Calling Any Chemists- How Do Ammonia Deoxifiers Work?

[hobby5]

You totally underestimate the rate of those reactions in water. Conversion between NH4+ and NH3 is nearly instantly, if your example were valid those 1538 reactions would happen within seconds - minutes. NH3 is the much more reactive species as it contains a free electron pair, therefore it is likely that this is the targe of those binders. But even if NH4+ was targeted, NH3 would be removed from the system as NH3 concentrations had to shrink due to the equilibrium regenerating NH4+ until finally all is gone. Again, it is not important which species you target you will always(!) remove both.
 
The quote about how prime works confirms all that. Somehow there must be a speeling error and the product in fact is an iminium salt. Those are not very stable and will dissipate over time releasing the NH3 again.
 
Concerning the pH: As I stated above imho those "binders" should change pH of a PURE NH3 solution but most likely will only marginally change pH of tap water which is buffered to some extend. Hence the claim it does not change pH, while it does but only to an extent which is not relevant.
 
I did not dive into the AOB theory yet, so cannot comment extensively atm. But as those products dissipate and release NH3 again it is of course available to the AOB again.

 

[NeonBlueLeon]

"Imidium salt" isn't a thing, so I also think they meant iminium.  Here is the formation of an iminium ion using an arbitrary ketone that would be found in Prime:
 

 

[TwoTankAmin]

It is not a mistake using the word imidium.
 

Reference
Arimitsu, S., Bo, X., Kishbaugh, T.L.S., Griffin, L., & Hammond, G. B.  Synthesis of a stable imidium complex derived from gamma-silyl-alpha, alpha-difluorobromopropyne: evaluation of AJA experimental parameters. Journal of Fluorine Chemistry, 125: 641-645. (Graduate Student Authors(s): Arimitsu,A.;Bo,X.) (2004).

from http/louisville.edu/research/for-faculty-staff/reference-search/2010-medicine/2004-references/arimitsu-et-al-2004-synthesis-of-a-stable-imidium-complex-derived-from-gamma-silyl-alpha-alpha-difluorobromopropyne-evaluation-of-aja-experimental-parameters
 
Go to this link to see them reference "imidium ion" http/pubs.acs.org/doi/pdf/10.1021/ja00835a066
 
But I will offer you this from the very lips of SeaChem (which sure is a lot of the same word over time and in many different parts of their site):

 
Thanks for the question. Prime converts ammonia into a complexed imidium salt. This salt is a nitrogenous compound that can still be utilized by aerobic bacteria. In the same way they consume ammonia, these bacteria consume the imidium salt and release nitrite as a byproduct. Prime will also bind with nitrite and nitrate, however, it will not prevent bacteria from consuming these compounds as well. Unfortunately, while we have researched it extensively in our laboratory, I do not have any documents that I can provide you as proof. However, if you wanted to test this, it would be very simple and could be done by treating tap water containing chloramine with Prime and adding it to an established aquarium. Also add a Seachem Ammonia Alert to give continuous free ammonia readings. Prime will break the chloramine bond, leaving behind ammonia. Unlike other water conditioners it will then bind to the ammonia, producing a non-toxic imidium salt. At this point you will see a 0.0 ammonia reading on the Ammonia Alert. After 24 hours, begin checking the Ammonia Alert every 30 minutes or so. After 24 hours, Prime will start to become inactive and if it is still binding any ammonia, it will begin to release it. If this is the case, the Ammonia Alert will begin changing color, giving you a reading for free ammonia.

If Prime works as we claim, which it alway does, you will not see any ammonia spikes. This is because, even when bound by Prime, the ammonia will be broken down by the biological filtration. Though not nearly as easy to test for, nitrite and nitrate are also still available for biological consumption in the aquarium even when they have been detoxified by Prime. Please let us know if you have any additional questions or if you need further clarification.

and in another post from the same page

 
The imidium salt refers to the ammonia detoxification and therefore we are speaking of bacteria that oxidize ammonia in this scenario. While nitrifying bacteria, in general, reproduce more slowly than other types of bacteria, you must understand that the bacteria do not take weeks to reproduce, instead they may take up to one day in order to double their colony size. Hobbyists do not experience ammonia spikes in the aquarium because there is no consumption of ammonia occuring, but instead because the rate of ammonia production exceeds the capacity of the bacteria present at the moment. Using Prime every 24-48 hours will ensure that any new ammonia being produced is detoxified accordingly. I am sure that tests were run with standard nitrifying bacteria many years ago when this product was produced. Currently, all aquariums as Seachem have been successfully cycled using Stability (and Prime when necessary).

from http/www.seachem.com/support/forums/showthread.php?p=9820
 
And I understood what was going on but wasn't sure how it worked and if the bacteria really could use the intermediary product in light of Dr. Hovanec's comment. The process involves replacing one or more of the Hs with something else. This effectively changes it from NH3 to N and one or two Hs and replaces the Hs with something that imitates an H.
 
I am not satisfied with the explanation regarding nitrogen, because the amount of N that goes in also comes out in the nitrite and again in the nitrate. As far as I can understand it, the N doesn't change. What changes are the other bits- the H and the O. There is also some charge related stuff, hence the - and + symbols we see. But to this untrained eye it does appear as if nitrogen is the key but is not being consumed. The nitrogen is consumed at other stages in its journey. Plants will use it, animals eat plants etc. The nitrifying bacteria aren't eating the nitrogen but rather using its electrons which may be lost or gained along the way through nitrification. This was interesting reading but I did not follow it all http/www.isws.illinois.edu/nitro/biogeofull.asp?lpg=biogeo

 

[hobby5]

Thx for all that research and the information you dug up! After some more research imidium could be an outdated term for iminium

 (using google you don't find recent documents using it)
 
Wow, your last paragraph reveals that you had not much chemical knowledge at all

But you managed to understand quiet a lot, congrats! For a better understanding read up on the nitrogen cycle. Yes, the nitrifying bacteria can retrieve energy and use it for growth by changing the bonding partners of N. Afterwards they pass it on (release it). For the aquarium setting it is only important, that there are enough bacteria which can quickly use NH3 (excreted by fish) and NO2-, as those are the toxic substances.

 

[TwoTankAmin]

hobby- The nitrogen cycle is a global phenomenon. However, when it comes to tanks, most of the information has little or no application. Soil bacteria or waste water treatment bacteria are part of the cycle, but the bacteria involved there are not found in tanks. The ones in the soil are not found in tanks. Aquaculture would be a more appropriate area in terms of sharing the same niches in terms of the nitrifying bacteria. And aquaculture is a more broad area because it is a larger scale and involves things that occur in nature rather than having to almost exclusively introduced or controlled by hobbyists or emplyees.
 
My interest in the nitrogen cycle is primarily as it relates to fresh water aquariums. Basically, if the information I find can and does apply to hobby tanks, huge public aquarium tanks or aquaculture, I read it. I even read the information related to drinking water treatment as is is also closely related, but open ocean nitrification would not be. However, I very rarely rely on fish keeping sites for my information. And on those few I might use, I always verify what I read via another source.
 
The problem with that Wiki page is it is all chemistry and the process that interests me is bio-chemistry. I know the bacteria need iron to oxidize yet I see nothing about Fe in the Wiki formulas. There are more ions and charges involved in what the bacteria do that that page even mentions.
 
But in the end I am still faced with trying to make sense of chemistry and biology I have neither the training nor the hands on experience that requires. And this is why I was lloking for some clarification on the issues in this thread. I was hoping to discover a backdoor way to explain to hobbyists what the actual dangers from ammonia or nitrite are to fish and how best to deal with them. I do not agree with what is most often stated on site like this one or Aquaria Central etc. Nor can I find any support in the literature for it.
 
My hope in investigating how the ammonia detoxifiers actually worked that it might turn out what they did was to lock up NH3 by converting it to NH4 and holding it that way for a while. Because the AOB in tanks prefer NH3 as their substrate, but likely also have some receptors for transporting NH4 inside. These allow the bacteria to use NH4, albeit less efficiently, and this might be the reason why microbiologists state that ammonia detoxifiers slow the cycle, especially when overdosed. In fact Tetra warns against using them or dechlors less than a day before adding Safe Start and not to do so for some time thereafter.
 
My hope was to offer easier to understand evidence about how to assess the actual dangers involved. When it came to cycling with fish, I got tired of reading when one has .25 or .5 ppm of total ammonia as measured on the average hobby kit, the only course of action was huge water changes. There is virtually no science I can find to support this. Everything revolves around NH3 levels not total ammonia, not NH4.
 
Unfortunately, ammonia detoxification will not supply the sort of simple easy to understand evidence on NH4 for which I was looking. If you know of any studies which deal exclusively with the potential harm from exposure to only NH4, please let me know or PM me the links or post them here.

 

[TwoTankAmin]

And now I have stumbled a bit farther into understanding things, but not in the detail I would like. I found this on Dr. Hovanec's site:
 

 
Why do ammonia removers inhibit the nitrifying bacteria? There are two major reasons for this and both may apply to your aquarium.
 
First, many ammonia removers are acids, so repeatedly adding them to the aquarium water will cause the pH to drop. This in turn means that the ammonia is in the ionized form (NH4+), which is the form the nitrifying bacteria CANNOT use. So the amount of ammonia converted to nitrite is less per day than if the pH were higher.
 
Second, some of the products have a chemical in them that inhibits the bacteria when the chemical is in a higher concentration, which occurs when the product is overdosed.
If your newly set-up tank is having problems cycling, consider how much ammonia remover you have been using; you may be overdosing and need to cut back.

from http/www.drtimsaquatics.com/using-an-ammonia-removerdechlorinator
 
I could contact Dr. H. and ask if the above would apply to which products, but wont for two reasons. First, as a competitor it would be a potentially tainted answer which would make it less trustworthy.  But as important, I would never want to ask somebody to state a competitor's product, did not work as advertised. No one in their right mind would open themselves to retribution in the courts. It simply isn't worth it. However, what the above does do is to explain why some ammonia detoxifiers when overdosed (by amount and/or frequency) can inhibit the cycle.
 
That second reason is what I would love to know more about. It is easy for us to measure pH, so the first way mentioned we can spot and correct easily. It is why any good article on cycling notes the need to insure pH is maintained (not allowed to drop much under 7.0 at worst).

 

[hobby5]

@TwoTankAmin

Ty very much for clarifying where u r coming from!

In fact I happen to be a biochemist working in research, but on totally different topics. Research is expensive, hence today only things of apparent importance like diseases threatening enough people in the western world or things which might have an economic impact are studied in great detail. Unfortunately for us nitrifying bacteria in aquariums do not belong in any of those categories and have therefore been poorly studied so far. Yet, the principles of the nitrogen cycle in hobby tanks are the same as described in the wikipedia. Maybe there are other species of bacteria doing the job, but the sequence of N-species is the same. If they use Iron to catalyse the reactions or something else is not important for our problem as those co-factors are not consumed and are not limited in our settings. They are needed in minute amounts only. I am afraid the backdoor you are looking for does not exist and you got trapped by thinking NH3 and NH4+ are totally different substances, but in water they are freely convertable, the ratio of both is only determined by pH and if you remove one of both it will regenerated from the other.
 
 

My hope in investigating how the ammonia detoxifiers actually worked that it might turn out what they did was to lock up NH3 by converting it to NH4 and holding it that way for a while. Because the AOB in tanks prefer NH3 as their substrate, but likely also have some receptors for transporting NH4 inside. These allow the bacteria to use NH4, albeit less efficiently, and this might be the reason why microbiologists state that ammonia detoxifiers slow the cycle, especially when overdosed. In fact Tetra warns against using them or dechlors less than a day before adding Safe Start and not to do so for some time thereafter.

No, as you found out those detoxifiers work by trapping NH3 in some organic nitrogen compound which contains an iminium salt. Bacteria grow quickly if they have plenty of their main nourishment (NH3 for AOB), but if you lower the concentration of that you inevitably also slow down their growth. They cannot grow with the same rate on less prefered substrates. Hence I would expect all ammonia detoxifiers to slow down the cycle. The tricky part doing a fish-in cyle is to keep NH3 low enough to not harm your fish, but high enough to progress with your cycle.
 
 

 
My hope was to offer easier to understand evidence about how to assess the actual dangers involved. When it came to cycling with fish, I got tired of reading when one has .25 or .5 ppm of total ammonia as measured on the average hobby kit, the only course of action was huge water changes. There is virtually no science I can find to support this. Everything revolves around NH3 levels not total ammonia, not NH4.

You are right, that only free NH3 is toxic and important. Therefore the same total amount of ammonia can be no problem at pH 6 while beeing totally toxic at pH 8. So you would suggest to calculate the free NH3 and only do the water change if this exceeds critical concentrations? (This is too complex for many people

) In addition you always have the nitrite levels elevated too as those are connected, hence huge water changes are the best.
 
 

 
Unfortunately, ammonia detoxification will not supply the sort of simple easy to understand evidence on NH4 for which I was looking. If you know of any studies which deal exclusively with the potential harm from exposure to only NH4, please let me know or PM me the links or post them here.

NH4+ is not toxic. But in water you always have a partial conversion to NH3, hence most likely there will be no such study.
 

That second reason is what I would love to know more about. It is easy for us to measure pH, so the first way mentioned we can spot and correct easily. It is why any good article on cycling notes the need to insure pH is maintained (not allowed to drop much under 7.0 at worst).

The rationale behind this is that the higher the pH the more of the NH3 will be in its uncharged form and accessible to AOB, leading to progression in the cycle.

 

[TwoTankAmin]

hobby- in pH 5 water there is 0 NH3 and 100% NH4. So the question you need to answer for me is simple. I have a tank with wild fish. I keep the pH in the mid 4s. I test for ammonia and learn I have .5 ppm. I know there is no NH3. How long can the fish live in that .5 ppm of NH4 and suffer 0 harm or damage? Suppose that level doubles? How about if its 4 ppm, all NH4. Can you answer this for me?
 
There is more to needing the pH kept up in nitrification than simply the pH and the acid factor. I can show you research that has autotrophic nitrification happening in pH 4.0. The Nitrosomonas europea  strain studied in it have receptors for NH4 which allows them to utilize it. There is also the fact that the dropping of pH usually happens because the carbonates in KH get used up. And they are usually a big source of the inorganic carbon for the bacteria. Remove that and they can't oxidize.
 
Hobby- I have been studying this topic in depth for several years. I do understand the nature of NH3 and NH4. I have not been trapped by anything. But you are making a statement here on which most of the membership will challenge you as they have me. In testing ammonia we get results for both forms. Most folks stop here and determine if that reading is harmful and how harmful based on the combined total ammonia reading. I have been arguing for some time now that this is not the proper approach.
 
You are not quite correct in what you state about research related to aquariums. While is it not an overriding issue, it is also not one where there is nothing to be found.:
 
Comparative Analysis of Nitrifying Bacteria Associated with Freshwater and Marine Aquaria. Applied and Environmental Microbiology Vol. 62, No. 8: 2888-2896.  Hovanec, T. A. and E. F. DeLong. 1996.
http/aem.asm.org/content/62/8/2888.full.pdf+html
 
Nitrospira- Like Bacteria Associated with Nitrite Oxidation in Freshwater Aquaria. Applied and Environmental Microbiology Vol. 64, No. 1: 258-264. Hovanec, T. A., L. T. Taylor, A. Blakis and E. F. DeLong. 1998.
http/aem.asm.org/content/64/1/258.full
 
Identification of Bacteria Responsible for Ammonia Oxidation in Freshwater Aquaria. Applied and Environmental Microbiology, Dec. 2001, p. 5791-5800. Paul C. Burrell, Carol M. Phalen, and Timothy A. Hovanec.
http/aem.asm.org/content/67/12/5791.full
 
And there are other studies that are related to aquariums. However, there are many more related to aquaculture and drinking water treatment. Here the same nitrifying bacteria are at work but now there is lots of impetus behind and funding for research. And we can extrapolate a lot of this to aquariums.
 
I have read countless abstracts or full studies on this topic, every one looks directly at NH3. I have seen studies for specific fish, for chronic exposure and for the effects of high ammonia and nitrite. I have read a Ph.D. thesis or two on the bacteria and biofilms and chlorine and chloramine. Trust me, I am not confused. I have been using ammonium chloride for some time to produce NH3 in tanks. What I am trying to do is explain to fish keepers that when it comes to ammonia, most fish sites have it all wrong. My hope was I could make this hit home if dechlors basically bound ammonia in the form of ammonium and prevented the interchange for some period. It would mean the fish were still exposed to the NH4 but not harmed. And this for me was a backdoor approach. If the product detoxified ammonia making it non-harmful and it did this as I just described, it would make it very hard for the doubters to continue doing so. Unfortunately, I struck out.
 
My error was in how I stated the NH3 - NH4 relationship. I know the two balance based on the pH and temp. However, I was trying to make the point that in taking up all the ammonia in a tank the bacteria only used the NH3 part. Because the bacteria will not process all the ammonia in a tank until they are present in sufficient numbers, they will take up only a part. They need to use up what they have taken in before they take in more. I was trying to say they will never use it all up in one fast go until the cycle is established, they are removing it in increments. What happens is they take it in smaller steps along the way. This lowers total ammonia, but it happens in steps. I stated this poorly (in terms of the actual chemical process) in my number of steps illustration.
 
There is a difference between how ammonia is produced and handled in a cycled tank vs how it is processed as it is added during a fishless cycle. My error was in how I tried to illustrate this.
 
However, much of what you noted about ammonia toxicity I have been saying for a long time on this site and others. I am not the one you need to be explaining this too, rather it is most of the rest of the membership here.
 
But as a microbiologist perhaps you can clarify something for me. The way the detoxifiers work is by changing the structue of the NH3 (and I presume the NH4 as well?). They substitue some number of the Hs with other things like this:
 

 
Comparing the structures of ammonia and primary amines
Each substance contains an -NH2 group. In ammonia, this is attached to a hydrogen atom. In a primary amine, it is attached to an alkyl group (shown by "R" in the diagram below) or a benzene ring.

from http/www.chemguide.co.uk/organicprops/anhydrides/nitrogen.html
 
What I was having difficulty understaning in relation to the bacteria realtes to what I wrote about the N being present all the way through but was changing its charge. My understanding is that the process was essential in a chain of fixing nitrogen. I believe what the bacteria are doing is helping to fix N in a form that can readily be consumed up the chain but that the bacteria were not consuming the N themselves. Plants love nitrate but can not use N directly, animals eat plants but do not use N directly. Have I understood this wrong? What I was trying to disover was how the process would still work on the bacterial level if the some of the H components were altered. First I wondered how the bacteria could take in the altered form and, second, if they did, how the process would still work in the absence of one of more of the Hs in NH3/NH4.
 
Finally, I agree with you that the average fish keeper doesn't have a clue about most of this and should never need to have one. However, I also believe that if one is going to opt for doing a fish in cycle, then they do need to know about the NH3/NH4 facts, they need to know how to do diluted nitrite testing, they need to know how to counteract nitrite with chloride. If they don't wish to have to learn and master so much more and to dedicate so much more work and time to cycling, they should simply be doing a fishless cycle. If they follow the directions in the cycling article on this site (which I wrote), they will cycle a tank in good time and with few problems. And they do not have to know anything about NH3/NH4 or how to test nitrite that is over 5 ppm on their API kits. But when it comes to fish in cycling, what they should not be doing is a lot of unneeded water changes which can also be harmful in terms of fish stress levels.

 

[hobby5]

Thx for this interesting discussion I am learning a lot too
 

There is more to needing the pH kept up in nitrification than simply the pH and the acid factor. I can show you research that has autotrophic nitrification happening in pH 4.0. The Nitrosomonas europea  strain studied in it have receptors for NH4 which allows them to utilize it. There is also the fact that the dropping of pH usually happens because the carbonates in KH get used up. And they are usually a big source of the inorganic carbon for the bacteria. Remove that and they can't oxidize.

Sorry I have no hard data for that and cannot say where the limit is. But, I would say there is no immidiate harm, even if the concentration doubles as there is nearly no NH3 present and only NH3 can diffuse passively through the gill epithelium, while charged NH4+ cannot. However, there might be long term effects as its more difficult for the fish to excrete excess ammonia themselfs. Thus, I would not advice to keep the fish for extended times at those concentrations. Moreover fish which normally live at those low pH also live in very soft water.
 

 
 
You are not quite correct in what you state about research related to aquariums. While is it not an overriding issue, it is also not one where there is nothing to be found.

Maybe I was a little too drastic with my statement, but compared to other topics with hundreds of papers a year, we only got marginal and superficial information on this.
 

 
However, I was trying to make the point that in taking up all the ammonia in a tank the bacteria only used the NH3 part. Because the bacteria will not process all the ammonia in a tank until they are present in sufficient numbers, they will take up only a part. They need to use up what they have taken in before they take in more. I was trying to say they will never use it all up in one fast go until the cycle is established, they are removing it in increments. What happens is they take it in smaller steps along the way. This lowers total ammonia, but it happens in steps. I stated this poorly (in terms of the actual chemical process) in my number of steps illustration.

I do not agree with you here. The process is rather a continuous flow. The AOB will metabolize the ammonia at their maximum capacity until their is less ammonia than capacity. During that process the capacity increases as the number of bacteria increases.
 

 
But as a microbiologist perhaps you can clarify something for me. The way the detoxifiers work is by changing the structue of the NH3 (and I presume the NH4 as well?). They substitue some number of the Hs with other things...
 
What I was having difficulty understaning in relation to the bacteria realtes to what I wrote about the N being present all the way through but was changing its charge. My understanding is that the process was essential in a chain of fixing nitrogen. I believe what the bacteria are doing is helping to fix N in a form that can readily be consumed up the chain but that the bacteria were not consuming the N themselves. Plants love nitrate but can not use N directly, animals eat plants but do not use N directly. Have I understood this wrong? What I was trying to disover was how the process would still work on the bacterial level if the some of the H components were altered. First I wondered how the bacteria could take in the altered form and, second, if they did, how the process would still work in the absence of one of more of the Hs in NH3/NH4.

If bacteria could use those products generated by the ammonia binders, they still had to uptake them actively and break them up to release the NH3 again to use that in the standard way. This will cost the bacteria energy and make the whole process less efficient. I rather hypothesis, that those products of binding are rather instable and will decompose releasing NH3 again spontaneously (over few days). But this process will give the bacteria more time to metabolize NH3 and there will not be such high peak levels in your tank.
 

 
Finally, I agree with you that the average fish keeper doesn't have a clue about most of this and should never need to have one. However, I also believe that if one is going to opt for doing a fish in cycle, then they do need to know about the NH3/NH4 facts, they need to know how to do diluted nitrite testing, they need to know how to counteract nitrite with chloride. If they don't wish to have to learn and master so much more and to dedicate so much more work and time to cycling, they should simply be doing a fishless cycle. If they follow the directions in the cycling article on this site (which I wrote), they will cycle a tank in good time and with few problems. And they do not have to know anything about NH3/NH4 or how to test nitrite that is over 5 ppm on their API kits. But when it comes to fish in cycling, what they should not be doing is a lot of unneeded water changes which can also be harmful in terms of fish stress levels.

Will add to this later sry.

 

[TwoTankAmin]

hobby- how can it be continuous? At the outset there are X barcrium present. The presence of ammonia first feeds them and then because there is more available, it enable them to have enough energy left over to reproduce. But it takes them 8-10 hours to double. So ammonia concentrations do not drop any more. The bacteria take time teo remove the ammonia which will become increasingly shorter the more they increase their numbers by repdorduction.
 
When one adds 3 ppm of ammonia in a fish less cycle and begins to test, the ammonia may show no change for a day or two and sometimes more. Of course this is the case using an API kit and not a Hach test with a colorimeter. Then one tests and the ammonia has gone down to 2 ppm. It took a number of days for this. Then next drop from 2 to 1 ppm takes less time and that last ppm is gone even faster. These are amplified steps. But the amount of time it takes to remove all of the ammonia is not being done at a constant rate. Cycling is the process of ramping up the bacteria to be able to handle the ammonia as fast as the the tank inhabitants etc. produce it. We could begin to chop the time into smaller intervals and if we could measure ammonia accurately, we would see that the minute effects as the number of total bacteria ramps up. We could actually see the rate of NH4 being converted to NH3 increasing. So, while you absolutely right it saying it is an onging and virtually instantaneous process on the one hand, it can also be seen as a series of steps from another perspective. My description of the steps was based on the idea that if the number of bacteria did not increase, removing the ammonia would involve a large number of small meals before it hit 0. I stated things badly/incorrectly as you observed.
 
An interesting thing about the AOB is they seem to have the ability to increase their capacity to oxidize by some amount before they need to reproduce in order to consume it all. This has been proposed as a possible explanation why AOA numbers often are so much greater in certain evironments than they are for AOB. The AOA may not be doing that much more of the oxidizing despite their apparent numerical superiority. The bacterial ability to increase their processing capacity is lacking in the AOA which must reproduce for this.
 
Yeah, I read about the AOA too. I am too much of a nerd for my own good sometimes.

 

[hobby5]

Finally, I agree with you that the average fish keeper doesn't have a clue about most of this and should never need to have one. However, I also believe that if one is going to opt for doing a fish in cycle, then they do need to know about the NH3/NH4 facts, they need to know how to do diluted nitrite testing, they need to know how to counteract nitrite with chloride. If they don't wish to have to learn and master so much more and to dedicate so much more work and time to cycling, they should simply be doing a fishless cycle. If they follow the directions in the cycling article on this site (which I wrote), they will cycle a tank in good time and with few problems. And they do not have to know anything about NH3/NH4 or how to test nitrite that is over 5 ppm on their API kits. But when it comes to fish in cycling, what they should not be doing is a lot of unneeded water changes which can also be harmful in terms of fish stress levels.

Promised response:
Agreed, keep it as simple as possible but not simpler

 
I only partially agree with you on water changes. If you got clean tap water (I am lucky

), which you don't have to use water purifier or dechlorinator on, nothing beats frequent and generous water changes in terms of fish health. You always reduce bacteria (not the substrate bound bacteria in the filter) and waste products and fish thrive.
 

hobby- how can it be continuous?

It is

Even if you could measure in very small steps you would not observe any steps. There are serveral reasons: First, the bacteria don't take up ammonia and then use it, but this happens simultaniosly. Its rather like a running engine using a certain amount of electricity per hour. This engine also is sucking electricity continuously.  When bacteria grow they increase in volume and split in two as soon as as they reach a certain volume, with the two daughter cells beeing only half the volume of the mother cell. The capacity to metabolize something is usually related to the cell volume. (If the uptake is the rate limiting step it will be related to cell surface.) Hence that doubling event does not change capacity dramatically. Second those bacterial cells do not grow synchronised, i.e. if the doubling time were 24h u don't have X bacteria from 0-23:59 and they will all double at 24 and u have 2X afterwards, but those 24h are an average and some will be a little quicker some a little slower. Furthermore at time 0, as the growth is not synchronised, u got bacteria, which just doubled, some which are half way through and all other stages, hence also the growth and with it the increase in metabolising capacity is rather continuous.
 
Fun fact at the end:
In the German speaking world, nobody knows or measures ammonia, but all centers around nitrite. I wonder what the French, the Spanish or the Chinese are doing?

 

[TwoTankAmin]

What about the fact that individual bacterium (and thus also a bacterial colony) is able to increase its processing capacity before reaching the point of "wanting" to reproduce? (I need to relocate the research I found on this.) And not via growth. What about the fact that they will only reproduce when their "food" source is greater than what is needed to meet all their other energy needs?
 
From what I have seen, one of the most difficult parts of studying bacteria is that they are generally studied as bacteria rather than as individual bacterium. Science can tell us at what rate a bacterial colony may be able to or is oxidizing, it is another thing to nail this down to the level of a single specific cell. This is one of the things I think makes the AOB vs AOA  studies fall short. Merely counting cell numbers, amo genes etc. may not be providing accurate analyses of how much of the load is being carried by each.
 
In the hobby, when one refers to doubling it isn't the actual number of individual cells that counts, it is the ability to process more ammonia or nitrite that is important. What ever number it takes to process 1 ppm of ammonia in 24 hours, double that capacity would be whatever number it takes to process 2 ppm in that time (or the same amount in half the time). In terms of cycling, this is all that counts. It is not the numerical size of the colony that matters rather its the capacity to process. And this happens in steps as far as hobbyists are concerned.
 
So you and I are basically looking at the same things from opposite ends of the issue. And for we hobbyists, there is really only one way we can see it, from my end. We can test ammonia and nitrite levels, we can not see or count the actual bacteria involved. For the scientist, it is a continuous process, for the hobbyist it goes in stages.
 
But what I would love to know more than anything about the nitrifyers in our tanks. What is their natural decay rate? Some portion of the bacteria must be dying all the time even if they are being replaced. Can you shed any light on this topic? I am also curious, if there is not sufficient energy for reproduction or growth but there is enough for survival, what % of them will die off over what period of time? Finally, when they go dormant because of "starvation" conditions, what is the death rate like then then? My understanding is it actually slows under this condition?
 
Fun fact question: How can one do a fishless cycle without ever testing for the level of ammonia at a few crucial points. How do you know how much ammonia you have added for certain without testing? Ammonia may have lost strength, been misdosed etc. And then I wonder when something goes awry in an established tank what they do. Over here it is common that the first step is to test ammonia to rule it out. Do they test for nitrite instead? Would this even be reliable if the issue were the bacteria being knocked back, there could be ammonia because of this and no nitrite for the very same reason?

 

[hobby5]

You have a lot of valid points there and u r right that only capacity is what is important and what we can measure easily. But I stick to my view if you would measure often enough u would see that there are no steps, but bacteria and capacity will grow exponentially until and flatten out as soon as  capacity meets demand.
 

But what I would love to know more than anything about the nitrifyers in our tanks. What is their natural decay rate? Some portion of the bacteria must be dying all the time even if they are being replaced. Can you shed any light on this topic? I am also curious, if there is not sufficient energy for reproduction or growth but there is enough for survival, what % of them will die off over what period of time? Finally, when they go dormant because of "starvation" conditions, what is the death rate like then then? My understanding is it actually slows under this condition?

This is a very good question! I have asked myself that a lot but in a different context, namely how long will your filter bacteria survive, when u have to turn off the filter for moving it. Interestingly, decades ago when I started with fish keeping I used to turn off the filter over night cos it was too loud for sleeping next to it. Today everybody will tell you the bacteria are dying don't do that, but my fish did not mind (at least not obviously or I was too inexperienced to see it).
But bacteria are rather hardy and only die quickly if you poison them with something or if a different species can outgrow them because the conditions changed.
 
No cannot answer that, sry.
 

 
Fun fact question: How can one do a fishless cycle without ever testing for the level of ammonia at a few crucial points. How do you know how much ammonia you have added for certain without testing? Ammonia may have lost strength, been misdosed etc. And then I wonder when something goes awry in an established tank what they do. Over here it is common that the first step is to test ammonia to rule it out. Do they test for nitrite instead? Would this even be reliable if the issue were the bacteria being knocked back, there could be ammonia because of this and no nitrite for the very same reason?

Nobody is adding ammonia. People put plants (nearly every tank is planted here, new plants will first decompose to some extend before starting to grow so there is some ammonia liberation too, btw plants can and will also use ammonia), snails and a flake of fish food once in a while and follow nitrite levels. And you do not fully stock your tank but begin slowly after the fish less cycle. And if there is a problem people test for nitrites. Once in a while there is a tank where u got no nitrite but still a problem and nobody has a clue

It would be intersting to test those for ammonia!

 

[TwoTankAmin]

Every time I get involved in one of these threads, something I thoroughly enjoy because often I learn more, it get smy juices flowing and I head over to Google scholar. I just bookmarked a few more AOB and AOB things today. Here are two snippets (I know it bad to cherry pick), But I will link to the complete papers so I don"t feel guilty. Both apply to the my earlier comment about the AOB being able to adjust their ammonia oxidizining capacity without growing bigger or having to reproduce. It also goes to towards the issue of AOA vs AOB based on counting amo genes.
 

 
We evaluate the relationships between the abundance of ammonia oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) amoA genes; potential nitrification rates and environmental variables to identify factors influencing AOA abundance and nitrifier activity in estuarine sediments. Our results showed that potential nitrification rates increased as abundance of AOA amoA increased. In contrast, there was no relationship between potential nitrification rates and AOB amoA abundance.

from http/www.researchgate.net/publication/5803565_Ammonia_oxidation_and_ammonia-oxidizing_bacteria_and_archaea_from_estuaries_with_differing_histories_of_hypoxia/file/79e41507ecc9b15de2.pdf
 

 
Between two and four copies of the amo gene have been observed in the AOB of the β subclass [41–43,45,65].......
Studies with insertional mutants of N. europaea, in which each copy of amoA alone was inactivated, showed that both copies were expressed. Inactivation of only one copy resulted in slower growth, less full-sized mRNA, and reduced AMO activity (measured as ammonia-dependent O2 consumption and [14C]acetylene incorporation). Thus, each copy had a distinct metabolic function, but was not essential for growth [66].

 And, as for how long the bacteria might last:

 
Ammonia limitation caused specific inhibition of the AMO but not of the HAO activity within 24 h, whereas little change in the ammonia oxidation activity occurred in a medium without ammonia [74]. Under long-term (342 days) ammonia starvation of N. europaea, the activity of AMO and HAO remained stable, and the cells maintained a high level of the enzyme. After the addition of ammonia or hydroxylamine, there was an immediate response, measured as nitrite production, without initial protein synthesis [76].

Both quotes from http/onlinelibrary.wiley.com/doi/10.1111/j.1574-6976.2000.tb00566.x/full
 

 
We show that although ammonia-oxidizing archaea are present in large numbers in these soils, neither their abundance nor their activity increased with the application of an ammonia substrate, suggesting that their abundance was not related to the rate of nitrification. In contrast, the number of ammonia-oxidizing bacteria increased 3.2–10.4-fold and their activity increased 177-fold, in response to ammonia additions.

from http/www.nature.com/ngeo/journal/v2/n9/full/ngeo613.html
 
I am still getting the impression that, at least, some of AOB are able to process additional ammonia without having to grow larger or to divide and then grow to do so.
 
I really wish I was able to understand more of what I read in these papers. I normally have to accept the methods used were appropriate for the results. And a lt of things I have to Google to understand what it means. I am trying to locate a study I recall on the decay rates. I could not understand the way the numbers were expressed so failed to bookmark it. DOH.

 

[hobby5]

Hm lots of things too read up
 
From your second link: Both groups of nitrifiers can survive under anoxic conditions for months (Refering to AOB and NOB).
 
This is very good news, so I can assume that filter bacteria (at least the nitrifying bacteria) surved while the filter was turned off, and I will never again worry about em