustering approaches—amplicon sequence variants (ASVs) and operational taxonomic units (OTUs)—affect the characterization of fungal communities. Despite minor differences, both approaches recovered consistent taxonomic patterns and community structure. Although both methods produced a similar total number of sequence clusters, they differed in representation of fungal community composition. All ASV representative sequences matched OTU representative sequences with at least 92.2% similarity, whereas several rare OTUs showed low similarity to ASV reads, suggesting differences in the detection of low-abundance taxa. However, only a small fraction of OTU reads (&lt; 0.1%) lacked a corresponding ASV, indicating that ASVs captured nearly all OTU-defined taxa. In contrast, 14% of ASV reads assigned to species hypotheses (SHs) did not match any OTU reads assigned to SHs, whereas only 1.3% of OTU SH-assigned reads lacked a corresponding ASV match. ASVs generally provided higher resolution than OTUs, as abundant SHs were often represented by multiple ASVs, suggesting that ASVs capture intraspecific diversity. Consequently, ASVs should not be used as direct species proxies but instead require post hoc grouping to reflect species-level diversity. OTUs-based community composition aligned more clearly with soil properties, particularly the N:C ratio. Overall, both approaches provided a similar overview of broad-scale species richness. The choice between two clustering methods depends on the research question and the desired level of taxonomic resolution, and our results provide little support for the claim that ASVs should categorically replace taxonomic units in marker-gene data analysis.</p>","PeriodicalId":52828,"journal":{"name":"Environmental DNA","volume":"8 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/edn3.70246","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146096603","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}