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

DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness

(2020) Alex Bush et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Are Environmental DNA Methods Ready for Aquatic Invasive Species Management?

(2020) Adam J. Sepulveda et al.   TRENDS IN ECOLOGY & EVOLUTION

Artificial substrates as sampling devices for marine epibenthic fauna: A quest for standardization

(2020) Diego Carreira-Flores et al.   Regional Studies in Marine Science

Gap-analysis and annotated reference library for supporting macroinvertebrate metabarcoding in Atlantic Iberia

(2020) B.R. Leite et al.   Regional Studies in Marine Science

DNA metabarcoding of stream invertebrates reveals spatio-temporal variation but consistent status class assessments in a natural and urban river

(2020) Vera M.A. Zizka 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

Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

(2020) Luna M. van der Loos et al.   MOLECULAR ECOLOGY

Environmental DNA allows upscaling spatial patterns of biodiversity in freshwater ecosystems

(2020) Luca Carraro et al.   Nature Communications

An Assessment of Environmental Metabarcoding Protocols Aiming at Favoring Contemporary Biodiversity in Inventories of Deep-Sea Communities

(2020) Miriam I. Brandt et al.   Frontiers in Marine Science

MinION-in-ARMS: Nanopore Sequencing to Expedite Barcoding of Specimen-Rich Macrofaunal Samples From Autonomous Reef Monitoring Structures

(2020) Jia Jin Marc Chang et al.   Frontiers in Marine Science

Human activities' fingerprint on multitrophic biodiversity and ecosystem functions across a major river catchment in China

(2020) Feilong Li et al.   GLOBAL CHANGE BIOLOGY

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

Assessing the impact of the threatened crucian carp ( Carassius carassius ) on pond invertebrate diversity: A comparison of conventional and molecular tools

(2020) Lynsey R. Harper et al.   MOLECULAR ECOLOGY

Pan‐regional marine benthic cryptobiome biodiversity patterns revealed by metabarcoding Autonomous Reef Monitoring Structures

(2020) J.K. Pearman et al.   MOLECULAR ECOLOGY

Comparison of markers for the monitoring of freshwater benthic biodiversity through DNA metabarcoding

(2020) Gentile Francesco Ficetola et al.   MOLECULAR ECOLOGY

Modelling technical and biological biases in macroinvertebrate community assessment from bulk preservative using multiple metabarcoding markers

(2020) Filipa M. S. Martins et al.   MOLECULAR ECOLOGY

Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities?

(2020) Adrià Antich et al.   MOLECULAR ECOLOGY

Assessment of stream macroinvertebrate communities with eDNA is not congruent with tissue‐based metabarcoding

(2020) Jennifer Erin Gleason et al.   MOLECULAR ECOLOGY

BAGS: an automated Barcode, Audit & Grade System for DNA barcode reference libraries

(2020) João T Fontes et al.   Molecular Ecology Resources

Takeaways from Mobile DNA Barcoding with BentoLab and MinION

(2020) Jia Jin Marc Chang et al.   Genes

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

(2020) Sofia Duarte et al.   SCIENCE OF THE TOTAL ENVIRONMENT

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

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

Assessing eukaryotic biodiversity in the Florida Keys National Marine Sanctuary through environmental DNA metabarcoding

(2019) Natalie A. Sawaya et al.   Ecology and Evolution

Beyond the visual: using metabarcoding to characterize the hidden reef cryptobiome

(2019) Susana Carvalho et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Metabarcoding a Diverse Arthropod Mock Community

(2019) Thomas W. A. Braukmann et al.   Molecular Ecology Resources

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

Multi-marker eDNA metabarcoding survey to assess the environmental impact of three offshore gas platforms in the North Adriatic Sea (Italy)

(2019) Tristan Cordier et al.   MARINE ENVIRONMENTAL RESEARCH

DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions

(2019) Lucie Zinger et al.   MOLECULAR 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

Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater

(2019) G. A. C. Singer et al.   Scientific Reports

High-throughput environmental DNA analysis informs a biological assessment of an urban stream

(2019) Mark Bagley et al.   ECOLOGICAL INDICATORS

Cobble community DNA as a tool to monitor patterns of biodiversity within kelp forest ecosystems

(2019) Peter Shum et al.   Molecular Ecology Resources

COI metabarcoding primer choice affects richness and recovery of indicator taxa in freshwater systems

(2019) Mehrdad Hajibabaei et al.   PLoS One

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

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

(2019) Zhenhua Sun et al.   Ecology and Evolution

Keeping up with introduced marine species at a remote biodiversity hotspot: awareness, training and collaboration across different sectors is key

(2019) Mareike Huhn et al.   BIOLOGICAL INVASIONS

A new approach to molecular biosurveillance of invasive species using DNA metabarcoding

(2019) Kristen Marie Westfall et al.   GLOBAL CHANGE BIOLOGY

Diversity of Wadden Sea macrofauna and meiofauna communities highest in DNA from extractions preceded by cell lysis

(2019) Lise Klunder et al.   JOURNAL OF SEA RESEARCH

Metabarcoding assessment of prokaryotic and eukaryotic taxa in sediments from Stellwagen Bank National Marine Sanctuary

(2019) Jennifer M. Polinski et al.   Scientific Reports

From metabarcoding to metaphylogeography: separating the wheat from the chaff

(2019) Xavier Turon et al.   ECOLOGICAL APPLICATIONS

Holistic pelagic biodiversity monitoring of the Black Sea via eDNA metabarcoding approach: From bacteria to marine mammals

(2019) Yan Zhang et al.   ENVIRONMENT INTERNATIONAL

Towards routine DNA metabarcoding of macroinvertebrates using bulk samples for freshwater bioassessment: Effects of debris and storage conditions on the recovery of target taxa

(2019) Susan J. Nichols et al.   FRESHWATER BIOLOGY

Successful molecular detection studies require clear communication among diverse research partners

(2019) Brittany A Mosher et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Watered-down biodiversity? A comparison of metabarcoding results from DNA extracted from matched water and bulk tissue biomonitoring samples

(2019) Mehrdad Hajibabaei et al.   PLoS One

Increased performance of DNA metabarcoding of macroinvertebrates by taxonomic sorting

(2019) Kevin K. Beentjes et al.   PLoS One

Stream water quality assessment by metabarcoding of invertebrates

(2019) Franziska Kuntke et al.   ECOLOGICAL INDICATORS

Can high-throughput sequencing detect macroinvertebrate diversity for routine monitoring of an urban river?

(2018) Melissa E. Carew et al.   ECOLOGICAL INDICATORS

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

Optimization and performance testing of a sequence processing pipeline applied to detection of nonindigenous species

(2018) Ryan Scott et al.   Evolutionary Applications

Metabarcoding and post-sampling strategies to discover non-indigenous species: A case study in the estuaries of the central south Bay of Biscay

(2018) Yaisel J. Borrell et al.   JOURNAL FOR NATURE CONSERVATION

More (or less?) bounce for the ounce: a comparison of environmental DNA and classical approaches for bioassessment

(2018) Paul J. McInerney et al.   MARINE AND FRESHWATER RESEARCH

Metagenomic sequencing of environmental DNA reveals marine faunal assemblages from the West Antarctic Peninsula

(2018) Dominique A. Cowart et al.   Marine Genomics

A cross-taxa study using environmental DNA/RNA metabarcoding to measure biological impacts of offshore oil and gas drilling and production operations

(2018) Olivier Laroche et al.   MARINE POLLUTION BULLETIN

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

(2018) Owen S. Wangensteen et al.   MARINE POLLUTION BULLETIN

Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples

(2018) Iliana Bista et al.   Molecular Ecology Resources

Optimal extraction methods for the simultaneous analysis of DNA from diverse organisms and sample types

(2018) Syrie M. Hermans et al.   Molecular Ecology Resources

The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems

(2018) Jan Pawlowski et al.   SCIENCE OF THE TOTAL ENVIRONMENT

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

(2018) Daniel Hering et al.   WATER RESEARCH

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity

(2018) David López-Escardó et al.   Scientific Reports

eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity

(2018) Anaïs Lacoursière-Roussel et al.   Ecology and Evolution

Identifying North American freshwater invertebrates using DNA barcodes: are existing COI sequence libraries fit for purpose?

(2018) Colin J. Curry et al.   Freshwater Science

Identifying North American freshwater invertebrates using DNA barcodes: are existing COI sequence libraries fit for purpose?

(2018) Colin J. Curry et al.   Freshwater Science

Estimating intraspecific genetic diversity from community DNA metabarcoding data

(2018) Vasco Elbrecht et al.   PeerJ

DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers

(2018) Owen S. Wangensteen et al.   PeerJ

Can non-destructive DNA extraction of bulk invertebrate samples be used for metabarcoding?

(2018) Melissa E. Carew et al.   PeerJ

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

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

Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring

(2018) Vasco Elbrecht et al.   FRESHWATER BIOLOGY

DNA metabarcoding from sample fixative as a quick and voucher-preserving biodiversity assessment method

(2018) Vera M A Zizka et al.   GENOME

The European Water Framework Directive facing current challenges: recommendations for a more efficient biological assessment of inland surface waters

(2018) Ana Filipa Filipe et al.   Inland Waters

Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities

(2017) Claudia Hollatz et al.   GENOME

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill

(2017) Carmelo Andújar et al.   MOLECULAR ECOLOGY

Detecting invertebrate species in archived collections using next-generation sequencing

(2017) Melissa E. Carew et al.   Molecular Ecology Resources

DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities

(2017) Jorge Lobo et al.   Scientific Reports

Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment

(2017) Michael Stat et al.   Scientific Reports

Sorting things out: Assessing effects of unequal specimen biomass on DNA metabarcoding

(2017) Vasco Elbrecht et al.   Ecology and Evolution

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

Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding

(2017) Matthieu Leray et al.   PeerJ

The importance of standardization for biodiversity comparisons: A case study using autonomous reef monitoring structures (ARMS) and metabarcoding to measure cryptic diversity on Mo’orea coral reefs, French Polynesia

(2017) Emma Ransome et al.   PLoS One

DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments

(2017) Anders Lanzén et al.   PLoS One

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

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

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

Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea

(2016) Mamoon M.D. Al-Rshaidat et al.   GENOME

Please mind the gap – Visual census and cryptic biodiversity assessment at central Red Sea coral reefs

(2016) John K. Pearman et al.   MARINE ENVIRONMENTAL RESEARCH

High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities

(2016) Anders Lanzén et al.   MOLECULAR ECOLOGY

Next-Generation Sequencing of Aquatic Oligochaetes: Comparison of Experimental Communities

(2016) Régis Vivien et al.   PLoS One

The ecologist's field guide to sequence-based identification of biodiversity

(2016) Simon Creer et al.   Methods in Ecology and Evolution

Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects

(2016) Vasco Elbrecht 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

Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries

(2015) Anthony A. Chariton et al.   ENVIRONMENTAL POLLUTION

Detecting nuisance species using NGST: Methodology shortcomings and possible application in ballast water monitoring

(2015) Anastasija Zaiko et al.   MARINE ENVIRONMENTAL RESEARCH

Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates

(2015) Eddy J. Dowle et al.   Molecular Ecology Resources

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

(2015) Matthieu Leray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol

(2015) Vasco Elbrecht et al.   PLoS One

Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons

(2015) Magdalena Guardiola et al.   PLoS One

Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing

(2015) Joel F. Gibson et al.   PLoS One

Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform

(2015) Shadi Shokralla et al.   Scientific Reports

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

(2015) Franck Lejzerowicz et al.   Scientific Reports

Stream biomonitoring using macroinvertebrates around the globe: a comparison of large-scale programs

(2014) Daniel F. Buss et al.   ENVIRONMENTAL MONITORING AND ASSESSMENT

Environmental Status Assessment Using DNA Metabarcoding: Towards a Genetics Based Marine Biotic Index (gAMBI)

(2014) Eva Aylagas et al.   PLoS One

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

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

(2013) Matthieu Leray et al.   Frontiers in Zoology

Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species

(2013) Melissa E Carew et al.   Frontiers in Zoology

Good Environmental Status of marine ecosystems: What is it and how do we know when we have attained it?

(2013) Angel Borja et al.   MARINE POLLUTION BULLETIN

Least Disturbed Condition for European Mediterranean rivers

(2013) M.J. Feio et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Comparability of ecological quality boundaries in the Mediterranean basin using freshwater benthic invertebrates. Statistical options and implications

(2013) M.J. Feio et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Enhanced primers for amplification of DNA barcodes from a broad range of marine metazoans

(2013) Jorge Lobo et al.   BMC ECOLOGY

Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing

(2012) DONALD J. BAIRD et al.   MOLECULAR ECOLOGY

Next-generation sequencing technologies for environmental DNA research

(2012) SHADI SHOKRALLA et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

(2012) Douglas W. Yu et al.   Methods in Ecology and Evolution

Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol

(2012) Mehrdad Hajibabaei et al.   BMC ECOLOGY

Three hundred ways to assess Europe's surface waters: An almost complete overview of biological methods to implement the Water Framework Directive

(2011) Sebastian Birk et al.   ECOLOGICAL INDICATORS

Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos

(2011) Mehrdad Hajibabaei et al.   PLoS One

Polychaete diversity and distribution patterns in Canadian marine waters

(2011) Christina May Carr   Marine Biodiversity

Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA

(2010) Anthony A Chariton et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

The European Water Framework Directive at the age of 10: A critical review of the achievements with recommendations for the future

(2010) Daniel Hering et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Current status of macroinvertebrate methods used for assessing the quality of European marine waters: implementing the Water Framework Directive

(2009) Angel Borja et al.   HYDROBIOLOGIA

A benthic perspective in assessing the ecological status of estuaries: The case of the Mondego estuary (Portugal)

(2007) H. Teixeira et al.   ECOLOGICAL INDICATORS