Toward a reliable assessment of potential ecological impacts of deep‐sea polymetallic nodule mining on abyssal infauna

Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding

(2021) Miriam I. Brandt et al.   Molecular Ecology Resources

Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA

(2021) Miriam I. Brandt et al.   Scientific Reports

Comparability between box-corer and epibenthic-sledge data on higher taxon level: A case study based on deep-sea samples from the NW Pacific

(2020) Lidia Lins et al.   PROGRESS IN OCEANOGRAPHY

Genus level molecular phylogeny of Aegisthidae Gisbrecht, 1893 (Copepoda: Harpacticoida) reveals morphological adaptations to deep-sea and plagic habitats

(2020) Sahar Khodami et al.   BMC EVOLUTIONARY BIOLOGY

Predicting meiofauna abundance to define preservation and impact zones in a deep-sea mining context using random forest modelling

(2020) Katja Uhlenkott et al.   JOURNAL OF APPLIED ECOLOGY

Unsupervised biodiversity estimation using proteomic fingerprints from MALDI‐TOF MS data

(2020) Sven Rossel et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

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

Two new species of paratanaoid tanaidaceans of the family incertae sedis (Crustacea: Peracarida) from polymetallic nodule fields in the eastern Clarion-Clipperton Fracture Zone

(2020) C. K. CHIM et al.   ZOOTAXA

Macrostylis metallicola spec. nov.—an isopod with geographically clustered genetic variability from a polymetallic-nodule area in the Clarion-Clipperton Fracture Zone

(2020) Torben Riehl et al.   PeerJ

High environmental stress and productivity increase functional diversity along a deep‐sea hydrothermal vent gradient

(2020) JM Alfaro‐Lucas et al.   ECOLOGY

Deep-Sea Misconceptions Cause Underestimation of Seabed-Mining Impacts

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

State of art and best practices for fatty acid analysis in aquatic sciences

(2020) Lydie I E Couturier et al.   ICES JOURNAL OF MARINE SCIENCE

Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities?

(2020) Adrià Antich et al.   MOLECULAR ECOLOGY

Convergent evolution of mouthparts morphology between Siphonostomatoida and a new genus of deep-sea Aegisthidae Giesbrecht, 1893 (Copepoda: Harpacticoida)

(2019) Nancy F. Mercado-Salas et al.   Marine Biodiversity

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

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

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

Role of spatial scales and environmental drivers in shaping nematode communities in the Blanes Canyon and its adjacent slope

(2019) Sara Román et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

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

(2019) Yoann Dufresne et al.   BMC BIOINFORMATICS

sFDvent: A global trait database for deep‐sea hydrothermal‐vent fauna

(2019) Abbie S. A. Chapman et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Revealing higher than expected diversity of Harpacticoida (Crustacea:Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding

(2019) S. Rossel et al.   Scientific Reports

High species richness and unique composition of the tanaidacean communities associated with five areas in the Pacific polymetallic nodule fields

(2019) Magdalena Błażewicz et al.   PROGRESS IN OCEANOGRAPHY

Effects of preservation methodology on stable isotope compositions of sea stars

(2019) Baptiste Le Bourg et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Biogeography and population structure of predominant macrofaunal taxa (Annelida and Isopoda) in abyssal polymetallic nodule fields: implications for conservation and management

(2019) Annika Janssen et al.   Marine Biodiversity

Dark Ophiuroid Biodiversity in a Prospective Abyssal Mine Field

(2019) Magdalini Christodoulou et al.   CURRENT BIOLOGY

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

Deep ocean seascape and Pseudotanaidae (Crustacea: Tanaidacea) diversity at the Clarion-Clipperton Fracture Zone

(2019) Aleksandra Jakiel et al.   Scientific Reports

From metabarcoding to metaphylogeography: separating the wheat from the chaff

(2019) Xavier Turon et al.   ECOLOGICAL APPLICATIONS

Epibenthic sled versus giant box corer – Comparison of sampling gears for tanaidacean species richness assessment in the abyssal benthic ecosystem

(2019) Piotr Jóźwiak et al.   PROGRESS IN OCEANOGRAPHY

Integrative systematics and ecology of a new deep-sea family of tanaidacean crustaceans

(2019) Magdalena Błażewicz et al.   Scientific Reports

High-resolution community analysis of deep-sea copepods using MALDI-TOF protein fingerprinting

(2018) Patricia Kaiser et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Determination of food sources for nematodes in the Kuril Basin and eastern slope of the Kuril Islands by stable isotope and fatty acid analyses

(2018) Vladimir V. Mordukhovich et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

The structure and organisation of integral marine benthic communities in relation to sieve mesh size

(2018) P.J. Somerfield et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Addressing biodiversity shortfalls in meiofauna

(2018) Gustavo Fonseca et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Identification of freshwater zooplankton species using protein profiling and principal component analysis

(2018) Radovan Hynek et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Towards robust and repeatable sampling methods in eDNA-based studies

(2018) Ian A. Dickie et al.   Molecular Ecology Resources

Species identification and connectivity of marine amphipods in Canada’s three oceans

(2018) Astrid Tempestini et al.   PLoS One

Using Biological Insight and Pragmatism When Thinking about Pseudoreplication

(2018) Nick Colegrave et al.   TRENDS IN ECOLOGY & EVOLUTION

Automatic specimen identification of Harpacticoids (Crustacea:Copepoda) using Random Forest and MALDI-TOF mass spectra, including a post hoc test for false positive discovery

(2018) Sven Rossel et al.   Methods in Ecology and Evolution

Characterization of Deep-sea Macrofauna in the Korean Exploration Claim Area in the Clarion-Clipperton Fracture Zone, Northeastern Pacific Ocean

(2018) Ok Hwan Yu et al.   Ocean Science Journal

Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences

(2018) Robert C. Edgar   PeerJ

Metabolic rates are significantly lower in abyssal Holothuroidea than in shallow-water Holothuroidea

(2018) Alastair Brown et al.   Royal Society Open Science

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

Phylogenetic and functional evidence suggests that deep-ocean ecosystems are highly sensitive to environmental change and direct human disturbance

(2018) Oliver S. Ashford et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

OUP accepted manuscript

(2018)   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Impacts of DNA extraction and PCR on DNA metabarcoding estimates of soil biodiversity

(2018) Andrew Dopheide et al.   Methods in Ecology and Evolution

Environmental DNA metabarcoding studies are critically affected by substrate selection

(2018) Adam Koziol et al.   Molecular Ecology Resources

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

(2018) Adrian G Glover et al.   eLife

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

Unravelling diversity of deep-sea copepods using integrated morphological and molecular techniques

(2017) Maya Bode et al.   JOURNAL OF PLANKTON RESEARCH

Mayfly and fish species identification and sex determination in bleak ( Alburnus alburnus ) by MALDI-TOF mass spectrometry

(2017) G. Maasz et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

(2017) Tobias Guldberg Frøslev et al.   Nature Communications

Sorting things out: Assessing effects of unequal specimen biomass on DNA metabarcoding

(2017) Vasco Elbrecht et al.   Ecology and Evolution

Taxonomy assignment approach determines the efficiency of identification of OTUs in marine nematodes

(2017) Oleksandr Holovachov et al.   Royal Society Open Science

Biological responses to disturbance from simulated deep-sea polymetallic nodule mining

(2017) Daniel O. B. Jones et al.   PLoS One

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

(2017) Anders Lanzén et al.   PLoS One

Metabarcoding of marine zooplankton: prospects, progress and pitfalls

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

Proteomics for the authentication of fish species

(2016) Maria Fiorella Mazzeo et al.   Journal of Proteomics

Comparison of sampling methods for deep-sea infauna

(2016) Paul A. Montagna et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Macrofaunal nematodes of the deep Whittard Canyon (NE Atlantic): assemblage characteristics and comparison with polychaetes

(2016) Laetitia M. Gunton et al.   Marine Ecology-An Evolutionary Perspective

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Environmental filtering and neutral processes shape octocoral community assembly in the deep sea

(2016) Andrea M. Quattrini et al.   OECOLOGIA

New Prionospio and Aurospio Species from the Deep Sea (Annelida: Polychaeta)

(2016) GORDON L. J. PATERSON et al.   ZOOTAXA

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

(2016) George D. F. Wilson   Marine Biodiversity

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

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

(2016) Ann Vanreusel et al.   Scientific Reports

Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA

(2015) Kristy Deiner et al.   BIOLOGICAL CONSERVATION

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

(2015) Jarmo Ritari et al.   BMC GENOMICS

High intraspecific variability in the diet of a deep-sea nematode: Stable isotope and fatty acid analyses of Deontostoma tridentum on Chatham Rise, Southwest Pacific

(2015) Daniel Leduc et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Fatty acid compositions and trophic relationships of shelled molluscs from the Kuril–Kamchatka Trench and the adjacent abyssal plain

(2015) Vladimir I. Kharlamenko et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Functional diversity patterns of abyssal nematodes in the Eastern Mediterranean: A comparison between cold seeps and typical deep sea sediments

(2015) V. Kalogeropoulou et al.   JOURNAL OF SEA RESEARCH

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

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

obitools: aunix-inspired software package for DNA metabarcoding

(2015) Frédéric Boyer et al.   Molecular Ecology Resources

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

(2015) Annika Janssen et al.   PLoS One

Nematode community composition and feeding shaped by contrasting productivity regimes in the Southern Ocean

(2015) Lidia Lins et al.   PROGRESS IN OCEANOGRAPHY

Managing mining of the deep seabed

(2015) L. M. Wedding et al.   SCIENCE

MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis

(2015) Neelja Singhal et al.   Frontiers in Microbiology

Is the meiofauna a good indicator for climate change and anthropogenic impacts?

(2015) Daniela Zeppilli et al.   Marine Biodiversity

A practical guide and power analysis for GLMMs: detecting among treatment variation in random effects

(2015) Morgan P. Kain et al.   PeerJ

Meiobenthos and macrobenthos are discrete entities and not artefacts of sampling a size continuum: Comment on Bett (2013)

(2014) RM Warwick   MARINE ECOLOGY PROGRESS SERIES

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

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

Accurate identification of Culicidae at aquatic developmental stages by MALDI-TOF MS profiling

(2014) Constentin Dieme et al.   Parasites & Vectors

Identification of European mosquito species by MALDI-TOF MS

(2014) Amina Yssouf et al.   PARASITOLOGY RESEARCH

Urstylidae - a new family of abyssal isopods (Crustacea: Asellota) and its phylogenetic implications

(2014) Torben Riehl et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Identification of fungal microorganisms by MALDI-TOF mass spectrometry

(2013) Jana Chalupová et al.   BIOTECHNOLOGY ADVANCES

Nematode feeding strategies and the fate of dissolved organic matter carbon in different deep-sea sedimentary environments

(2013) Ellen Pape et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Unusually high food availability in Kaikoura Canyon linked to distinct deep-sea nematode community

(2013) D. Leduc et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Comparison of molecular species identification for North Sea calanoid copepods (Crustacea) using proteome fingerprints and DNA sequences

(2013) S. Laakmann et al.   Molecular Ecology Resources

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

Latitudinal and temporal variability in the community structure and fatty acid composition of deep-sea nematodes in the Southern Ocean

(2013) Katja Guilini et al.   PROGRESS IN OCEANOGRAPHY

Carbon and nitrogen stable isotope signatures of deep-sea meiofauna follow oceanographical gradients across the Southern Ocean

(2013) Gritta Veit-Köhler et al.   PROGRESS IN OCEANOGRAPHY

Discrimination of freshwater fish species by Matrix-Assisted Laser Desorption/Ionization- Time Of Flight Mass Spectrometry (MALDI-TOF MS): a pilot study

(2012) Pietro Volta et al.   JOURNAL OF LIMNOLOGY

Environmental DNA

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

The seven deadly sins of DNA barcoding

(2012) R. A. Collins et al.   Molecular Ecology Resources

Disturbance-diversity models: what do they really predict and how are they tested?

(2012) J. R. Svensson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Sequencing our way towards understanding global eukaryotic biodiversity

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

Deep-sea nematode assemblage has not recovered 26 years after experimental mining of polymetallic nodules (Clarion-Clipperton Fracture Zone, Tropical Eastern Pacific)

(2011) Dmitry M. Miljutin et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

(2011) Jeffrey J Werner et al.   ISME Journal

Comparing isotopic niche widths among and within communities: SIBER - Stable Isotope Bayesian Ellipses in R

(2011) Andrew L. Jackson et al.   JOURNAL OF ANIMAL ECOLOGY

Fatty acids as dietary tracers in benthic food webs

(2011) JR Kelly et al.   MARINE ECOLOGY PROGRESS SERIES

Advances, challenges and a developing synthesis of ecological community assembly theory

(2011) E. Weiher et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Do Meio- and Macrobenthic Nematodes Differ in Community Composition and Body Weight Trends with Depth?

(2011) Jyotsna Sharma et al.   PLoS One

Deep-Sea Nematodes Actively Colonise Sediments, Irrespective of the Presence of a Pulse of Organic Matter: Results from an In-Situ Experiment

(2011) Katja Guilini et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Live (stained) benthic foraminifera in the Whittard Canyon, Celtic margin (NE Atlantic)

(2010) P. Duros et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Diet insights of deep-sea polychaetes derived from fatty acid analyses

(2010) Laura Würzberg et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

A distance-based framework for measuring functional diversity from multiple traits

(2010) Etienne Laliberté et al.   ECOLOGY

Functional diversity measures: an overview of their redundancy and their ability to discriminate community assembly rules

(2010) Maud A. Mouchet et al.   FUNCTIONAL ECOLOGY

Tentative Characterization of New Environmental Giant Viruses by MALDI-TOF Mass Spectrometry

(2010) Bernard La Scola et al.   INTERVIROLOGY

Diversity of larger free-living nematodes from macrobenthos (>250 μm) in the Arctic deep-sea Canada Basin

(2010) Jyotsna Sharma et al.   Marine Biodiversity

Species Distribution Models: Ecological Explanation and Prediction Across Space and Time

(2009) Jane Elith et al.   Annual Review of Ecology Evolution and Systematics

Effects of preservatives on stable isotope analyses of four marine species

(2009) Sirka Carabel et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Composition of macrobenthos from the Central Indian Ocean Basin

(2009) S. Pavithran et al.   Journal of Earth System Science

Deep-sea nematode assemblages of the Clarion-Clipperton Nodule Province (Tropical North-Eastern Pacific)

(2009) Maria A. Miljutina et al.   Marine Biodiversity

Metazoan meiofauna biomass, grazing, and weight-dependent respiration in the Northern Gulf of Mexico deep sea

(2008) Jeffrey G. Baguley et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

NEW MULTIDIMENSIONAL FUNCTIONAL DIVERSITY INDICES FOR A MULTIFACETED FRAMEWORK IN FUNCTIONAL ECOLOGY

(2008) Sébastien Villéger et al.   ECOLOGY

Description of Oncholaimus moanae sp. nov. (Nematoda: Oncholaimidae), with notes on feeding ecology based on isotopic and fatty acid composition

(2008) Daniel Leduc   JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM

Abyssal food limitation, ecosystem structure and climate change

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