Tara Oceans: towards global ocean ecosystems biology

Phytoplankton in the Tara Ocean

(2020) Juan José Pierella Karlusich et al.   Annual Review of Marine Science

Phage-specific metabolic reprogramming of virocells

(2020) Cristina Howard-Varona et al.   ISME Journal

Community-Level Responses to Iron Availability in Open Ocean Planktonic Ecosystems

(2019) Luigi Caputi et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Microbial abundance, activity and population genomic profiling with mOTUs2

(2019) Alessio Milanese et al.   Nature Communications

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands

(2019) Joanna Warwick-Dugdale et al.   PeerJ

Scientists’ warning to humanity: microorganisms and climate change

(2019) Ricardo Cavicchioli et al.   NATURE REVIEWS MICROBIOLOGY

Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host

(2019) Takuro Nakayama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MerMAIDs: a family of metagenomically discovered marine anion-conducting and intensely desensitizing channelrhodopsins

(2019) Johannes Oppermann et al.   Nature Communications

Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems

(2019) M. E. Sieracki et al.   Scientific Reports

The Tara Pacific expedition—A pan-ecosystemic approach of the “-omics” complexity of coral reef holobionts across the Pacific Ocean

(2019) Serge Planes et al.   PLOS BIOLOGY

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

(2019) Guillem Salazar et al.   CELL

Global Trends in Marine Plankton Diversity across Kingdoms of Life

(2019) Federico M. Ibarbalz et al.   CELL

Ecological and functional capabilities of an uncultured Kordia sp.

(2019) M. Royo-Llonch et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Assessing the Diversity and Distribution of Apicomplexans in Host and Free-Living Environments Using High-Throughput Amplicon Data and a Phylogenetically Informed Reference Framework

(2019) Javier del Campo et al.   Frontiers in Microbiology

Marine microbes in 4D — using time series observation to assess the dynamics of the ocean microbiome and its links to ocean health

(2018) Pier Luigi Buttigieg et al.   CURRENT OPINION IN MICROBIOLOGY

The epibiotic life of the cosmopolitan diatom Fragilariopsis doliolus on heterotrophic ciliates in the open ocean

(2018) Flora J. Vincent et al.   ISME Journal

Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan

(2018) Takashi Yoshida et al.   ISME Journal

Taxon Richness of “Megaviridae” Exceeds those of Bacteria and Archaea in the Ocean

(2018) Tomoko Mihara et al.   MICROBES AND ENVIRONMENTS

Marine biodiversity and the chessboard of life

(2018) Grégory Beaugrand et al.   PLoS One

Light color acclimation is a key process in the global ocean distribution ofSynechococcus cyanobacteria

(2018) Théophile Grébert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The biomass distribution on Earth

(2018) Yinon M. Bar-On et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export

(2018) Karine Leblanc et al.   Nature Communications

High resolution time series reveals cohesive but short-lived communities in coastal plankton

(2018) Antonio M. Martin-Platero et al.   Nature Communications

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

(2018) Yoann Seeleuthner et al.   Nature Communications

A global ocean atlas of eukaryotic genes

(2018) Quentin Carradec et al.   Nature Communications

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

(2018) Benjamin J. Tully et al.   Scientific Data

Coccolithovirus facilitation of carbon export in the North Atlantic

(2018) Christien P. Laber et al.   Nature Microbiology

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

(2018) Tom O. Delmont et al.   Nature Microbiology

UCYN-A3, a newly characterized open ocean sublineage of the symbiotic N2 -fixing cyanobacterium Candidatus Atelocyanobacterium thalassa

(2018) Francisco M. Cornejo-Castillo et al.   ENVIRONMENTAL MICROBIOLOGY

A distinct abundant group of microbial rhodopsins discovered using functional metagenomics

(2018) Alina Pushkarev et al.   NATURE

Deep mitochondrial origin outside the sampled alphaproteobacteria

(2018) Joran Martijn et al.   NATURE

Oceanographic boundaries constrain microbial diversity gradients in the South Pacific Ocean

(2018) Eric J. Raes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters

(2018) Yanze Li et al.   Viruses-Basel

Marine microbial metagenomes sampled across space and time

(2018) Steven J. Biller et al.   Scientific Data

Worldwide Occurrence and Activity of the Reef-Building Coral Symbiont Symbiodinium in the Open Ocean

(2018) Johan Decelle et al.   CURRENT BIOLOGY

Discovering Millions of Plankton Genomic Markers from the Atlantic Ocean and the Mediterranean Sea

(2018) Majda Arif et al.   Molecular Ecology Resources

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

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

(2017) Tristan Biard et al.   ISME Journal

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

(2017) Benjamin J Callahan et al.   ISME Journal

New insights into global biogeography, population structure and natural selection from the genome of the epipelagic copepod Oithona

(2017) Mohammed-Amin Madoui et al.   MOLECULAR ECOLOGY

Influence of diatom diversity on the ocean biological carbon pump

(2017) Paul Tréguer et al.   Nature Geoscience

Virus taxonomy in the age of metagenomics

(2017) Peter Simmonds et al.   NATURE REVIEWS MICROBIOLOGY

Single-virus genomics reveals hidden cosmopolitan and abundant viruses

(2017) Francisco Martinez-Hernandez et al.   Nature Communications

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data

(2017) Zachary S. L. Foster et al.   PLoS Computational Biology

Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes

(2017) Sebastien Colin et al.   eLife

Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes

(2017) Marta Royo-Llonch et al.   Frontiers in Microbiology

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept

(2017) Melissa B. Duhaime et al.   Frontiers in Microbiology

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria

(2017) Benjamin Bolduc et al.   PeerJ

A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells

(2017) Svetlana Fridman et al.   Nature Microbiology

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean

(2017) Yosuke Nishimura et al.   mSphere

Morphological Identification and Single-Cell Genomics of Marine Diplonemids

(2016) Ryan M.R. Gawryluk et al.   CURRENT BIOLOGY

Extreme Diversity of Diplonemid Eukaryotes in the Ocean

(2016) Olga Flegontova et al.   CURRENT BIOLOGY

Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters

(2016) Adriana Lopes dos Santos et al.   ISME Journal

Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus

(2016) Cristina Howard-Varona et al.   ISME Journal

Global genetic capacity for mixotrophy in marine picocyanobacteria

(2016) Alexis P Yelton et al.   ISME Journal

iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure

(2016) Benjamin Bolduc et al.   ISME Journal

Plankton networks driving carbon export in the oligotrophic ocean

(2016) Lionel Guidi et al.   NATURE

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

In situ imaging reveals the biomass of giant protists in the global ocean

(2016) Tristan Biard et al.   NATURE

Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria

(2016) Gregory K. Farrant et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights into global diatom distribution and diversity in the world’s ocean

(2016) Shruti Malviya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Decoupling function and taxonomy in the global ocean microbiome

(2016) S. Louca et al.   SCIENCE

Linking Virus Genomes with Host Taxonomy

(2016) Tomoko Mihara et al.   Viruses-Basel

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton

(2016) Francisco M. Cornejo-Castillo et al.   Nature Communications

The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates

(2016) Anna Gimmler et al.   Scientific Reports

Survey of the green picoalga Bathycoccus genomes in the global ocean

(2016) Thomas Vannier et al.   Scientific Reports

Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding

(2015) Noan Le Bescot et al.   ENVIRONMENTAL MICROBIOLOGY

A new look at ocean carbon remineralization for estimating deepwater sequestration

(2015) Lionel Guidi et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages

(2015) Magali Lescot et al.   ISME Journal

The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.)

(2015) Solenn Mordret et al.   ISME Journal

Global distribution and vertical patterns of a prymnesiophyte–cyanobacteria obligate symbiosis

(2015) Ana M Cabello et al.   ISME Journal

PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy

(2015) Johan Decelle et al.   Molecular Ecology Resources

Computational eco-systems biology in Tara Oceans: translating data into knowledge

(2015) S. Sunagawa et al.   Molecular Systems Biology

Rising to the challenge: accelerated pace of discovery transforms marine virology

(2015) Jennifer R. Brum et al.   NATURE REVIEWS MICROBIOLOGY

Light-driven synchrony ofProchlorococcusgrowth and mortality in the subtropical Pacific gyre

(2015) Francois Ribalet 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

Environmental characteristics of Agulhas rings affect interocean plankton transport

(2015) E. Villar et al.   SCIENCE

Tara Oceans studies plankton at planetary scale

(2015) P. Bork et al.   SCIENCE

Patterns and ecological drivers of ocean viral communities

(2015) J. R. Brum et al.   SCIENCE

Determinants of community structure in the global plankton interactome

(2015) G. Lima-Mendez et al.   SCIENCE

Deep sequencing of amplifiedPrasinovirusand host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes

(2015) Camille Clerissi et al.   Environmental Microbiology Reports

Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards

(2015) Petra ten Hoopen et al.   Standards in Genomic Sciences

The ocean sampling day consortium

(2015) Anna Kopf et al.   GigaScience

Open science resources for the discovery and analysis of Tara Oceans data

(2015) Stéphane Pesant et al.   Scientific Data

Comprehensive Model of Annual Plankton Succession Based on the Whole-Plankton Time Series Approach

(2015) Jean-Baptiste Romagnan et al.   PLoS One

Unveiling of the Diversity of Prasinoviruses (Phycodnaviridae) in Marine Samples by Using High-Throughput Sequencing Analyses of PCR-Amplified DNA Polymerase and Major Capsid Protein Genes

(2014) Camille Clerissi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evolutionary history of Chaetognatha inferred from molecular and morphological data: a case study for body plan simplification

(2014) Samah Gasmi et al.   Frontiers in Zoology

Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton

(2014) Peter von Dassow et al.   ISME Journal

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

(2014) Bonnie L Hurwitz et al.   ISME Journal

Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years

(2014) Jacob A Cram et al.   ISME Journal

Brandtodiniumgen. nov. andB. nutriculacomb. Nov. (Dinophyceae), a dinoflagellate commonly found in symbiosis with polycystine radiolarians

(2014) Ian Probert et al.   JOURNAL OF PHYCOLOGY

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Microbial oceanography and the Hawaii Ocean Time-series programme

(2014) David M. Karl et al.   NATURE REVIEWS MICROBIOLOGY

Prasinovirus distribution in the Northwest Mediterranean Sea is affected by the environment and particularly by phosphate availability

(2014) Camille Clerissi et al.   VIROLOGY

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

(2013) Ramiro Logares et al.   ENVIRONMENTAL MICROBIOLOGY

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

(2013) Pascal Hingamp et al.   ISME Journal

Phylogenetic Analysis of Thecosomata Blainville, 1824 (Holoplanktonic Opisthobranchia) Using Morphological and Molecular Data

(2013) Emmanuel Corse et al.   PLoS One

Metabolic reprogramming by viruses in the sunlit and dark ocean

(2013) Bonnie L Hurwitz et al.   GENOME BIOLOGY

Global patterns in efficiency of particulate organic carbon export and transfer to the deep ocean

(2012) Stephanie A. Henson et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Are we missing half of the viruses in the ocean?

(2012) Grieg F Steward 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

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

(2012) Jens Roat Kultima et al.   PLoS One

Marine Protistan Diversity

(2011) David A. Caron et al.   Annual Review of Marine Science

A Holistic Approach to Marine Eco-Systems Biology

(2011) Eric Karsenti et al.   PLOS BIOLOGY

Light-dependent adsorption of photosynthetic cyanophages to Synechococcus  sp. WH7803

(2010) Ying Jia et al.   FEMS MICROBIOLOGY LETTERS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation

(2010) Jack A. Gilbert et al.   PLoS One

Diversity dynamics of marine planktonic diatoms across the Cenozoic

(2009) Daniel L. Rabosky et al.   NATURE

The impact of remineralization depth on the air–sea carbon balance

(2009) Eun Young Kwon et al.   Nature Geoscience

Four stages of a scientific discipline; four types of scientist

(2009) Alexander M. Shneider   TRENDS IN BIOCHEMICAL SCIENCES

Molecular eco-systems biology: towards an understanding of community function

(2008) Jeroen Raes et al.   NATURE REVIEWS MICROBIOLOGY

A latitudinal diversity gradient in planktonic marine bacteria

(2008) J. A. Fuhrman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA