The containment of genetically modified microorganisms (GMMs) is a major bottleneck for achieving the promise of biotechnologies in the environment. While biological strategies have been implemented to restrict the growth and replication of GMMs, there is a need for deployable physical containment technologies to achieve redundant, multi-layered, and robust containment. To address this challenge, we developed a hydrogel-based encapsulation system for GMMs that incorporates a biocompatible multilayer tough shell and an alginate-based core. This DEployable Physical COntainment Strategy (DEPCOS) allows no detectable GMM escape, samples to be easily retrieved, bacteria to be protected against environmental insults including antibiotics and low pH, and the lifespan of genetically recoded bacteria to be controlled.

Cell-free synthetic biology has made advancements in genetic circuit design, biomanufacturing, and diagnostics yet there is still a need to combine those capabilities to create advanced biosensing. Here we show that multiple biosensors can be combined to create logic gates or classifiers with visual or bioactive outputs. Multi-input cell-free diagnostics have the ability to sense, compute, and respond to complex sets of biomarkers, opening the door to new applications in microbiome composition, antibiotic tolerance, or inflammation markers.