Scientific publications

A machine learning algorithm for high throughput identification of FTIR spectra: Application on microplastics collected in the Mediterranean Sea

A machine learning algorithm for high throughput identification of FTIR spectra: Application on microplastics collected in the Mediterranean Sea

This article proposes a protocol for analyzing the huge number of microplastics present in samples taken from the marine environment. This analysis currently requires a great deal of time and advanced skills. This new protocol therefore proposes an automated machine learning approach based on spectrophotometric analysis. First, the spectra of pure plastics are entered into

Predicting global distributions of eukaryotic plankton communities from satellite data

Predicting global distributions of eukaryotic plankton communities from satellite data

Satellite remote sensing is a powerful tool to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here, we present an approach to identify community types from a global plankton network that includes phytoplankton and heterotrophic protists and to predict their

Genomic adaptation of giant viruses in polar oceans

Genomic adaptation of giant viruses in polar oceans

Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phyla Nucleocytoviricota and Mirusviricota are groups of eukaryote-infecting large and giant DNA viruses with genomes encoding a variety of functions. Here, by leveraging the

Mirusviruses link herpesviruses to giant viruses

Mirusviruses link herpesviruses to giant viruses

DNA viruses have a major influence on the ecology and evolution of cellular organisms1,2,3,4, but their overall diversity and evolutionary trajectories remain elusive5. Here we carried out a phylogeny-guided genome-resolved metagenomic survey of the sunlit oceans and discovered plankton-infecting relatives of herpesviruses that form a putative new phylum dubbed Mirusviricota. The virion morphogenesis module of this

Phylogenetics and taxonomy of the scleractinian coral family Euphylliidae

Phylogenetics and taxonomy of the scleractinian coral family Euphylliidae

The family Euphylliidae consists of reef-building zooxanthellate scleractinian corals distributed across the Indo-Pacific. Seven extant genera comprising a total of 22 valid species are currently recognised. Recent studies have re-organised the taxonomy of the family at the genus level based on molecular and morphological data, including a comprehensive revision of Euphyllia and the resurrection of Fimbriaphyllia. Here, three

Global Distribution and Diversity of Marine Parmales

Global Distribution and Diversity of Marine Parmales

Parmales (Bolidophyceae) is a minor eukaryotic phytoplankton group, sister to diatoms, which exists as two distinct forms of unicellular organisms: silicified cells and naked flagellates. Since their discovery, many field studies on Parmales have been performed; however, their global distribution has not yet been examined in detail. We herein compiled more than 3,000 marine DNA

Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities

Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities

Marine microorganisms form complex communities of interacting organisms that influence central ecosystem functions in the ocean such as primary production and nutrient cycling. Identifying the mechanisms controlling their assembly and activities is a major challenge in microbial ecology. Here, we integrated Tara Oceans meta-omics data to predict genome-scale community interactions within prokaryotic assemblages in the euphotic ocean.

Linking satellites to genes with machine learning to estimate phytoplankton community structure from space

Linking satellites to genes with machine learning to estimate phytoplankton community structure from space

Ocean color remote sensing has been used for more than 2 decades to estimate primary productivity. Approaches have also been developed to disentangle phytoplankton community structure based on spectral data from space, in particular when combined with in situ measurements of photosynthetic pigments. Here, we propose a new ocean color algorithm to derive the relative cell

New plastids, old proteins: repeated endosymbiotic acquisitions in kareniacean dinoflagellates.

New plastids, old proteins: repeated endosymbiotic acquisitions in kareniacean dinoflagellates.

Dinoflagellates are a diverse group of ecologically significant micro-eukaryotes that can serve as a model system for plastid symbiogenesis due to their susceptibility to plastid loss and replacement via serial endosymbiosis. Kareniaceae harbor fucoxanthin-pigmented plastids instead of the ancestral peridinin-pigmented ones and support them with a diverse range of nucleus-encoded plastid-targeted proteins originating from the haptophyte

Complementary environmental analysis and functional characterization of lower glycolysis-gluconeogenesis in the diatom plastid 

Complementary environmental analysis and functional characterization of lower glycolysis-gluconeogenesis in the diatom plastid 

Organic carbon fixed in chloroplasts through the Calvin–Benson–Bassham Cycle can be diverted toward different metabolic fates, including cytoplasmic and mitochondrial respiration, gluconeogenesis, and synthesis of diverse plastid metabolites via the pyruvate hub. In plants, pyruvate is principally produced via cytoplasmic glycolysis, although a plastid-targeted lower glycolytic pathway is known to exist in non-photosynthetic tissue. Here,

Complex Genomes of Early Nucleocytoviruses Revealed by Ancient Origins of Viral Aminoacyl-tRNA Synthetases

Complex Genomes of Early Nucleocytoviruses Revealed by Ancient Origins of Viral Aminoacyl-tRNA Synthetases

Aminoacyl-tRNA synthetases (aaRSs), also known as tRNA ligases, are essential enzymes in translation. Owing to their functional essentiality, these enzymes are conserved in all domains of life and used as informative markers to trace the evolutionary history of cellular organisms. Unlike cellular organisms, viruses generally lack aaRSs because of their obligate parasitic nature, but several

Diatom phytochromes integrate the underwater light spectrum to sense depth

Diatom phytochromes integrate the underwater light spectrum to sense depth

Aquatic life is strongly structured by the distribution of light, which, besides attenuation in intensity, exhibits a continuous change in the spectrum with depth1. The extent to which these light changes are perceived by phytoplankton through photoreceptors is still inadequately known. We addressed this issue by integrating functional studies of diatom phytochrome (DPH) photoreceptors in

A genomic approach to Porites (Anthozoa: Scleractinia) megadiversity fromthe Indo-Pacific

A genomic approach to Porites (Anthozoa: Scleractinia) megadiversity fromthe Indo-Pacific

Unveiling the link between phytoplankton molecular physiology and biogeochemical cycling via genome-scale modeling

Unveiling the link between phytoplankton molecular physiology and biogeochemical cycling via genome-scale modeling

Earth system models (ESMs) highly simplify their representation of biological processes, leading to major uncertainty in the impacts of climate change. Despite a growing understanding of molecular networks from genomic data, describing how changing phytoplankton physiology affects biogeochemical processes remains elusive. Here, we embed genome-scale models within a state-of-the-art ESM to deliver an integrated understanding

Bioprospecting Marine Plankton

Bioprospecting Marine Plankton

Decomposition of in situ particulate absorption spectra

Decomposition of in situ particulate absorption spectra

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

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

Phylogenetic relationships and revision of the genus Blastomussa (Cnidaria Anthozoa Scleractinia) with description of a new species

Phylogenetic relationships and revision of the genus Blastomussa (Cnidaria Anthozoa Scleractinia) with description of a new species

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

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

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

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