Looks like water damage for sure. Pretty sure the black stuff is mold. Job #1 is finding out where the water is coming from, as reko said, it may be a drain trap or fitting that leaks intermittently, so may take some investigation.
As far as repair. I would disconnect and remove those gas lines, cut out the damaged area, and replace the plywood, then add another patch sheet below that bridges the patch seam in the floor. The re-drill the gas line holes and reinstall.
Alternatively, if you wanted to keep it simpler, you could just add a patch piece underneath that is notched to go around the gas lines, but it will need to braced somehow so you can take the bounce out of the floor.
