Routes for sustainable bacterial bioplastics production: an integrative assessment of carbon sources and fermentation strategies.

Carbon dioxide emissions and plastic pollution represent major environmental challenges, which can be addressed through circular economy solutions aimed at the production of biodegradable materials. Cupriavidus necator is a model bacterial species capable of converting diverse carbon sources into polyhydroxyalkanaoates, biodegradable polymers with excellent mechanical properties and high market value. This positions C. necator as a key organism for circular economy applications employing anaerobic digestion products as sources of carbon dioxide and volatile fatty acids. However, these applications remain underexplored due to several practical challenges related to safety measures, process control and substrate pretreatment. The aim of this thesis is to expand the knowledge on biorefinery approaches involving anaerobic digestion byproducts utilization by C. necator. The collection of studies presented here explores the metabolic flexibility of the bacterium, its adaptation to carbon sources, and demonstrates novel applications for resource valorization, integrating multi-scale approaches. The first study reviews the genetic and metabolic diversity of C. necator, identifying knowledge gaps in strain characterization and modeling that limit its broader application. The review also recapitulates existing applications of C. necator in circular economy, highlighting underexplored opportunities for waste-to-bioplastics conversions. The second study demonstrates the feasibility of using carbon dioxide from biogas as the sole carbon source for C. necator growth. Additionally, it identifies transcriptomic signatures associated with the transition to autotrophic metabolism. The third article investigates the use of anaerobic digestion byproducts, particularly volatile fatty acids, as low-cost feedstocks for polyhydroxyalkanoates production. Volatile fatty acid utilization is characterized at a macroscopic scale in a continuously stirred reactor, and at a molecular level by studying the state of the transcriptome, underlining substrate-specific responses. Lastly, the fourth study provides a preliminary characterization of a novel bioreactor design for gas fermentation, suitable for the treatment of hazardous gas mixtures, in view of devising a biogas upgrading approach with concurrent polyhydroxyalkanoate production. Together, these studies advance the understanding of C. necator as a chassis organism for circular economy applications, offering strategies to enhance bioplastics production from diverse and sustainable carbon sources.