The effects of exposure to ammonia and nitrite have been studied extensively in a laboratory setting. There are many such studies. These studies do not support the sort of statements seen so often here and many other fish sites about what levels of ammonia or nitrite exposure may be toxic and what damage both temporary or long term are caused.
For example a study on silver perch (Bidyanus bidyanus) exposed for 39days to various ammonia concentrations:
"Concentrations tested were control, 0.03, 0.04, 0.07, 0.14 and 0.36 mg l-1 UAN (control, 0.29, 0.5, 0.8, 1.7 and 4.3 mg l-1 total ammonia–nitrogen [TAN])"
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Note: 4.3 mg l-1 total ammonia–nitrogen would read 5.5 ppm on an API kit. The ammonia levels tested were all over .25 ppm of ammonia on the API kit.
For the most part the only "harm" they noticed at the end of the study was:
"No gross pathology of gill tissue was observed. The filaments of all fish were straight and the lamellae were arranged evenly and parallel. Mucous cells were located distally in all preparations. No chloride cells were observed. Examination of histological material, however, revealed changes to gill filaments following exposure to ammonia Table 3.. The most significant change was an increase in the percentage of filaments exhibiting epithelial lifting."
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Now this might be significant until one reads at the end of the study:
"Epitheliocystis observed in the present study occurred as a benign infection and had no apparent effect on survival or growth rate. Subsequent histopathological examination of cohort silver perch retained at NSW Fisheries’ Grafton Research Centre showed no
evidence of epitheliocystis (Frances and Nowak, unpubl. data)."
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*from
http/directory.umm.ac.id/Data%20Elmu/jurnal/A/Aquaculture/Vol183.Issue1-2.Mar2000/61096.pdf
So the minimal effect in gills they noted was reversed, i.e. not permanent.
I can quote and cite more such research not only for ammonia, but for nitrite and even nitrate. What they show is that it isn't possible to make a blanket statement about what levels of ammonia or nitrite exposure will cause harm. It is definitely species specific and also age and fish size specific. What the research indicates is that it should be possible to do a fish in cycle which allows the levels to rise well beyond .25 or .50 ppm on API kits and not cause the fish any permanent harm or long term damage.
I can also find research showing that stressed fish do not handled ammonia or nitrite as well as when stress is minimized. Can anybody show that daily water changes in a tank cycling with fish in it is not stressful to the fish? It can be easy to assess- if the fish bolt- they are stressed, if the fish hide, they are stressed. In fact, the flight reflex is one of the reactions studied to show the effects of elevated toxins.
The upshot of this is that doing a fish in cycle requires using those fish that are most resistant to the effects of ammonia and nitrite. Fish in cycles can be done without causing permanent harm/damage to the fish.
Despite all of these facts, I will still always suggest that people opt for doing fishless cycles. There are any number of reasons for this, but the two best are it is faster and, if one makes a mistake, no fish suffer or die. The risk in doing fish in cycles are not when they are done right, but when things go wrong. And for an inexperienced fish keeper, things can go wrong in a hurry.