We could also look for 16S RNAs by RT-PCR, which would tell us if something biological was present even if we couldn't culture it.
I saw an intriguingly small qPCR unit today in "Biotechniques", but still expensive ($10,000). I'll look into it further. With something like this we could at least detect a 16S signature in flight - and then sequence the amplicon back on the ground? (Sequencing in flight I think if for the deluxe version!)