Is there any proof of beneficial mutations?

No, there is no evidence of a direct environment-to-genome mechanism.What comes close, though, is the fact that when under environmental stress a colony of bacteria will often quicken their individual mutation rates in hopes of hitting on some useful mutation before the colony dies out completely (Adaptive Mutation). But this is normal random mutation (though sped up) without any targeted goal.I do not know enough about Flavobacterium to say with certainty, but Adaptive Mutation may have been the vector of the nylon munchers.

Environment does indeed cause mutations (mutagens, cosmic rays, etc.) but the resultant mutations are random, not specifically targeted toward a result.Use caution here. Any place in the genome is a mutation candidate, but, some areas are more robustly repaired than others. Also, outside the bacteria species, in the true multi-cellular creatures like trees, turtles and people, it is only a mutation in a germ-line cell that may get passed on to the offspring. A mutation in a somatic cell will have little to no effect on the organism (unless it's cancerous).Regardless, all are random and have no predetermined value.

Here, this might help.A bacterium can, of course, "feel" its environment. Too hot/cold, dry/wet, food/no food. Different genes are switched on or off depending upon the "stress" felt. All this was "learned" by the bacteria through random mutation/natural selection over many billions of years.

Really? Did you ever have a course of penicillin cure a cold?Do you know of anyone on the planet who had their cold cured by penicillin?I was there too ICANT. In the 50's penicillin was lousy on colds. To this day it's still lousy on colds. So are amoxicillin, oxacillin, methecillin and all the other derivatives of penicillin produced anywhere ever.Even in the 50's, ICANT, doctors know better than to prescribe penicillin for a cold.Do you know why?