In broad terms there are two types of biodegradation – aerobic and anaerobic, with and without oxygen respectively.
By far the more common is aerobic, mainly because there is plenty of oxygen around and also aerobic biodegradation is fast. For this reason, this approach is used quite a lot industrially. Typically, an industrial waste treatment plant will involve a chemical dosing step, followed by a biodegradation plant. This normally simply involves a large vat with aerators. The aerators provide the oxygen for the bugs to do their stuff, and they successfully remove both the carbon (as CO2) and nitrogen (as N2). Essentially, aerobic digestors are pretty foolproof.
And these are used in sewage treatment plants – massive treatment vats with banks of aerators blast air through the waste day and night. These plants have a substantial amount of sludge, of course, and this sludge is tapped off at various points and sent to an anaerobic digestor. The anaerobic digestor consumes this solid sludge with about 96% efficiency, and converts it all to methane, ammonia, and hydrogen sulphide.
Interestingly, I recently heard of one of these facilities that is being set up commercially, using food waste, to generate methane that can be used as fuel to generate power.
So the world around us is an incredibly efficient biological reactor, using several mechanisms, to recycle pretty much everything.