OK. Obviously you will remove the stem. It looks like a form of black brush algae. If you see this elsewhere, you need to take action to restrain it, meaning, stop it from increasing. It will be everywhere. It is caused by an imbalance of light and nutrients. This means the light has to be sufficient in intenisty for the plants, and nutrients have to be available. If this is not balanced, the plants cannot grow and algae takes advantage.
The Java Fern looks in trouble. Is the rhizome buried in the sand? And what is the light, this is a low light plant. Are you adding any plant fertilizer?