Alginate-ϵPLL core-shell hydrogel beads as a tool for an effective, stable and scalable microbial encapsulation

Synthetic microbial consortia have a significant potential for novel biotechnological applications such as the upgrade of complex feedstocks. However, achieving stable and reproducible co-cultures is challenging due to competitive dynamics and unbalanced growth rates among species. Here, we present an effective method for microbial encapsulation relying on alginate core-shell hydrogel beads coated with {varepsilon}-poly-L-lysine ({varepsilon}PLL-HB). This procedure ensures complete containment of several microbial species (prokaryotic and eukaryotic) while allowing for consistent growth inside the beads. Compared to chitosan and -poly-L-lysine, two of the biomaterials most used as coating agents for this kind of encapsulation, {varepsilon}PLL demonstrated superior performance in avoiding cellular escape across diverse culture conditions and for all the microbial strains tested. {varepsilon}PLL-HB enabled the construction of spatially distributed co-cultures, effectively balancing populations between microorganisms with different growth rates. Furthermore, microbial encapsulation inside {varepsilon}PLL-HB provided protection against toxic compounds in lignocellulosic-derived media and maintained the encapsulation efficacy and cell viability after long-term storage at -80 {degrees}C. The superior microbial containment, structural integrity and chemical resistance of {varepsilon}PLL-HB, combined with their cost-effective and simple preparation, makes them a versatile tool for synthetic microbial consortia engineering, with broad applicability in biotechnological processes.