Could be a sign of some anaerobic bacterial activity. Sulfate release (H2S) is probably the biggest concern and can poison fish. I suggest a water change with every gravel vacuum if you can.
As flight50 mentioned, poking the sub periodically helps a lot.
It may be that your soil or gravel or both may be a little deep, creating anaerobic areas.
Are there plants near where the bubbles come from? Plants also help by oxygenating the soil, encouraging aerobic bacteria.