Lucie Bittner, PhD
Bioinformatics, Environmental and Evolutionary Genomics
Emile Faure PhD’s defense – December 2nd 2020
Contributions of meta-omics data to the detection of functional traits in planktonic ecosystems
The defense is available on youtube.
The jury was composed of:
- Sébastien Monchy, Professeur (Université du Littoral Côte d’Opale), Rapporteur
- Christian Tamburini, DR CNRS (Mediterranean Institute of Oceanography), Rapporteur
- Thomas Mock, Professor (University of East Anglia), Examinateur
- Ingrid Obernosterer, DR CNRS (Sorbonne Université), Examinatrice
- Sakina-Dorothée Ayata, MC (Sorbonne Université), Co-Directrice de thèse
- Lucie Bittner, MC (Sorbonne Université), Co-Directrice de thèse
Abstract: Marine planktonic organisms play a crucial role in trophic networks, global biogeochemical cycles, and climate regulation. Biogeochemical models simulate planktonic ecosystems dynamics to understand and predict climate change. In most biogeochemical models, planktonic diversity is implemented either through plankton functional types (PFT), i.e. theoretical entities grouping planktonic organisms according to shared functional capacities (e.g., calcifiers, nitrogen fixers or silicifiers), or functional traits, i.e. morphological, physiological or phenological features measurable at the individual level that effect growth, reproduction or survival (e.g. feeding modes, production of toxins or body size). These methods imply an a priori and restricted choice of the considered types or traits of planktonic organisms, potentially leading to oversimplified representations of planktonic diversity in models. Unprecedented amounts of meta-omics data on marine planktonic communities were recently collected at global scales, calling for the use of data-driven methodologies to determine and quantify the potential and realized functional traits of planktonic organisms in-situ. My objective in this thesis was therefore to determine how to use meta-omics data to quantify the distribution of functional traits in the environment. In a first part, I present how omics data can be used to describe and quantify specific, a priori selected traits in the global ocean. A particular focus is made on two functional traits: mixotrophy, from which the genomic basis is poorly known, and dimethyl sulfide (DMS) production, from which the genomic basis is well understood. I show how metabarcoding data on one hand and functional genomic markers on the other hand allow to decipher the biogeography of functional traits, identifying limits and advantages of the two types of data. In a second part, I present an approach allowing to detect putative protein families in metagenomics data that can be associated with functional traits, without any a priori choice of functional traits of interest. By quantifying the response of these emergent clusters to physico-chemical gradients in the global ocean, I show how this approach could allow to predict the functional composition of planktonic communities from environmental data in the near future. Finally, I use my results to discuss the potential of meta-omics data as a means of realistically representing the diversity of planktonic communities in biogeochemical models.
Pavla Debeljak has joined the lab ! – September 15th, 2020
As a post-doc, she will study the functional and taxonomical, unknown omics from the planktonic ecosystems.
She is founded by the H2020 Blue-Cloud project, and will contribute to the Plankton Genomics demonstrator.
Collaborations between the Institut de Systématique, Évolution, Biodiversité (Paris), the LAGE team at the CEA Genoscope (Evry) and the Laboratoire d’Océanographie de Villefranche (Villefranche-sur-mer)
Master 2 internship [ January 2021 – June 2021 ] – September 2020
Dynamics of aquatic microbial interactions involved in the degradation of terrestrial organic matter
Detailed description here
Keywords: co-occurrence networks, interactions, metabarcoding, bioinformatics/biostatistics, microbial ecology, organic matter degradation, temperature