A review on the applications and recent advances in environmental DNA (eDNA) metagenomics
Published 2019 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
A review on the applications and recent advances in environmental DNA (eDNA) metagenomics
Authors
Keywords
Biodiversity, Ecosystem, Environmental DNA, eDNA, Freshwater habitats, Invasive species, Marine habitats, Next-generation sequencing, High throughput sequencing, Species monitoring
Journal
REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY
Volume -, Issue -, Pages -
Publisher
Springer Science and Business Media LLC
Online
2019-07-29
DOI
10.1007/s11157-019-09501-4
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding
- (2019) Natalie A. Sawaya et al. Ecology and Evolution
- Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA
- (2019) Krista M. Ruppert et al. Global Ecology and Conservation
- Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient
- (2019) Joseph D. DiBattista et al. PeerJ
- Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool?
- (2019) Clare I.M. Adams et al. Genes
- Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods
- (2019) Philip Francis Thomsen et al. Ecology and Evolution
- Influence of accuracy, repeatability and detection probability in the reliability of species-specific eDNA based approaches
- (2019) Quentin Mauvisseau et al. Scientific Reports
- Retrospective eDNA assessment of potentially harmful algae in historical ship ballast tank and marine port sediments
- (2019) Jennifer L. A. Shaw et al. MOLECULAR ECOLOGY
- Development and preliminary validation of a multi-trophic metabarcoding biotic index for monitoring benthic organic enrichment
- (2018) Nigel Keeley et al. ECOLOGICAL INDICATORS
- eDNA-based bioassessment of coastal sediments impacted by an oil spill
- (2018) Yuwei Xie et al. ENVIRONMENTAL POLLUTION
- Molecular-Assisted Pollen Grain Analysis Reveals Spatiotemporal Origin of Long-Distance Migrants of a Noctuid Moth
- (2018) Hong Chang et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- A Comparison of Different Ciliate Metabarcode Genes as Bioindicators for Environmental Impact Assessments of Salmon Aquaculture
- (2018) Dominik Forster et al. JOURNAL OF EUKARYOTIC MICROBIOLOGY
- Evaluation of marine zooplankton community structure through environmental DNA metabarcoding
- (2018) Anni Djurhuus et al. LIMNOLOGY AND OCEANOGRAPHY-METHODS
- Early detection of marine invasive species, Bugula neritina (Bryozoa: Cheilostomatida), using species-specific primers and environmental DNA analysis in Korea
- (2018) Philjae Kim et al. MARINE ENVIRONMENTAL RESEARCH
- Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula
- (2018) Dominique A. Cowart et al. Marine Genomics
- Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis
- (2018) Maxime Galan et al. Molecular Ecology Resources
- Effects of bioturbation on environmental DNA migration through soil media
- (2018) Christopher M. Prosser et al. PLoS One
- DNA metabarcoding uncovers fungal diversity of mixed airborne samples in Italy
- (2018) Elisa Banchi et al. PLoS One
- A tool for finding rare marine species
- (2018) Ellen K. Pikitch SCIENCE
- Biofilms as a sink for antibiotic resistance genes (ARGs) in the Yangtze Estuary
- (2018) Xing-pan Guo et al. WATER RESEARCH
- Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys
- (2018) Erin K. Grey et al. Scientific Reports
- Demonstration of the potential of environmental DNA as a tool for the detection of avian species
- (2018) Masayuki Ushio et al. Scientific Reports
- eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity
- (2018) Anaïs Lacoursière-Roussel et al. Ecology and Evolution
- Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation
- (2018) Melania E. Cristescu et al. Annual Review of Ecology Evolution and Systematics
- Pollen metabarcoding as a tool for tracking long-distance insect migrations
- (2018) Tomasz Suchan et al. Molecular Ecology Resources
- Water, water everywhere: environmental DNA can unlock population structure in elusive marine species
- (2018) Kim M. Parsons et al. Royal Society Open Science
- Environmental DNA Metabarcoding Supporting Community Assessment of Environmental Stressors in a Field-Based Sediment Microcosm Study
- (2018) Jianghua Yang et al. ENVIRONMENTAL SCIENCE & TECHNOLOGY
- Environmental DNA for the enumeration and management of Pacific salmon
- (2018) Taal Levi et al. Molecular Ecology Resources
- Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement
- (2018) Gert-Jan Jeunen et al. Molecular Ecology Resources
- Shotgun metagenomics of honey DNA: Evaluation of a methodological approach to describe a multi-kingdom honey bee derived environmental DNA signature
- (2018) Samuele Bovo et al. PLoS One
- Minimal Influence of Extracellular DNA on Molecular Surveys of Marine Sedimentary Communities
- (2018) Gustavo A. Ramírez et al. Frontiers in Microbiology
- Environmental DNA (eDNA) Shedding and Decay Rates to Model Freshwater Mussel eDNA Transport in a River
- (2017) Brandon J. Sansom et al. ENVIRONMENTAL SCIENCE & TECHNOLOGY
- Predicting the Ecological Quality Status of Marine Environments from eDNA Metabarcoding Data Using Supervised Machine Learning
- (2017) Tristan Cordier et al. ENVIRONMENTAL SCIENCE & TECHNOLOGY
- The importance of molecular markers and primer design when characterizing biodiversity from environmental DNA
- (2017) Joanna R. Freeland GENOME
- Transcription of mcrA Gene Decreases Upon Prolonged Non-flooding Period in a Methanogenic Archaeal Community of a Paddy-Upland Rotational Field Soil
- (2017) Dongyan Liu et al. MICROBIAL ECOLOGY
- Revegetation rewilds the soil bacterial microbiome of an old field
- (2017) Nicholas J. C. Gellie et al. MOLECULAR ECOLOGY
- Environmental DNA metabarcoding: Transforming how we survey animal and plant communities
- (2017) Kristy Deiner et al. MOLECULAR ECOLOGY
- Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past
- (2017) Clio Der Sarkissian et al. Molecular Ecology Resources
- Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring
- (2017) Laure Apothéloz-Perret-Gentil et al. Molecular Ecology Resources
- Ancient plant DNA in lake sediments
- (2017) Laura Parducci et al. NEW PHYTOLOGIST
- eDNA for detection of five highly invasive molluscs. A case study in urban rivers from the Iberian Peninsula
- (2017) Laura Clusa et al. PLoS One
- Bacterial natural product biosynthetic domain composition in soil correlates with changes in latitude on a continent-wide scale
- (2017) Christophe Lemetre et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Integrated field, laboratory, and theoretical study of PKD spread in a Swiss prealpine river
- (2017) Luca Carraro et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Making sense of the noise: The effect of hydrology on silver carp eDNA detection in the Chicago area waterway system
- (2017) Jeffery W. Song et al. SCIENCE OF THE TOTAL ENVIRONMENT
- A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater
- (2017) Flavia Flaviani et al. Viruses-Basel
- Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity
- (2017) Iliana Bista et al. Nature Communications
- Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment
- (2017) Michael Stat et al. Scientific Reports
- DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea )
- (2017) Tina E. Berry et al. Ecology and Evolution
- Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis
- (2017) Nam-Il Won et al. International Journal of Environmental Research and Public Health
- Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities
- (2017) Olivier Laroche et al. PeerJ
- Application of environmental DNA to detect an endangered marine skate species in the wild
- (2017) Kay Weltz et al. PLoS One
- Monitoring of noble, signal and narrow-clawed crayfish using environmental DNA from freshwater samples
- (2017) Sune Agersnap et al. PLoS One
- Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes
- (2017) Katy E. Klymus et al. PLoS One
- Persistence of marine fish environmental DNA and the influence of sunlight
- (2017) Elizabeth A. Andruszkiewicz et al. PLoS One
- Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications
- (2017) Xavier Pochon et al. PLoS One
- Controls on eDNA movement in streams: Transport, Retention, and Resuspension
- (2017) Arial J. Shogren et al. Scientific Reports
- Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system
- (2016) Jennifer L.A. Shaw et al. BIOLOGICAL CONSERVATION
- Quantification of Environmental DNA (eDNA) Shedding and Decay Rates for Three Marine Fish
- (2016) Lauren M. Sassoubre et al. ENVIRONMENTAL SCIENCE & TECHNOLOGY
- The sequence of sequencers: The history of sequencing DNA
- (2016) James M. Heather et al. GENOMICS
- Quantifying relative fish abundance with eDNA: a promising tool for fisheries management
- (2016) Anaïs Lacoursière-Roussel et al. JOURNAL OF APPLIED ECOLOGY
- Laboratory and field validation of a simple method for detecting four species of non-native freshwater fish using eDNA
- (2016) P. I. Davison et al. JOURNAL OF FISH BIOLOGY
- Can environmental DNA (eDNA) be used for detection and monitoring of introduced crab species in the Baltic Sea?
- (2016) Tiia Forsström et al. MARINE POLLUTION BULLETIN
- A Global eDNA Comparison of Freshwater Bacterioplankton Assemblages Focusing on Large-River Floodplain Lakes of Brazil
- (2016) Michael Tessler et al. MICROBIAL ECOLOGY
- Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding
- (2016) Alice Valentini et al. MOLECULAR ECOLOGY
- Real-time PCR detection of Didemnum perlucidum (Monniot, 1983) and Didemnum vexillum (Kott, 2002) in an applied routine marine biosecurity context
- (2016) Tiffany J. S. Simpson et al. Molecular Ecology Resources
- Detecting the movement and spawning activity of bigheaded carps with environmental DNA
- (2016) Richard A. Erickson et al. Molecular Ecology Resources
- How to limit false positives in environmental DNA and metabarcoding?
- (2016) Gentile Francesco Ficetola et al. Molecular Ecology Resources
- Analysis of soil eDNA functional genes: potential to increase profitability and sustainability of pastoral agriculture
- (2016) SA Wakelin et al. NEW ZEALAND JOURNAL OF AGRICULTURAL RESEARCH
- NCBI prokaryotic genome annotation pipeline
- (2016) Tatiana Tatusova et al. NUCLEIC ACIDS RESEARCH
- Environmental DNA reveals that rivers are conveyer belts of biodiversity information
- (2016) Kristy Deiner et al. Nature Communications
- Critical considerations for the application of environmental DNA methods to detect aquatic species
- (2016) Caren S. Goldberg et al. Methods in Ecology and Evolution
- In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River
- (2016) M. V. Cannon et al. Scientific Reports
- Genetic signatures of ecological diversity along an urbanization gradient
- (2016) Ryan P. Kelly et al. PeerJ
- Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA
- (2016) Magdalena Guardiola et al. PeerJ
- Next-generation freshwater bioassessment: eDNA metabarcoding with a conserved metazoan primer reveals species-rich and reservoir-specific communities
- (2016) Nicholas K. M. Lim et al. Royal Society Open Science
- An eDNA Assay to Monitor a Globally Invasive Fish Species from Flowing Freshwater
- (2016) Irene Adrian-Kalchhauser et al. PLoS One
- Evaluation of the Environmental DNA Method for Estimating Distribution and Biomass of Submerged Aquatic Plants
- (2016) Saeko Matsuhashi et al. PLoS One
- Potential of Environmental DNA to Evaluate Northern Pike (Esox lucius) Eradication Efforts: An Experimental Test and Case Study
- (2016) Kristine J. Dunker et al. PLoS One
- An Easy Phylogenetically Informative Method to Trace the Globally Invasive Potamopyrgus Mud Snail from River’s eDNA
- (2016) Laura Clusa et al. PLoS One
- Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA
- (2015) Kristy Deiner et al. BIOLOGICAL CONSERVATION
- Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity
- (2015) Philip Francis Thomsen et al. BIOLOGICAL CONSERVATION
- Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus)
- (2015) Jeremy Biggs et al. BIOLOGICAL CONSERVATION
- The ecology of environmental DNA and implications for conservation genetics
- (2015) Matthew A. Barnes et al. CONSERVATION GENETICS
- The downside of eDNA as a survey tool in water bodies
- (2015) Jean-Marc Roussel et al. JOURNAL OF APPLIED ECOLOGY
- An eDNA assay for IrishPetromyzon marinusandSalmo truttaand field validation in running water
- (2015) M. S. Gustavson et al. JOURNAL OF FISH BIOLOGY
- Culture-independent discovery of natural products from soil metagenomes
- (2015) Micah Katz et al. JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
- The impact of debris on marine life
- (2015) S.C. Gall et al. MARINE POLLUTION BULLETIN
- Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA
- (2015) Johan Pansu et al. MOLECULAR ECOLOGY
- Environmental DNA particle size distribution from Brook Trout (Salvelinus fontinalis)
- (2015) Taylor M. Wilcox et al. Conservation Genetics Resources
- Spatial and temporal dynamics of virus occurrence in two freshwater lakes captured through metagenomic analysis
- (2015) Mohammad Mohiuddin et al. Frontiers in Microbiology
- Environmental DNA (eDNA) Sampling Improves Occurrence and Detection Estimates of Invasive Burmese Pythons
- (2015) Margaret E. Hunter et al. PLoS One
- Development and Validation of Environmental DNA (eDNA) Markers for Detection of Freshwater Turtles
- (2015) Christina M. Davy et al. PLoS One
- Molecular detection of trophic interactions: emerging trends, distinct advantages, significant considerations and conservation applications
- (2014) Elizabeth L. Clare Evolutionary Applications
- REVIEW: The detection of aquatic animal species using environmental DNA - a review of eDNA as a survey tool in ecology
- (2014) Helen C. Rees et al. JOURNAL OF APPLIED ECOLOGY
- Identifying airborne fungi in Seoul, Korea using metagenomics
- (2014) Seung-Yoon Oh et al. JOURNAL OF MICROBIOLOGY
- Recent advances in genomic DNA sequencing of microbial species from single cells
- (2014) Roger S. Lasken et al. NATURE REVIEWS GENETICS
- Evaluating multiplexed next-generation sequencing as a method in palynology for mixed pollen samples
- (2014) A. Keller et al. PLANT BIOLOGY
- Using Environmental DNA to Census Marine Fishes in a Large Mesocosm
- (2014) Ryan P. Kelly et al. PLoS One
- Defaunation in the Anthropocene
- (2014) R. Dirzo et al. SCIENCE
- Harnessing DNA to improve environmental management
- (2014) R. P. Kelly et al. SCIENCE
- From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity
- (2014) Melania E. Cristescu TRENDS IN ECOLOGY & EVOLUTION
- Ten years of next-generation sequencing technology
- (2014) Erwin L. van Dijk et al. TRENDS IN GENETICS
- Particle size distribution and optimal capture of aqueous macrobial eDNA
- (2014) Cameron R. Turner et al. Methods in Ecology and Evolution
- The application of eDNA for monitoring of the Great Crested Newt in the UK
- (2014) Helen C. Rees et al. Ecology and Evolution
- Utility of environmental DNA for monitoring rare and indicator macroinvertebrate species
- (2014) Elvira Mächler et al. Freshwater Science
- Robust Detection of Rare Species Using Environmental DNA: The Importance of Primer Specificity
- (2013) Taylor M. Wilcox et al. PLoS One
- Environmental DNA
- (2012) PIERRE TABERLET et al. MOLECULAR ECOLOGY
- A global synthesis reveals biodiversity loss as a major driver of ecosystem change
- (2012) David U. Hooper et al. NATURE
- Investigating the Potential Use of Environmental DNA (eDNA) for Genetic Monitoring of Marine Mammals
- (2012) Andrew D. Foote et al. PLoS One
- From molecules to management: Adopting DNA-based methods for monitoring biological invasions in aquatic environments
- (2011) John A. Darling et al. ENVIRONMENTAL RESEARCH
- Monitoring endangered freshwater biodiversity using environmental DNA
- (2011) PHILIP FRANCIS THOMSEN et al. MOLECULAR ECOLOGY
- Recent advances in DNA sequencing methods – general principles of sample preparation
- (2010) Sten Linnarsson EXPERIMENTAL CELL RESEARCH
- Global Biodiversity: Indicators of Recent Declines
- (2010) S. H. M. Butchart et al. SCIENCE
- Scenarios for Global Biodiversity in the 21st Century
- (2010) H. M. Pereira et al. SCIENCE
- Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures
- (2009) Eeva M Soininen et al. Frontiers in Zoology
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started