Simply use a heavy duty caustic detergent (sodium silicate, etc. based detergent) pour in/ spray on and let it sit a few days, then scrub. The caustic will dissolve the bacteria and other microorganisms. Spray the adjacent areas with the same and scrub. If your are environmentally aware/concerned add a large amount vinegar to the mix to neutralize before discharging. Br sure to wear a respirator and rubber gloves when scrubbing as many of the microorganisms found in ''dark places'' on boats can be toxic mildews.
..... you might want to tighten your prop shaft packing gland a bit so that you lessen the entrance of ''bugs'' ... or get a dripless packing gland; the less stagnant bilge water the less the bacterial, etc. growth.