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 ε-poly-L-lysine (εPLL-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 α-poly-L-lysine, two of the biomaterials most used as coating agents for this kind of encapsulation, εPLL demonstrated superior performance in avoiding cellular escape across diverse culture conditions and for all the microbial strains tested. εPLL-HB enabled the construction of spatially distributed co-cultures, effectively balancing populations between microorganisms with different growth rates. Furthermore, microbial encapsulation inside εPLL-HB provided protection against toxic compounds in lignocellulosic-derived media and maintained the encapsulation efficacy and cell viability after long-term storage at −80 °C. The superior microbial containment, structural integrity and chemical resistance of εPLL-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.