I have referenced this in a couple of threads, but given the immense significance I think it deserves its own thread.
Nitrification is the oxidation of ammonia into nitrite and then the oxidation of nitrite into nitrate. For decades, aquarists have assumed that nitrification was carried out by bacteria, usually deemed to be Nitrosomonas
(ammonia to nitrite) and Nitrobacter
(nitrite to nitrate). Dr. Tim Hovanec (1996) led a team of scientists that determined the second stage was actually carried out by Nitrospira
in aquatic (as opposed to soil) environments. Nitrosomonas
was confirmed to be present in marine environments but could not be detected in freshwater; subsequent research (2001) confirmed that Nitrosomonas
bacteria could be enriched from freshwater, so it was assumed to be the bacteria strain responsible for FW nitrification.
[Edit: Just occurred to me to mention here that prior to Dr. Hovanec's work, or perhaps a bit earlier, most had assumed aquatic nitrification followed soil nitrification, hence the "assumed" bacteria. Dr. H proved that absolutely incorrect, and several subsequent studies by other scientists have not proven him wrong but confirmed his findings.]
Since the discovery of ammonia-oxidizing archaea (AOA) in 2008, scientists have been studying anew the nitrification process in marine and freshwater habitats. Earlier this year (2012), a team of biologists at the University of Waterloo (Waterloo, Ontario) published the results of their study which revealed that, based on amoA
gene abundances, AOA were the dominant putative ammonia oxidizers in the majority of freshwater and saltwater aquaria. These results provide first evidence for the important role of AOA in freshwater aquarium filtration and suggest possible niche adaptation of AOA to conditions associated with freshwater aquarium biofilters [cited from the Introduction to the scientific paper].
For those interested, here is the complete study; the Introduction and Results sections are easier to follow and contain some very useful information. PLOS ONE: Aquarium Nitrification Revisited: Thaumarchaeota Are the Dominant Ammonia Oxidizers in Freshwater Aquarium Biofilters
Archaea used to be classed with bacteria in the prokaryote group of organisms, but they now constitute a distinct domain of single-celled organisms.
What this means in terms of many of the oft-repeated assumptions on nitrification and bacteria I don't know, but we should be prepared for some significant re-thinking in this area.