Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates

(2021) Sofia Duarte et al.   Water

Meta‐analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards

(2021) Julija Fediajevaite et al.   Ecology and Evolution

Uncovering the complete biodiversity structure in spatial networks: the example of riverine systems

(2020) Florian Altermatt et al.   OIKOS

Monitoring freshwater fish communities in large rivers using environmental DNA ( eDNA ) metabarcoding and a long‐term electrofishing survey

(2020) Aurélie Goutte et al.   JOURNAL OF FISH BIOLOGY

Genetic and morphologic determination of diatom community composition in surface sediments from glacial and thermokarst lakes in the Siberian Arctic

(2020) S. Huang et al.   JOURNAL OF PALEOLIMNOLOGY

Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape

(2020) Bryan N. Nguyen et al.   Scientific Reports

Effects of sampling seasons and locations on fish environmental DNA metabarcoding in dam reservoirs

(2020) Kana Hayami et al.   Ecology and Evolution

Combining morphological and metabarcoding approaches reveals the freshwater eukaryotic phytoplankton community

(2020) Shouliang Huo et al.   Environmental Sciences Europe

18S-V9 DNA metabarcoding detects the effect of water-quality impairment on stream biofilm eukaryotic assemblages

(2020) Alison D. Minerovic et al.   ECOLOGICAL INDICATORS

Advances in metabarcoding techniques bring us closer to reliable monitoring of the marine benthos

(2020) Margaux Steyaert et al.   JOURNAL OF APPLIED ECOLOGY

Evaluation and sensitivity analysis of diatom DNA metabarcoding for WFD bioassessment of Mediterranean rivers

(2020) Javier Pérez-Burillo et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Monitoring of biofouling communities in a Portuguese port using a combined morphological and metabarcoding approach

(2020) Joana Azevedo et al.   Scientific Reports

Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment

(2020) Noriko Uchida et al.   PeerJ

Biodiversity and Community Structure of Mesozooplankton in the Marine and Coastal National Park Areas of Korea

(2020) Heesoo Kim et al.   Diversity-Basel

DNA metabarcoding and morphological analysis - Assessment of zooplankton biodiversity in transitional waters

(2020) Anna Schroeder et al.   MARINE ENVIRONMENTAL RESEARCH

Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring

(2020) Jan Pawlowski et al.   MOLECULAR ECOLOGY

Monitoring the ecological status of rivers with diatom eDNA metabarcoding: a comparison of taxonomic markers and analytical approaches for the inference of a molecular diatom index

(2020) Laure Apothéloz‐Perret‐Gentil et al.   MOLECULAR ECOLOGY

Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness

(2020) Mary E. McElroy et al.   Frontiers in Ecology and Evolution

Comparative analysis of morphological and molecular approaches integrated into the study of the dinoflagellate biodiversity within the recently deposited Black Sea sediments – benefits and drawbacks

(2020) Nina Dzhembekova et al.   Biodiversity Data Journal

Determining an effective sampling method for eDNA metabarcoding: a case study for fish biodiversity monitoring in a small, natural river

(2020) Masayuki K. Sakata et al.   LIMNOLOGY

A Marine Biodiversity Observation Network for Genetic Monitoring of Hard-Bottom Communities (ARMS-MBON)

(2020) Matthias Obst et al.   Frontiers in Marine Science

Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities

(2020) Wengang Kang et al.   ECOLOGICAL INDICATORS

Metabarcoding reveals hidden species and improves identification of marine zooplankton communities in the North Sea

(2020) Ilias Semmouri et al.   ICES JOURNAL OF MARINE SCIENCE

Exploring the capacity of aquatic biofilms to act as environmental DNA samplers: Test on macroinvertebrate communities in rivers

(2020) Sinziana F. Rivera et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Environmental DNA metabarcoding for fish community analysis in backwater lakes: A comparison of capture methods

(2019) Kazuya Fujii et al.   PLoS One

Have the cake and eat it: Optimising non‐destructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring

(2019) Filipa M.S. Martins et al.   Molecular Ecology Resources

Ground-truthing of a fish-based environmental DNA metabarcoding method for assessing the quality of lakes

(2019) Jianlong Li et al.   JOURNAL OF APPLIED ECOLOGY

Comparison of DNA metabarcoding and morphological identification for stream macroinvertebrate biodiversity assessment and monitoring

(2019) Joeselle M. Serrana et al.   ECOLOGICAL INDICATORS

Metabarcoding of storage ethanol vs. conventional morphometric identification in relation to the use of stream macroinvertebrates as ecological indicators in forest management

(2019) Maitane Erdozain et al.   ECOLOGICAL INDICATORS

Environmental DNA metabarcoding as an effective and rapid tool for fish monitoring in canals

(2019) Allan D. McDevitt et al.   JOURNAL OF FISH BIOLOGY

Morphology and metabarcoding: a test with stream diatoms from Mexico highlights the complementarity of identification methods

(2019) Demetrio Mora et al.   Freshwater Science

Diversity and Spatial Distribution of Chromophytic Phytoplankton in the Bay of Bengal Revealed by RuBisCO Genes (rbcL)

(2019) Laxman Pujari et al.   Frontiers in Microbiology

Environmental DNA reveals landscape mosaic of wetland plant communities

(2019) M.E. Shackleton et al.   Global Ecology and Conservation

How Does eDNA Compare to Traditional Trapping? Detecting Mosquito Communities in South-African Freshwater Ponds

(2019) Louie Krol et al.   Frontiers in Ecology and Evolution

DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

(2019) Hannah Weigand et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Non‐specific amplification compromises environmental DNA metabarcoding with COI

(2019) Rupert A. Collins et al.   Methods in Ecology and Evolution

DNA metabarcoding adds valuable information for management of biodiversity in roadside stormwater ponds

(2019) Zhenhua Sun et al.   Ecology and Evolution

Comparison of Water Sampling between Environmental DNA Metabarcoding and Conventional Microscopic Identification: A Case Study in Gwangyang Bay, South Korea

(2019) Kim et al.   Applied Sciences-Basel

Testing different (e)DNA metabarcoding approaches to assess aquatic oligochaete diversity and the biological quality of sediments

(2019) Régis Vivien et al.   ECOLOGICAL INDICATORS

Predicting the fate of eDNA in the environment and implications for studying biodiversity

(2019) Jori B. Harrison et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Diat.barcode, an open-access curated barcode library for diatoms

(2019) Frédéric Rimet et al.   Scientific Reports

A comparison between the morphological and molecular approach to identify the benthic diatom community in the St Lucia Estuary, South Africa

(2019) M Nunes et al.   AFRICAN JOURNAL OF MARINE SCIENCE

Metabarcoding reveals a more complex cyanobacterial community than morphological identification

(2019) XiaoChuang Li et al.   ECOLOGICAL INDICATORS

Stream water quality assessment by metabarcoding of invertebrates

(2019) Franziska Kuntke et al.   ECOLOGICAL INDICATORS

Unlocking biodiversity and conservation studies in high-diversity environments using environmental DNA (eDNA): A test with Guianese freshwater fishes

(2018) Kévin Cilleros et al.   Molecular Ecology Resources

Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles

(2018) François Keck et al.   Molecular Ecology Resources

Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation

(2018) Inger Greve Alsos et al.   PLoS One

DNA metabarcoding and microscopic analyses of sea turtles biofilms: Complementary to understand turtle behavior

(2018) Sinziana F. Rivera et al.   PLoS One

Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive

(2018) Daniel Hering et al.   WATER RESEARCH

Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks

(2018) Eva Aylagas et al.   ECOLOGICAL INDICATORS

Comparison of environmental DNA and bulk-sample metabarcoding using highly degenerate cytochrome c oxidase I primers

(2018) Jan-Niklas Macher et al.   Molecular Ecology Resources

Evaluating freshwater macroinvertebrates from eDNA metabarcoding: A river Nalón case study

(2018) Sara Fernández et al.   PLoS One

Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation

(2018) Didier Pont et al.   Scientific Reports

Ecological influence of sediment bypass tunnels on macroinvertebrates in dam-fragmented rivers by DNA metabarcoding

(2018) Joeselle M. Serrana et al.   Scientific Reports

A comparative analysis of metabarcoding and morphology-based identification of benthic communities across different regional seas

(2018) Abigail E. Cahill et al.   Ecology and Evolution

How quantitative is metabarcoding: A meta‐analytical approach

(2018) Philip D. Lamb et al.   MOLECULAR ECOLOGY

Biodiversity increases and decreases ecosystem stability

(2018) Frank Pennekamp et al.   NATURE

The diversity and structure of marine protists in the coastal waters of China revealed by morphological observation and 454 pyrosequencing

(2017) Yun Liu et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Molecular and morphological characterization of the Achnanthidium minutissimum complex (Bacillariophyta) in Petuniabukta (Spitsbergen, High Arctic) including the description of A. digitatum sp. nov.

(2017) Eveline Pinseel et al.   EUROPEAN JOURNAL OF PHYCOLOGY

Freshwater biomonitoring in the Information Age

(2017) François Keck et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Metabarcoding of lake benthic diatoms: from structure assemblages to ecological assessment

(2017) S. F. Rivera et al.   HYDROBIOLOGIA

Haptophyte Diversity and Vertical Distribution Explored by 18S and 28S Ribosomal RNA Gene Metabarcoding and Scanning Electron Microscopy

(2017) Sandra Gran-Stadniczeñko et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Comparison of morphological and next generation DNA sequencing methods for assessing zooplankton assemblages

(2017) Julio B.J. Harvey et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

Genetic monitoring of open ocean biodiversity: An evaluation of DNA metabarcoding for processing continuous plankton recorder samples

(2017) Bruce E. Deagle 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

DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities

(2017) Jorge Lobo et al.   Scientific Reports

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

(2017) Laurence J. Clarke et al.   Ecology and Evolution

DNA in a bottle—Rapid metabarcoding survey for early alerts of invasive species in ports

(2017) Yaisel J. Borrell et al.   PLoS One

Zooplankton Community Profiling in a Eutrophic Freshwater Ecosystem-Lake Tai Basin by DNA Metabarcoding

(2017) Jianghua Yang et al.   Scientific Reports

DNA metabarcoding and morphological macroinvertebrate metrics reveal the same changes in boreal watersheds across an environmental gradient

(2017) Caroline E. Emilson 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

Is metabarcoding suitable for estuarine plankton monitoring? A comparative study with microscopy

(2016) David Abad et al.   MARINE BIOLOGY

Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods

(2016) Bernd Hänfling et al.   MOLECULAR ECOLOGY

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

(2016) Alice Valentini et al.   MOLECULAR ECOLOGY

Environmental DNA reveals that rivers are conveyer belts of biodiversity information

(2016) Kristy Deiner et al.   Nature Communications

Estimating species richness using environmental DNA

(2016) Brett P. Olds et al.   Ecology and Evolution

Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System

(2016) Raphaël Civade et al.   PLoS One

Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data

(2015) Joana Amorim Visco et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Effects of plankton net characteristics on metagenetic community analysis of metazoan zooplankton in a coastal marine ecosystem

(2015) Junya Hirai et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

(2015) Jesse A. Port et al.   MOLECULAR ECOLOGY

MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

(2015) M. Miya et al.   Royal Society Open Science

Metabarcoding Is Powerful yet Still Blind: A Comparative Analysis of Morphological and Molecular Surveys of Seagrass Communities

(2015) Dominique A. Cowart et al.   PLoS One

High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems

(2015) Franck Lejzerowicz et al.   Scientific Reports

Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods

(2014) J. Piñol et al.   Molecular Ecology Resources

Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies

(2014) Jonas Zimmermann et al.   Molecular Ecology Resources

Transport Distance of Invertebrate Environmental DNA in a Natural River

(2014) Kristy Deiner et al.   PLoS One

Using Environmental DNA to Census Marine Fishes in a Large Mesocosm

(2014) Ryan P. Kelly et al.   PLoS One

Use of High Throughput Sequencing and Light Microscopy Show Contrasting Results in a Study of Phytoplankton Occurrence in a Freshwater Environment

(2014) Xi Xiao et al.   PLoS One

A next-generation sequencing approach to river biomonitoring using benthic diatoms

(2014) Lenaïg Kermarrec et al.   Freshwater Science

Big data and the future of ecology

(2013) Stephanie E Hampton et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Unveiling Distribution Patterns of Freshwater Phytoplankton by a Next Generation Sequencing Based Approach

(2013) Alexander Eiler et al.   PLoS One

Next Generation Sequencing Reveals the Hidden Diversity of Zooplankton Assemblages

(2013) Penelope K. Lindeque et al.   PLoS One

Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study

(2012) Charles Bachy et al.   ISME Journal

Environmental DNA

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples

(2012) Philip Francis Thomsen et al.   PLoS One

Persistence of Environmental DNA in Freshwater Ecosystems

(2011) Tony Dejean et al.   PLoS One

“Sight-unseen” detection of rare aquatic species using environmental DNA

(2011) Christopher L. Jerde et al.   Conservation Letters

Cost-efficiency of biodiversity indicators for Mediterranean ecosystems and the effects of socio-economic factors

(2010) Yael Mandelik et al.   JOURNAL OF APPLIED ECOLOGY

Species detection using environmental DNA from water samples

(2008) G. F. Ficetola et al.   Biology Letters