This interests me more than it should
The bugs form a biofilm, which for all intents and purposes will then be there forever (issue with surgical implants, as even autoclaving isnt guaranteed to kill it all, i.e why house hold sprays say kills 99.9% of bacteria)
The layers of bacteria, yeasts, algae etc generally work together. aerobic will be on top, anerobes will be deeper in the layer.
Now heres the neeto part - throw some poison on them, it may get some of the first layer, but as they die they will send out signals which tell the surrounding layers to shut up shop/start producing compounds to break down the toxins, or to form spores (the0.01% you will have a near impossible job of killing)
As a biotechnologist my advice is; remove one of these
carbon for food (cant do it, your fuel is hydrocarbons)
oxygen and sulphur for respiration (not practical)
trace elements for growth and propagation (perhaps, the main one would be iron, which unless you have plastic tanks you are shit outta luck)
dissolved water for germination - this, watertraps and perhaps a cup of meths in the tank to bind up any free water