If the fuel is suspect, hire a qualified pro to come clean your fuel or "polish" it for you. They can usually clean out your tank at the same time. If that is impossible....
Filters are what should protect your motor from things in diesel that your motor will be damaged by. Namely that is water or debris (organic or otherwise). If there is biological matter in your fuel it will quickly accumulate in a filter, clogging the filter, then the motor will die due to fuel starvation. Of course the "fix" is to clean up the fuel and then change the filter, then bleed the system.
Most boats have at least 2 fuel filters. One filter will be mounted on the engine itself. Generally it will be immediately in line after the hand priming pump and before the injector pump. It should be a spin on type filter.
Trace the supply side of your fuel line back to the tank. There will usually be another filter between the motor and the tank. That is the filter you should be most concerned with. It will clog first. If you do not have a filter there, you should consider installing one to protect your motor.
Organisms grow in the fuel because water is introduced into the fuel. If this is a problem often for you, investigate ways water could be entering your fuel. Was your jerry jug left outside for a long time? Are the seals tight? Did it expand and contract many times in the sun?
If you add something to the fuel to kill the infestation, it will result in a lot of organic matter dying and drifting to the bottom of the tank. This will speed up the process of clogging, so be prepared. Ie, don't go out on a big sail with suspect fuel. (carry spare fuel filters!) Most additives combat the problem by removing water from the fuel. Some are actual biocides that kill what is growing. If you decide to use it, do not over use it. And add it on a regular basis. Think of it as a preventative medicine rather than a "quick fix".
Hope this helps.
Tate