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Environmental DNA metabarcoding of rivers: Not all eDNA is everywhere, and not all the time

https://doi.org/10.1101/164046
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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/ece3.1272openalex-snapshot
The application of eDNA for monitoring of the Great Crested Newt in the UK
inferredcites →https://doi.org/10.1002/ece3.2165openalex-snapshot
Environmental context and magnitude of disturbance influence trait‐mediated community responses to wastewater in streams
inferredcites →https://doi.org/10.1002/iroh.200390030openalex-snapshot
The Development of a System to Assess the Ecological Quality of Streams Based on Macroinvertebrates – Design of the Sampling Programme within the AQEM Project
inferredcites →https://doi.org/10.1007/978-1-4020-5493-8_34openalex-snapshot
Assessing the impact of errors in sorting and identifying macroinvertebrate samples
inferredcites →https://doi.org/10.1007/bf00378456openalex-snapshot
Experimental disturbance and the maintenance of species diversity in a stream community
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/s10750-006-0075-6openalex-snapshot
Assessing the impact of errors in sorting and identifying macroinvertebrate samples
inferredcites →https://doi.org/10.1007/s10750-007-9145-7openalex-snapshot
Beta diversity in stream macroinvertebrate assemblages: among-site and among-microhabitat components
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.2014.11.018openalex-snapshot
Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA
inferredcites →https://doi.org/10.1016/j.ecolind.2015.08.024openalex-snapshot
Multiple-stressor effects on stream invertebrates: DNA barcoding reveals contrasting responses of cryptic mayfly species
inferredcites →https://doi.org/10.1016/j.protis.2009.07.003openalex-snapshot
Barcoding Amoebae: Comparison of SSU, ITS and COI Genes as Tools for Molecular Identification of Naked Lobose Amoebae
inferredcites →https://doi.org/10.1038/nature09440openalex-snapshot
Global threats to human water security and river biodiversity
inferredcites →https://doi.org/10.1038/ncomms12544openalex-snapshot
Environmental DNA reveals that rivers are conveyer belts of biodiversity information
inferredcites →https://doi.org/10.1038/ncomms14087openalex-snapshot
Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity
inferredcites →https://doi.org/10.1038/nmeth.2604openalex-snapshot
UPARSE: highly accurate OTU sequences from microbial amplicon reads
inferredcites →https://doi.org/10.1038/s41598-017-05223-1openalex-snapshot
Controls on eDNA movement in streams: Transport, Retention, and Resuspension
inferredcites →https://doi.org/10.1086/678128openalex-snapshot
Utility of environmental DNA for monitoring rare and indicator macroinvertebrate species
inferredcites →https://doi.org/10.1093/bioinformatics/btq461openalex-snapshot
Search and clustering orders of magnitude faster than BLAST
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025612openalex-snapshot
Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae)
inferredcites →https://doi.org/10.1101/gr.5969107openalex-snapshot
MEGAN analysis of metagenomic data
inferredcites →https://doi.org/10.1111/1755-0998.12159openalex-snapshot
Factors influencing detection of eDNA from a stream‐dwelling amphibian
inferredcites →https://doi.org/10.1111/1755-0998.12459openalex-snapshot
Comparative study of the validity of three regions of the 18S‐ rRNA gene for massively parallel sequencing‐based monitoring of the planktonic eukaryote community
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/10.1111/2041-210x.12789openalex-snapshot
Assessing strengths and weaknesses of DNA metabarcoding‐based macroinvertebrate identification for routine stream monitoring
inferredcites →https://doi.org/10.1111/2041-210x.12836openalex-snapshot
Long‐range PCR allows sequencing of mitochondrial genomes from environmental DNA
inferredcites →https://doi.org/10.1111/ddi.12427openalex-snapshot
Metabarcoding reveals strong spatial structure and temporal turnover of zooplankton communities among marine and freshwater ports
inferredcites →https://doi.org/10.1111/fwb.12592openalex-snapshot
Resilience of a stream community to extreme climatic events and long‐term recovery from a catastrophic flood
inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05418.xopenalex-snapshot
Monitoring endangered freshwater biodiversity using environmental DNA
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05542.xopenalex-snapshot
Environmental DNA
inferredcites →https://doi.org/10.1111/j.1462-2920.2012.02785.xopenalex-snapshot
Temporal variability in the diversity and composition of stream bacterioplankton communities
inferredcites →https://doi.org/10.1111/j.1469-185x.2007.00027.xopenalex-snapshot
Effect size, confidence interval and statistical significance: a practical guide for biologists
inferredcites →https://doi.org/10.1111/j.1471-8286.2007.01678.xopenalex-snapshot
bold : The Barcode of Life Data System (http://www.barcodinglife.org)
inferredcites →https://doi.org/10.1111/j.1574-6941.2008.00548.xopenalex-snapshot
Spatial and temporal heterogeneity of the bacterial communities in stream epilithic biofilms
inferredcites →https://doi.org/10.1111/j.1755-0998.2011.03041.xopenalex-snapshot
DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer
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.13660openalex-snapshot
Environmental DNA metabarcoding of lake fish communities reflects long‐term data from established survey methods
inferredcites →https://doi.org/10.1111/mec.13973openalex-snapshot
Genomewide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids‐adapted clade of cichlids from the Congo River
inferredcites →https://doi.org/10.1111/pre.12179openalex-snapshot
Utility of mitochondrial‐encoded cytochrome c oxidase I gene for phylogenetic analysis and species identification of the planktonic diatom genus Skeletonema
inferredcites →https://doi.org/10.1139/f00-239openalex-snapshot
What controls who is where in freshwater fish communities the roles of biotic, abiotic, and spatial factors
inferredcites →https://doi.org/10.1186/s12862-016-0723-zopenalex-snapshot
Widely distributed and regionally isolated! Drivers of genetic structure in Gammarus fossarum in a human-impacted landscape
inferredcites →https://doi.org/10.1371/journal.pbio.1001419openalex-snapshot
CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms
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.0130324openalex-snapshot
Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol
inferredcites →https://doi.org/10.1371/journal.pone.0157366openalex-snapshot
Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System
inferredcites →https://doi.org/10.1371/journal.pone.0175186openalex-snapshot
Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.1643/0045-8511(2002)002[0333:codraa]2.0.co;2openalex-snapshot
Comparison of Deep-River and Adjacent Sandy-Beach Fish Assemblages in the Napo River Basin, Eastern Ecuador
inferredcites →https://doi.org/10.2307/3671211openalex-snapshot
Habitat Partitioning in the Fish Community of a Southwestern River
inferredcites →https://doi.org/10.2307/3671663openalex-snapshot
Epiphytic Diatoms on Cladophora glomerata in the Colorado River, Arizona: Longitudinal and Vertical Distribution in a Regulated River
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/fenvs.2017.00038openalex-snapshot
Corrigendum: Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment
inferredcites →https://doi.org/10.7717/peerj.1966openalex-snapshot
Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects
inferredcites →https://doi.org/10.7717/peerj.3006openalex-snapshot
Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding

What points at this work

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

inferred← citeshttps://doi.org/10.1002/aqc.3208openalex-snapshot
Taxonomic and geographical representation of freshwater environmental DNA research in aquatic conservation
inferred← citeshttps://doi.org/10.1002/aqc.3254openalex-snapshot
Using occupancy models to assess the effectiveness of underwater cameras to detect rare stream fishes
inferred← citeshttps://doi.org/10.1002/edn3.14openalex-snapshot
Influence of preservation methods, sample medium and sampling time on eDNA recovery in a neotropical river
inferred← citeshttps://doi.org/10.1002/edn3.155openalex-snapshot
Detecting community change in Arctic marine ecosystems using the temporal dynamics of environmental DNA
inferred← citeshttps://doi.org/10.1002/edn3.156openalex-snapshot
Monitoring for freshwater mussel presence in rivers using environmental DNA
inferred← citeshttps://doi.org/10.1002/edn3.33openalex-snapshot
Assessing different components of diversity across a river network using eDNA
inferred← citeshttps://doi.org/10.1002/edn3.5openalex-snapshot
Temporal and spatial variation in distribution of fish environmental DNA in England’s largest lake
inferred← citeshttps://doi.org/10.1002/edn3.525openalex-snapshot
Comparing cost, effort, and performance of environmental DNA sampling and trapping for detecting an elusive freshwater turtle
inferred← citeshttps://doi.org/10.1002/edn3.90openalex-snapshot
Macroinvertebrate community diversity and habitat quality relationships along a large river from targeted eDNA metabarcode assays
inferred← citeshttps://doi.org/10.1002/rra.3947openalex-snapshot
Monitoring invasive alien macroinvertebrate species with environmental DNA
inferred← citeshttps://doi.org/10.1002/rra.4265openalex-snapshot
Environmental DNA time series analysis of a temperate stream reveals distinct seasonal community and functional shifts
inferred← citeshttps://doi.org/10.1007/s10531-026-03333-9openalex-snapshot
Rivers run through it – exploring drivers of aquatic macrozoobenthic diversity in an inner alpine dry valley
inferred← citeshttps://doi.org/10.1021/acs.est.8b06829openalex-snapshot
Stream Transport and Retention of Environmental DNA Pulse Releases in Relation to Hydrogeomorphic Scaling Factors
inferred← citeshttps://doi.org/10.1101/2023.05.30.542510openalex-snapshot
Comparison of eDNA, bulk-sample metabarcoding, and morphological approaches: A case study of riverine benthic macroinvertebrate communities
inferred← citeshttps://doi.org/10.1101/546549openalex-snapshot
Assessing different components of biodiversity across a river network using eDNA
inferred← citeshttps://doi.org/10.1111/1755-0998.12982openalex-snapshot
Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement
inferred← citeshttps://doi.org/10.1111/1755-0998.70213openalex-snapshot
Simplifying Macroinvertebrate Biodiversity Assessment: A Standardised Metabarcoding Method for Invertebrate Samples With High Volumes of Debris
inferred← citeshttps://doi.org/10.1111/mec.15597openalex-snapshot
Assessment of stream macroinvertebrate communities with eDNA is not congruent with tissue‐based metabarcoding
inferred← citeshttps://doi.org/10.1111/mec.15623openalex-snapshot
Thermal stratification and fish thermal preference explain vertical eDNA distributions in lakes
inferred← citeshttps://doi.org/10.1111/mec.15725openalex-snapshot
Decision‐making and best practices for taxonomy‐free environmental DNA metabarcoding in biomonitoring using Hill numbers
inferred← citeshttps://doi.org/10.1139/cjfas-2020-0224openalex-snapshot
Comparison of larval fish detections using morphology-based taxonomy versus high-throughput sequencing for invasive species early detection
inferred← citeshttps://doi.org/10.1139/gen-2018-0048openalex-snapshot
DNA metabarcoding from sample fixative as a quick and voucher-preserving biodiversity assessment method
inferred← citeshttps://doi.org/10.1186/s12859-018-2419-4openalex-snapshot
SEDE-GPS: socio-economic data enrichment based on GPS information
inferred← citeshttps://doi.org/10.1186/s13071-024-06591-0openalex-snapshot
Genus Bithynia: morphological classification to molecular identification
inferred← citeshttps://doi.org/10.22541/au.168060917.72845952/v1openalex-snapshot
Environmental DNA time series analysis of a temperate stream reveals distinct seasonal community and functional shifts but no influence of within-stream sampling position
inferred← citeshttps://doi.org/10.22541/au.168060917.72845952/v2openalex-snapshot
Environmental DNA time series analysis of a temperate stream reveals distinct seasonal community and functional shifts but no influence of within-stream sampling position
inferred← citeshttps://doi.org/10.3389/fmars.2019.00621openalex-snapshot
Linking Environmental DNA and RNA for Improved Detection of the Marine Invasive Fanworm Sabella spallanzanii
inferred← citeshttps://doi.org/10.3391/mbi.2020.11.2.04openalex-snapshot
Simple, sensitive and species-specific assays for detecting quagga and zebra mussels (Dreissena rostriformis bugensis and D. polymorpha) using environmental DNA
inferred← citeshttps://doi.org/10.3897/mbmg.1.22262openalex-snapshot
Combining NCBI and BOLD databases for OTU assignment in metabarcoding and metagenomic datasets: The BOLD_NCBI _Merger
inferred← citeshttps://doi.org/10.3897/mbmg.2.26869openalex-snapshot
A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy
inferred← citeshttps://doi.org/10.70675/8723eba5z6f92z4a72z84dez1f21bbd2a07dopenalex-snapshot
Exploring temporal patterns of marine plankton communities in the Western English Channel through the analyses of morphological and metabarcoding time-series
inferred← citeshttps://doi.org/10.7717/peerj.18016openalex-snapshot
Is it worth the extra mile? Comparing environmental DNA and RNA metabarcoding for vertebrate and invertebrate biodiversity surveys in a lowland stream
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