Patterns of eukaryotic diversity from the surface to the deep-ocean sediment

Microbial dynamics of elevated carbon flux in the open ocean’s abyss

(2021) Kirsten E. Poff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes

(2021) L. Armbrecht et al.   Scientific Reports

Eukaryotic Biodiversity and Spatial Patterns in the Clarion-Clipperton Zone and Other Abyssal Regions: Insights From Sediment DNA and RNA Metabarcoding

(2021) Franck Lejzerowicz et al.   Frontiers in Marine Science

A metagenomic assessment of microbial eukaryotic diversity in the global ocean

(2020) Aleix Obiol et al.   Molecular Ecology Resources

Ecological variables for developing a global deep-ocean monitoring and conservation strategy

(2020) Roberto Danovaro et al.   Nature Ecology & Evolution

Extraordinary diversity of viruses in deep‐sea sediments as revealed by metagenomics without prior virion separation

(2020) Xiaowei Zheng et al.   ENVIRONMENTAL MICROBIOLOGY

Protist diversity and function in the dark ocean – Challenging the paradigms of deep-sea ecology with special emphasis on foraminiferans and naked protists

(2020) Andrew J. Gooday et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Deep-Sea Misconceptions Cause Underestimation of Seabed-Mining Impacts

(2020) Craig R. Smith et al.   TRENDS IN ECOLOGY & EVOLUTION

Challenges to the sustainability of deep-seabed mining

(2020) Lisa A. Levin et al.   Nature Sustainability

Global diversity of microbial communities in marine sediment

(2020) Tatsuhiko Hoshino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2020) Olivier Laroche et al.   Frontiers in Marine Science

Ecological variables for deep-ocean monitoring must include microbiota and meiofauna for effective conservation

(2020) Jeroen Ingels et al.   Nature Ecology & Evolution

SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data

(2019) Yoann Dufresne et al.   BMC BIOINFORMATICS

Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants

(2019) Dominik Forster et al.   ENVIRONMENTAL MICROBIOLOGY

The potential of sedimentary ancient DNA for reconstructing past sea ice evolution

(2019) Stijn De Schepper et al.   ISME Journal

Effects of intragenomic polymorphism in the SSU rRNA gene on estimating marine microeukaryotic diversity: A test for ciliates using single‐cell high‐throughput DNA sequencing

(2019) Feng Zhao et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Global Trends in Marine Plankton Diversity across Kingdoms of Life

(2019) Federico M. Ibarbalz et al.   CELL

DNA metabarcoding reveals organisms contributing to particulate matter flux to abyssal depths in the North East Pacific ocean

(2019) Christina M. Preston et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Phytoplankton size diversity and ecosystem function relationships across oceanic regions

(2018) Esteban Acevedo-Trejos et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Declining oxygen in the global ocean and coastal waters

(2018) Denise Breitburg et al.   SCIENCE

Biogeography and diversity of Collodaria (Radiolaria) in the global ocean

(2017) Tristan Biard et al.   ISME Journal

ranger: A Fast Implementation of Random Forests for High Dimensional Data in C++ and R

(2017) Marvin N. Wright et al.   Journal of Statistical Software

Revealing higher than expected meiofaunal diversity in Antarctic sediments: a metabarcoding approach

(2017) V. G. Fonseca et al.   Scientific Reports

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

From the Surface to the Deep-Sea: Bacterial Distributions across Polymetallic Nodule Fields in the Clarion-Clipperton Zone of the Pacific Ocean

(2017) Markus V. Lindh et al.   Frontiers in Microbiology

Microbial Eukaryote Diversity and Activity in the Water Column of the South China Sea Based on DNA and RNA High Throughput Sequencing

(2017) Dapeng Xu et al.   Frontiers in Microbiology

Extreme Diversity of Diplonemid Eukaryotes in the Ocean

(2016) Olga Flegontova et al.   CURRENT BIOLOGY

Fossil DNA persistence and decay in marine sediment over hundred-thousand-year to million-year time scales

(2016) John B. Kirkpatrick et al.   GEOLOGY

Plankton networks driving carbon export in the oligotrophic ocean

(2016) Lionel Guidi et al.   NATURE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

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

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems

(2016) R. Danovaro et al.   Science Advances

Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria

(2016) Christina Bienhold et al.   PLoS One

Seafloor heterogeneity influences the biodiversity–ecosystem functioning relationships in the deep sea

(2016) Daniela Zeppilli et al.   Scientific Reports

Toward a Conceptual Understanding of β-Diversity in the Deep-Sea Benthos

(2015) Craig R. McClain et al.   Annual Review of Ecology Evolution and Systematics

A new look at ocean carbon remineralization for estimating deepwater sequestration

(2015) Lionel Guidi et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans

(2015) Massimo C Pernice et al.   ISME Journal

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

The deep ocean under climate change

(2015) Lisa A. Levin et al.   SCIENCE

Ubiquitous healthy diatoms in the deep sea confirm deep carbon injection by the biological pump

(2015) S. Agusti et al.   Nature Communications

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

Patchiness of deep-sea benthic Foraminifera across the Southern Ocean: Insights from high-throughput DNA sequencing

(2014) Franck Lejzerowicz et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

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

Ecology: Protect the deep sea

(2014) Edward B. Barbier et al.   NATURE

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

A Call for Deep-Ocean Stewardship

(2014) K. J. Mengerink et al.   SCIENCE

Diversity and distribution of microbial eukaryotes in the deep tropical and subtropical North Atlantic Ocean

(2013) Danielle Morgan-Smith et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

The biogeography of marine plankton traits

(2013) Andrew D. Barton et al.   ECOLOGY LETTERS

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

A proposed biogeography of the deep ocean floor

(2012) Les Watling et al.   PROGRESS IN OCEANOGRAPHY

A reduced estimate of the strength of the ocean's biological carbon pump

(2011) Stephanie A. Henson et al.   GEOPHYSICAL RESEARCH LETTERS

Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing

(2011) Jan Pawlowski et al.   PLoS One

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems

(2011) Lucie Zinger 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

Local-scale faunal turnover on the deep Pacific seafloor

(2010) CR McClain et al.   MARINE ECOLOGY PROGRESS SERIES

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

(2010) Roberto Danovaro et al.   PLoS One

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

(2009) Linda A. Amaral-Zettler et al.   PLoS One

Pan-oceanic distribution of new highly diverse clades of deep-sea diplonemids

(2008) Enrique Lara et al.   ENVIRONMENTAL MICROBIOLOGY

Abyssal food limitation, ecosystem structure and climate change

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