This isn't to say that nitrifying bacteria are absent on a natural coral reef, or that they are completely insignificant ecologically, but rather to show that they're not particularly abundant (and therefore exert a limited influence). Check out this list of top 18 microbial genera sampled from 4 major reef microhabitats ("Variability in Microbial Community Composition and Function Between Different Niches Within a Coral Reef"
https://core.ac.uk/download/pdf/78071687.pdf).
In addition to those ubiquitous and massively abundant chemoheterotrophic genera such as
Pelagibacter, there's a considerable representation of
photoheterotrophs (
Roseobacter,
Rhodopseudomonas,
Rhodospirillum,
Rhodobacter and perhaps at least some
Roseovarius sp.) in the list.
So yeah, while I wouldn't be against adding nitrifying bacteria to a new system, I wouldn't work so hard to replace them at a later stage if they fail to persist (i.e., eventually get outcompeted by certain heterotrophs).
I get that the microbiome in an aquarium is generally very different than that of a natural reef. But for those folks that are using the natural ecosystem as a model for their captive system, and use the similarity between their system and the natural system as a metric of success, you might find this list interesting.
Maybe I'm biased because I have a huge interest in photoheterotrophs, but it appears to me from personal experience (successfully conditioning new systems exclusively with
Rhodopseudomonas,
Rhodospirillum and
Rhodobacter) that nitrifiers such as
Nitrosomonas and
Nitrobacter are not absolutely essential to "cycle" a system. Actually, I'd totally be one to advocate for updating and elaborating upon what we term "cycling" to better reflect what occurs in the natural environment.
