Biofilms: The Microbial Megacities
Introduction
Biofilms are the assemblage of associated microbial cells enclosed in an extracellular polymeric substance matrix composed of polysaccharides, proteins, lipids, and nucleic acids that enhance surface adherence and microbial aggregation.
Biofilms form on both biotic and abiotic surfaces. Micro-organisms that form biofilms are bacteria, fungi, and protists. Generally, they are created by the single cell or small groups of cells, and then they divide and differentiate.
Biofilms account for nearly 80% of all bacteria on the planet, occupying environments spanning from miles underneath the ocean floor to inside the human gastrointestinal tract.
Bacteria within biofilms can undergo significant shifts in gene expression and participate in emergent social behaviours, including division of labour and coordinated growth.
Due to their prevalence in nature and natural emergent properties, biofilms present synthetic biology with the attractive opportunity to deliver and operate engineered gene circuits in a range of desired target environments, such as soil and the microbiome.
The collective organization has been a goal for the field of synthetic biology, and tapping into the native capabilities found in biofilms may enable the next generation of spatiotemporally controlled gene circuit designs.
While domesticated bacterial strains can be used to prototype new synthetic designs in the lab, installing these cells into nature remains a challenge as they experience diverse environmental conditions that can impact cellular fitness. To address this, recent efforts have focused on expanding synthetic biology toward new bacterial species beyond Escherichia coli. The field of synthetic biology has begun to utilize non-model and undomesticated bacterial species by creating new genetic parts and a broad range of genetic transformation methods.
Challenges
Future challenges will include maintaining and containment of these engineered functions in their native contexts, such as soil and the microbiome. Challenges that must be considered for engineering biofilms include extracting microscopic and macroscopic measurements among millions of biofilm cells and contending with bacterial cell fate changes during biofilm community development.
Opportunities
Bacterial biofilms currently provide benefits for wastewater treatment and microbial fuel cells due to their ability to adhere, densely pack and persist in the environment.
With an improved understanding of biofilm biology and creating new synthetic biology tools, biofilms are poised to advance artificial biology efforts in medicine.
Potential applications for synthetic biology in biofilms are:
- Environmental remediation: Removal of heavy metals and hazardous compounds by storing them safely in the biofilm matrix.
- Biofouling prevention: Seeding surfaces with engineered biofilms to prevent attachment of microbial species.
- Novel biomaterials: Biofilm ECM (Extracellular Matrix) with engineered biochemical properties to enable novel biomaterials.
- Biomanufacturing: Metabolic burden split across multiple cell populations within a biofilm for increased efficiency.
- Microbiome diagnostics: Biofilms as sentinel organisms in the mammalian gut to sense pathogens.
- Microbiome therapeutics: Engineered biofilms regulate host-microbiome through therapeutic production and environmental remediation.
Conclusion and Future Perspectives
Developing biofilms as next-generation synthetic biology holds great promise, yet to realize this vision, several important challenges remain.
Current tools have only begun to address non-model biofilm-forming bacterial species and their complex social behaviours. The heterogeneity and temporal dynamics associated with cell state and species composition in biofilms remain poorly understood.
Furthermore, the environmental persistence of biofilms raises some concern about biocontainment, as biofilms have been associated with chronic infections and biofouling.
Despite these challenges, the opportunity remains to adapt the complex social behaviours of biofilms (e.g., cell-to-cell signalling, division of labour, and matrix production) for medicine, biomanufacturing, and environmental remediation. The physical robustness and environmental persistence of biofilms could enable new living materials and proper deployment of engineered bacteria into target environments. These advances may also prove valuable way beyond synthetic biology, ecology, and medicine.
References:
https://aiche.onlinelibrary.wiley.com/doi/abs/10.1002/btpr.3123
