There is a lot of hype about programming single cells by editing their genetic code, which in turn alters the dynamics of their regulatory or metabolic networks. However, using these engineered microbes in the real world is a very skeptical step, simply because we cannot predict exactly what can happen.
An alternative is to not edit the microbes themselves at all. Instead of building networks using enzymes inside the microbe, why not see a cell itself as a complex catalyst. A living cell converts some chemicals into others (environmental conditions apply).
Using microfluidics, it might be possible to completely characterize the "catalytic" profile of hundreds of microbial species, including bacteria, fungi, amoeba, algae, archaea. Then, build a "network" of different species such that the whole system is stable and performs some metabolic process that is of use to us, such as bio-remediation. This "engineered" network should be safer in the real world.