Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

Metabarcoding improves detection of eukaryotes from early biofouling communities: implications for pest monitoring and pathway management

(2016) Anastasija Zaiko et al.   BIOFOULING

Hidden diversity of Acoelomorpha revealed through metabarcoding

(2016) Alicia S. Arroyo et al.   Biology Letters

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

Protist metabarcoding and environmental biomonitoring: Time for change

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

Metabarcoding of marine zooplankton: prospects, progress and pitfalls

(2016) Ann Bucklin et al.   JOURNAL OF PLANKTON RESEARCH

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

Genetic assessment of meiobenthic community composition and spatial distribution in coastal sediments along northern Gulf of Mexico

(2016) Pamela M. Brannock et al.   MARINE ENVIRONMENTAL RESEARCH

Censusing marine eukaryotic diversity in the twenty-first century

(2016) Matthieu Leray et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

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

Early detection of eukaryotic communities from marine biofilm using high-throughput sequencing: an assessment of different sampling devices

(2015) Xavier Pochon et al.   BIOFOULING

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

The ecology of environmental DNA and implications for conservation genetics

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

Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing

(2015) Ramon Massana et al.   ENVIRONMENTAL MICROBIOLOGY

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

Meiofaunal community analysis by high-throughput sequencing: Comparison of extraction, quality filtering, and clustering methods

(2015) Pamela M. Brannock et al.   Marine Genomics

Metagenetic tools for the census of marine meiofaunal biodiversity: An overview

(2015) Laura Carugati et al.   Marine Genomics

obitools: aunix-inspired software package for DNA metabarcoding

(2015) Frédéric Boyer 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

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

(2015) Magdalena Guardiola 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

REVIEW: The detection of aquatic animal species using environmental DNA - a review of eDNA as a survey tool in ecology

(2014) Helen C. Rees et al.   JOURNAL OF APPLIED ECOLOGY

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

eulerAPE: Drawing Area-Proportional 3-Venn Diagrams Using Ellipses

(2014) Luana Micallef et al.   PLoS One

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

Swarm: robust and fast clustering method for amplicon-based studies

(2014) Frédéric Mahé et al.   PeerJ

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

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

(2013) William Orsi 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

Deep flow variability in a deeply incised Mediterranean submarine valley (Blanes canyon)

(2013) G. Jorda 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

Multiple drivers of particle fluxes in the Blanes submarine canyon and southern open slope: Results of a year round experiment

(2013) Pilar Lopez-Fernandez et al.   PROGRESS IN OCEANOGRAPHY

Surviving in a Marine Desert: The Sponge Loop Retains Resources Within Coral Reefs

(2013) Jasper M. de Goeij et al.   SCIENCE

Identifying active foraminifera in the Sea of Japan using metatranscriptomic approach

(2012) Franck Lejzerowicz et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

A functional and morphological approach to evaluate the vertical migration of estuarine intertidal nematodes during a tidal cycle

(2012) M. C. Brustolin et al.   HELGOLAND MARINE RESEARCH

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

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

(2012) C. Q. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequencing our way towards understanding global eukaryotic biodiversity

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

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

(2011) Xiaolin Hao et al.   BIOINFORMATICS

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   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

Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing

(2011) Jan Pawlowski et al.   PLoS One

Man and the Last Great Wilderness: Human Impact on the Deep Sea

(2011) Eva Ramirez-Llodra 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

Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis

(2010) Tim van Zutphen et al.   BMC GENOMICS

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

Preservation, origin and genetic imprint of extracellular DNA in permanently anoxic deep-sea sediments

(2010) C. CORINALDESI 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

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

Temporal changes (1989–1999) in deep-sea metazoan meiofaunal assemblages on the Porcupine Abyssal Plain, NE Atlantic

(2009) V. Kalogeropoulou et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

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

Dynamics of benthic copepods and other meiofauna in the benthic boundary layer of the deep NW Mediterranean Sea

(2009) LD Guidi-Guilvard et al.   MARINE ECOLOGY PROGRESS SERIES

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

New Insights into the Diversity of Marine Picoeukaryotes

(2009) Fabrice Not et al.   PLoS One

Particle fluxes dynamics in Blanes submarine canyon (Northwestern Mediterranean)

(2009) Diana Zúñiga et al.   PROGRESS IN OCEANOGRAPHY

Effect of commercial trawling on the deep sedimentation in a Mediterranean submarine canyon

(2008) J. Martín et al.   MARINE GEOLOGY