It looks like the algae or something related to it from your media has traveled up your stem. I have been rooting confederate rose cuttings, & if algae develops in the bubbler tank, they develop a dark green color like your stem & destroys the whole batch of cuttings. I have learned to get them out of the tank before it develops.
I doubt if you can effectively treat it. I clean my tanks daily, & have tried cleaning the cuttings. but once it sets up there is no stopping it. Hopefully your tomatoes are near fruiting so it will not be much of an issue.