It feels next would be trying isolate the component that make CO2. Try to use smaller sample. Put them under microscope, etc.
I might be dumb, but I figured they would just continuously subdivide the sample until they isolated it. Maybe CO2 sensors wont be sensitive enough?
Maybe it's the very molecules that the live cells were using, just doing their thing without the cells. Cells concentrate things by confining them in a small volume, but otoh, if you have damp particles, the thin water layer on the particles would be a kind of confining space, with the added advantage of surface area to exchange gases with.