Is any attempt made to decontaminate oil drilling equipment between uses? I know that aquifers can be contaminated by iron bacteria introduced by water well drilling. Could some of the bacteria in deep reservoirs have been conveyed from shallower levels by the drills? (Somewhat similar to drug addicts getting AIDS or hepatitis from reused needles)
The equipment used to drill surface sits out in the open during the rest of the hole. On large, oilwell drilling rigs, that means they are exposed to air which kills most anerobes. The rest of the drill string (at least around) here is commonly in saturated salt mud or diesel based invert mud (an 80/20 diesel/saturated salt water emulsion).
Pit water is monitored for bacteria and biocides run in the drilling fluid if any are detected. That way the pumps, mud tanks, pits, wellbore, and drilling equipment all get purged.
The shallower ("surface" hole--as deep as 5000 ft.) is cased prior to drilling the rest of the hole to protect near surface aquifers, and the drilling fluid changed from fresh water/native mud to a saturated salt water or invert drilling fluid afterwards. Not much chance for a critter which does well in one environment to survive in the other.
The field I cited was most likely contaminated by frac fluid hauled in a truck which had either hauled sour salt water to a disposal well or sour crude. Usually, water/salt water/ disposal water/crude oil haulers and the like haul the same fluids consistently, and do not mix what goes into the truck from load to load.
Over the life of the field, the difference in price has cost the operators millions because the sour crude is worth less than it would have been if it stayed sweet, so bacterial monitoring is a cheap form of insurance.