A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis

Microbial ecologists are increasingly turning to small, synthesized ecosystems^1-5 as a reductionist tool to probe the complexity of native microbiomes^6,7. Concurrently, synthetic biologists have gone from single-cell gene circuits^8-11 to controlling whole populations using intercellular signalling^12-16. The intersection of these fields is giving rise to new approaches in waste recycling¹⁷, industrial fermentation¹⁸, bioremediation¹⁹ and human health^16,20. These applications share a common challenge⁷ well-known in classical ecology^21,22-stability of an ecosystem cannot arise without mechanisms that prohibit the faster-growing species from eliminating the slower. Here, we combine orthogonal quorum-sensing systems and a population control circuit with diverse self-limiting growth dynamics to engineer two 'ortholysis' circuits capable of maintaining a stable co-culture of metabolically competitive Salmonella typhimurium strains in microfluidic devices. Although no successful co-cultures are observed in a two-strain ecology without synthetic population control, the 'ortholysis' design dramatically increases the co-culture rate from 0% to approximately 80%. Agent-based and deterministic modelling reveal that our system can be adjusted to yield different dynamics, including phase-shifted, antiphase or synchronized oscillations, as well as stable steady-state population densities. The 'ortholysis' approach establishes a paradigm for constructing synthetic ecologies by developing stable communities of competitive microorganisms without the need for engineered co-dependency.