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

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

(2018) Daniel Hering et al.   WATER RESEARCH

Predicting the Ecological Quality Status of Marine Environments from eDNA Metabarcoding Data Using Supervised Machine Learning

(2017) Tristan Cordier et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Suitability of PCR primers for characterizing invertebrate communities from soil and leaf litter targeting metazoan 18S ribosomal or cytochrome oxidase I (COI) genes

(2017) Dean J. Horton et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Freshwater biomonitoring in the Information Age

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

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

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

Environmental DNA enables detection of terrestrial mammals from forest pond water

(2017) Masayuki Ushio 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

Utility of mitochondrial-encoded cytochrome c oxidase I gene for phylogenetic analysis and species identification of the planktonic diatom genus Skeletonema

(2017) Machiko Yamada et al.   PHYCOLOGICAL RESEARCH

DNA metabarcoding of unfractionated water samples relates phyto-, zoo- and bacterioplankton dynamics and reveals a single-taxon bacterial bloom

(2017) Christian Wurzbacher et al.   Environmental Microbiology Reports

Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity

(2017) Iliana Bista et al.   Nature Communications

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

Detection of a global aquatic invasive amphibian, Xenopus laevis, using environmental DNA

(2016) Jean Secondi et al.   AMPHIBIA-REPTILIA

Scale and scope matter when explaining varying patterns of community diversity in riverine metacommunities

(2016) Mathew Seymour et al.   BASIC AND APPLIED ECOLOGY

Distribution and population genetic variation of cryptic species of the Alpine mayfly Baetis alpinus (Ephemeroptera: Baetidae) in the Central Alps

(2016) Marie Leys et al.   BMC EVOLUTIONARY BIOLOGY

Widely distributed and regionally isolated! Drivers of genetic structure in Gammarus fossarum in a human-impacted landscape

(2016) Martina Weiss et al.   BMC EVOLUTIONARY BIOLOGY

Metabarcoding reveals strong spatial structure and temporal turnover of zooplankton communities among marine and freshwater ports

(2016) Frédéric J. J. Chain et al.   DIVERSITY AND DISTRIBUTIONS

Multiple-stressor effects on stream invertebrates: DNA barcoding reveals contrasting responses of cryptic mayfly species

(2016) Jan N. Macher et al.   ECOLOGICAL INDICATORS

Protist metabarcoding and environmental biomonitoring: Time for change

(2016) J. Pawlowski et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Detecting signatures of competition from observational data: a combined approach using DNA barcoding, diversity partitioning and checkerboards at small spatial scales

(2016) Trevor T. Bringloe et al.   FRESHWATER 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

Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA

(2016) Lucie Zinger et al.   SOIL BIOLOGY & BIOCHEMISTRY

Environmental DNA reveals that rivers are conveyer belts of biodiversity information

(2016) Kristy Deiner et al.   Nature Communications

Environmental context and magnitude of disturbance influence trait-mediated community responses to wastewater in streams

(2016) Francis J. Burdon et al.   Ecology and Evolution

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

(2016) Vasco Elbrecht et al.   PeerJ

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

The ecology of environmental DNA and implications for conservation genetics

(2015) Matthew A. Barnes et al.   CONSERVATION GENETICS

www.freshwaterecology.info – An online tool that unifies, standardises and codifies more than 20,000 European freshwater organisms and their ecological preferences

(2015) Astrid Schmidt-Kloiber et al.   ECOLOGICAL INDICATORS

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

Tag jumps illuminated - reducing sequence-to-sample misidentifications in metabarcoding studies

(2015) Ida Baerholm Schnell et al.   Molecular Ecology Resources

Planetary boundaries: Guiding human development on a changing planet

(2015) W. Steffen et al.   SCIENCE

Managing aquatic ecosystems and water resources under multiple stress — An introduction to the MARS project

(2015) Daniel Hering et al.   SCIENCE OF THE TOTAL ENVIRONMENT

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

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

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

DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match

(2014) B. E. Deagle et al.   Biology Letters

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

(2014) Jonas Zimmermann et al.   Molecular Ecology Resources

Cryptic biodiversity in streams: a comparison of macroinvertebrate communities based on morphological and DNA barcode identifications

(2014) John K. Jackson et al.   Freshwater Science

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

Patterns of benthic algae and cyanobacteria along twin-stressor gradients of nutrients and fine sediment: a stream mesocosm experiment

(2013) Annika Wagenhoff et al.   FRESHWATER BIOLOGY

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

Effects of connectivity, dispersal directionality and functional traits on the metacommunity structure of river benthic diatoms

(2013) Jing Liu et al.   JOURNAL OF BIOGEOGRAPHY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Macroinvertebrate responses along broad stressor gradients of deposited fine sediment and dissolved nutrients: a stream mesocosm experiment

(2012) Annika Wagenhoff et al.   JOURNAL OF APPLIED ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & EVOLUTION

CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

(2012) Jan Pawlowski et al.   PLOS BIOLOGY

Subsidy-stress and multiple-stressor effects along gradients of deposited fine sediment and dissolved nutrients in a regional set of streams and rivers

(2011) ANNIKA WAGENHOFF et al.   FRESHWATER BIOLOGY

DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer

(2011) GREGG P. ROBIDEAU et al.   Molecular Ecology Resources

THE IMPACT OF FINE SEDIMENT ON MACRO-INVERTEBRATES

(2011) J. I. Jones et al.   RIVER RESEARCH AND APPLICATIONS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Multiple stressors in agricultural streams: interactions among sediment addition, nutrient enrichment and water abstraction

(2010) Christoph D. Matthaei et al.   JOURNAL OF APPLIED ECOLOGY

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

(2010) S. CREER et al.   MOLECULAR ECOLOGY

Global threats to human water security and river biodiversity

(2010) C. J. Vörösmarty et al.   NATURE

Do insects lose flight before they lose their wings? Population genetic structure in subalpine stoneflies

(2009) GRAHAM A. McCULLOCH et al.   MOLECULAR ECOLOGY

Barcoding Amoebae: Comparison of SSU, ITS and COI Genes as Tools for Molecular Identification of Naked Lobose Amoebae

(2009) Elena Nassonova et al.   PROTIST

Barcoding Bamboozled by Bacteria: Convergence to Metazoan Mitochondrial Primer Targets by Marine Microbes

(2009) Mark E. Siddall et al.   SYSTEMATIC BIOLOGY

Individual and combined responses of stream ecosystems to multiple stressors

(2008) Colin R. Townsend et al.   JOURNAL OF APPLIED ECOLOGY