Julia CANTUTI GENDRE

Composition of the jury:

• Véronique BROUSSOLLE, INRAE, Reviewer

• Rémy FROISSART, CNRS, Reviewer

• Clara TORRES-BARCELO, INRAE,Examiner

• Céline DELBÈS, INRAE, Examiner

Keywords : Bacteriophage, fermented vegetables, microbial ecology, viral metagenomic, epifluorescence microscopy, synthetic ecology

Abstract : Fermented vegetables are generally produced through spontaneous fermentation, which involves various microorganisms. Their successive development follows a well-defined sequence. The natural community present on the surface of the vegetable, mainly composed of Enterobacteria and yeasts, is progressively replaced by heterofermentative lactic acid bacteria, such as Leuconostoc mesenteroides, and then by homofermentative lactic acid bacteria, such as Lactiplantibacillus plantarum. Bacteriophages, viruses that infect bacteria, could play a key role in this microbial dynamic. However, although their ability to regulate bacterial populations is well documented in various environments, their role in vegetable fermentation remains poorly understood. This work aims to provide new insights supporting the hypothesis that bacteriophages play a role in microbial dynamics during vegetable fermentation. First, the diversity and abundance of viruses were explored in three types of fermented vegetables. This revealed a high viral diversity and structural differences in the communities depending on the vegetable used as raw material. Then, experimental spontaneous fermentations conducted under controlled conditions allowed the description of viral population successions throughout the fermentation process. These analyses highlighted a viral dynamic synchronized with that of bacteria, suggesting a potential regulatory role of phages on bacterial populations. Finally, a synthetic ecology approach was implemented using a model of fermented carrots inoculated with a simplified microbial community to assess the effect of adding a virulent phage on microbial dynamics and the biochemical characteristics of the product. In this highly simplified model, the results revealed the resilience of the bacterial community to phage attack, demonstrating the limited impact of this phage on the fermentation process. This work thus provides new insights into the microbial ecology of fermented vegetables and the potential role of phages in microbial dynamics during fermentation.