I would quibble with the use of "contaminated" for something that's always been there.

In fact, the atmosphere had quite a lot of carbon dioxide a billion years before there was any significant quantity of oxygen.

E. coli, staph and salmonella are everywhere and all over you, but we still call things that have them "contaminated".

We don't, except in some narrow contexts, like "Large quantities of E.c. found in bottled water". Looking at pristine lake far in woods one wouldn't say "Look, such a contaminated water!" just because there are bacteria. We also don't say "My intestines is contaminated with E.Coli" in spite of the fact it's there too.

But if there was too much bacteria it would be contaminated. It's about there being an inappropriately high amount of something.