Design of an exclusive obligate symbiosis for organism-based biological containment

Biological containment is a critical safeguard for genetically engineered microbes prior to their environmental release to prevent proliferation in unintended regions. However, few biocontainment strategies can support the longer-term microbial survival that may be desired in a target environment without repeated human intervention. Here, we introduce the concept of an orthogonal obligate commensalism for the autonomous creation of environments that are permissive for survival of a biocontained microbe. We engineer one microbe to produce a non-standard amino acid (nsAA), and we engineer synthetic auxotrophy in a second microbe via reliance on this nsAA for growth. We show that this obligate commensalism is highly effective, with the survival of our commensal organism during co-culture dependent on the presence of our producer strain. We also show that this commensalism is orthogonal to a small microbial consortium isolated from maize roots, with survival of the synthetic auxotroph conditional upon the presence of the nsAA-producing strain in the consortium. Overall, our study demonstrates a transition from a chemical to a biological dependence for biocontained organisms that could lay the groundwork for biocontained synthetic ecologies.