Organic acid driven bacterial interactions in arctic snow

• Main Author: Bergk Pinto, Benoit
• Other Authors: Ampère (AMPERE), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ampère, Département Bioingénierie (BioIng), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École Centrale de Lyon (ECL), Université de Lyon, Catherine Larose
• Format: Doctoral or Postdoctoral Thesis
• Language: French
• Published: HAL CCSD 2020
• Subjects: Competition; Cooperation; Networks; Snow; Organic acids; Microbiologie; Compétition; Coopération; Réseaux; Neige; Acides organiques; [SPI.OTHER]Engineering Sciences [physics]/Other; Arctic; Svalbard
• Online Access: https://theses.hal.science/tel-03411873; https://theses.hal.science/tel-03411873/document; https://theses.hal.science/tel-03411873/file/TH_T2764_bbpinto_optimise.pdf

Bacterial interactions are ubiquitous in the environment. For a long time, microbiologists have been considering mostly negative interactions (mainly competition) between microorganisms as the natural selection would only select the most adapted bacteria in the environment. But nowadays, bacterial cooperation is starting to attract more and more attention as microbiologist realize that a significant number of microorganisms are auxotroph for one or more biomolecules and need the presence of other microorganisms in order to grow. This new field of microbiology has been mostly developing thanks to lab controlled co-cultures. Thus we face now the challenge to try to validate the acquired knowledge from the wet lab experiments in the environment.In this thesis, we wanted to validate some observations that had been made in lab controlled co-cultures at the level of an environmental bacterial community. We considered the effect of organic acids (a carbon source) and hypothesized that an increase of organic acids would increase bacterial competition and that bacterial cooperation would drop at the same time. To test this hypothesis we selected two methods to assess bacterial interactions in order to strength our observations. First, we tracked genes reported as being proxy of cooperation (plasmids) or competition (antibiotics resistance genes =ARG) in metagenomes. We used also co-variance networks of 16S rRNA to assess bacterial interactions. This hybrid approach was then used on a bacterial community from the Arctic snow. We decided to study this community because the Arctic snow environment is reported as being highly dynamic and a seasonal increase of organic acids had been previously reported.During our first study, carried out on a time series of snow, we applied successfully our methodology to track bacterial interactions and how it was impacted by the increase of organic acids. In the snow metagenomes, we observed that the ARGs were retrieved in higher abundance in the snow samples having a higher organic acids ...