From Sea Surface to Seafloor: A Benthic Allochthonous eDNA Survey for the Abyssal Ocean

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

Ecology of a polymetallic nodule occurrence gradient: Implications for deep‐sea mining

(2019) Erik Simon‐Lledó et al.   LIMNOLOGY AND OCEANOGRAPHY

Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean

(2019) Dominique Boeuf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Coupling carbon and energy fluxes in the North Pacific Subtropical Gyre

(2019) Eric Grabowski et al.   Nature Communications

Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation

(2019) Linda H. Armbrecht et al.   EARTH-SCIENCE REVIEWS

Larval assemblages over the abyssal plain in the Pacific are highly diverse and spatially patchy

(2019) Oliver Kersten et al.   PeerJ

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

Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys

(2018) Erin K. Grey et al.   Scientific Reports

Natural spatial variability of depositional conditions, biogeochemical processes and element fluxes in sediments of the eastern Clarion-Clipperton Zone, Pacific Ocean

(2018) Jessica B. Volz et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

(2018) Sina M. Adl et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing

(2018) Francisco J. A. Nascimento et al.   Scientific Reports

Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes

(2018) Babett Günther et al.   Scientific Reports

Spatial Variability of Picoeukaryotic Communities in the Mariana Trench

(2018) Hongmei Jing et al.   Scientific Reports

Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement

(2018) Gert-Jan Jeunen et al.   Molecular Ecology Resources

Minimal Influence of Extracellular DNA on Molecular Surveys of Marine Sedimentary Communities

(2018) Gustavo A. Ramírez et al.   Frontiers in Microbiology

Seawater environmental DNA reflects seasonality of a coastal fish community

(2017) Eva Egelyng Sigsgaard et al.   MARINE BIOLOGY

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

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

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

(2017) Michael Stat et al.   Scientific Reports

Mechanisms and Regulation of Extracellular DNA Release and Its Biological Roles in Microbial Communities

(2017) Alejandra L. Ibáñez de Aldecoa et al.   Frontiers in Microbiology

Editorial: Biodiversity of the Clarion Clipperton Fracture Zone

(2017) Stefanie Kaiser et al.   Marine Biodiversity

Major impacts of climate change on deep-sea benthic ecosystems

(2017) Andrew K. Sweetman et al.   Elementa-Science of the Anthropocene

Dendrogramma is a siphonophore

(2016) Timothy D. O’Hara et al.   CURRENT BIOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

A primer for use of genetic tools in selecting and testing the suitability of set-aside sites protected from deep-sea seafloor massive sulfide mining activities

(2016) Rachel E. Boschen et al.   OCEAN & COASTAL MANAGEMENT

iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)

(2016) T. C. Hsieh et al.   Methods in Ecology and Evolution

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

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

Polymetallic nodules, sediments, and deep waters in the equatorial North Pacific exhibit highly diverse and distinct bacterial, archaeal, and microeukaryotic communities

(2016) Christine N. Shulse et al.   MicrobiologyOpen

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

(2016) Magdalena Guardiola et al.   PeerJ

Threatened by mining, polymetallic nodules are required to preserve abyssal epifauna

(2016) Ann Vanreusel et al.   Scientific Reports

Insights into the abundance and diversity of abyssal megafauna in a polymetallic-nodule region in the eastern Clarion-Clipperton Zone

(2016) Diva J. Amon et al.   Scientific Reports

Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms

(2015) Katherine M. Strickler et al.   BIOLOGICAL CONSERVATION

The ecology of environmental DNA and implications for conservation genetics

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

Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries

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

Origin, dynamics, and implications of extracellular DNA pools in marine sediments

(2015) Andrea Torti et al.   Marine Genomics

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

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

Metagenome skimming for phylogenetic community ecology: a new era in biodiversity research

(2015) Anna Papadopoulou et al.   MOLECULAR ECOLOGY

Making environmental DNA count

(2015) Ryan P. Kelly   Molecular Ecology Resources

Comparative study of the validity of three regions of the 18S-rRNA gene for massively parallel sequencing-based monitoring of the planktonic eukaryote community

(2015) Akifumi S. Tanabe et al.   Molecular Ecology Resources

Unveiling the Biodiversity of Deep-Sea Nematodes through Metabarcoding: Are We Ready to Bypass the Classical Taxonomy?

(2015) Antonio Dell’Anno et al.   PLoS One

Managing mining of the deep seabed

(2015) L. M. Wedding et al.   SCIENCE

Spatial and temporal changes in cumulative human impacts on the world’s ocean

(2015) Benjamin S. Halpern et al.   Nature Communications

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

(2015) Magdalena Guardiola et al.   PLoS One

Impact of depositional and biogeochemical processes on small scale variations in nodule abundance in the Clarion‐Clipperton Fracture Zone

(2014) K. Mewes et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Environmental Conditions Influence eDNA Persistence in Aquatic Systems

(2014) Matthew A. Barnes et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

(2014) Gentile F. Ficetola 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

The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol-chloroform-isoamyl alcohol DNA extraction

(2014) Mark A. Renshaw et al.   Molecular Ecology Resources

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

(2014) Kenan Hadziavdic et al.   PLoS One

Ancient DNA complements microfossil record in deep-sea subsurface sediments

(2013) F. Lejzerowicz et al.   Biology Letters

Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies

(2013) Anne Chao et al.   ECOLOGICAL MONOGRAPHS

Deep-sea macroplankton distribution (at 400 to 2300m) in the northwestern Mediterranean in relation to environmental factors

(2013) J.E. Cartes et al.   JOURNAL OF MARINE SYSTEMS

Mining of deep-sea seafloor massive sulfides: A review of the deposits, their benthic communities, impacts from mining, regulatory frameworks and management strategies

(2013) R.E. Boschen et al.   OCEAN & COASTAL MANAGEMENT

From principles to practice: a spatial approach to systematic conservation planning in the deep sea

(2013) L. M. Wedding et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities

(2013) Aibin Zhan et al.   Methods in Ecology and Evolution

Coverage-based rarefaction and extrapolation: standardizing samples by completeness rather than size

(2012) Anne Chao et al.   ECOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Philip Francis Thomsen et al.   PLoS One

Motion, Commotion, and Biophysical Connections at Deep Ocean Seamounts

(2011) J. William Lavelle et al.   OCEANOGRAPHY

A supervised clustering approach for fMRI-based inference of brain states

(2011) Vincent Michel et al.   PATTERN RECOGNITION

Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing

(2011) Jan Pawlowski et al.   PLoS One

The bathypelagic community of Monterey Canyon

(2010) Bruce H. Robison et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Paradigms in seamount ecology: fact, fiction and future

(2010) Ashley A. Rowden et al.   Marine Ecology-An Evolutionary Perspective

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

(2010) C. CORINALDESI et al.   MOLECULAR ECOLOGY

Second-generation environmental sequencing unmasks marine metazoan biodiversity

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

The Ecology of Seamounts: Structure, Function, and Human Impacts

(2009) Malcolm R. Clark et al.   Annual Review of Marine Science

Vertical distribution and relative abundance of gelatinous zooplankton, in situ observations near the Mid-Atlantic Ridge

(2008) M. Youngbluth et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Phylogenetic diversity of cyanobacterialnarBgenes from various marine habitats

(2008) Ryan W. Paerl et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2008) C. CORINALDESI et al.   MOLECULAR ECOLOGY

Abyssal food limitation, ecosystem structure and climate change

(2008) C SMITH et al.   TRENDS IN ECOLOGY & EVOLUTION