Before the development of RNA libraries we were reliant on culturing bacteria (from sewage treatment etc) to find out what organisms were involved in nitrification, which led to many of the assumptions about aquarium cycling that we now know to be incorrect. It isn't surprising, if you look at raw sewage it is a very different medium, from even very polluted, aquarium water. Dr Tim Hovanec talks about this is in <"
Bacteria revealed">, and there are a number of papers specifically on the nitrifying organisms in aquarium filters which suggest that their assemblage shows a fluid response to varying ammonia loadings, with a stable core of archaea and an ever changing cast of nitrifying bacteria. This is described in <"
Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira">.