We need to sample upwind, or make sure the UVC LEDs are turned off for a good period before sampling so that the plume dissipates. And how long would that be? Again, we really need some way to simulate plumes, eddies etc. We need to monitor air currents and direction at altitude, perhaps using a tell-tale. But how to sterilise it? Oh dear... perhaps something cool like a segmented area of canopy and you mention the pressure in each segment, so you can see which segment is being distorted by the wind blowing against it?
Another thing we could do is to fire a probe out of the gondola, for instance on a small rocket, trailing a sample line well clear of the gondola and any possible plume. Since this would have been stored inside the gondola it could have been pretty easily sterilised on the ground. Does a model rocket engine withstand autoclaving? Gamma irradiation? Ethylene dioxide? An interesting experiment to find out :-)
As a simple experiment, we could imagine drawing the sample line (made of what? Coated with what?) back into the gondola and then over the different culture mediums that my colleague was discussing, so inoculating them.