Other gases: methane and hydrogen sulfide
Other gases. Besides the dissolved atmospheric gases, natural water may also include minute amounts of bacterially-produced gases: methane, hydrogen sulfide and nitrous oxide, for example. The bacteria that produce these gases all have anaerobic metabolisms, for aerobic respiration only gives off carbon dioxide.
In practice, as soon as these bacterial by-products encounter certain other bacteria with aerobic metabolisms, they are quickly oxidized to harmless end-products. Thus, all the gases produced by bacterial metabolisms are normally taken up by other bacteria or by plants. Little ordinarily survives to be outgassed at the water surface.
Methane. One of these bacterially produced gases is methane. Aquarists sometimes needlessly worry about poisonous methane, that it might diffuse into the water from anoxic substrate levels. Methane is only slightly soluble in water, which is one reason why it can accumulate in sediment and rise as a bubble. Methane is actually very stable; it takes lots of oxygen and a spark to combust it. But the only way methane could come in contact with aquarium water would be by violent stirring of rich deep anoxic sediment. A bubble rising from the substrate is much more likely to be carbon dioxide.
Hydrogen sulfide. Bacterially-produced hydrogen sulfide (H2S) is a natural part of sulfate/sulfide cycling. It is produced in minute quantities in the processes of decomposition in low oxygen microzones throughout the aquarium system and is rapidly scavenged and oxidized by bacteria. Hydrogen sulfide is abiotically oxidized too, when it encounters hydroxy radicals. Faint skunky sulfurous smells produced by sulfur-bearing thiols ("mercaptans") in some aquaria are often mistaken for the choking odor of rotten eggs given off by H2S. And odors associated with iron bacteria in the substrate could set off needless H2S alarms too.
The quick way to deal with H2S is to oxidize it to sulfate with hydrogen peroxide. The permanent way to reduce hydrogen sulfide production in the system is with more thorough sanitation and better water circulation.