Lucie Bittner
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View article: Omics to Study and Manage Aquatic Environments: A Snapshot From the <scp>A</scp>qua<scp>E</scp>c<scp>O</scp>mics Meeting (Evian‐les‐Bains, 2025)
Omics to Study and Manage Aquatic Environments: A Snapshot From the <span>A</span>qua<span>E</span>c<span>O</span>mics Meeting (Evian‐les‐Bains, 2025) Open
The AquaEcOmics meeting brought together 280 scientists applying omics tools to aquatic research in March 2025 (Evian‐les‐Bains, France). We synthesised here the main outcomes from the 167 presentations which were given. A similar number o…
View article: Ancient Microbiomes as Mirrored by DNA Extracted From Century‐Old Herbarium Plants and Associated Soil
Ancient Microbiomes as Mirrored by DNA Extracted From Century‐Old Herbarium Plants and Associated Soil Open
Numerous specimens stored in natural history collections have been involuntarily preserved together with their associated microbiomes. We propose exploiting century‐old soils occasionally found on the roots of herbarium plants to assess th…
View article: The genomic potential of photosynthesis in piconanoplankton is functionally redundant but taxonomically structured at a global scale
The genomic potential of photosynthesis in piconanoplankton is functionally redundant but taxonomically structured at a global scale Open
Carbon fixation is a key metabolic function shaping marine life, but the underlying taxonomic and functional diversity involved is only partially understood. Using metagenomic resources targeted at marine piconanoplankton, we provide a rep…
View article: Life cycle strategies in free‐living unicellular eukaryotes: Diversity, evolution, and current molecular tools to unravel the private life of microorganisms
Life cycle strategies in free‐living unicellular eukaryotes: Diversity, evolution, and current molecular tools to unravel the private life of microorganisms Open
An astonishing range of morphologies and life strategies has arisen across the vast diversity of protists, allowing them to thrive in most environments. In model protists, like Tetrahymena , Dictyostelium , or Trypanosoma , life cycles inv…
View article: Single-cell transcriptomics highlights sexual cues among reproductive life stages of uncultivated Acantharia (Radiolaria)
Single-cell transcriptomics highlights sexual cues among reproductive life stages of uncultivated Acantharia (Radiolaria) Open
As an innate property of life, the ability to reproduce is a key process for the perpetuation of organisms. Along the evolution of protist reproductive strategies, the molecular machinery of sexual recombination is estimated to have been i…
View article: Picoeukaryotic photosynthetic potential is functionally redundant but taxonomically structured at global scale
Picoeukaryotic photosynthetic potential is functionally redundant but taxonomically structured at global scale Open
Primary production, performed by RUBISCO, and often associated with carbon concentration mechanisms, is of major importance in the oceans. Thanks to growing metagenomic resources (e.g., eukaryotic Metagenome-Assembled-Genomes; MAGs), we pr…
View article: SENSE-PPI reconstructs protein-protein interactions of various complexities, within, across, and between species, with sequence-based evolutionary scale modeling and deep learning
SENSE-PPI reconstructs protein-protein interactions of various complexities, within, across, and between species, with sequence-based evolutionary scale modeling and deep learning Open
Ab initio computational reconstructions of protein-protein interaction (PPI) networks will provide invaluable insights on cellular systems, enabling the discovery of novel molecular interactions and elucidating biological mechanisms within…
View article: Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of Syndiniales marine parasites
Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of Syndiniales marine parasites Open
Marine protists are major components of the oceanic microbiome that remain largely unrepresented in culture collections and genomic reference databases. The exploration of this uncharted protist diversity in oceanic communities relies esse…
View article: Genomic differentiation of three pico‐phytoplankton species in the Mediterranean Sea
Genomic differentiation of three pico‐phytoplankton species in the Mediterranean Sea Open
For more than a decade, high‐throughput sequencing has transformed the study of marine planktonic communities and has highlighted the extent of protist diversity in these ecosystems. Nevertheless, little is known relative to their genomic …
View article: Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of marine parasites
Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of marine parasites Open
Marine protists are major components of the oceanic microbiome that remain largely unrepresented in culture collections and genomic reference databases. The exploration of this uncharted protist diversity in oceanic communities relies esse…
View article: MAGs protein functional clusters data
MAGs protein functional clusters data Open
Tab_PFCLevel_Faureetal2020_PRTable with 233,756 lines corresponding to protein functional clusters, and 67 columns : PFC ID | Size of the PFC | KEGG-based unctional homogeneity | EggNOG-based functional homogeneity | Taxonomical homogeneit…
View article: Functional trait‐based approaches as a common framework for aquatic ecologists
Functional trait‐based approaches as a common framework for aquatic ecologists Open
Aquatic ecologists face challenges in identifying the general rules of the functioning of ecosystems. A common framework, including freshwater, marine, benthic, and pelagic ecologists, is needed to bridge communication gaps and foster know…
View article: Functional trait-based approaches as a common framework for freshwater and marine ecologists
Functional trait-based approaches as a common framework for freshwater and marine ecologists Open
International audience
View article: Mixotrophic protists display contrasted biogeographies in the global ocean
Mixotrophic protists display contrasted biogeographies in the global ocean Open
Mixotrophy, or the ability to acquire carbon from both auto- and heterotrophy, is a widespread ecological trait in marine protists. Using a metabarcoding dataset of marine plankton from the global ocean, 318,054 mixotrophic metabarcodes re…
View article: Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems
Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems Open
Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of…
View article: On the use of networks to link molecules to ecosystems: Investigating the uncultured lineages and/or the unknown functions from protists for a better understanding of ecosystems
On the use of networks to link molecules to ecosystems: Investigating the uncultured lineages and/or the unknown functions from protists for a better understanding of ecosystems Open
Our understanding of the microbial world is living a true paradigm shift. The advent of next generation sequencing in molecular biology, offers, via metagenomics and metatranscriptomics, unprecedent measures of both taxonomic and functiona…
View article: Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome‐based sequence similarity network
Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome‐based sequence similarity network Open
Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high‐throughput sequencing resources can be used to cha…
View article: The epibiotic life of the cosmopolitan diatom <i>Fragilariopsis doliolus</i> on heterotrophic ciliates in the open ocean
The epibiotic life of the cosmopolitan diatom <i>Fragilariopsis doliolus</i> on heterotrophic ciliates in the open ocean Open
Diatoms are a diverse and ecologically important group of phytoplankton. Although most species are considered free living, several are known to interact with other organisms within the plankton. Detailed imaging and molecular characterizat…
View article: Additional file 2: of A de novo approach to disentangle partner identity and function in holobiont systems
Additional file 2: of A de novo approach to disentangle partner identity and function in holobiont systems Open
Taxonomic assignment of SRC assembled contigs with MEGAN6 for the holobiont models M1 and M2. (XLSX 23Â kb)
View article: Additional file 7: of A de novo approach to disentangle partner identity and function in holobiont systems
Additional file 7: of A de novo approach to disentangle partner identity and function in holobiont systems Open
SRC_c library content information and data sources. Table with detailed information of SRC_c libraries contents. The type of data and the total library sizes are displayed. It includes taxonomic contents and links to data repositories for …