The best way to control micro-organisms is to make their living conditions/environment inhospitable. Protecting the fuel from moisture or water ingress and draining off any water from the fuel and tank system is fundamental to control.
Once growth has become established, chemical, mechanical and possibly even physical (tank entry) intervention will be needed to clean both fuel and tank system to restore a healthy balance. Preventative measures often called “Housekeeping”are the best solution.
These involve designing “appropriate to risk” fuel cleanliness programs, which combine regular drainage of water from the system and testing for levels of microbial growth. This should be backed by appropriate chemical or mechanical treatments when testing indicates the need. This strategy should avoid costly physical intervention.