There are a variety of bacteria that can reduce dimethyl sulfoxide (DMSO) to
dimethyl sulfide which has a very characteristic odor. I do not know if you
consider DMSO an organic compound or not.
There are also bacteria that can produce volatile smelly compounds from
selenium salts. But there may be a toxicity issue with these. Similarly for
the release of cyanide from amygdalin by a variety of fairly common bacteria.