Machine learning helps construct an evolutionary timeline of bacteria

As other researchers have pointed out, genes for handling oxygen (and metabolic cycles in general) are often repurposed (with cycles even reversing direction over evolutionary time scales). So the lineages that apparently "used" oxygen may in reality have simply had the ability to tolerate it or safely dispose of it.

'"Results show that at least 3 aerobic lineages appeared before the GOE -- by nearly 900 million years -- suggesting that a capacity for using oxygen evolved well before its widespread accumulation in the atmosphere," Professor Hugenholtz said.'