Diversity and biotechnological potential of endophytic bacteria associated with Origanum species: insights into essential oil modulation and antibacterial activity

Endophytic bacteria associated with medicinal plants are an underexplored source of bioactive compounds. These microorganisms significantly contribute to plant growth, stress resilience, and secondary metabolite production, making them valuable candidates for drug discovery. In this thesis, the culturable endophytic bacterial communities of four Origanum species—O. vulgare, O. vulgare ssp. vulgare, O. vulgare ssp. hirtum, and O. heracleoticum were characterized from a molecular and phenotypic point of view. The aim of this work was to understand the evolutionary forces shaping plant-microbe interactions and identify endophytic strains with the potential to modulate Origanum essential oil composition and/or produce bioactive secondary metabolites with antibacterial activity. The study revealed that Origanum plants host diverse bacterial communities, selectively recruiting specific strains based on plant species and tissues. Notably, O. heracleoticum seeds harbored a specific endophytic community with interesting antimicrobial properties. Additionally, bacteria isolated from different compartments of O. heracleoticum displayed distinct compositions, along with varying metabolic plasticity and antagonistic potential, supporting the idea of niche-specific adaptation. The establishment of an in vitro axenic model of O. heracleoticum confirmed that the endophytes are well-adapted to their compartment of origin. The screening of endophytic strains for antibacterial activity against multidrug-resistant human pathogens, combined with genome mining, highlighted the potential of the endophytes for bioactive secondary metabolite production, further linking them to the composition of essential oils. Overall, this study highlighted the specific adaptation of bacterial endophytes to Origanum plants' inner tissues and demonstrated their ability to produce antibacterial molecules. These findings lay the groundwork for future research into the role of endophytic bacteria in influencing plant physiology and secondary metabolite production, and highlight their biotechnological potential in sustainable agriculture practices and the development of novel antimicrobial agents.