Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient

Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity

(2018) Michal Stat et al.   CONSERVATION BIOLOGY

Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority

(2018) J. K. Pearman et al.   Scientific Reports

Urban coral reefs: Degradation and resilience of hard coral assemblages in coastal cities of East and Southeast Asia

(2018) Eliza C. Heery et al.   MARINE POLLUTION BULLETIN

Environmental DNA metabarcoding studies are critically affected by substrate selection

(2018) Adam Koziol et al.   Molecular Ecology Resources

Stolonifera from shallow waters in the north-western Pacific: a description of a new genus and two new species within the Arulidae (Anthozoa, Octocorallia)

(2018) Yee Wah Lau et al.   ZooKeys

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

(2017) Michael Stat et al.   Scientific Reports

Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan

(2017) Taha Soliman et al.   Frontiers in Microbiology

Spatial distribution of environmental DNA in a nearshore marine habitat

(2017) James L. O’Donnell et al.   PeerJ

The importance of standardization for biodiversity comparisons: A case study using autonomous reef monitoring structures (ARMS) and metabarcoding to measure cryptic diversity on Mo’orea coral reefs, French Polynesia

(2017) Emma Ransome et al.   PLoS One

Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding

(2017) Elizabeth A. Andruszkiewicz et al.   PLoS One

Environmental DNA reveals tropical shark diversity in contrasting levels of anthropogenic impact

(2017) Judith Bakker et al.   Scientific Reports

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

Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea

(2016) Mamoon M.D. Al-Rshaidat et al.   GENOME

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

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

(2016) Magdalena Guardiola et al.   PeerJ

Coral mucus fuels the sponge loop in warm- and cold-water coral reef ecosystems

(2016) Laura Rix et al.   Scientific Reports

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

(2015) Andrea Torti et al.   Marine Genomics

Effects of causeway construction on environment and biota of subtropical tidal flats in Okinawa, Japan

(2015) James Davis Reimer et al.   MARINE POLLUTION BULLETIN

Accurate multiplexing and filtering for high-throughput amplicon-sequencing

(2015) Philippe Esling et al.   NUCLEIC ACIDS RESEARCH

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

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows

(2015) Dáithí C. Murray et al.   PLoS One

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

(2015) Magdalena Guardiola et al.   PLoS One

Fishes associated with mesophotic coral ecosystems in La Parguera, Puerto Rico

(2014) I. Bejarano et al.   CORAL REEFS

Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes

(2014) Vera G. Fonseca et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Fast-Evolving Mitochondrial DNA in Ceriantharia: A Reflection of Hexacorallia Paraphyly?

(2014) Sérgio N. Stampar et al.   PLoS One

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Sharing the slope: depth partitioning of agariciid corals and associated Symbiodinium across shallow and mesophotic habitats (2-60 m) on a Caribbean reef

(2013) Pim Bongaerts et al.   BMC EVOLUTIONARY BIOLOGY

Phylogeny and Systematics of Demospongiae in Light of New Small-Subunit Ribosomal DNA (18S) Sequences

(2013) N. E. Redmond et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Species-Specific Responses of Corals to Bleaching Events on Anthropogenically Turbid Reefs on Okinawa Island, Japan, over a 15-year Period (1995–2009)

(2013) Chuki Hongo et al.   PLoS One

Evaluating Detection Limits of Next-Generation Sequencing for the Surveillance and Monitoring of International Marine Pests

(2013) Xavier Pochon et al.   PLoS One

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

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

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Patterns of Diversity in Soft-Bodied Meiofauna: Dispersal Ability and Body Size Matter

(2012) Marco Curini-Galletti et al.   PLoS One

Global Diversity of Sponges (Porifera)

(2012) Rob W. M. Van Soest et al.   PLoS One

Different zooxanthellae types in populations of the zoanthid Zoanthus sansibaricus along depth gradients in Okinawa, Japan

(2012) Minaho Kamezaki et al.   Marine Biodiversity

Changes in scleractinian coral Seriatopora hystrix morphology and its endocellular Symbiodinium characteristics along a bathymetric gradient from shallow to mesophotic reef

(2011) O. Nir et al.   CORAL REEFS

Connectivity and stability of mesophotic coral reefs

(2011) M. Slattery et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Photoacclimatization by the coral Montastraea cavernosa in the mesophotic zone: light, food, and genetics

(2010) Michael P. Lesser et al.   ECOLOGY

Global patterns and predictors of marine biodiversity across taxa

(2010) Derek P. Tittensor et al.   NATURE

Second-generation environmental sequencing unmasks marine metazoan biodiversity

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

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

Ecology of mesophotic coral reefs

(2009) Michael P. Lesser et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Slow Mitochondrial COI Sequence Evolution at the Base of the Metazoan Tree and Its Implications for DNA Barcoding

(2008) Danwei Huang et al.   JOURNAL OF MOLECULAR EVOLUTION

Descending to the twilight-zone: changes in coral reef fish assemblages along a depth gradient down to 65 m

(2008) E Brokovich et al.   MARINE ECOLOGY PROGRESS SERIES

Distribution and Possible Impacts of Toxic Organic Pollutants on Coral Reef Ecosystems around Okinawa Island, Japan1

(2008) S. T. Imo et al.   PACIFIC SCIENCE