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Optimizing an eDNA protocol for estuarine environments: Balancing sensitivity, cost and time

https://doi.org/10.1371/journal.pone.0233522
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/aqc.2494openalex-snapshot
Relative importance of chinook salmon abundance on resident killer whale population growth and viability
inferredcites →https://doi.org/10.1002/ece3.2083openalex-snapshot
Evaluating the effects of laboratory protocols on eDNA detection probability for an endangered freshwater fish
inferredcites →https://doi.org/10.1002/edn3.25openalex-snapshot
A system for rapid eDNA detection of aquatic invasive species
inferredcites →https://doi.org/10.1007/3-540-29449-x_7openalex-snapshot
Stabilization of Extracellular DNA and Proteins by Transient Binding to Various Soil Components
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Extremely randomized trees
inferredcites →https://doi.org/10.1007/s11222-016-9696-4openalex-snapshot
Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC
inferredcites →https://doi.org/10.1016/j.biocon.2014.11.018openalex-snapshot
Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA
inferredcites →https://doi.org/10.1016/j.biocon.2015.12.023openalex-snapshot
Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis
inferredcites →https://doi.org/10.1016/j.biocon.2018.01.030openalex-snapshot
Concentrations of environmental DNA (eDNA) reflect spawning salmon abundance at fine spatial and temporal scales
inferredcites →https://doi.org/10.1016/s1568-2692(00)80130-8openalex-snapshot
Influence of salinity, bottom topography, and tides on locations of estuarine turbidity maxima in northern San Francisco Bay
inferredcites →https://doi.org/10.1080/10641269908951361openalex-snapshot
A History of Salmon and People in the Central Valley Region of California
inferredcites →https://doi.org/10.1093/nar/23.22.4742openalex-snapshot
Solid-phase reversible immobilization for the isolation of PCR products
inferredcites →https://doi.org/10.1093/oso/9780198767220.001.0001openalex-snapshot
Environmental DNA
inferredcites →https://doi.org/10.1111/1365-2664.12598openalex-snapshot
Quantifying relative fish abundance with eDNA : a promising tool for fisheries management
inferredcites →https://doi.org/10.1111/1755-0998.12305openalex-snapshot
Ten real‐time PCR assays for detection of fish predation at the community level in the San Francisco Estuary–Delta
inferredcites →https://doi.org/10.1111/2041-210x.12206openalex-snapshot
Particle size distribution and optimal capture of aqueous macrobial eDNA
inferredcites →https://doi.org/10.1111/2041-210x.12683openalex-snapshot
Comparison of capture and storage methods for aqueous macrobial eDNA using an optimized extraction protocol: advantage of enclosed filter
inferredcites →https://doi.org/10.1111/j.1365-2672.2012.05384.xopenalex-snapshot
PCR inhibitors - occurrence, properties and removal
inferredcites →https://doi.org/10.1111/j.1755-263x.2010.00158.xopenalex-snapshot
“Sight‐unseen” detection of rare aquatic species using environmental DNA
inferredcites →https://doi.org/10.1111/jfb.12863openalex-snapshot
Sampling large geographic areas for rare species using environmental DNA : a study of bull trout Salvelinus confluentus occupancy in western Montana
inferredcites →https://doi.org/10.1126/science.1251156openalex-snapshot
Harnessing DNA to improve environmental management
inferredcites →https://doi.org/10.1128/aem.02291-05openalex-snapshot
Rapid One-Step Quantitative Reverse Transcriptase PCR Assay with Competitive Internal Positive Control for Detection of Enteroviruses in Environmental Samples
inferredcites →https://doi.org/10.1371/journal.pbio.2003916openalex-snapshot
Nucleic acid purification from plants, animals and microbes in under 30 seconds
inferredcites →https://doi.org/10.1371/journal.pone.0114329openalex-snapshot
Improved Methods for Capture, Extraction, and Quantitative Assay of Environmental DNA from Asian Bigheaded Carp (Hypophthalmichthys spp.)
inferredcites →https://doi.org/10.1371/journal.pone.0121655openalex-snapshot
Environmental DNA (eDNA) Sampling Improves Occurrence and Detection Estimates of Invasive Burmese Pythons
inferredcites →https://doi.org/10.1371/journal.pone.0179251openalex-snapshot
Methods to maximise recovery of environmental DNA from water samples
inferredcites →https://doi.org/10.1371/journal.pone.0179282openalex-snapshot
Clearing muddied waters: Capture of environmental DNA from turbid waters
inferredcites →https://doi.org/10.1577/1548-8675(1998)018<0487:haadoc>2.0.co;2openalex-snapshot
Historical Abundance and Decline of Chinook Salmon in the Central Valley Region of California
inferredcites →https://doi.org/10.2174/1874940201003010038openalex-snapshot
Assessing PCR Inhibition from Humic Substances
inferredcites →https://doi.org/10.2174/1874940201003010046openalex-snapshot
Assessing PCR Inhibition from Humic Substances
inferredcites →https://doi.org/10.21775/9781912530243.12openalex-snapshot
MIQE: Guidelines for the Design and Publication of a Reliable Real-time PCR Assay
inferredcites →https://doi.org/10.3133/tm2a13openalex-snapshot
Environmental DNA sampling protocol - filtering water to capture DNA from aquatic organisms
inferredcites →https://doi.org/10.3389/fpubh.2017.00307openalex-snapshot
Sensitivity, Specificity, and Predictive Values: Foundations, Pliabilities, and Pitfalls in Research and Practice
inferredcites →https://doi.org/10.4319/lom.2004.2.365openalex-snapshot
Optimization of DNA extraction for quantitative marine bacterioplankton community analysis
inferredcites →https://doi.org/10.7717/peerj-cs.55openalex-snapshot
Probabilistic programming in Python using PyMC3

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.3897/mbmg.8.115512zenodo-depositor-declared
Optimising eDNA analysis for urban otter monitoring: seasonal patterns, detection strategies and prey availability
inferred← citeshttps://doi.org/10.1002/9781119742975.ch26openalex-snapshot
Emerging Frameworks and Tools for Environmental Risk Assessment
inferred← citeshttps://doi.org/10.1002/aff2.70104openalex-snapshot
Turning Trash Into Treasure: Leveraging Discarded Filters for National‐Scale Aquatic eDNA Biomonitoring
inferred← citeshttps://doi.org/10.1002/ece3.73925openalex-snapshot
Trends in Aquatic Environmental DNA Research in Alaska
inferred← citeshttps://doi.org/10.1002/edn3.241openalex-snapshot
Biodiversity assessment across a dynamic riverine system: A comparison of eDNA metabarcoding versus traditional fish surveying methods
inferred← citeshttps://doi.org/10.1002/edn3.279openalex-snapshot
Practical eDNA sampling methods inferred from particle size distribution and comparison of capture techniques for a Critically Endangered elasmobranch
inferred← citeshttps://doi.org/10.1002/edn3.365openalex-snapshot
Characterizing the distribution of the critically endangered estuarine pipefish (Syngnathus watermeyeri) across its range using environmental DNA
inferred← citeshttps://doi.org/10.1002/edn3.392openalex-snapshot
Optimized DNA isolation from marine sponges for natural sampler DNA metabarcoding
inferred← citeshttps://doi.org/10.1002/edn3.409openalex-snapshot
Maximizing sampling efficiency to detect differences in fish community composition using environmental DNA metabarcoding in subarctic fjords
inferred← citeshttps://doi.org/10.1002/edn3.476openalex-snapshot
Environmental DNA and RNA in aquatic community ecology: Toward methodological standardization
inferred← citeshttps://doi.org/10.1002/edn3.486openalex-snapshot
High frequency environmental DNA metabarcoding provides rapid and effective monitoring of fish community dynamics
inferred← citeshttps://doi.org/10.1002/edn3.500openalex-snapshot
Unveiling the hidden diversity of marine eukaryotes in the Ross Sea: A comparative analysis of seawater and sponge eDNA surveys
inferred← citeshttps://doi.org/10.1002/edn3.535openalex-snapshot
Environmental DNA reveals the ecology and seasonal migration of a rare sturgeon species in the Ural River
inferred← citeshttps://doi.org/10.1002/edn3.560openalex-snapshot
A comparison of eDNA sampling methods in an estuarine environment on presence of longfin smelt (Spirinchus thaleichthys) and fish community composition
inferred← citeshttps://doi.org/10.1002/edn3.70002openalex-snapshot
A Guide to Environmental DNA Extractions for Non‐Molecular Trained Biologists, Ecologists, and Conservation Scientists
inferred← citeshttps://doi.org/10.1002/edn3.70180openalex-snapshot
Unveiling Structure of Tropical Estuarine Communities Through eDNA and Implications for Biomonitoring
inferred← citeshttps://doi.org/10.1002/edn3.70197openalex-snapshot
Significant Improvement of Environmental DNA Assay by Targeting Retrotransposon Sequences Characteristic to Anguilla Eels
inferred← citeshttps://doi.org/10.1002/edn3.70206openalex-snapshot
Performance of eDNA Filtration Methods for Monitoring Fish Diversity in a Hyper‐Tidal Estuary
inferred← citeshttps://doi.org/10.1002/edn3.70287openalex-snapshot
Locating Little Larvae: Environmental DNA Methods Can Detect a Rare Fish Species Under Field Estuarine Conditions
inferred← citeshttps://doi.org/10.1002/fsh.11038openalex-snapshot
Environmental DNA as a Tool for Better Understanding the Distribution, Abundance, And Health of Atlantic Salmon and Pacific Salmon
inferred← citeshttps://doi.org/10.1002/nafm.10937openalex-snapshot
Environmental DNA compliments traditional sampling for monitoring fish communities in a Texas estuary
inferred← citeshttps://doi.org/10.1007/s00027-025-01222-xopenalex-snapshot
Which filter should I use? A comparative study of environmental DNA concentration methods for detection of freshwater species
inferred← citeshttps://doi.org/10.1007/s10661-025-14596-0openalex-snapshot
Using eDNA as a viable fish monitoring approach in Northern Gulf estuarine habitats
inferred← citeshttps://doi.org/10.1007/s12237-022-01080-yopenalex-snapshot
Environmental DNA Methods for Ecological Monitoring and Biodiversity Assessment in Estuaries
inferred← citeshttps://doi.org/10.1016/b978-0-443-38325-0.00009-5openalex-snapshot
Clustered regularly interspaced short palindromic repeats associated protein systems in environmental biotechnology: Applications in pollution management
inferred← citeshttps://doi.org/10.1016/j.aquaculture.2026.744118openalex-snapshot
Methodological limitations in eDNA-based detection of Bonamia ostreae: Implications for non-invasive oyster health monitoring
inferred← citeshttps://doi.org/10.1016/j.ecolind.2021.107916openalex-snapshot
Targeted non-invasive bioindicator species detection in eDNA water samples to assess and monitor the integrity of vulnerable alpine freshwater environments
inferred← citeshttps://doi.org/10.1016/j.ecss.2026.109968openalex-snapshot
Comparing beam trawl sampling and eDNA metabarcoding for assessing fish diversity in turbid tropical seagrass habitats
inferred← citeshttps://doi.org/10.1016/j.envint.2026.110086openalex-snapshot
Flow conditions govern the efficiency of passive environmental DNA sampling
inferred← citeshttps://doi.org/10.1016/j.fsisyn.2026.100722openalex-snapshot
Protocols and challenges in managing multi-source biological evidence at the crime scene: a scoping review
inferred← citeshttps://doi.org/10.1016/j.jip.2025.108462openalex-snapshot
Exploring the environmental distribution of the oyster parasite Haplosporidium costale
inferred← citeshttps://doi.org/10.1016/j.marenvres.2025.107041openalex-snapshot
Biodiversity monitoring in remote marine environments: Advancing environmental DNA/RNA sampling workflows
inferred← citeshttps://doi.org/10.1016/j.marenvres.2026.107926openalex-snapshot
Testing the waters: A comparison of DNA extraction methods for the metabarcoding of microbial communities
inferred← citeshttps://doi.org/10.1016/j.marenvres.2026.108259openalex-snapshot
Unveiling Ross Sea eukaryotic diversity through environmental DNA metabarcoding
inferred← citeshttps://doi.org/10.1016/j.margeo.2025.107562openalex-snapshot
Hydrodynamic processes and extreme events recognized from the sedimentary records at ancient Port Shuomen in the Oujiang River mouth, Southeast China
inferred← citeshttps://doi.org/10.1016/j.marpolbul.2022.113860openalex-snapshot
The use of environmental DNA to monitor impacted coastal estuaries
inferred← citeshttps://doi.org/10.1016/j.mex.2024.103020openalex-snapshot
A simple and cost-effective extraction for piscine environmental DNA metabarcoding using guanidine hydrochloride method
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2024.172900openalex-snapshot
Species-specific eDNA assay development for enhanced box jellyfish risk management in coastal environments
inferred← citeshttps://doi.org/10.1038/s41598-025-85176-yopenalex-snapshot
An optimized eDNA protocol for fish tracking in estuarine environments
inferred← citeshttps://doi.org/10.1039/d5ew00886gopenalex-snapshot
Emerging investigator series: why we should care about the fate of biological contaminants from municipal wastewater in reverse osmosis concentrate
inferred← citeshttps://doi.org/10.1051/bioconf/202414701013openalex-snapshot
Bibliometric analysis: Environmental DNA (eDNA) methods in marine biodiversity research in the world and Indonesia
inferred← citeshttps://doi.org/10.1093/biosci/biab027openalex-snapshot
The Promise and Pitfalls of Environmental DNA and RNA Approaches for the Monitoring of Human and Animal Pathogens from Aquatic Sources
inferred← citeshttps://doi.org/10.1093/icesjms/fsab273openalex-snapshot
Current laboratory protocols for detecting fish species with environmental DNA optimize sensitivity and reproducibility, especially for more abundant populations
inferred← citeshttps://doi.org/10.1101/2022.07.11.499619openalex-snapshot
Optimised DNA isolation from marine sponges for natural sampler DNA (nsDNA) metabarcoding
inferred← citeshttps://doi.org/10.1101/2025.06.07.656140openalex-snapshot
Recovering historical fish eDNA from museum-preserved Antarctic filter feeders via non-destructive metabarcoding
inferred← citeshttps://doi.org/10.1111/1755-0998.13754openalex-snapshot
Assessing the utility of marine filter feeders for environmental DNA ( eDNA ) biodiversity monitoring
inferred← citeshttps://doi.org/10.1111/1755-0998.13942openalex-snapshot
Optimizing waterborne eDNA capture from waterholes in savanna systems under remote field conditions
inferred← citeshttps://doi.org/10.1111/1755-0998.70132openalex-snapshot
Recovering Historical eDNA From Museum‐Preserved Filter Feeders via Non‐Destructive Metabarcoding
inferred← citeshttps://doi.org/10.11614/ksl.2021.54.4.272openalex-snapshot
Development of the Filterable Water Sampler System for eDNA Filtering and Performance Evaluation of the System through eDNA Monitoring at Catchment Conduit Intake-Reservoir
inferred← citeshttps://doi.org/10.11614/ksl.2025.58.3.298openalex-snapshot
Application of the QuickConcTM Concentration System for Environmental DNA Analysis in Lakes: Case Study on Genetic Diversity of Freshwater Bivalves
inferred← citeshttps://doi.org/10.1371/journal.pone.0318046openalex-snapshot
Citizen science-based biodiversity monitoring in oil palm plantations
inferred← citeshttps://doi.org/10.1371/journal.pone.0350111openalex-snapshot
Cost-efficient filtration and replication strategies match or exceed detection sensitivity for marine eDNA diversity at an intertidal site under a standardized laboratory workflow
inferred← citeshttps://doi.org/10.14775/ksmpe.2021.20.08.0074openalex-snapshot
Effect of the Internal Shape of eDNA Filter Case made by the PBF method Metal 3D Printer on Water Sampling Performance
inferred← citeshttps://doi.org/10.21203/rs.3.rs-3643693/v1openalex-snapshot
eDNA reveals the ecology and seasonal migration of a rare sturgeon species in the Ural River
inferred← citeshttps://doi.org/10.21203/rs.3.rs-4611874/v1openalex-snapshot
Effects of abiotic variables on DNA degradation in a limnic environment
inferred← citeshttps://doi.org/10.22541/au.164783670.08001593/v1openalex-snapshot
Red fish, blue fish, native fish, new fish: eDNA as a tool to monitor fish in estuarine systems
inferred← citeshttps://doi.org/10.24018/ejbio.2023.4.2.451openalex-snapshot
Detection of Limnoperna fortunei DNA From Plankton Samples: A New Protocol
inferred← citeshttps://doi.org/10.3390/app14062641openalex-snapshot
The eDNA-Container App: A Simple-to-Use Cross-Platform Package for the Reproducible Analysis of eDNA Sequencing Data
inferred← citeshttps://doi.org/10.3390/d15030322openalex-snapshot
Investigating the Potential Utility of Environmental DNA to Provide a Relative Abundance Index for the Depleted Teleost, Mulloway, Argyrosomus japonicus
inferred← citeshttps://doi.org/10.3390/fishes9110422openalex-snapshot
Evaluation of Fish Biodiversity in Estuaries Through Environmental DNA Metabarcoding: A Comprehensive Review
inferred← citeshttps://doi.org/10.3390/w13081113openalex-snapshot
Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance
inferred← citeshttps://doi.org/10.6027/temanord2023-505openalex-snapshot
DNA metabarcoding - Guidelines to monitor phytoplankton diversity and distribution in marine and brackish waters
inferred← citeshttps://doi.org/10.64898/2026.05.07.723600openalex-snapshot
Molecular Star Gazing: Development and Validation of an Environmental DNA Assay for the Imperiled Sunflower Sea Star ( Pycnopodia helianthoides )
inferred← citeshttps://doi.org/10.7717/peerj.14071openalex-snapshot
A manager’s guide to using eDNA metabarcoding in marine ecosystems
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Optimization of environmental DNA-based methods: a case study for detecting brook trout ( Salvelinus fontinalis )
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