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

Next-Generation Environmental Diversity Surveys of Foraminifera: Preparing the Future

(2016) J. Pawlowski et al.   BIOLOGICAL BULLETIN

High-Throughput Sequencing Characterizes Intertidal Meiofaunal Communities in Northern Gulf of Mexico (Dauphin Island and Mobile Bay, Alabama)

(2016) Pamela M. Brannock et al.   BIOLOGICAL BULLETIN

Unreliable quantitation of species abundance based on high-throughput sequencing data of zooplankton communities

(2015) C Sun et al.   Aquatic Biology

Fish environmental DNA is more concentrated in aquatic sediments than surface water

(2015) Cameron R. Turner 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

How will the ‘molecular revolution’ contribute to biological recording?

(2015) Lori Lawson Handley   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries

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

Scraping the bottom of the barrel: are rare high throughput sequences artifacts?

(2015) Shawn P. Brown et al.   Fungal Ecology

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

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

(2015) Jullien M. Flynn 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

Patterns of Rare and Abundant Marine Microbial Eukaryotes

(2014) Ramiro Logares et al.   CURRENT BIOLOGY

Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes

(2014) Vera G. Fonseca et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

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

(2014) Delphine Lallias et al.   ISME Journal

Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data

(2014) Gentile F. Ficetola et al.   Molecular Ecology Resources

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

(2014) Jonas Zimmermann et al.   Molecular Ecology Resources

Chronic and intensive bottom trawling impairs deep-sea biodiversity and ecosystem functioning

(2014) A. Pusceddu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Harnessing DNA to improve environmental management

(2014) R. P. Kelly et al.   SCIENCE

Challenging the paradigms of deep-sea ecology

(2014) Roberto Danovaro et al.   TRENDS IN ECOLOGY & EVOLUTION

Environmental DNA for wildlife biology and biodiversity monitoring

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

Ancient DNA complements microfossil record in deep-sea subsurface sediments

(2013) F. Lejzerowicz et al.   Biology Letters

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

Down under the tunic: bacterial biodiversity hotspots and widespread ammonia-oxidizing archaea in coral reef ascidians

(2013) Patrick M Erwin et al.   ISME Journal

Bryozoan faunal composition and community structure from the continental shelf off Cap de Creus (Northwestern Mediterranean)

(2013) T. Madurell et al.   JOURNAL OF SEA RESEARCH

Trophic Dynamics of Deep-Sea Megabenthos Are Mediated by Surface Productivity

(2013) Samuele Tecchio et al.   PLoS One

Evaluating Detection Limits of Next-Generation Sequencing for the Surveillance and Monitoring of International Marine Pests

(2013) Xavier Pochon et al.   PLoS One

Integrated study of Mediterranean deep canyons: Novel results and future challenges

(2013) M. Canals et al.   PROGRESS IN OCEANOGRAPHY

Spatial and temporal variability of meiobenthic density in the Blanes submarine canyon (NW Mediterranean)

(2013) C. Romano et al.   PROGRESS IN OCEANOGRAPHY

Spatial and temporal infaunal dynamics of the Blanes submarine canyon-slope system (NW Mediterranean); changes in nematode standing stocks, feeding types and gender-life stage ratios

(2013) Jeroen Ingels et al.   PROGRESS IN OCEANOGRAPHY

Seasonal fluctuations of deep megabenthos: Finding evidence of standing stock accumulation in a flux-rich continental slope

(2013) Samuele Tecchio et al.   PROGRESS IN OCEANOGRAPHY

The future of environmental DNA in ecology

(2012) NIGEL G. YOCCOZ   MOLECULAR ECOLOGY

Cosmopolitanism of microbial eukaryotes in the global deep seas

(2012) SIMON CREER et al.   MOLECULAR 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

Bioinformatic challenges for DNA metabarcoding of plants and animals

(2012) ERIC COISSAC et al.   MOLECULAR ECOLOGY

DNA from soil mirrors plant taxonomic and growth form diversity

(2012) N. G. YOCCOZ et al.   MOLECULAR ECOLOGY

Environmental DNA

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Ploughing the deep sea floor

(2012) Pere Puig et al.   NATURE

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Holly M. Bik et al.   PLoS One

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

(2012) Philip Francis Thomsen et al.   PLoS One

Determining the Diet of Larvae of Western Rock Lobster (Panulirus cygnus) Using High-Throughput DNA Sequencing Techniques

(2012) Richard O'Rorke et al.   PLoS One

Sequencing our way towards understanding global eukaryotic biodiversity

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

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

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

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

The seven impediments in invertebrate conservation and how to overcome them

(2011) Pedro Cardoso et al.   BIOLOGICAL CONSERVATION

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments

(2011) HOLLY M. BIK et al.   MOLECULAR ECOLOGY

Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity

(2011) KENNETH ANDERSEN et al.   MOLECULAR ECOLOGY

ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis

(2011) Tiayyba Riaz et al.   NUCLEIC ACIDS RESEARCH

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing

(2011) Jan Pawlowski et al.   PLoS One

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments

(2011) Béatrice Lecroq et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toward routine, DNA-based detection methods for marine pests

(2010) Nathan J. Bott et al.   BIOTECHNOLOGY ADVANCES

An In silico approach for the evaluation of DNA barcodes

(2010) Gentile Ficetola et al.   BMC GENOMICS

Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA

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

Understanding sediment dynamics of two large submarine valleys from seafloor data: Blanes and La Fonera canyons, northwestern Mediterranean Sea

(2010) G. Lastras et al.   MARINE GEOLOGY

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

(2010) S. CREER et al.   MOLECULAR ECOLOGY

Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms

(2010) RALPH MEDINGER et al.   MOLECULAR ECOLOGY

Deep-Sea Biodiversity in the Mediterranean Sea: The Known, the Unknown, and the Unknowable

(2010) Roberto Danovaro et al.   PLoS One

Second-generation environmental sequencing unmasks marine metazoan biodiversity

(2010) Vera G. Fonseca et al.   Nature Communications

Metazoan meiofauna in deep-sea canyons and adjacent open slopes: A large-scale comparison with focus on the rare taxa

(2009) S. Bianchelli et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Organic matter in sediments of canyons and open slopes of the Portuguese, Catalan, Southern Adriatic and Cretan Sea margins

(2009) Antonio Pusceddu et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities

(2009) Anders F Andersson et al.   ISME Journal

Universal DNA-Based Methods for Assessing the Diet of Grazing Livestock and Wildlife from Feces

(2009) Anthony Pegard et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Megabenthic diversity patterns and community structure of the Blanes submarine canyon and adjacent slope in the Northwestern Mediterranean: a human overprint?

(2009) Eva Ramirez-Llodra et al.   Marine Ecology-An Evolutionary Perspective

a-, β-, γ-, δ- and ε-diversity of deep-sea nematodes in canyons and open slopes of Northeast Atlantic and Mediterranean margins

(2009) R Danovaro et al.   MARINE ECOLOGY PROGRESS SERIES

Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure

(2009) DOROTA L. PORAZINSKA et al.   Molecular Ecology Resources

Damage and degradation rates of extracellular DNA in marine sediments: implications for the preservation of gene sequences

(2008) C. CORINALDESI et al.   MOLECULAR ECOLOGY