It is probably infected with fungus and there is not much you can do about it. You can try spraying with a fungicide.

First, off William, when you say, "Orange tree in trouble" some people like me, who know a little about orange trees open this to find what you have is an baby orange seedling. First thing is get it out of that terra cotta pot and put it in plastic/ceramic/composite pot MUCH smaller. Next is water it from the bottom; that is, put it in a larger container of water almost to the top of the soil line until the soil is wet. That is the best way to avoid damp off, which is the number one killer of seedlings of all sorts.