Over the years, a great number of strains of bacteria have developed resistance to the once deadly antibiotics. Is this not evidence that such bacteria had the ability to deal with a new and trying situation, one of the indications of intelligence?
No, because individual bacteria aren't adapting to the presence of the antibiotic; they're either born able to resist the antibiotic, or they die. Only as a population have they adapted to the antibiotic. Individually, none of them have reacted to the presence of the antibiotic at all.
The possibility is open that some of the life-related molecules are themselves alive.
Maybe you're working on a different definition of consciousness, but I don't see how a single molecule could possibly contain enough state to represent consciousness.