Black spots aren't necessarily growing organisms. You might just have some diesel buildup in the tank or lines that broke loose and ended up in your prefilter. I've found the same stuff in fuel level sending units, and on tank screens. Keep any eye on it and if it starts getting worse I'd start worrying about it.

You can put some biocide in the tank if you are worried but prepare to change filters a few times. The biocide will kill all the gooy growers and they'll end up in your filters.

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