Animals keep to the surface and bacteria keeps to the underground... problem solved.
I love being underground. It's cool and quiet. Those facilities also last a very long time. I found many "Kilroy was here" scribbles in tunnels in the military and some of them were dated back to WWII.
Another option would be to deprecate trains. Instead people travel through pressurized maglev modules in tubes at 800 mph / 1200 kph. Transcontinental tubes accelerate the modules to 8000 mph / 12,000 kph. Interplanetary offramps eject the module from earth at mach 50+ where it is caught by a sub-orbital robot ship that matches speed and takes the module to the interplanetary colony ship.
It's significant.
I think I've read a book about this. Or ten.