That article was more for
Ichthys who asked if I had research about the bacteria and using NH# v.s. NH4. The "cycle" does not stop at acid pH levels.
While NH3 is the really toxic form of ammonia as compared to ammonium which is actually an ion as it has a negative charge, this does not mean there is 0 danger from elevated levels of NH4. And this matters in environments where the water is very acid and there are fish thriving in it.
The best way I can explain this is to related the story of my Altum angels and needing to cycle a tank which started at 4.2 pH and was targetted to be at 6.o eventually. I had a grand plan. I knew that TA at pH 4.2 was pretty safe over the shorter term. I also knew that it took time for the bactreria to reset to process NH4. So here was my plan. I brought the fish into a tank set at 4.2 pH but which was not cycled. Before the fish even arrived I put in motion the second part of my plan. I set up a small bio farm tank at pH 7.0 which was my tap. I added some Dr. Tim's One and Only to start a fishless cycle dosing ammonium chloride. Once the tank was cycled, I began a gradual process of dropping the pH by a .2 while continuing to add ammonia. When the tank was again cycled at 6.8, I again dropped the pH. The goal was to end up with the filters in the farm tank to be cycled for water at 6.0 pH.
The plan was to raise the Altum tank pH over time to 6.0 and and have the bio-farm cycling at 6 .0. The time frame for this was about 6 months. it all made perfect sense to me except for one thing on which I did not count. The Altum tank cycled itself on the way up to 6.0. I could not test any ammonia in it as I approached the time when I would move the cycled filters from the biofarm tank to the tank with the fish.
The altum tank held no plants. So there was only one way that the TA could test at 0 and that was the tank was cycled on its own without my doing anything and without any harm coming to the fish. I cannot explain why there was no issue from nitrite. Perhaps it was due to the bacteria that began colonizing favored Nitrospira, the bacteria originally though only to process nitrite. It turned out they can process ammonia straight to nitrate as well as processing nitrite to nitrate. This was revealed in a paper published in 2015. Don't worry about the technical terms, look at what they actually mean. I have underlined the key sentence.
van Kessel, M. A., Speth, D. R., Albertsen, M., Nielsen, P. H., Op den Camp, H. J., Kartal, B., Jetten, M. S., & Lücker, S. (2015). Complete nitrification by a single microorganism.
Nature,
528(7583), 555–559.
https://doi.org/10.1038/nature16459
Summary
Nitrification is a two-step process where ammonia is considered to first be oxidized to nitrite by ammonia-oxidizing bacteria (AOB) and/or archaea (AOA), and subsequently to nitrate by nitrite-oxidizing bacteria (NOB). Described by Winogradsky already in 1890
1, this division of labour between the two functional groups is a generally accepted characteristic of the biogeochemical nitrogen cycle
2. Complete oxidation of ammonia to nitrate in one organism (complete ammonia oxidation; comammox) is energetically feasible and it was postulated that this process could occur under conditions selecting for species with lower growth-rates but higher growth-yields than canonical ammonia-oxidizing microorganisms
3. Still, organisms catalysing this process have not yet been discovered.
Here, we report the enrichment and initial characterization of two Nitrospira species that encode all enzymes necessary for ammonia oxidation via nitrite to nitrate in their genomes, and indeed completely oxidize ammonium to nitrate to conserve energy. Their ammonia monooxygenase (AMO) enzymes are phylogenetically distinct from currently identified AMOs, rendering recent acquisition by horizontal gene transfer from known ammonia-oxidizing microorganisms unlikely. We also found highly similar
amoA sequences (encoding the AMO subunit A) in public sequence databases, which were apparently misclassified as methane monooxygenases. This recognition of a novel
amoA sequence group will lead to an improved understanding on the environmental abundance and distribution of ammonia-oxidizing microorganisms. Furthermore, the discovery of the long-sought-after comammox process will change our perception of the nitrogen cycle
from
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878690/
This is the beauty of science. It expects to learn new things over time that change what was thought to be known. A perfect example of this re cycling was that there are Archaea, (another microorganism) which can process ammonia to nitrite. So what science knew about the nitrogen cycle and how it work was revised. It was no longer solely the province of bacteria.
Fortunately, for us as fish keepers, it doesn't mater what specific microorganisms may do the job of keeping our tanks safe from ammonia and what it can become. It doesn't matter that a lot of this may be done by live plants in a tank. What matters is that ammonia etc. ceases to be a threat to our fish and inverts. It is important that we know how to act at various stages of the cycle.
What does matter is that we have a basic understanding of what is going on at the microscopic level in our tanks so that we can know things are safe and healthy. This understanding makes it a whole lot easier to cycle a tank and to know how this process is progressing along the way. So we need to know that ammonia comes first then nitrite and then nitrate. We need to know how much ammonia to add in a fishless cycle- i.e not to exceed 5 ppm as nitrogen which is 6.4 ppm on the total ion scale used by most hobby test kits.
We do not need to be master chemists nor biologists to get a tank cycled, we just need to understand the real basics as opposed to a lot of the urban aquarium myths one can find all over the net. This is also why I wrote the cycling articles. I wanted to eliminate the misinformation. I wanted to create easy to follow step by step instructions which, when followed exactly, will always result in a tank becoming cycled in a reasonable amount of time. It was designed to be fail-safe. By that I mean one could not over dose ammonia which would then create too much nitrite which is usually what actually stalls a cycle. It is knowing the science behind the nitrogen cycle which mades it possible to create this sort of system for cycling.
How many times have you been told any amount of ammonia is harmful and requires water changes? It is not true. What matters is how much of it is NH3. I am telling you do not change water for nitrite, use chloride to block the nitrite from entering the fish and doing the harm. Consider the aquaculture industry or a public aquarium which has huge tanks. Water changes are not a possibility when 100s of thousands of gallons are involved. It was the science which showed these areas how to deal with ammonia and nitrite in other ways. And those ways will also work in a tank. Here is how I learned to use chloride for nitrite, the paper is from 1997.
Nitrite in Fish Ponds Robert M. Durborow1, David M. Crosby2 and Martin W. Brunson3
Consider this, the science tells us that any paper written on nitrite needs to include information on the amount of chloride present. Without this critical piece of information, a paper re nitrite without this information is considered to have no scientific value. This is because of how chloride blocks nitrite.
edited for spelling and typos
