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Low PH Nitrogen Cycle
August 21, 2013
1:02 am
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amazonrain
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Hello, my name is Adam. I have a question about how the nitrogen cycle occurs in an aquarium with a PH of 5.3. A little history about my tank...I have a 35 gallon Paludarium with all wild caught fish. I have 9 similius corydoras catfish, a pair or blue german rams, 10 rummynose tetras, 10 single lined pencil fish, 2 clams, 5 amano shrimp and 5 otocinclus catfish with a Caribsea Sunset Gold sand substrate 1 3/4 inches deep. I keep a steady PH of 5.3 with a GH of 100ppm and a KH of 120ppm with a temp of 76 degrees F. I am using RO water and a Product called Amazon Rain by Tropical Science. I do not consider myself an expert by any means however I am very knowledgable. This topic however alludes me no matter how much research I do. That being said I want to know how the nitrogen cycle occurs in an aquarium with a PH less than 6.0. I know that all nitrification of ammonia and nitrite and nitrates stop when a PH is lower than 6.0 so why do i have nitrates. I test for ammonium with the api ammonia test kit and there is ammonium in my tank which is removed with a water change. So why do I have nitrates if my tank is not supposed to cycle.

Anyone who can give me any knowledge about this topic will be greatly appreciated. If you have any questions for me about my setup let me know. Thanks guys.

August 21, 2013
11:27 pm
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BillT
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I have often wondered about this, but have not done anything more than think about it.

 

Is there a lot of ammonia and nitrite in natural low pH waters?

If not is it because:

rapid water turnover (vs. rate of ammonia production)?

low production of nitrogenous wastes in low pH water?

or ???

 

For 30 or 40 years the wrong bacteria was identified as being responsible for one of the nitrification steps in aquaria. I am not sure what is the current understanding of this stuff but it would not surprise me if the story is more complex than is commonly understood.

Personally I would expect different sets of bacteria to be adapted to different environments and fill the nitrogen processing nitches available there. I know from talking with a bacterial ecologist that different bacteria that process nitrogen compounds in different environments. Those that work best in aquariums come from similar environments where bacteria are processing levels of nitrogen compounds similar to those found in aquariums. Lots of bacteria can do this, but not all of them will do so efficiently in an aquarium setting.

Therefore I would expect (predict) that there would be different bacteria in more extreme environments to fulfill the same function. Getting your tank colonized by these might require inoculating with water from such a natural environment. If you do not live in an area with a low pH natural environment than it might be very unlikely that these bacteria could drift in on the wind to colonize your tank's ecosystem.

Bill Trevarrow [email protected]
August 24, 2013
7:24 am
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amazonrain
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Thank you that actually helps. In the dry season in Venezuela some of the tributaries are trapped off from the main river in turn having no water flow. There has to be some way the ammonia or ammonium is consumed or the fish would surely die. Most fish do not die until the water actually dries completely and they get eaten or dried out. Maybe you are right about the bacteria that we use being wrong. I have read about that in another article but I didnt think anything of it until now. Any thoughts on a test kit that will tell me whether I have ammonia or ammonium?  

I experimented and found a dosage of the "Amazon Rain" that makes my PH a stable 6.4 so I can have a slow but occuring cycle. I have a 100G Marineland 360 canister filter with all 3 trays filled with Seachem "Matrix" biological filtration media. Since my tank is only about 40 gallons at most this should be sufficient while adding "Nitromax" bacteria from Tropical Science. 

I also added a ton of plants because I think plants like ammonium more than nitrates. I read a very good article which i conveniently forgot the name of about how plants will actually compete for ammonia or ammonium with the nitrifying bacteria in filter and in your tank. Not sure how credible this is however it was stated in multiple articles in some way or another. I know that it isnt the most natural environment for some of my fish but I dont think they will be unhappy if they are in there. 

 

What bacteria do you use in your tank(s)? 

August 25, 2013
7:35 pm
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Byron Hosking
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I may be able to add a bit.

As has been mentioned, the low fish load to water volume in nature plus the ever-moving water (in streams and rivers) means that ammonia is not likely going to affect fish, barring some disaster.

Turning to the aquarium, the pH of the water being acidic means that ammonia is changed into ammonium, and this is basically harmless to fish.  My several tanks have for more than 20 years had a pH around 5 in some, 6 in others, and they are full of fish (mostly wild caught).  I have never had ammonia or nitrite above zero when I tested.  I also have live plants which grab the ammonium fast, and actually out-compete the bacteria/archaea all else being equal.  So in your (amazonrain) situation, I wouldn't worry at all.

On the bacteria itself, from my admittedly not exhaustive research I have found that with respect to pH, the nitrifying bacteria operate at close to 100% effectiveness at a pH of 8.3, and this level of efficiency decreases as the pH lowers.  At pH 7.0 efficiency is only 50%, at 6.5 only 30%, and at 6.0 only 10%.  Below 6.0 the bacteria enter a state of dormancy and cease functioning. Fortunately, in acidic water (pH below 7.0) ammonia automatically ionizes into ammonium which is basically harmless, as I mentioned above.  And since nitrite will not be produced when the ammonia-oxidizing bacteria are in “hibernation,” this decrease in their effectiveness poses no immediate danger to the fish and other life forms. 

Temperature also affects the rate of growth of nitrifying bacteria.  It will be optimal at a temperature between 25 and 30C/77 and 86F.  At a temperature of 18C/64F it will be 50%.  Above 35C/95F the bacteria has extreme difficulty.  At both 0C/32F (freezing) and 100C/212F (boiling) the bacteria die.

A study published only last year suggests that in established aquaria, it is not bacteria but rather archaea that perform the nitrification.  I'm fairly certain that Matt posted about this a while back, but you can read the entire paper here:

http://www.plosone.org/article.....ne.0023281

Hope this is of some help.

Byron.

Byron Hosking, BMus, MA Vancouver, BC Canada
August 26, 2013
10:01 pm
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Gloups
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Byron Hosking said

A study published only last year suggests that in established aquaria, it is not bacteria but rather archaea that perform the nitrification.  I'm fairly certain that Matt posted about this a while back, but you can read the entire paper here:

http://www.plosone.org/article.....ne.0023281

Byron.

This is a nice paper that brings a new view on an old topic. Unfortunately for this thread, no one of the sampled tanks were on the acidic side.

My guess is that one will soon heard about many new discoveries in this field, given the increasingly popular technologies for metagenome sequencing, on the one side and the ongoing progresses in genome sequencing from a single bacterial cell, on the other side.

September 9, 2013
4:04 am
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BillT
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I asked Tim Hovanec, my bacterial ecologist friend, about low pH nitrifiers.

This is his explanation:

"It is true that nitrifiers - more specially ammonia-oxidizing bacteria (AOB) don't do well in low pH environments.

The reason is that in water there are two forms - ammonia (NH3) and ammonium (NH4+).  The lower the pH the more the total ammonia is in the ammonium form while at higher pH values the more that the total ammonia exists in the NH3 form.

The AOB use the NH3 form.  So when the pH is low and most to nearly all the total ammonia is in the NH4+ form the bacteria do not have much substrate to convert and so the rate of oxidation to nitrite is very slow and therefore in a fish tank total ammonia builds up at low pH values."

 

However he did say he had heard of someone with a AOB/NOB processing bacterial culture adapted to low pH, so that remains a possibility. N=nitrite

Bill Trevarrow [email protected]
September 9, 2013
10:15 pm
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Gloups
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I am aware that many experienced killie keepers skip any cycling before introducing their precious fishes (e.g. Aphyosemion or "Rivulus") in tanks just setup and filled with acidified rain water. And I recently learned that the same practice is also common among Parosphromenus enthusiasts. Both these groups of aquarists are however not claiming this practice too loudly, possibly to avoid being flamed by "main stream" aquarists. But, I have no reason to doubt that this is actually working, as this has been reported by more than one very experienced specialist of these uneasy and delicate fishes from acidic biotopes.

Looking for some possible explanations, regarding the chemistry and the microbiology, I consider the following points:

* At low pH, NH4+ is the very predominant form of the NH4+/NH3 conjugate acid-base pairs and NH4+ is essentially and definitely non-toxic

* Nitrification from NH4+ to NO2- is either completely inhibited at low pH: NO2- is never produced and NH4+ is consumed by the plants and fungi. Or alternatively, and this is pure speculation, at low pH the bacteria responsible for nitrification from NH4+ to NO2- grow much slowly than those responsible for the next nitrification step from NO2- to NO3-, hence NO2- has no chance to accumulate at low pH, on the the contrary to what is observed at higher pH. Again, this last idea is purely speculative, but the microbiology paper previously mentioned in this thread clearly indicates that there is still much to learn in this domain.

It is a pleasure to discuss such topics on SF, thank you

September 10, 2013
6:56 am
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amazonrain
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Thank you all for your replies! I would like to know more about this acidified rain water and how you come about that if anyone wants to enlighten me. 

September 10, 2013
7:46 am
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BillT
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It is a pleasure to discuss such topics on SF

 

Yes I agree. It's nice to have a serious discussion on water chemistry or whatever.

It would be nice if these discussions could be triggered more frequently. This discussion seems to me to be concerned with a seriously unresolved question on an issue of basic knowledge for anyone keeping fish.

Not resolved but interesting to discuss.

 

Nitrification from NH4+ to NO2- is either completely inhibited at low pH: NO2- is never produced and NH4+ is consumed by the plants and fungi.

What plants do well at low pH's? They might make a good biofilter.

 

 

Another nitrification "rule" that may present problems at low pH's:

In the "normal" nitrification cycle (that which is referenced in textbooks), 7 carbonate molecules are consumed for each molecule of ammonia processed to nitrate. (I don't know the chemical details of this or how much occurs in which step.) For this reason, active biological filters need carbonate in the water to function efficiently. By this logic, carbonate deprived biofilters should not work well. Active biofilters will absorb carbonate out of the water, allowing the pH to more easily change

So how does this work at low pH? One would not expect much carbonate there, because carbonate is usually associated with alkalinity, the ability to slow a shift in the acid direction when acid is added.

Carbonic acid (H2CO3) can be derived from CO2 dissolved in the water or from other sources, like metabolism. Dissolved carbon dioxide reacts with water to make carbonic acid (CO2 + H2O ⇌ H2CO3). In any solution, there will be an equilibrium will form between different forms of carbonate: H2CO3 vs. H+ and HCO3- vs. 2H+ and CO3=. This equilibrium is different at different pHs. Higher pH's should favor H2CO3.

Perhaps this is the source of carbonate for/if nitrification occurs at low pH's.

Bill Trevarrow [email protected]
September 10, 2013
9:53 am
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Matt
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BillT said

What plants do well at low pH's? They might make a good biofilter.

No expert here but many Cryptocoryne species do, Barclaya as well. Pitcher plants?

Also have a question to add - if ammonia is primarily stored as non-toxic NH4+ in acidic systems, what effect(s) do its accumulation have in the long term?

Cake or death?
September 10, 2013
10:50 am
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BigTom
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What plants do well at low pH's? 

My experience is that most of the traditional low tech varieties will do OK... I've grown java fern, bolbitis, lilleaopsis, hair grass, mosses, anubias, crypts and various floaters such as Amazon frogbit and Phyllanthus fluitans around pH5. Paro breeders are all very keen on Ceratopsis thalictroides.

 

Plus you always have the option of using riparian plants, unless you need a tight fitting lid.

September 11, 2013
11:04 pm
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oaken
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Gloups said
I am aware that many experienced killie keepers skip any cycling before introducing their precious fishes (e.g. Aphyosemion or "Rivulus") in tanks just setup and filled with acidified rain water. And I recently learned that the same practice is also common among Parosphromenus enthusiasts. Both these groups of aquarists are however not claiming this practice too loudly, possibly to avoid being flamed by "main stream" aquarists. But, I have no reason to doubt that this is actually working, as this has been reported by more than one very experienced specialist of these uneasy and delicate fishes from acidic biotopes.

I do this quite often. Coincidentally I keep a lot of "Rivulus". But I feel that even if skipping the cycling part works, there is a need for some extra caution during the first weeks as the tank is still nowhere as stable as an established tank. I think there is more to an aquarium than bacteria, even if they do play a huge role. Algae is one of those things, plants as well. Like mentioned earlier, plants do make for a good biofilter and some plants (also mentioned already) like Ceratopteris are extremely good at removing nutrients from the water. I used to have a lot of Ceratopteris cornuta in my tanks, but I find that this plant develops extremely long roots when there's not enough nutrients in the water, and these roots eventually take over the tank. So nowadays I mostly use Salvinia spp. I also like to use Microsorium and different types of moss. In a setup like this you don't actually need a normal filter, but I think some aeration of the water is always beneficial. 

Most plants do quite well in "low" pH. The problems start to arise when you want to go really low, in my experience. Like under pH 5. And as far as I can remember most plants actually prefer a lowish pH value. Some plants don't seem to like it all though, Ceratophyllum, for example. 

 

September 12, 2013
3:36 am
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BillT
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Most plants do quite well in "low" pH. The problems start to arise when you want to go really low, in my experience. Like under pH 5.

 

What is your preferred method of measuring pH in these tanks.

I don't think my pH strips work well in weakly buffered water.

Bill Trevarrow [email protected]
September 13, 2013
10:24 am
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oaken
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To be honest I stopped measuring pH in my tanks a long time ago. But when I did I did actually buy some decent eletronic equipment (they don't last very long however if you don't take very good care of them).  When I did measure I made some notes for how how much acid I need to lower my tapwater to certain values. And I'm not sure pH strips are ever reliable? At least that is what I've Heard. If I ever feel the need to measure pH these days I use a normal drip test. It's not very exact but then again very few fish are going to care.

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