{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T19:42:02Z","timestamp":1792784522804,"version":"4.5.0"},"reference-count":68,"publisher":"American Chemical Society (ACS)","issue":"36","license":[{"start":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T00:00:00Z","timestamp":1787788800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T00:00:00Z","timestamp":1787788800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T00:00:00Z","timestamp":1787788800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/na","name":"National Basic Research Program of China","doi-asserted-by":"publisher","award":["2022YFC3202100"],"award-info":[{"award-number":["2022YFC3202100"]}],"id":[{"id":"10.13039\/na","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/na","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["42377277"],"award-info":[{"award-number":["42377277"]}],"id":[{"id":"10.13039\/na","id-type":"DOI","asserted-by":"publisher"},{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Megarivers support high biodiversity but challenge monitoring efforts, as conventional low-frequency environmental DNA (eDNA) surveys often miss rare taxa and may misclassify transient exogenous DNA. Here, we conducted daily eDNA monitoring for 1 year at a fixed site on the Yangtze River to evaluate the effects of sampling frequency and distinguish native from exogenous signals. Among 210 detected fish taxa, 124 were verified as native. Fish diversity exhibited strong temporal variation, peaking in warm seasons. Downsampling analyses revealed that quarterly sampling recovered only \u223c30% of annual diversity\u2500primarily missing rare taxa\u2500whereas sampling every \u22643 days recovered &amp;gt;90%. To address exogenous contamination, we trained a Random Forest classifier using daily eDNA profiles. An \u201cenvironmental coupling score\u201d, which quantifies synchrony between eDNA and water-quality dynamics, emerged as the strongest predictor. Achieving an AUC of 0.727, this model substantially outperformed conventional abundance-based thresholding. Together, our results demonstrate that continuous daily eDNA monitoring substantially improves the detection of rare species in hydrodynamically complex rivers. This study offers quantitative guidance on sampling design and provides a robust machine-learning framework to reduce misclassification of exogenous signals in large-river biomonitoring.<\/jats:p>","DOI":"10.1021\/acs.est.6c07489","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T15:42:23Z","timestamp":1788277343000},"page":"25309-25321","source":"Crossref","is-referenced-by-count":0,"title":["Continuous eDNA\nMonitoring Reveals Rare Fish Diversity\nand Enables Filtering of Exogenous DNA Signals in a Megariver"],"prefix":"10.1021","volume":"60","author":[{"given":"Jianghua","family":"Yang","sequence":"first","affiliation":[{"name":"Nanjing Normal University , , ,","place":["Nanjing, China, 210046"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Wen","sequence":"additional","affiliation":[{"name":"Nanjing Environmental Monitoring Center of Jiangsu Province , ,","place":["Nanjing, China, 211000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0688-5359","authenticated-orcid":true,"given":"Yan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Nanjing University , , ,","place":["Nanjing, China, 210023"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3469-9855","authenticated-orcid":true,"given":"Lijuan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Yunnan University , , ,","place":["Kunming, China, 650500"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8974-9963","authenticated-orcid":true,"given":"Xiaowei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Yunnan University , , ,","place":["Kunming, China, 650500"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,27]]},"reference":[{"key":"2026091511121933900_cit1","doi-asserted-by":"publisher","first-page":"3585","DOI":"10.1038\/s41467-020-17337-8","article-title":"Environmental\nDNA allows upscaling spatial patterns of biodiversity in freshwater\necosystems","volume":"11","author":"Carraro","year":"2020","journal-title":"Nat. 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Soc."},{"key":"2026091511121933900_cit4","doi-asserted-by":"publisher","first-page":"719","DOI":"10.1126\/science.adu5160","article-title":"Fishing ban halts seven\ndecades of biodiversity decline in the Yangtze River","volume":"391","author":"Xiong","year":"2026","journal-title":"Science"},{"key":"2026091511121933900_cit5","doi-asserted-by":"publisher","DOI":"10.1111\/gcb.70617","article-title":"Effects Of Biodiversity\nLoss On Freshwater Ecosystem Functions Increase With The Number Of\nStressors","volume":"31","author":"Schafer","year":"2025","journal-title":"Glob Chang Biol."},{"key":"2026091511121933900_cit6","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1038\/s43017-024-00596-0","article-title":"Hydropower\nimpacts on riverine biodiversity","volume":"5","author":"He","year":"2024","journal-title":"Nat. Rev.\nEarth Environ."},{"key":"2026091511121933900_cit7","doi-asserted-by":"publisher","first-page":"3806","DOI":"10.1021\/acs.est.5c09855","article-title":"Hidden Genetic Erosion: eDNA Exposes Chemical Stressors as Silent\nDrivers of Freshwater Biodiversity Loss","volume":"60","author":"Jiang","year":"2026","journal-title":"Environ.\nSci. Technol."},{"key":"2026091511121933900_cit8","doi-asserted-by":"publisher","first-page":"117198","DOI":"10.1016\/j.envres.2023.117198","article-title":"Environmental DNA\nunveiling the fish community structure and diversity features in the\nYangtze River basin","volume":"239","author":"Qian","year":"2023","journal-title":"Environ. Res."},{"key":"2026091511121933900_cit9","doi-asserted-by":"publisher","first-page":"136242","DOI":"10.1016\/j.scitotenv.2019.136242","article-title":"Extinction\nof one of the world\u2019s\nlargest freshwater fishes: Lessons for conserving the endangered Yangtze\nfauna","volume":"710","author":"Zhang","year":"2020","journal-title":"Sci. Total Environ."},{"key":"2026091511121933900_cit10","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1038\/s44358-024-00012-x","article-title":"Successes\nand failures\nof conservation actions to halt global river biodiversity loss","volume":"1","author":"Haase","year":"2025","journal-title":"Nat. Rev. Biodiversity"},{"key":"2026091511121933900_cit11","doi-asserted-by":"publisher","first-page":"1036","DOI":"10.1007\/s10661-025-14504-6","article-title":"Comparative\nperformance\nof eDNA and conventional capture-based monitoring approaches to detect\nriverine fish assemblages","volume":"197","author":"Stern","year":"2025","journal-title":"Environ. Monit. Assess."},{"key":"2026091511121933900_cit12","doi-asserted-by":"publisher","first-page":"121238","DOI":"10.1016\/j.envres.2025.121238","article-title":"Freshwater\nfish community assessment\nusing eDNA metabarcoding vs. capture-based methods: Differences in\nefficiency and resolution coupled to habitat and ecology","volume":"274","author":"Curto","year":"2025","journal-title":"Environ. Res."},{"key":"2026091511121933900_cit13","doi-asserted-by":"publisher","first-page":"276","DOI":"10.3389\/fevo.2020.00276","article-title":"Calibrating Environmental DNA Metabarcoding\nto Conventional Surveys for Measuring Fish Species Richness","volume":"8","author":"McElroy","year":"2020","journal-title":"Front. Ecol. Evolu."},{"key":"2026091511121933900_cit14","doi-asserted-by":"publisher","first-page":"150088","DOI":"10.1098\/rsos.150088","article-title":"MiFish,\na set of universal PCR primers for metabarcoding\nenvironmental DNA from fishes: detection of more than 230 subtropical\nmarine species","volume":"2","author":"Miya","year":"2015","journal-title":"Royal Society Open Sci."},{"key":"2026091511121933900_cit15","doi-asserted-by":"publisher","first-page":"5872","DOI":"10.1111\/mec.14350","article-title":"Environmental\nDNA metabarcoding: Transforming how we survey animal and plant communities","volume":"26","author":"Deiner","year":"2017","journal-title":"Mol. 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Ecol."},{"key":"2026091511121933900_cit19","doi-asserted-by":"publisher","first-page":"1773","DOI":"10.1038\/s41598-017-01808-y","article-title":"Zooplankton\nCommunity Profiling in a Eutrophic Freshwater\nEcosystem-Lake Tai Basin by DNA Metabarcoding","volume":"7","author":"Yang","year":"2017","journal-title":"Sci. Rep."},{"key":"2026091511121933900_cit20","doi-asserted-by":"publisher","first-page":"29460","DOI":"10.1038\/s41598-024-80907-z","article-title":"eDNA metabarcoding\nreveals differences in fish diversity and community structure in Danjiang\nRiver","volume":"14","author":"Deng","year":"2024","journal-title":"Sci. Rep."},{"key":"2026091511121933900_cit21","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1002\/edn3.387","article-title":"Small changes make\nbig progress: A more efficient eDNA monitoring method for freshwater\nfish","volume":"5","author":"Yang","year":"2023","journal-title":"Environ. 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Rep."},{"key":"2026091511121933900_cit30","doi-asserted-by":"publisher","first-page":"21524","DOI":"10.1038\/s41598-022-25274-3","article-title":"Quantitative\nenvironmental DNA metabarcoding\nshows high potential as a novel approach to quantitatively assess\nfish community","volume":"12","author":"Tsuji","year":"2022","journal-title":"Sci. Rep."},{"key":"2026091511121933900_cit31","doi-asserted-by":"publisher","DOI":"10.1002\/edn3.506","article-title":"CRISPR-based environmental\nDNA detection for a rare endangered estuarine species","volume":"6","author":"Nagarajan","year":"2024","journal-title":"Environ. DNA"},{"key":"2026091511121933900_cit32","doi-asserted-by":"publisher","first-page":"23433","DOI":"10.1021\/acs.est.5c02209","article-title":"Temporal Tracing of Pollution Source\nUsing a Continuous eDNA Approach","volume":"59","author":"Jiang","year":"2025","journal-title":"Environ. Sci.\nTechnol."},{"key":"2026091511121933900_cit33","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00003-15","article-title":"Open-Source\nSequence Clustering Methods Improve the State Of the Art","volume":"1","author":"Kopylova","year":"2016","journal-title":"Msystems"},{"key":"2026091511121933900_cit34","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis\nof high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat. Methods"},{"key":"2026091511121933900_cit35","doi-asserted-by":"publisher","first-page":"107950","DOI":"10.1016\/j.envint.2023.107950","article-title":"Unsupervised biological integrity assessment by eDNA biomonitoring\nof multi-trophic aquatic taxa","volume":"175","author":"Yang","year":"2023","journal-title":"Environ. Int."},{"key":"2026091511121933900_cit36","doi-asserted-by":"publisher","first-page":"774","DOI":"10.3390\/w15040774","article-title":"Next-Generation\nDNA Barcoding for Fish Identification Using High-Throughput Sequencing\nin Tai Lake, China","volume":"15","author":"Mu","year":"2023","journal-title":"Water"},{"key":"2026091511121933900_cit37","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1111\/1755-0998.12961","article-title":"DNA barcoding the ichthyofauna of\nthe Yangtze River: Insights from the molecular inventory of a mega-diverse\ntemperate fauna","volume":"19","author":"Shen","year":"2019","journal-title":"Mol. Ecol. Resour."},{"key":"2026091511121933900_cit38","first-page":"119314","article-title":"Species identification\nrates of commonly\nused Environmental DNA primers for Yangtze River fishes","volume":"49","author":"Jinyi","year":"2025","journal-title":"Eng. Version"},{"key":"2026091511121933900_cit39","volume-title":"Ecology and Environment Quality\nReport of Nanjing 2021\u20132025","author":"Government, N. M.","year":"2025"},{"key":"2026091511121933900_cit40","doi-asserted-by":"publisher","first-page":"833","DOI":"10.1016\/j.aaf.2023.06.004","article-title":"Status of aquatic organisms resources and their environments\nin the\nYangtze River system (2017\u25002021)","volume":"9","author":"Yang","year":"2024","journal-title":"Aquacult.\nFish."},{"key":"2026091511121933900_cit41","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1111\/1755-0998.12338","article-title":"Replication levels,\nfalse presences and the estimation of the presence\/absence from eDNA\nmetabarcoding data","volume":"15","author":"Ficetola","year":"2015","journal-title":"Molecular Ecol. Res."},{"key":"2026091511121933900_cit42","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1016\/j.tree.2018.09.003","article-title":"Environmental DNA Time\nSeries in Ecology","volume":"33","author":"Ba\u0301lint","year":"2018","journal-title":"Trends Ecol. Evol."},{"key":"2026091511121933900_cit43","doi-asserted-by":"publisher","first-page":"1819","DOI":"10.1021\/es404734p","article-title":"Environmental Conditions\nInfluence eDNA Persistence\nin Aquatic Systems","volume":"48","author":"Barnes","year":"2014","journal-title":"Environ. Sci. Technol."},{"key":"2026091511121933900_cit44","doi-asserted-by":"publisher","first-page":"2783","DOI":"10.1890\/07-0539.1","article-title":"Random forests for\nclassification in ecology","volume":"88","author":"Cutler","year":"2007","journal-title":"Ecology"},{"key":"2026091511121933900_cit45","first-page":"571","article-title":"On fish composition\nand dominant species in the Yangtze River in Jiangsu Province","volume":"16","author":"Chen","year":"2007","journal-title":"Res. Environ. Yangtze Basin"},{"key":"2026091511121933900_cit47","doi-asserted-by":"publisher","first-page":"150","DOI":"10.1111\/j.1755-263X.2010.00158.x","article-title":"\u201cSight-unseen\u201d\ndetection of rare aquatic species using environmental DNA","volume":"4","author":"Jerde","year":"2011","journal-title":"Conservation Lett."},{"key":"2026091511121933900_cit48","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1002\/edn3.7","article-title":"Meta-analysis\nsupports further refinement\nof eDNA for monitoring aquatic species-specific abundance in nature","volume":"1","author":"Yates","year":"2019","journal-title":"Environ. DNA"},{"key":"2026091511121933900_cit49","doi-asserted-by":"publisher","first-page":"6651282","DOI":"10.1155\/jai\/6651282","article-title":"Using Environmental\nDNA to Assess Fish Communities Post-Waterway Regulation in the Yangtze\nRiver","volume":"2025","author":"Zheng","year":"2025","journal-title":"J. Appl. Ichthyol."},{"key":"2026091511121933900_cit50","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1080\/03632415.2017.1276329","article-title":"Comparative\nCost and Effort of Fish Distribution Detection via Environmental DNA\nAnalysis and Electrofishing","volume":"42","author":"Evans","year":"2017","journal-title":"Fisheries"},{"key":"2026091511121933900_cit51","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1111\/1755-0998.12483","article-title":"A framework for\nestimating the sensitivity of eDNA surveys","volume":"16","author":"Furlan","year":"2016","journal-title":"Mol. Ecol. Resour."},{"key":"2026091511121933900_cit52","first-page":"3161","article-title":"Assessing fish diversity in the Nanjing section of\nthe Yangtze River by fish larvae survey and eDNA technology","volume":"44","author":"Tianyou","year":"2025","journal-title":"Chinese J. Ecol."},{"key":"2026091511121933900_cit53","doi-asserted-by":"publisher","first-page":"108706","DOI":"10.1016\/j.envint.2024.108706","article-title":"Passive eDNA sampling facilitates\nbiodiversity monitoring and rare species detection","volume":"187","author":"Chen","year":"2024","journal-title":"Environ. Int."},{"key":"2026091511121933900_cit54","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0328280","article-title":"Seasonal changes\nin the structure of river fish communities in temperate Japan depicted\nusing quantitative eDNA metabarcoding","volume":"20","author":"Ito","year":"2025","journal-title":"PLoS\nOne"},{"key":"2026091511121933900_cit55","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1016\/j.biocon.2014.11.038","article-title":"Quantifying\neffects of UV-B, temperature,\nand pH on eDNA degradation in aquatic microcosms","volume":"183","author":"Strickler","year":"2015","journal-title":"Biol. Conserv."},{"key":"2026091511121933900_cit56","doi-asserted-by":"publisher","DOI":"10.1002\/edn3.530","article-title":"Quantifying the\neffect of water quality\non eDNA degradation using microcosm and bioassay experiments","volume":"6","author":"McKnight","year":"2024","journal-title":"Environ. DNA"},{"key":"2026091511121933900_cit57","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0035868","article-title":"Estimation\nof fish biomass using environmental DNA","volume":"7","author":"Takahara","year":"2012","journal-title":"PLoS\nOne"},{"key":"2026091511121933900_cit58","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0088786","article-title":"Transport\ndistance of invertebrate environmental DNA\nin a natural river","volume":"9","author":"Deiner","year":"2014","journal-title":"PLoS One"},{"key":"2026091511121933900_cit59","doi-asserted-by":"publisher","first-page":"10361","DOI":"10.1038\/s41598-018-28424-8","article-title":"Environmental DNA reveals\nquantitative patterns of\nfish biodiversity in large rivers despite its downstream transportation","volume":"8","author":"Pont","year":"2018","journal-title":"Sci. Rep."},{"key":"2026091511121933900_cit60","doi-asserted-by":"publisher","first-page":"11559","DOI":"10.1038\/s41598-019-47899-7","article-title":"Detection of introduced\nand resident marine species using environmental\nDNA metabarcoding of sediment and water","volume":"9","author":"Holman","year":"2019","journal-title":"Sci.\nRep."},{"key":"2026091511121933900_cit61","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1038\/s41559-016-0004","article-title":"Population characteristics of a large whale\nshark aggregation inferred from seawater environmental DNA","volume":"1","author":"Sigsgaard","year":"2016","journal-title":"Nat. Ecol. Evol."},{"key":"2026091511121933900_cit62","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1002\/edn3.185","article-title":"Environmental DNA (eDNA) as a tool for assessing fish\nbiomass: A review of approaches and future considerations for resource\nsurveys","volume":"4","author":"Rourke","year":"2022","journal-title":"Environ. 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Manage."},{"key":"2026091511121933900_cit64","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0224119","article-title":"Validating metabarcoding-based biodiversity\nassessments with multi-species occupancy models: A case study using\ncoastal marine eDNA","volume":"15","author":"McClenaghan","year":"2020","journal-title":"PLoS One"},{"key":"2026091511121933900_cit65","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/j.biocon.2014.11.020","article-title":"Quantification of eDNA\nshedding rates from invasive bighead carp Hypophthalmichthys nobilis\nand silver carp Hypophthalmichthys molitrix","volume":"183","author":"Klymus","year":"2015","journal-title":"Biol. 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