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

Patterns of Macrofaunal Biodiversity Across the Clarion-Clipperton Zone: An Area Targeted for Seabed Mining

(2021) Travis W. Washburn et al.   Frontiers in Marine Science

The Biodiversity and Distribution of Abyssal Benthic Foraminifera and Their Possible Ecological Roles: A Synthesis Across the Clarion-Clipperton Zone

(2021) Andrew J. Gooday et al.   Frontiers in Marine Science

Climate‐induced changes in the suitable habitat of cold‐water corals and commercially important deep‐sea fishes in the North Atlantic

(2020) Telmo Morato et al.   GLOBAL CHANGE BIOLOGY

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

High diversity and pan-oceanic distribution of deep-sea polychaetes: Prionospio and Aurospio (Annelida: Spionidae) in the Atlantic and Pacific Ocean

(2020) Theresa Guggolz et al.   ORGANISMS DIVERSITY & EVOLUTION

Correction: Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform

(2020)   PLoS One

Digenean parasites of deep-sea teleosts: A progress report

(2020) Rodney A. Bray   International Journal for Parasitology-Parasites and Wildlife

Environmental DNA surveys detect distinct metazoan communities across abyssal plains and seamounts in the western Clarion Clipperton Zone

(2020) Olivier Laroche et al.   MOLECULAR ECOLOGY

Phylogenetic clustering and rarity imply risk of local species extinction in prospective deep-sea mining areas of the Clarion–Clipperton Fracture Zone

(2020) Lara Macheriotou et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Effects of a deep-sea mining experiment on seafloor microbial communities and functions after 26 years

(2020) T. R. Vonnahme et al.   Science Advances

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

Climate change considerations are fundamental to management of deep‐sea resource extraction

(2020) Lisa A. Levin et al.   GLOBAL CHANGE BIOLOGY

Perspectives from Ten Years of Protist Studies by High‐Throughput Metabarcoding

(2020) Luciana Santoferrara et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Discovery of widely available abyssal rock patches reveals overlooked habitat type and prompts rethinking deep-sea biodiversity

(2020) Torben Riehl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The heterogeneous abyss

(2020) Craig R. Smith   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Subtle variation in abyssal terrain induces significant change in benthic megafaunal abundance, diversity, and community structure

(2020) Jennifer M. Durden et al.   PROGRESS IN OCEANOGRAPHY

Deep-Sea Misconceptions Cause Underestimation of Seabed-Mining Impacts

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

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

Meiofauna Life on Loggerhead Sea Turtles-Diversely Structured Abundance and Biodiversity Hotspots That Challenge the Meiofauna Paradox

(2020) Jeroen Ingels et al.   Diversity-Basel

Challenges to the sustainability of deep-seabed mining

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

Large scale patterns of marine diatom richness: Drivers and trends in a changing ocean

(2020) Greta Busseni et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Benthic monitoring of oil and gas offshore platforms in the North Sea using environmental DNA metabarcoding

(2020) Florian Mauffrey et al.   MOLECULAR ECOLOGY

Significant taxon sampling gaps in DNA databases limit the operational use of marine macrofauna metabarcoding

(2020) Jon Thomassen Hestetun et al.   Marine Biodiversity

Sedimentary DNA tracks decadal-centennial changes in fish abundance

(2020) Michinobu Kuwae et al.   Communications Biology

Metabarcoding on both environmental DNA and RNA highlights differences between fungal communities sampled in different habitats

(2020) Martino Adamo et al.   PLoS One

Using Habitat Classification to Assess Representativity of a Protected Area Network in a Large, Data-Poor Area Targeted for Deep-Sea Mining

(2020) Kirsty A. McQuaid et al.   Frontiers in Marine Science

A Novel Sparse Compositional Technique Reveals Microbial Perturbations

(2019) Cameron Martino et al.   mSystems

Metabarcoding free‐living marine nematodes using curated 18S and CO1 reference sequence databases for species‐level taxonomic assignments

(2019) Lara Macheriotou et al.   Ecology and Evolution

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

(2019) Yoann Dufresne et al.   BMC BIOINFORMATICS

Diversity and spatial patterns of foraminiferal assemblages in the eastern Clarion–Clipperton zone (abyssal eastern equatorial Pacific)

(2019) Aurélie Goineau et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Can Environmental RNA Revolutionize Biodiversity Science?

(2019) Melania E. Cristescu   TRENDS IN ECOLOGY & EVOLUTION

Marked changes in diversity and relative activity of picoeukaryotes with depth in the world ocean

(2019) Caterina R. Giner et al.   ISME Journal

Release and degradation of environmental DNA and RNA in a marine system

(2019) Susanna A. Wood et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Abyssal fauna of polymetallic nodule exploration areas, eastern Clarion-Clipperton Zone, central Pacific Ocean: Annelida: Capitellidae, Opheliidae, Scalibregmatidae, and Travisiidae

(2019) Helena Wiklund et al.   ZooKeys

Insights into the ecology of epibenthic calcareous foraminifera from a colonization study at 4000 m (Station M) in the NE Pacific Ocean

(2019) Ashley Burkett et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Understanding sequencing data as compositions: an outlook and review

(2018) Thomas P Quinn et al.   BIOINFORMATICS

Supervised machine learning outperforms taxonomy-based environmental DNA metabarcoding applied to biomonitoring

(2018) Tristan Cordier et al.   Molecular Ecology Resources

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Habitat filtering of bacterioplankton communities above polymetallic nodule fields and sediments in the Clarion-Clipperton zone of the Pacific Ocean

(2018) Markus V. Lindh et al.   Environmental Microbiology Reports

Extracellular DNA as a genetic recorder of microbial diversity in benthic deep-sea ecosystems

(2018) C. Corinaldesi et al.   Scientific Reports

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

(2018) Stefan Janssen et al.   mSystems

American Gut: an Open Platform for Citizen Science Microbiome Research

(2018) Daniel McDonald et al.   mSystems

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

Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks

(2018) Eva Aylagas et al.   ECOLOGICAL INDICATORS

Diversity and distribution of peracarid crustaceans (Malacostraca) from the abyss adjacent to the Kuril-Kamchatka Trench

(2018) Olga A. Golovan et al.   Marine Biodiversity

Striped UniFrac: enabling microbiome analysis at unprecedented scale

(2018) Daniel McDonald et al.   NATURE METHODS

Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring

(2018) Tristan Cordier et al.   TRENDS IN MICROBIOLOGY

Managing a sustainable deep-sea ‘blue economy’ requires knowledge of what actually lives there

(2018) Adrian G Glover et al.   eLife

An updated classification of rotaliid foraminifera based on ribosomal DNA phylogeny

(2017) Maria Holzmann et al.   MARINE MICROPALEONTOLOGY

Abyssal fauna of the UK-1 polymetallic nodule exploration area, Clarion-Clipperton Zone, central Pacific Ocean: Mollusca

(2017) Helena Wiklund et al.   ZooKeys

Marine biogeographic realms and species endemicity

(2017) Mark J. Costello et al.   Nature Communications

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

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

Balance Trees Reveal Microbial Niche Differentiation

(2017) James T. Morton et al.   mSystems

DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments

(2017) Anders Lanzén et al.   PLoS One

Novel benthic foraminifera are abundant and diverse in an area of the abyssal equatorial Pacific licensed for polymetallic nodule exploration

(2017) Aurélie Goineau et al.   Scientific Reports

It's all relative: analyzing microbiome data as compositions

(2016) Gregory B. Gloor et al.   ANNALS OF EPIDEMIOLOGY

The distribution of deep-sea sponge aggregations in the North Atlantic and implications for their effective spatial management

(2016) Kerry-Louise Howell et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

First evaluation of foraminiferal metabarcoding for monitoring environmental impact from an offshore oil drilling site

(2016) Olivier Laroche et al.   MARINE ENVIRONMENTAL RESEARCH

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

(2016) Anders Lanzén et al.   MOLECULAR ECOLOGY

New deep-sea species of Xenoturbella and the position of Xenacoelomorpha

(2016) Greg W. Rouse et al.   NATURE

Abyssal hills: Influence of topography on benthic foraminiferal assemblages

(2016) Paris V. Stefanoudis et al.   PROGRESS IN OCEANOGRAPHY

Macrofauna abundance, species diversity and turnover at three sites in the Clipperton-Clarion Fracture Zone

(2016) George D. F. Wilson   Marine Biodiversity

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

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

The German–Russian deep-sea expedition KuramBio (Kurile Kamchatka biodiversity studies) on board of the RV Sonne in 2012 following the footsteps of the legendary expeditions with RV Vityaz

(2015) Angelika Brandt et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Manganese-Cycling Microbial Communities Inside Deep-Sea Manganese Nodules

(2015) Marco Blöthe et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

An abyssal hill fractionates organic and inorganic matter in deep-sea surface sediments

(2015) Robert Turnewitsch et al.   GEOPHYSICAL RESEARCH LETTERS

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

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

PFR2: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution

(2015) Raphaël Morard et al.   Molecular Ecology Resources

Accurate multiplexing and filtering for high-throughput amplicon-sequencing

(2015) Philippe Esling et al.   NUCLEIC ACIDS RESEARCH

A Reverse Taxonomic Approach to Assess Macrofaunal Distribution Patterns in Abyssal Pacific Polymetallic Nodule Fields

(2015) Annika Janssen et al.   PLoS One

The deep ocean under climate change

(2015) Lisa A. Levin et al.   SCIENCE

Swarm v2: highly-scalable and high-resolution amplicon clustering

(2015) Frédéric Mahé et al.   PeerJ

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

(2015) Magdalena Guardiola 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

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

Intensity of pelagic–benthic coupling in different regions along the Antarctic Polar Front – Clues from abyssal megafauna

(2014) Laura Würzberg 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

The biodiversity of species and their rates of extinction, distribution, and protection

(2014) S. L. Pimm et al.   SCIENCE

Ancient DNA complements microfossil record in deep-sea subsurface sediments

(2013) F. Lejzerowicz et al.   Biology Letters

Community structure and species diversity of Harpacticoida (Crustacea: Copepoda) at two sites in the deep sea of the Angola Basin (Southeast Atlantic)

(2013) Kai Horst George et al.   ORGANISMS DIVERSITY & EVOLUTION

marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R

(2013) Eric Pante et al.   PLoS One

Evolution of the plankton paleome in the Black Sea from the Deglacial to Anthropocene

(2013) M. J. L. Coolen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

EMPeror: a tool for visualizing high-throughput microbial community data

(2013) Yoshiki Vázquez-Baeza et al.   GigaScience

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

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

Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing

(2012) Ramiro Logares et al.   ISME Journal

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Structure, function and diversity of the healthy human microbiome

(2012)   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

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Deep-ocean mineral deposits as a source of critical metals for high- and green-technology applications: Comparison with land-based resources

(2012) James R. Hein et al.   ORE GEOLOGY REVIEWS

A proposed biogeography of the deep ocean floor

(2012) Les Watling et al.   PROGRESS IN OCEANOGRAPHY

Services from the deep: Steps towards valuation of deep sea goods and services

(2012) Claire W. Armstrong et al.   Ecosystem Services

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Submarine ridges do not prevent large-scale dispersal of abyssal fauna: A case study of Mesocletodes (Crustacea, Copepoda, Harpacticoida)

(2011) Lena Menzel et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

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

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

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

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

Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA

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

Short rDNA Barcodes for Species Identification in Foraminifera

(2010) JAN PAWLOWSKI et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

The dynamics of biogeographic ranges in the deep sea

(2010) C. R. McClain et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Molecular analyses reveal high levels of eukaryotic richness associated with enigmatic deep-sea protists (Komokiacea)

(2009) B. Lecroq et al.   Marine Biodiversity

Abyssal food limitation, ecosystem structure and climate change

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