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Evaluation of Fish Biodiversity in Estuaries Through Environmental DNA Metabarcoding: A Comprehensive Review

https://doi.org/10.3390/fishes9110422
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What this work says

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

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Toward an ecoregion scale evaluation of eDNA metabarcoding primers: A case study for the freshwater fish biodiversity of the Murray–Darling Basin (Australia)
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A review of applications of environmental DNA for reptile conservation and management
inferredcites →https://doi.org/10.1002/edn3.21openalex-snapshot
The detection of aquatic macroorganisms using environmental DNA analysis—A review of methods for collection, extraction, and detection
inferredcites →https://doi.org/10.1002/edn3.221openalex-snapshot
Fish community shifts along a strong fluvial environmental gradient revealed by eDNA metabarcoding
inferredcites →https://doi.org/10.1002/edn3.241openalex-snapshot
Biodiversity assessment across a dynamic riverine system: A comparison of eDNA metabarcoding versus traditional fish surveying methods
inferredcites →https://doi.org/10.1002/edn3.25openalex-snapshot
A system for rapid eDNA detection of aquatic invasive species
inferredcites →https://doi.org/10.1002/edn3.74openalex-snapshot
Maximizing fish detection with eDNA metabarcoding
inferredcites →https://doi.org/10.1002/edn3.75openalex-snapshot
Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA
inferredcites →https://doi.org/10.1007/978-1-4684-1528-5openalex-snapshot
The Estuarine Ecosystem
inferredcites →https://doi.org/10.1007/bf02804905openalex-snapshot
“A strikingly rich zone”—Nutrient enrichment and secondary production in coastal marine ecosystems
inferredcites →https://doi.org/10.1007/s00338-012-0984-yopenalex-snapshot
The importance of structural complexity in coral reef ecosystems
inferredcites →https://doi.org/10.1007/s10201-011-0362-4openalex-snapshot
Surveillance of fish species composition using environmental DNA
inferredcites →https://doi.org/10.1007/s10592-015-0775-4openalex-snapshot
The ecology of environmental DNA and implications for conservation genetics
inferredcites →https://doi.org/10.1007/s11356-024-33523-3openalex-snapshot
Assessing spatiotemporal risks of nonpoint source pollution via soil erosion: a coastal case in the Yellow River Delta, China
inferredcites →https://doi.org/10.1007/s12237-022-01080-yopenalex-snapshot
Environmental DNA Methods for Ecological Monitoring and Biodiversity Assessment in Estuaries
inferredcites →https://doi.org/10.1016/j.biocon.2014.11.017openalex-snapshot
Fish environmental DNA is more concentrated in aquatic sediments than surface water
inferredcites →https://doi.org/10.1016/j.biocon.2014.11.019openalex-snapshot
Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity
inferredcites →https://doi.org/10.1016/j.biocon.2014.11.020openalex-snapshot
Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix
inferredcites →https://doi.org/10.1016/j.biocon.2014.11.023openalex-snapshot
Monitoring the near-extinct European weather loach in Denmark based on environmental DNA from water samples
inferredcites →https://doi.org/10.1016/j.biocon.2014.11.038openalex-snapshot
Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms
inferredcites →https://doi.org/10.1016/j.bse.2014.05.003openalex-snapshot
Detection of invasive freshwater fish species using environmental DNA survey
inferredcites →https://doi.org/10.1016/j.ecss.2005.09.010openalex-snapshot
Temperature and salinity as primary determinants influencing the biogeography of fishes in South African estuaries
inferredcites →https://doi.org/10.1016/j.ecss.2012.09.018openalex-snapshot
Importance of estuarine mangroves to juvenile banana prawns
inferredcites →https://doi.org/10.1016/j.ecss.2023.108522openalex-snapshot
Environmental DNA metabarcoding for fish diversity assessment in a macrotidal estuary: A comparison with established fish survey methods
inferredcites →https://doi.org/10.1016/j.jembe.2012.06.013openalex-snapshot
Optimisation of baited remote underwater video sampling designs for estuarine fish assemblages
inferredcites →https://doi.org/10.1016/j.marenvres.2007.02.002openalex-snapshot
Food web analysis in two permanently open temperate estuaries: Consequences of saltmarsh loss?
inferredcites →https://doi.org/10.1016/j.marpolbul.2022.113860openalex-snapshot
The use of environmental DNA to monitor impacted coastal estuaries
inferredcites →https://doi.org/10.1016/j.scitotenv.2019.134704openalex-snapshot
eDNA metabarcoding as a promising conservation tool for monitoring fish diversity in a coastal wetland of the Pearl River Estuary compared to bottom trawling
inferredcites →https://doi.org/10.1016/j.scitotenv.2019.135314openalex-snapshot
Release and degradation of environmental DNA and RNA in a marine system
inferredcites →https://doi.org/10.1016/j.scitotenv.2023.166469openalex-snapshot
Environmental DNA (eDNA) removal rates in streams differ by particle size under varying substrate and light conditions
inferredcites →https://doi.org/10.1016/j.tree.2014.04.003openalex-snapshot
Environmental DNA for wildlife biology and biodiversity monitoring
inferredcites →https://doi.org/10.1016/s0272-7714(02)00305-0openalex-snapshot
Fish assemblages across the marine to low salinity transition zone of a temperate estuary
inferredcites →https://doi.org/10.1017/s0376892902000127openalex-snapshot
The future of seagrass meadows
inferredcites →https://doi.org/10.1017/s0376892902000322openalex-snapshot
Kelp forest ecosystems: biodiversity, stability, resilience and future
inferredcites →https://doi.org/10.1021/acs.est.6b01761openalex-snapshot
Influence of Stream Bottom Substrate on Retention and Transport of Vertebrate Environmental DNA
inferredcites →https://doi.org/10.1021/acs.est.6b03114openalex-snapshot
Quantification of Environmental DNA (eDNA) Shedding and Decay Rates for Three Marine Fish
inferredcites →https://doi.org/10.1021/acs.est.8b01822openalex-snapshot
Water Flow and Biofilm Cover Influence Environmental DNA Detection in Recirculating Streams
inferredcites →https://doi.org/10.1038/nclimate1539openalex-snapshot
Thermal tolerance and the global redistribution of animals
inferredcites →https://doi.org/10.1038/s41587-019-0209-9openalex-snapshot
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
inferredcites →https://doi.org/10.1038/s41598-017-12501-5openalex-snapshot
Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment
inferredcites →https://doi.org/10.1038/s41598-019-44402-0openalex-snapshot
New PCR primers for metabarcoding environmental DNA from freshwater eels, genus Anguilla
inferredcites →https://doi.org/10.1038/s41598-019-47899-7openalex-snapshot
Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water
inferredcites →https://doi.org/10.1038/s41598-019-50571-9openalex-snapshot
Combining ddPCR and environmental DNA to improve detection capabilities of a critically endangered freshwater invertebrate
inferredcites →https://doi.org/10.1038/s41598-020-71238-wopenalex-snapshot
Aquatic suspended particulate matter as source of eDNA for fish metabarcoding
inferredcites →https://doi.org/10.1038/s41598-020-77304-7openalex-snapshot
Field application of an improved protocol for environmental DNA extraction, purification, and measurement using Sterivex filter
inferredcites →https://doi.org/10.1038/s41598-022-06889-yopenalex-snapshot
Comparing DNA yield from fish scales following different extraction protocols
inferredcites →https://doi.org/10.1038/s41598-022-15488-wopenalex-snapshot
eDNA metabarcoding as a promising conservation tool to monitor fish diversity in Beijing water systems compared with ground cages
inferredcites →https://doi.org/10.1038/s41598-024-75863-7openalex-snapshot
The effect of urbanization on planktonic and biofilm bacterial communities in different water bodies of the Danube River in Hungary
inferredcites →https://doi.org/10.1038/s42003-018-0192-6openalex-snapshot
Persistence of environmental DNA in marine systems
inferredcites →https://doi.org/10.1038/sdata.2014.7openalex-snapshot
Systematic global assessment of reef fish communities by the Reef Life Survey program
inferredcites →https://doi.org/10.1093/nar/gkr732openalex-snapshot
ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis
inferredcites →https://doi.org/10.1098/rsbl.2008.0118openalex-snapshot
Species detection using environmental DNA from water samples
inferredcites →https://doi.org/10.1098/rspb.2002.2218openalex-snapshot
Biological identifications through DNA barcodes
inferredcites →https://doi.org/10.1098/rspb.2004.2813openalex-snapshot
Review Paper. Ancient DNA
inferredcites →https://doi.org/10.1111/1749-4877.12832openalex-snapshot
Validation and development of eDNA metabarcoding primers for comprehensive assessment of Chinese amphibians
inferredcites →https://doi.org/10.1111/1755-0998.12285openalex-snapshot
Distance, flow and PCR inhibition: e DNA dynamics in two headwater streams
inferredcites →https://doi.org/10.1111/1755-0998.12421openalex-snapshot
Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish
inferredcites →https://doi.org/10.1111/1755-0998.12501openalex-snapshot
Using occupancy modelling to compare environmental DNA to traditional field methods for regional‐scale monitoring of an endangered aquatic species
inferredcites →https://doi.org/10.1111/1755-0998.12619openalex-snapshot
Detection limits of quantitative and digital PCR assays and their influence in presence–absence surveys of environmental DNA
inferredcites →https://doi.org/10.1111/1755-0998.13055openalex-snapshot
A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR and metabarcoding for species‐specific detection in environmental DNA
inferredcites →https://doi.org/10.1111/1755-0998.13657openalex-snapshot
Filtration extraction method using a microfluidic channel for measuring environmental DNA
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.13276openalex-snapshot
Non‐specific amplification compromises environmental DNA metabarcoding with COI
inferredcites →https://doi.org/10.1111/2041-210x.13485openalex-snapshot
A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish
inferredcites →https://doi.org/10.1111/ddi.13228openalex-snapshot
Large‐scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north‐western Australia
inferredcites →https://doi.org/10.1111/gcb.16057openalex-snapshot
Temperature‐mediated acquisition of rare heterologous symbionts promotes survival of coral larvae under ocean warming
inferredcites →https://doi.org/10.1111/j.1365-2664.2012.02171.xopenalex-snapshot
Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus
inferredcites →https://doi.org/10.1111/j.1365-2699.2011.02613.xopenalex-snapshot
A realignment of marine biogeographic provinces with particular reference to fish distributions
inferredcites →https://doi.org/10.1111/j.1365-294x.2008.03880.xopenalex-snapshot
Damage and degradation rates of extracellular DNA in marine sediments: implications for the preservation of gene sequences
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05542.xopenalex-snapshot
Environmental DNA
inferredcites →https://doi.org/10.1111/j.1525-142x.2009.00381.xopenalex-snapshot
Morphological integration and developmental progress during fish ontogeny in two contrasting habitats
inferredcites →https://doi.org/10.1111/jfb.12975openalex-snapshot
Fish diversity in the Río de la Plata and adjacent waters: an overview of environmental influences on its spatial and temporal structure
inferredcites →https://doi.org/10.1111/jfb.14843openalex-snapshot
Habitat type and complexity drive fish assemblages in a tropical seascape
inferredcites →https://doi.org/10.1111/mec.13481openalex-snapshot
Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA
inferredcites →https://doi.org/10.1111/mec.15661openalex-snapshot
Environmental DNA effectively captures functional diversity of coastal fish communities
inferredcites →https://doi.org/10.1126/science.1067728openalex-snapshot
Marine Biodiversity Hotspots and Conservation Priorities for Tropical Reefs
inferredcites →https://doi.org/10.1126/science.1117475openalex-snapshot
Extracellular DNA Plays a Key Role in Deep-Sea Ecosystem Functioning
inferredcites →https://doi.org/10.1126/science.1122039openalex-snapshot
Scaling of Connectivity in Marine Populations
inferredcites →https://doi.org/10.1128/jcm.28.3.495-503.1990openalex-snapshot
Rapid and simple method for purification of nucleic acids
inferredcites →https://doi.org/10.1186/1742-9994-10-34openalex-snapshot
A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents
inferredcites →https://doi.org/10.1186/s41021-023-00295-0openalex-snapshot
Absolute quantification of DNA damage response proteins
inferredcites →https://doi.org/10.1371/journal.pone.0035868openalex-snapshot
Estimation of Fish Biomass Using Environmental DNA
inferredcites →https://doi.org/10.1371/journal.pone.0041732openalex-snapshot
Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples
inferredcites →https://doi.org/10.1371/journal.pone.0088786openalex-snapshot
Transport Distance of Invertebrate Environmental DNA in a Natural River
inferredcites →https://doi.org/10.1371/journal.pone.0119645openalex-snapshot
Do Reef Fish Habituate to Diver Presence? Evidence from Two Reef Sites with Contrasting Historical Levels of SCUBA Intensity in the Bay Islands, Honduras
inferredcites →https://doi.org/10.1371/journal.pone.0122763openalex-snapshot
Use of Droplet Digital PCR for Estimation of Fish Abundance and Biomass in Environmental DNA Surveys
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/10.1371/journal.pone.0210357openalex-snapshot
Environmental DNA metabarcoding for fish community analysis in backwater lakes: A comparison of capture methods
inferredcites →https://doi.org/10.1371/journal.pone.0219700openalex-snapshot
Detection of an invasive aquatic plant in natural water bodies using environmental DNA
inferredcites →https://doi.org/10.1371/journal.pone.0231127openalex-snapshot
Evaluation of fish biodiversity in estuaries using environmental DNA metabarcoding
inferredcites →https://doi.org/10.1371/journal.pone.0233522openalex-snapshot
Optimizing an eDNA protocol for estuarine environments: Balancing sensitivity, cost and time
inferredcites →https://doi.org/10.1371/journal.pone.0250452openalex-snapshot
eDNA as a tool for non-invasive monitoring of the fauna of a turbid, well-mixed system, the Elbe estuary in Germany
inferredcites →https://doi.org/10.1371/journal.pone.0259084openalex-snapshot
The update and optimization of an eDNA assay to detect the invasive rusty crayfish (Faxonius rusticus)
inferredcites →https://doi.org/10.1641/0006-3568(2001)051[0633:ticamo]2.0.co;2openalex-snapshot
The Identification, Conservation, and Management of Estuarine and Marine Nurseries for Fish and Invertebrates
inferredcites →https://doi.org/10.1641/0006-3568(2003)053[1048:aepotb]2.0.co;2openalex-snapshot
An Ecological Perspective on the Biodiversity of Tropical Island Streams
inferredcites →https://doi.org/10.2307/1352731openalex-snapshot
Estimating Densities of Small Fishes and Decapod Crustaceans in Shallow Estuarine Habitats: A Review of Sampling Design with Focus on Gear Selection
inferredcites →https://doi.org/10.24272/j.issn.2095-8137.2021.331openalex-snapshot
Effects of sampling strategies and DNA extraction methods on eDNA metabarcoding: A case study of estuarine fish diversity monitoring
inferredcites →https://doi.org/10.3354/esr00880openalex-snapshot
Surveys of environmental DNA (eDNA): a new approach to estimate occurrence in Vulnerable manatee populations
inferredcites →https://doi.org/10.3389/fenvs.2017.00011openalex-snapshot
Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment
inferredcites →https://doi.org/10.3389/fmicb.2021.665664openalex-snapshot
Influence of Filter Pore Size on Composition and Relative Abundance of Bacterial Communities and Select Host-Specific MST Markers in Coastal Waters of Southern Lake Michigan
inferredcites →https://doi.org/10.3390/ani13040683openalex-snapshot
Environmental DNA Assay for the Detection of the American Bullfrog (Lithobates catesbeianus) in the Early Stages of the Invasion in the Ebre Delta
inferredcites →https://doi.org/10.3390/fishes7050257openalex-snapshot
Environmental DNA Metabarcoding Reflects Fish DNA Dynamics in Lentic Ecosystems: A Case Study of Freshwater Ponds
inferredcites →https://doi.org/10.3390/ijms232213690openalex-snapshot
The Origin, Function, Distribution, Quantification, and Research Advances of Extracellular DNA
inferredcites →https://doi.org/10.3391/mbi.2018.9.3.07openalex-snapshot
Tradeoffs of a portable, field-based environmental DNA platform for detecting invasive northern pike (Esox lucius) in Alaska
inferredcites →https://doi.org/10.3791/54741openalex-snapshot
Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA
inferredcites →https://doi.org/10.3791/60967openalex-snapshot
Capture of Environmental DNA (eDNA) from Water Samples by Flocculation
inferredcites →https://doi.org/10.7717/peerj.2584openalex-snapshot
VSEARCH: a versatile open source tool for metagenomics
inferredcites →https://doi.org/10.7717/peerj.5871openalex-snapshot
An experimental comparison of composite and grab sampling of stream water for metagenetic analysis of environmental DNA

What points at this work

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

inferred← citeshttps://doi.org/10.1111/jfb.70056zenodo-depositor-declared
Aquatic eDNA outperforms sedimentary eDNA for the detection of estuarine fish communities in subtropical coastal vegetated ecosystems
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/10.1016/j.rsma.2026.105411openalex-snapshot
SAS eDNA complements traditional sampling in detecting fish diversity along river-estuarine-coastal continuum
inferred← citeshttps://doi.org/10.1016/j.watbs.2026.100661openalex-snapshot
Deciphering temporal variation and community stability of marine fish assemblages using environmental DNA metabarcoding
inferred← citeshttps://doi.org/10.1109/tfr.2025.3648380openalex-snapshot
Integrating Robotics, Remote Sensing, and Machine Learning for Scalable Biodiversity Monitoring in Tropical Rainforests
inferred← citeshttps://doi.org/10.3389/fmars.2025.1686361openalex-snapshot
Environmental DNA-based metabarcoding reveals a high animal biodiversity level within Red Sea mangrove beds
inferred← citeshttps://doi.org/10.3390/ijms27031483openalex-snapshot
Marine Ranching Systems Exhibit Higher Multi-Trophic Biodiversity: Evidence from Three Ranching Areas
inferred← citeshttps://doi.org/10.3390/w17182667openalex-snapshot
Assessment of Stock Enhancement Efficacy for Hypophthalmichthys molitrix and Aristichthys nobilis in the Xixi of Jiulong River Basin
inferred← citeshttps://doi.org/10.34133/ehs.0551openalex-snapshot
Integrating Aquatic Environmental DNA and Remote Sensing for Ecological Security Pattern in the Dongjiang River Basin, China
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