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Hi,
A mechanical centrifuge will not clean out 100% of a Microbiological Infestation.
The cladosporium resinae microbes can pass through the centrifugal process and get into the fuel filters where they continue to grow and multiply.
If you are finding that you have problems with this a first step remedy is to slug dose your remaining fuel stocks with a Fuel Biocide, There are several on the market I like Biobor because it come in handy sized cans and use a product called Amerstat 10 from Drew Ameriod when I cant get Biobor.
Once you have knocked the bugs off a lot more will separate out in the bowl and what's left will pass through your filters and burn in the combustion chamber.
You should also try to remove as much of the free water in the bottom of the tanks as possible as it is in the interface between fuel and water that these little things thrive.
I don't know what model of separator you are running but I have seen a plastic bowl liner( I can't remember if it was Alfa or Westfalia) that allows for a quick bowl clean by just yanking it out and chucking it away, you still have to clean the disc stack but it definitely saves time and mess.
You can further improve the condition of your fuel by throttling back the Separators throughput and batch purifying all the time. Unfortunately a lot of boats are not set up for this so you have to transfer fuel around with the Seperator to run it through it, a process that requires a lot more user input than a simple recirc to and from the same tank.
Don't forget once you have it under control to continue to use a Biocide as part of your housekeeping and fuel management program.
If your problem is really severe the only proper way to get it sorted is to have someone come along and take all your fuel off, centrifuge it, put it through a polishing filter and clean your tanks before returning it onboard. Don't forget to change all your fuel filters and blow out the lines if it is really bad.
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Cheers,
K1W1
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