It is not quite accurate to say the bacteria in sw and fw are the same. At best they are similar. In an established freshwater tank the ammonia oxidizers are not one strain of bacteria, over time different strains colonize. In sw the variety is way less diverse. So the odds are fairly decent that some of those in fw may survive a medication while in sw they are killed.
I can post a paper which measured the AOA, AOB and NOB in FW and SW aquariums. Here is what they found.
McKnight, M.M. and Neufeld, J.D., 2021. Microbial community analysis of biofilters reveals a dominance of either comammox Nitrospira or archaea as ammonia oxidizers in freshwater aquaria. BioRxiv, pp.2021-11.
Abstract
Nitrification by aquarium biofilters transforms toxic ammonia waste (NH3/NH4+) to less toxic nitrate (NO3-) via nitrite (NO2-). Ammonia oxidation is mediated by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the recently discovered complete ammonia oxidizing (comammox) Nitrospira. Prior to the discovery of comammox Nitrospira, previous research revealed that AOA dominate among ammonia oxidizers in freshwater biofilters. Here, we characterized the composition of aquarium filter microbial communities and quantified the abundance of all three known groups of ammonia oxidizers. Aquarium biofilter and water samples were collected from representative freshwater and saltwater systems in Southwestern Ontario, Canada. Using extracted DNA, we performed
16S rRNA gene sequencing and quantitative PCR (qPCR) to assess community composition and quantify the abundance of amoA genes, respectively. Our results show that aquarium biofilter microbial communities were consistently represented by putative heterotrophs of the Proteobacteria and Bacteroides phyla, with distinct profiles associated with fresh versus saltwater biofilters. Among
nitrifiers, comammox Nitrospira amoA genes were detected in all 38 freshwater aquarium biofilter samples and were the most abundant ammonia oxidizer in 30 of these samples, with the remaining biofilters dominated by AOA, based on amoA gene abundances. In saltwater biofilters, AOA or AOB were differentially abundant, with no comammox Nitrospira detected. These results demonstrate that comammox Nitrospira play an important role in biofilter nitrification that has been previously overlooked and such microcosms are useful for exploring the ecology of nitrification for future research.
Basically, the recently discovered Nitrospira strains that can process ammonia to nitrate directly turn out to be the major ammonia oxidizers in FW tanks. I had been thought that AOA (ammonia oxidizing archaea) were the dominant ammonia oxidizers in FW aquariums until the new Nitrospira strains were discovered. But there are still AOB and NOB in tanks at work as well.
The more the science discovers in this respect, the more we understand about what is keeping our fish safe from ammonia etc. in our tanks.
When I got ino the hobby the 3rd of Dr, Hovanec's papers on the bacteria in our tanks was published. These basically showed the bacteria in waste treatment were not the ones in tanks, Then he identified Nitrospira as being the dominant nitrite converters and varieties of Nitrosomonas were the dominant ammmonia oxidisers.
Then the ammonia oxidizing archaea were discovered and what we new changed. They were initially found on the underside of a rock in a sw tank in a public aaquarium, It turns out they are everywhere, not just in SW.
Almost a decade later it was discovered that some strains of Nitrospira were able to process ammonia straight to nitrate (these are called comammox Nitrospira). And, again what we knew changed.
And then the above paper concluded that the not only were there differences in the strains of ammonia oxidizers but that the Nitrospira in fw and sw were different strains. In fw the comammox Nitrospira dominated but were not in sw. There they only found the Nitrospira which only converts nitrite to nitrate. And, again we knew has changed.
There is one other big difference between nitrite levels in fw and sw which has been know for some time. Chloride in the water blocks nitrite from entering fish. This is why nitrite is not usually an issue for fish in sw.
I have been looking at research trying discover if their is any difference in the composition and nature of the nitrifying biofilms in fw vs. sw. I have had no luck so far. What I do know is that in fw, the biofilm can protect the inhabitants against antibiotics. "Most nitrifiers, the bacteria responsible for nitrification, are Gram Negative." So this would suggest that antibiotics which work against gram negative bacter would do a lot of damage to out bio-filtration. So might some of the full spectrum antibiotics. But, the science has shown that the biofilms actually protect the bacteria from many of these. I know this is the case for fw.
Since I have never had brackish or sw tanks, I have not focused on them bacteria in them. It is hard enough trying to learn about and understand fw. I know there are similarities and difference and some of the general explanations but that is all.
edited for a number of egregious typos and incomplete words. I need an editor.