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

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

(2016) Rosalinda D’Amore et al.   BMC GENOMICS

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

(2016) Alice Valentini et al.   MOLECULAR ECOLOGY

A comparison of DNA extraction methods for biodiversity studies of eukaryotes in marine sediments

(2015) K Lekang et al.   AQUATIC MICROBIAL ECOLOGY

Depth shapes α- and β-diversities of microbial eukaryotes in surficial sediments of coastal ecosystems

(2015) Jun Gong et al.   ENVIRONMENTAL MICROBIOLOGY

Accurate assessment of the impact of salmon farming on benthic sediment enrichment using foraminiferal metabarcoding

(2015) X. Pochon et al.   MARINE POLLUTION BULLETIN

High-Throughput Sequencing—The Key to Rapid Biodiversity Assessment of Marine Metazoa?

(2015) Inga Mohrbeck et al.   PLoS One

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?

(2015) Emily A. Brown et al.   Ecology and Evolution

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

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

(2015) Franck Lejzerowicz et al.   Scientific Reports

Investigating Microbial Eukaryotic Diversity from a Global Census: Insights from a Comparison of Pyrotag and Full-Length Sequences of 18S rRNA Genes

(2014) Alle A. Y. Lie et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A molecular-based approach for examining responses of eukaryotes in microcosms to contaminant-spiked estuarine sediments

(2014) Anthony A. Chariton et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems

(2014) Delphine Lallias et al.   ISME Journal

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

(2014) Jonas Zimmermann et al.   Molecular Ecology Resources

Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities

(2014) Jan Pawlowski et al.   Molecular Ecology Resources

Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers

(2014) Kenan Hadziavdic et al.   PLoS One

Environmental DNA for wildlife biology and biodiversity monitoring

(2014) Kristine Bohmann et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2014) Lenaïg Kermarrec et al.   Freshwater Science

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Marine monitoring during an economic crisis: The cure is worse than the disease

(2013) Ángel Borja et al.   MARINE POLLUTION BULLETIN

Genomics in marine monitoring: New opportunities for assessing marine health status

(2013) Sarah J. Bourlat et al.   MARINE POLLUTION BULLETIN

Deep Sequencing of Subseafloor Eukaryotic rRNA Reveals Active Fungi across Marine Subsurface Provinces

(2013) William Orsi et al.   PLoS One

Extremely High Copy Numbers and Polymorphisms of the rDNA Operon Estimated from Single Cell Analysis of Oligotrich and Peritrich Ciliates

(2013) Jun Gong et al.   PROTIST

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

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

Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil Spill

(2012) Holly M. Bik et al.   PLoS One

Testing the Limits of 454 Pyrotag Sequencing: Reproducibility, Quantitative Assessment and Comparison to T-RFLP Fingerprinting of Aquifer Microbes

(2012) Giovanni Pilloni et al.   PLoS One

CREST – Classification Resources for Environmental Sequence Tags

(2012) Anders Lanzén et al.   PLoS One

Sequencing our way towards understanding global eukaryotic biodiversity

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

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

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

(2011) Mehrdad Hajibabaei et al.   PLoS One

Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA

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

18S rDNA Sequences from Microeukaryotes Reveal Oil Indicators in Mangrove Sediment

(2010) Henrique F. Santos et al.   PLoS One

Improving aquatic ecological assessments

(2010) Anthony A Chariton et al.   Integrated Environmental Assessment and Management

Counterintuitive carbon-to-nutrient coupling in an Arctic pelagic ecosystem

(2008) T. F. Thingstad et al.   NATURE