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JDM 12-12-2012 02:37 PM

Ammonia and plants, just a little research and chemistry
Some probably saw my 25H cycle post where it was recommended that I use plants instead of cycling my tank the classic way. I sat down and worked out the chemical reactions to see what was happening to the various components of ammonia, ammonium, nitrites and nitrates and perhaps get a better handle on why.

Another thread prompted me to look at this closer as someone there was vehemently opposed to plants.

My old chemistry is a bit rusty I found, so I had to do some research.

A few things that I learned:

Ammonia is more toxic than ammonium for whatever reason, I didn't investigate that.

Ammonia (NH3) and ammonium(NH4) are both present in water in an equilibrium. At higher water pH levels, the amount of toxic ammonia is higher than ammonium and at lower levels the reverse is the case... there are other ions in the mix but this is the main point. Both likely show up in the testing process so the ammonia test will show the total.

Plants use ammonium, not ammonia, to produce their building blocks. The more ammonium they draw from the water, the more is created from the the water and ammonia/ammonium balanced reaction which in turn reduces the toxicity to the fish until the levels reach zero, or near zero.

Seeing as a) the plants use the ammonium directly and don't need to convert it to something else first and b) they also use nitrates but need to convert it to ammonium first; it only stands to reason that the plants will not use nitrates if ammonium is present. Seeing as ammonium is in the water more so than in the substrate, I expect that not much is absorbed through the root systems which explains why so many aquatic plants are not well rooted, if at all.

I didn't look at the bacterial involvement so I don't know if the nitrosomona eat the ammonia or ammonium, I think the latter so the balance works the same as for the plants. Either way this puts the bacteria and plants in direct competition for the ammonium. This would put an established old school cycled tank at a disadvantage when it comes to incorporating plants after the fact. (yes guys, you were right to guide me to plants at the beginning)

Aquatic plants act as an ammonia sink rather than converting it to something else that requires processing into yet something else that just needs to be removed from the water later. No nitrites are produced (not by the plants anyway) that need to be converted to less harmful nitrates. What nitrites are produced in the tank can be easily handled by the nitrospira bacteria that do develop over time.

I did find a compilation of studies that found that not only do the plants prefer ammonium, they will not even touch the Nitrates until the ammonium levels are zero and they suck up the ammonium fast. That's good for the fish but means that it is tough to remove the nitrates that do develop in any way other than water changes. Perhaps a plant that roots in the substrate but all of it's greenery is above water would be able to do some of this job... I haven't looked at natural ways to remove nitrates yet. Maybe someone else can point me in the right direction.


Byron 12-12-2012 03:51 PM

You have a very good grasp of things, indeed. Your research has paid off.:-)

One minor correction, and that is that plants will take up ammonia and ammonium, whichever is present. They change ammonia to ammonium to use as a nutrient. So as you said, plants are an ammonia sink in effect, and they can take up a considerable amount beyond what they use as nutrient. I am not a chemist and I haven't bothered to fuss over the precise chemistry on ammonia/ammonium and pH, but ammonia does change into ammonium in acidic water, and in basic the reverse. But the plants grab whichever fast.

Ammonia/ammonium is taken up via the leaves of aquatic plants, as are several other nutrients (CO2, O, potassium, hydrogen, etc). The roots are needed for other nutrients, and the plant expels copious amounts of oxygen via the roots during photosynthesis.

Studies suggest that nitrites will be taken up next, by many plants, even before nitrates. But only if ammonia/ammonium is exhausted. Nitrates can also be used, but as their third choice. The internal conversion of nitrate back into ammonium that the plants must use consumes a considerable amount of energy, which is thus "wasted" because it cannot be applied to direct photosynthesis and growth.

As for nitrates building, they should not, or at least not in appreciable numbers. Many planted tank aquarists have zero nitrates. My tanks run around 5ppm, one is <10ppm. But I have a lot of fish, more than some might, and I do 50% water changes every week. Nitrates are actually part of the complete bacterial cycle as there are bacteria in the substrate that use nitrates to produce oxygen, and other bacteria convert nitrates back into nitrogen gas to fully complete the cycle. But nitrates should never be allowed above 20ppm, and for any fish the lower the better in all cases.

Nitrosomonas will grab ammonia or ammonium, equally if either is present. Water conditioners and similar ammonia-detoxifying products usually work by changing ammonia to ammonium, but the bacteria doesn't care which. Although interestingly, recent studies indicate that bacteria actually are not involved in this, it is archaea, another life form that used to be considered in the bacteria but is now distinct. Just to keep us on our toes.


JDM 12-12-2012 04:54 PM

Always new stuff. I kept running into references to nitrobacter or something, turns out that is the bacteria that used to be considered the ammonia gulper... old news.

I'm not so sure that the plants or nitrosomona (or archaea as the case may be) do use ammonia, not trying to argue or make a particular point other than the way that the ammonia/ammonium balancing act occurs automatically in the water... and in both directions... it is as likely as not that consuming the ammonium forces the conversion of ammonia into ammonium, and there is no easy way of determining if the plant is responsible or not... both compounds would disappear at roughly the same rate either way. Seeing as one cannot be present without the other, naturally anyway, in some ratio determined by the pH, ammonium could not be consumed totally without the corresponding ammonia being ionized to keep up with the depletion which could easily appear as though both were being consumed by the plants.

I suppose, just like the ammonia de-tox chemicals converting to ammonium, some other chemical could force ammonium into ammonia to force feed the plants to prove that they will use it. I just expect that there is less energy expense in using NH3 when both are present... why bother?

I know that I will never likely prove this myself so beyond this, I won't worry about it again. My daughter's science project is due before Christmas or we might have done something aquarium related... this would have been a good topic. So we are down to breaking craft sticks to plot the breaking point of statically loaded composite materials. It's amazing how much of a difference there is even in little sticks of wood. I didn't anticipate having to lug around 50-100lbs of weights though.


beaslbob 12-12-2012 04:58 PM

+1 with bryon

(hope he doesn't faint). :lol:

Your research is correct and explains the "silent" planted cycle where a cycling tank with heavy plants experience little or no ammonia spikes but can have an initial nitrate spike.

What happens is the aerobic bacteria are still there (even introduced by the plants themselves) and start building up and consuming the ammonia. So that after a time the bacteria get the ammonia and the plants start consuming nitrates. So after a few weeks that possible nitrate spike drops down.

And eventually the tank runs with ammonia and nitrItes being reduced by bacteria and nitrates, phosphates and carbon dioxide beign consumed by the plants which in turn return oxygen.

During the entire process the tank is safe for fish expecially compared to the ammonia->nitrIte->nitrate bacteria cycle.

Now consider this (which I consider extremely important), say something goes bump in the night. A fish dies. Over feeding whatever. Ammonia bumps up.

So what happens?.

Just like in the cycling tank the plants switch to consuming the ammonia preventing the dangerous spikes and tank crashes. And in the process nitrates bump also but that is much safer. Then as things are brought back into line the plants resume consuming nitrates.

So the tank rapidily returns back to the starting point in a safe manner. Hence my personal emphasis on stability. The tank is basically very forgiving of my type errors. :lol:

my .02

Byron 12-12-2012 05:15 PM

Bob, I honestly do mean it when I say I am sorry for having to correct something, after you agreed with me...but ...:sob:

First JDM, on the Nitrobacter, this is the bacteria that we used to believe consumed nitrite and changed it to nitrate, but Dr. Tim Hovanec and others proved this wrong, and Nitrospira is the actual bacteria. Nitrosomonas handles ammonia to nitrite, then Nitrospira nitrite to nitrate. Except it is now archaea...:roll:

And also JDM, the ammonia/ammonium balance is non-existent in most cases. Fish produce ammonia; in acidic water it immediately changes to ammonium, but in basic water it remains ammonia. The plants grab it in both cases and use it, either directly as ammonium in acidic water, or as ammonia in basic water and in this case they change some into ammonium internally, and take up the rest as a toxin and detoxify it. [More on this below]

To Bob's post. If the tank is well planted with relatively fast-growing plants, almost all of the ammonia produced by fish during respiration or by the breakdown of organics will be taken up by the plants. Studies have shown that plants actually do this faster than Nitrosomonas [or whatever they are;-)]. And the amount of ammonia plants can take up is quite amazing. I once raised this with Tom Barr, and he came back with a figure that I would have to dig for hours to get, but he said not to worry about levels because it would take a disaster to create too much ammonia for the plants to deal with. They not only use some as their nitrogen, but they can take up and detoxify lots as well. Which is why your "ammonia bumps" won't occur, or more correctly, the ammonia will appear and be gobbled up before it can do damage to fish.

Second, these plants will not use nitrates unless the ammonia is exhausted, as I think I explained previously. There will be no nitrate spike in a new planted tank, just as there will be no ammonia or nitrite visible at all. The nitrates will, or may, perhaps build up relatively slowly, depending upon the organic load.

The bacteria/archaea will still be present, but in greatly lower numbers with live plants.


beaslbob 12-12-2012 09:55 PM

actually bryon we agrre more then you think.

I have noticed an initial nitrate spike in my tanks started with plants. but I suspect that was coming from the organics like peat moss in the substrate. Not from the bioload. So there was an initial source of nitrates.

Then after awhile the nitrates drop down. Which I suspect happens when the bacteria build up and anr then csonuming the ammonia. So the plants then start consuming the nitrates.

I also noticed a minor nitrIte spike a few days after adding a fish or a week later when I started very light feeding. I suspect that spike would have been much more pronounced had I added more fish and/or did heavier feeding.

but overall I think we are on the same page.

my .02

pop 12-14-2012 08:49 AM

salutations dr. stanley:
Has anyone considered the possibility of removing ammonia by using air bubbles to collect the dissolved ammonia, the idea here as the bubbles rise through the water column they react with the water exchanging not only carbon dioxide but ammonia as well on there ride to the surface releasing the adsorbed ammonia and carbon dioxide into the air. Would this be desorption of ammonia from the water column? Just an idea from the thread.

JDM 12-14-2012 09:05 AM

For sake of argument,

I'm pretty sure that the exchange would be too little to make any appreciable difference compared to how much and how fast the plants can absorb it.

Seeing as CO2 is often injected into the water to accommodate the plants (not sure who here as done it but it seems to come up often with heavily planted tanks) and the bubbling effectively removes CO2, this would be counter productive anyway... from a planted tank angle at least. The plants will grow and operate based on the least available factor (light, various nutrients etc) so pulling out CO2 could slow down the plants even if everything else is available in plentitude but CO2 is not. I can't recall who determined this but there is some named law I think.

So between the minimal ammonium/ammonia gas exchange and the potential to reduce the plants capability to absorb the same....


pop 12-14-2012 11:29 AM

good observation about benefits. i don't test for ammonia so i don't have a test kit, it would be fun to see how much ammonia is removed by tiny little bubbles in about 2 gals of water. You are mostly right about the benefit.

equatics 12-17-2012 04:12 PM


Originally Posted by JDM (Post 1346565)
Some probably saw my 25H cycle post where it was recommended that I use .
I haven't looked at natural ways to remove nitrates yet. Maybe someone else can point me in the right direction.


Jeff, thank you for bringing your research and the concepts up. I hope the "silent cycle" is now accessible to more people.

I have another question. What does 0 ammonia/um 0 nitrite and 0 nitrate mean, like what things are happenning in the tank when nitrate is 0? I have pondered on this and I think that it's because the ammonia/um is not continuing in the Nitrogen Cycle but instead is being consumed by the plants. I understand that plants are able to consume nitrate that have already been converted by archaia (typo) and I have no way to prove it but I think it's the first case and that would be the default. There are a lot of nitrifying bacteria around a tank, though, and if there is no or not enough ammonia/um available, they start to die back.

Thanks for your important work.

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