Influence of Regional Oceanography and Hydrothermal Activity on Protist Diversity and Community Structure in the Okinawa Trough

A metagenomic assessment of microbial eukaryotic diversity in the global ocean

(2020) Aleix Obiol et al.   Molecular Ecology Resources

Ciliate diversity and distribution across horizontal and vertical scales in the open ocean

(2020) Oriol Canals et al.   MOLECULAR ECOLOGY

Compositional characteristics and sources of DIC and DOC in seawater of the Okinawa Trough, East China Sea

(2019) Xianrong Zhang et al.   CONTINENTAL SHELF RESEARCH

SSU-rRNA Gene Sequencing Survey of Benthic Microbial Eukaryotes from Guaymas Basin Hydrothermal Vent

(2019) Alexis Pasulka et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally

(2019) Gregory J. Dick   NATURE REVIEWS MICROBIOLOGY

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

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

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

Insights into protist diversity and biogeography in intertidal sediments sampled across a range of spatial scales

(2019) Yongbo Pan et al.   LIMNOLOGY AND OCEANOGRAPHY

Temporal and Spatial Scales of Correlation in Marine Phytoplankton Communities

(2019) A. M. Kuhn et al.   JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS

EukRef-Ciliophora: a manually curated, phylogeny-based database of small subunit rRNA gene sequences of ciliates

(2018) Vittorio Boscaro et al.   ENVIRONMENTAL MICROBIOLOGY

A large-scale view of oceanic variability from 2007 to 2015 in the global high resolution monitoring and forecasting system at Mercator Océan

(2018) Florent Gasparin et al.   JOURNAL OF MARINE SYSTEMS

Consistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists

(2018) Guillaume Lentendu et al.   MOLECULAR ECOLOGY

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Intra-host Symbiont Diversity and Extended Symbiont Maintenance in Photosymbiotic Acantharea (Clade F)

(2018) Margaret Mars Brisbin et al.   Frontiers in Microbiology

A globally distributed Syndiniales parasite dominates the Southern Ocean micro-eukaryote community near the sea-ice edge

(2018) Laurence J. Clarke et al.   ISME Journal

Dispersal of Hydrothermal Vent Larvae at East Pacific Rise 9-10°N Segment

(2018) Guangyu Xu et al.   JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS

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

(2017) Benjamin J Callahan et al.   ISME Journal

Contrasting the relative importance of species sorting and dispersal limitation in shaping marine bacterial versus protist communities

(2017) Wenxue Wu et al.   ISME Journal

Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea)

(2017) Luciana F. Santoferrara et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Microbiome Datasets Are Compositional: And This Is Not Optional

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

It's all relative: analyzing microbiome data as compositions

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

Marine protist associations and environmental impacts across trophic levels in the twilight zone and below

(2016) VP Edgcomb   CURRENT OPINION IN MICROBIOLOGY

Molecular diversity and distribution pattern of ciliates in sediments from deep-sea hydrothermal vents in the Okinawa Trough and adjacent sea areas

(2016) Feng Zhao et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Geochemical characteristics of hydrothermal fluids at Hatoma Knoll in the southern Okinawa Trough

(2016) Tomohiro Toki et al.   GEOCHEMICAL JOURNAL

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Quantifying dispersal from hydrothermal vent fields in the western Pacific Ocean

(2016) Satoshi Mitarai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) Massimo C Pernice et al.   ISME Journal

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

An adaptive, Courant-number-dependent implicit scheme for vertical advection in oceanic modeling

(2015) Alexander F. Shchepetkin   OCEAN MODELLING

Post-Drilling Changes in Seabed Landscape and Megabenthos in a Deep-Sea Hydrothermal System, the Iheya North Field, Okinawa Trough

(2015) Ryota Nakajima et al.   PLoS One

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

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

Diversity and abundance of haptophytes in the East China Sea

(2014) YC Lin et al.   AQUATIC MICROBIAL ECOLOGY

The rise and fall of Picobiliphytes: How assumed autotrophs turned out to be heterotrophs

(2014) David Moreira et al.   BIOESSAYS

Scale evolution in Paraphysomonadida (Chrysophyceae): Sequence phylogeny and revised taxonomy of Paraphysomonas, new genus Clathromonas, and 25 new species

(2014) Josephine Margaret Scoble et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Observations of flow variability through the Kerama Gap between the East China Sea and the Northwestern Pacific

(2014) Hanna Na et al.   JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS

Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles

(2013) Ramon Massana et al.   ISME Journal

Diversity and Distributional Patterns of Ciliates in Guaymas Basin Hydrothermal Vent Sediments

(2013) Kathryn J. Coyne et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Phylogenetic diversity of eukaryotic marine microbial plankton on the Scotian Shelf Northwestern Atlantic Ocean

(2013) Cindy R. Dasilva et al.   JOURNAL OF PLANKTON RESEARCH

Picomonas judraskeda Gen. Et Sp. Nov.: The First Identified Member of the Picozoa Phylum Nov., a Widespread Group of Picoeukaryotes, Formerly Known as ‘Picobiliphytes’

(2013) Ramkumar Seenivasan et al.   PLoS One

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Biogeography of Persephonella in deep-sea hydrothermal vents of the Western Pacific

(2013) Sayaka Mino et al.   Frontiers in Microbiology

Intermediate and deep water formation in the Okinawa Trough

(2013) Hirohiko Nakamura et al.   JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS

Effect of oxygen minimum zone formation on communities of marine protists

(2012) William Orsi et al.   ISME Journal

Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank

(2012) Sean P Jungbluth et al.   ISME Journal

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

Morphological description of three marine ciliates (Ciliophora, Scuticociliatia), with establishment of a new genus and two new species

(2011) Xinpeng Fan et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness

(2011) Virginia Edgcomb et al.   ISME Journal

Protist community composition during spring in an Arctic flaw lead polynya

(2011) Ramon Terrado et al.   POLAR BIOLOGY

Drivers of bacterial  -diversity depend on spatial scale

(2011) J. B. H. Martiny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eukaryotic Picoplankton in Surface Oceans

(2010) Ramon Massana   Annual Review of Microbiology

Emerging concepts on microbial processes in the bathypelagic ocean – ecology, biogeochemistry, and genomics

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

Comparative analysis between protist communities from the deep-sea pelagic ecosystem and specific deep hydrothermal habitats

(2010) Anne-Laure Sauvadet et al.   ENVIRONMENTAL MICROBIOLOGY

Interaction between the East China Sea Kuroshio and the Ryukyu Current as revealed by the self-organizing map

(2010) Baogang Jin et al.   JOURNAL OF GEOPHYSICAL RESEARCH

Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing

(2010) HÉLÈNE AGOGUÉ et al.   MOLECULAR ECOLOGY

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

Testing the significance of canonical axes in redundancy analysis

(2010) Pierre Legendre et al.   Methods in Ecology and Evolution

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Quantifying connectivity in the coastal ocean with application to the Southern California Bight

(2009) S. Mitarai et al.   JOURNAL OF GEOPHYSICAL RESEARCH

Groups without Cultured Representatives Dominate Eukaryotic Picophytoplankton in the Oligotrophic South East Pacific Ocean

(2009) Xiao Li Shi et al.   PLoS One

Widespread occurrence and genetic diversity of marine parasitoids belonging toSyndiniales(Alveolata)

(2008) L. Guillou et al.   ENVIRONMENTAL MICROBIOLOGY

Use of stable isotope-labelled cells to identify active grazers of picocyanobacteria in ocean surface waters

(2008) Jorge Frias-Lopez et al.   ENVIRONMENTAL MICROBIOLOGY