Bacteria that live in oxygen-lacking, or oxygen-deficient areas are known as anaerobic bacteria, whilst those that grow in conditions where oxygen is readily available are known as aerobic bacteria.
The bacteria responsible for converting ammonia into nitrites, and nitrites into nitrates are aerobic bacteria, this is why a good flow of water through a filter is required; it is the flow of water which provides the bacteria with oxygen.
All bacteria require oxygen to metabolise so anaerobic bacteria which grow in oxygen lacking areas must find another source. In the case of a useful group of bacteria, this source is nitrate (NO3), which is split into nitrogen gas and oxygen (2NO3 = 2N + 6O2)
Using this principle; some specialised filters are designed for low oxygen conditions in order to remove nitrates. These filters work by providing a large surface area for the bacteria, much like normal filters, but the water is only passed through very slowly. A small population of aerobic bacteria quickly use up the waters oxygen, allowing a large number of anaerobic bacteria to colonise the filter and remove nitrates.
If you have a large external filter, you may be able to encourage anaerobic bacteria to grow by leaving the last sponge in the filter to get clogged and dirty. The clogged areas will have an uneven flow of water and some areas will develop a lower oxygen level, so anaerobic bacteria should thrive. Under this situation, the filter will be removing ammonia, nitrites and nitrates although water changes will still be required for reasons other than nitrate control.