Cycling and microbial interactions in aquariums below pH 6.0

[Dennis Wong]

TLDR: In the pH 5+ range, with no plants/substrate, with just a filter, the system eventually processed 0.8ppm of ammonia within 24 hours. And this rate would probably speed up with more ammonia fed to the system.

Recently I shifted the contents of a planted tank away and used the matured filter and setup to test the age old idea that "a tank stops cycling below pH 6" or that "bacteria stops processing ammonia below pH 6". I had a matured filter, and the empty tank was still connected up to a CO2 injection system that I used to suppress the pH down to between 5.2(at peak saturation) to 5.9 (when CO2 is turned off). GH was around 3 and KH was <1. Ammonium sulphate was dosed and tested across many days.




Ammonia readings subsided slowly at the start (but decreased each day), then sped up after a few days had passed. Eventually, after a week or so, the system could digest 1+ppm of ammonia over a 24hr window.

Due to the plant mass that existed before the tank was cleared, it is likely that most of the ammonia produced in the tank was taken up by plants. When ammonia was first added to the now empty tank, it took many days for the microbial system to process the ammonia. However, as the microbial communities ramped up, now that they are not competing with plants for ammonia, the processing of ammonia quickened to digest more than 1ppm in a 24hr window. The test is still on-going as it it.

My hypothesis is that in acidic systems, species that operate well in acidic environments become the primary ammonia oxidisers over time. These microbial strains can be quite different from the ones used by fishery industries - which are more efficient but dependent on higher alkalinity ranges to function. So acidic tanks do cycle and mature with time, but with their own microbial mix that is suited to that kind of environment.

The actual reading and dates:
18/7/2025
Added Ammonia
Ammonia test 1.10ppm 2pm
19/7/2025
Ammonia test 0.9ppm 2.30ppm
20/7/2025
Ammonia test 0.71ppm 1.00pm
21/7/2025
Ammonia test 0.31ppm 2.30pm
22/7/2025
Ammonia test 0.03ppm 3pm
Dosed ammonia again to 1.2ppm 3pm
23/7/2025
Ammonia test 0.80ppm 1.30pm
24/72025
Ammonia test 0.0ppm 2.30pm
Dosed 1.30ppm ammonia 2.30pm

In aquariums where there is no CO2 injection/generation, such as fish-only aquariums without plants, non-intentional changes in pH can signal deteriorating biological conditions which can be major red flags. A mass fish die off for example, will drive up carbon dioxide levels through decomposition, while depleting oxygen levels at the same time. This results in the pH dropping precipitously. The depletion of oxygen and deterioration of water quality is what affects aquarium inhabitants. The change in pH is merely a symptom of underlying problems. I suspect this is why low pH is such as scary thing for the generic aquarium crowd.

 

[Pepere]

I love reading write ups of testing like this.

Thank you for researching and sharing this.

 

[Sb1415]

Thank you very helpful to know, and love the scientific approach to this.

As a hobbyist my comments are,
1. What about those of us who have alkaline water to start with and inert substrate that our pH does not go below 7. Do you think this would still hold true ? Not the question you were trying to answer but curious.

2. Isn’t this in essence talking about what happens in dark start ?

As a person with scientific background and with an immense appreciation for what you do and your goals to bring aquascaping knowledge in an accessible way to everyone, my questions are

1. To prove causation an additional layer of support would come from another tank with only water and co2 and some way of producing just flow to show that the ammonia does not automatically dissipate.

2. I would encourage you to publish this not only on the 2hr aquarist website but also in a peer reviewed journal

 

[ElleDee]

2. I would encourage you to publish this not only on the 2hr aquarist website but also in a peer reviewed journal

I don't think what Dennis is demonstrating here is new to science at large, but rather combating misinformation that persists in the hobby. If you want to get into where the current science is, Darryl at UKAPS has a series that digs into newer research that shows that nitrification in the aquarium goes beyond the traditional view of cycling we learned when we were new to the hobby. He even has some direct correspondence with some of the researchers. I'm pulling from memory, but this includes stuff like the importance of nitrifying archea and comammox bacteria which can completely oxidize ammonia to nitrate. It's good reading.

That information hasn't really filtered down into the hobby though, so we still have to contend with hoary old myths about low pH preventing nitrification. Dennis's demonstration will hopefully help with that, at least among planted tank people.

I think it's also worth pointing out that changing your aquarium parameters during start up to speed up cycling may be counterproductive. There are many species that can oxidize nitrogen products that are competing for resources, but because of natural selection which ones thrive vary depending on the environment. If you run the tank very warm, with higher pH than usual, you are selecting for microbes that do best in those conditions. Once you change your parameters back, the population will have to adjust again.

 

[Bubble]

The idea that "bacteria stops processing ammonia below pH 6"" is indeed old and the main issue with it is the use of just the word "bacteria" or in other words oversimplification for the sake of accessibility. It would be just like saying "Aquascapers use high light for their aquariums"... there is no uniform group of aquascapers, just like there is no uniformity with bacteria.

We know that there is bacterial ammonia oxidation at lower pH values for many years now. It exists, it's proven, it's happening and there are many organisms capable of it, for example a relatively new paper:
Picone et al , Nature, 2020

In this work, we report on the discovery, cultivation, {...} of a novel gammaproteobacterial ammonia-oxidizing bacterium enriched via continuous bioreactor cultivation from an acidic air biofilter that was able to grow and oxidize ammonia at pH 2.5

Nevertheless, without going into the weeds, I would still argue that it's sound advice to have a pH higher than 6, or rather having some detectable KH , say 3-4 when first starting a tank , for most beginner aquarists. And this last part is the most important one, if you are an expert, you should be the expert and not use thumb rules meant for beginners. If you have a niche tank, with certain fish or plants that need no KH and extremely low pH then it's no use starting a tank with KH 4... that is an exception though.
As you say, you have an established filter adjusted to no KH and acidic environment and still after a week of increased dosing it's not able to deal with 1.2 mg/L TAN in a day. I have started a new tank with a new filter and no added (or measured) KH. We'll see how it develops. For the majority, with a new tank, new filter, a need to add fish as fast as possible, it would be preferred to establish the "common bacteria", as they are... well... common (as in easily introduced), good first colonizers, grow fast, are robust and process many ppm of ammonia. And we know they do better in higher pH, room temperature, well oxygenated water with abundant KH (HCO3) as a source of buffer and of carbon.

So I guess, I'm saying we know ammonia oxidation can take place under extreme conditons and at the same time we need to show beginners the easy way.

 

[ElleDee]

Nevertheless, without going into the weeds, I would still argue that it's sound advice to have a pH higher than 6, or rather having some detectable KH , say 3-4 when first starting a tank , for most beginner aquarists. And this last part is the most important one, if you are an expert, you should be the expert and not use thumb rules meant for beginners. If you have a niche tank, with certain fish or plants that need no KH and extremely low pH then it's no use starting a tank with KH 4... that is an exception though.
As you say, you have an established filter adjusted to no KH and acidic environment and still after a week of increased dosing it's not able to deal with 1.2 mg/L TAN in a day. I have started a new tank with a new filter and no added (or measured) KH. We'll see how it develops. For the majority, with a new tank, new filter, a need to add fish as fast as possible, it would be preferred to establish the "common bacteria", as they are... well... common (as in easily introduced), good first colonizers, grow fast, are robust and process many ppm of ammonia. And we know they do better in higher pH, room temperature, well oxygenated water with abundant KH (HCO3) as a source of buffer and of carbon.

So I guess, I'm saying we know ammonia oxidation can take place under extreme conditons and at the same time we need to show beginners the easy way.

I didn't take this post as giving recommendations for beginners, but I don't think that going full RO and high CO2 is for casual beginners anyway. That's already a niche tank. If you are going that route from the jump you need to be committed to keeping up with it or there are a million ways to fail outside of a pH crash.

I have 1.5 dkh out of the tap and don't inject CO2 and I can barely get south of 7.0 in normal operations. I see this recommendation for adding more dkh, but it seems like it's not based in practice, at least for planted tanks. It seems like it would be better advice to, like, not overstock rather than to keep the water so over buffered.

 

[GreggZ]

Great write up Dennis!

I remember back years ago when I announced I was going to basically zero dKH with pure RO water people thought I was nuts.

The pH crash police were all over me.

Now many years later there are loads of examples out there of excellent tanks running with very little to no dKH.

I think your article years ago about very low pH tanks helped people gain a better understanding.

As always keep up the good work!

 

[Dennis Wong]

Thank you very helpful to know, and love the scientific approach to this.

As a hobbyist my comments are,
1. What about those of us who have alkaline water to start with and inert substrate that our pH does not go below 7. Do you think this would still hold true ? Not the question you were trying to answer but curious.

2. Isn’t this in essence talking about what happens in dark start ?

As a person with scientific background and with an immense appreciation for what you do and your goals to bring aquascaping knowledge in an accessible way to everyone, my questions are

1. To prove causation an additional layer of support would come from another tank with only water and co2 and some way of producing just flow to show that the ammonia does not automatically dissipate.

2. I would encourage you to publish this not only on the 2hr aquarist website but also in a peer reviewed journal

1. if ammonia automatically dissipate the readings would be completely linear, however, it accelerates at a certain point (similar to how cycled tanks work).
2. I'm not scientist lol. As long as there is enough evidence for folks to use it in practice, I'm happy to publish the results on my own websites. Folks are totally free to believe whose advice they choose to follow or not.

The idea that "bacteria stops processing ammonia below pH 6"" is indeed old and the main issue with it is the use of just the word "bacteria" or in other words oversimplification for the sake of accessibility. It would be just like saying "Aquascapers use high light for their aquariums"... there is no uniform group of aquascapers, just like there is no uniformity with bacteria.

We know that there is bacterial ammonia oxidation at lower pH values for many years now. It exists, it's proven, it's happening and there are many organisms capable of it, for example a relatively new paper:
Picone et al , Nature, 2020


Nevertheless, without going into the weeds, I would still argue that it's sound advice to have a pH higher than 6, or rather having some detectable KH , say 3-4 when first starting a tank , for most beginner aquarists. And this last part is the most important one, if you are an expert, you should be the expert and not use thumb rules meant for beginners. If you have a niche tank, with certain fish or plants that need no KH and extremely low pH then it's no use starting a tank with KH 4... that is an exception though.
As you say, you have an established filter adjusted to no KH and acidic environment and still after a week of increased dosing it's not able to deal with 1.2 mg/L TAN in a day. I have started a new tank with a new filter and no added (or measured) KH. We'll see how it develops. For the majority, with a new tank, new filter, a need to add fish as fast as possible, it would be preferred to establish the "common bacteria", as they are... well... common (as in easily introduced), good first colonizers, grow fast, are robust and process many ppm of ammonia. And we know they do better in higher pH, room temperature, well oxygenated water with abundant KH (HCO3) as a source of buffer and of carbon.

So I guess, I'm saying we know ammonia oxidation can take place under extreme conditons and at the same time we need to show beginners the easy way.

What is extreme conditions for one group of folks is the default condition for another group of folks. Due to 2hrAquarist's spread, I have customer side data across 4 continents. And also took data from various shops across countries where we have a presence. Many countries are pre-dominantly soft water or very soft water (between 0-2 dKH out of tap). Japan, thailand, parts of Indonesia, Singapore, Malaysia all have soft tap water in most areas.

Due to costs differences (as in aquasoil is cheaper in asia due to proximity to where they are produced - China/japan), its rare to actually see non-aquasoil planted tanks. As in almost every planted aquarium here uses aquasoil, and is combined with soft tap water (resulting in super low KH values). There are thousands of tanks set up this way across the entire continent. Some shops use planted tanks as their holding tanks for fish, so they are quite well stocked. So even before I did the experiments above, I can kinda already guess what the answer was - that these tanks worked perfectly fine for the large groups of even inexperienced hobbyists.

In most of these countries buffering KH was never an idea that spread (these folks did not spend time browsing english forums), so folks just did not do it. None the less, virtually all these tanks ran pretty normally (between pH 5 to low 6+, less than 1dKH) and from the shop/customer point of view we never got reports of tanks crashing due to low pH. Any reports that came in to do with "pH crashes", weirdly came from tanks that run inert substrate (but too few datapoints for it to be commented on with any significance). Not only that, an overwhelming number of complaints pertaining to pH issues we get comes from 1 single country (also the one country that has been more obsessed with KH buffering than any other). It could well be that that country just has poorer tap water in general, or that hobbyist's self-diagnosis carry the bias of what they read online and that their issues isn't related to pH at all.

I think that for aquasoil tanks in soft water countries, over-buffering the water actually causes issues. Rather than propagating microbes that are suited to the naturally low pH environment, you would be trying to promote strains that are suited for a higher pH/KH level. And you would be fighting the aquasoil all the time. Adding 3 to 4dKH to an aquasoil tank will see it quickly reduce to 1 or less within the week in a tank with fresh aquasoil. This is the exact kind of advice I would be warning against.

 

[acino]

Thank you for the write up, Dennis. I really enjoy reading about the perspective dissonance that evolved within Western audience vs. the audience in Asia!

 

[daa13157]

Life will find a way...

Thank you for sharing!

 

[Dennis Wong]

I asked Sudipta shaw the question whether one should buffer low pH/KH tanks and I thought his answer was very informative, as he actually did studies of bacteria in aquarium so I'm pasting his answer here for folks to read also:

"I don't see any compelling reason to increase KH for plant centric tanks with livestock not requiring alkaline conditions, especially if someone is using aquasoil. I think there are two primary reasons why many people advocate for high KH; One is this so called fascination about select groups of nitrifying bacteria, which don't exist in any meaningful way in most healthy tanks including tanks with higher KH (in plant centric tanks with livestock not picky about KH). As far as I know, healthy tanks generally don't produce enough ammonia to sustain a huge population of these bacteria because their enzymes have low affinity for ammonia, they need higher ammonia concentration to thrive. That's why these are primarily found in decent numbers in waste water treatment facilities and contaminated water bodies. There are several scientific studies on healthy freshwater systems including aquariums which show that these popular nitrifying bacteria (in the hobby) are not the primary nitrifying microbes (particularly for the first and the most difficult reaction that is conversion of ammonia to nitrite). I have done two separate DNA analysis from multiple tanks and I see the same thing. Not even a single tank showed any meaningful presence of these legendary nitrifying bacteria. Another reason for many people to stay obsessed with this higher KH theory is that they find it difficult to comprehend that KH is not the only factor that can maintain a stable pH (buffering capacity). Tanks with aquasoil also maintain a stable but low pH for decent amount of time. There are other factors as well such as application of phosphate as fertilizers for plants. Phosphate is a common buffer and is one of the primary buffers used in biochemical research. When applied on a regular basis as fertilizer in tanks with regular maintenance (weekly water change, substrate cleaning etc.), it can also maintain a stable pH in tanks with inert substrates with almost 0 dKH as well. This would mainly apply to people who dose ei. The point is, it is certainly possible to maintain low and stable pH in planted tanks which should be the main objective rather than getting obsessed about achieving some magical pH by increasing KH. I have not even mentioned about the effects on CO2 uptake by plants in higher KH water and potential negative effects on Fe and other metal uptake mechanism. There is a reason why most people struggle to grow plants in relatively higher KH water."

 

[Burr740]

Good stuff. I'd throw a wild guess and say the "pH crash" the inert substrate people saw was more a tank crash in general, not related to PH/KH. Especially if aquasoil subs are the norm there, they likely tried to apply methods designed for rich subs

I keep 4 or 5 sand tanks at 0 kh for years now. The only crashes Ive seen is when Ive gotten lazy on something

Adding; Reading Sudipta's input on po4, my sand tanks do get pretty heavy dosing, around 5 ppm PO4 between 50% water changes. The water column probably rolls with 7-9 ppm total. So that may offer a buffer like he mentioned

I have never ran a sand tank with little to zero PO4 in the water, cant say what itd do without it. Plants would go to shit though, I know that! lol

 

[acino]

Interesting points on the DNA analysis, thanks!

However, I am not convinced about PO4 being a meaningful buffer in our tanks. Even at 5 ppm concentration in water, the buffering capacity (c ~50 μM) is way smaller compared to KH (1 °dKH corresponds to c ~ 180 μM). The parallel of using PO4 as a buffer in biochemical research should be taken with caution. Although it is true, the concentrations used are way higher than what we have in tanks (10 mM vs ~50 μM, i.e. 200 times higher).

 

[Pepere]

In aquariums where there is no CO2 injection/generation, such as fish-only aquariums without plants, non-intentional changes in pH can signal deteriorating biological conditions which can be major red flags. A mass fish die off for example, will drive up carbon dioxide levels through decomposition, while depleting oxygen levels at the same time. This results in the pH dropping precipitously. The depletion of oxygen and deterioration of water quality is what affects aquarium inhabitants. The change in pH is merely a symptom of underlying problems. I suspect this is why low pH is such as scary thing for the generic aquarium crowd.

This is interesting and certainly a possibility… but it does beg the question as to what precipitated the mass did off in the first place if the ph “crash” was merely a result of the decomposition that occurred.

Ie did the low kh water have any supportive affects on the chain of events that led up to the die off?

I suspect low KH tanks with regular significant water changes fare better than low KH tanks that predominantly see mostly water top offs.. I can see where just doing a top off of low kh water especially in inert substrate might be more prone to ph falling from accumulation of acids not being water changed out.

 

[Dennis Wong]

Interestingly I inserted the question into AI prompt and this was the answer that I got:

Does ammonia oxidation by microbes stop below below pH6.0?​

Does ammonia oxidation by microbes stop below below pH6.0?



https://pmc.ncbi.nlm.nih.gov/articles/PMC106468/
https://pmc.ncbi.nlm.nih.gov/articles/PMC92966/
https://pmc.ncbi.nlm.nih.gov/articles/PMC525248/
https://www.abdn.ac.uk/staffpages/uploads/mbi010/Soil Biology and Biochemistry 25, 935-941.pdf

Ammonia Oxidation by Microbes and pH 6.0: A Complex Relationship​

Ammonia oxidation by microbes does not categorically stop below pH 6.0, but the relationship between pH and microbial ammonia oxidation is complex and depends on several factors including the specific microorganisms involved, environmental conditions, and whether the microbes are in pure culture or natural communities.

Traditional Understanding vs. Recent Discoveries​

Pure Culture Laboratory Studies

Traditional laboratory studies with pure cultures of ammonia-oxidizing bacteria (AOB) have consistently shown that ammonia oxidation becomes severely limited or ceases at pH values around 6.0 or below. The pH range for growth of pure cultures of ammonia oxidizers is typically 5.8 to 8.5, with most studies indicating that growth of pure cultures in liquid culture does not occur below pH 6.5. For Nitrosomonas europaea, a common laboratory strain, the pH minimum for growth in liquid culture is pH 7, though it can show activity in biofilm systems at pH 6.

The cessation of ammonia oxidation at low pH in pure cultures is attributed to several mechanisms:

• Energy limitation: At low pH values, the energy available from the proton motive force becomes too small for NADH production, causing an energy-limited state in the bacterial cells
• Substrate limitation: Free ammonia (NH₃), the actual substrate for ammonia monooxygenase, becomes severely limited due to protonation to ammonium (NH₄⁺) at low pH
• Toxicity effects: Accumulation of nitrous acid (HNO₂) at low pH can inhibit microbial activity

Natural Environment Exceptions

Despite these laboratory limitations, nitrification has been consistently observed in natural environments at pH values well below 6.0, including:

• Acid soils with pH values as low as 3.7-4.0
• Some of the highest rates of soil nitrification occurring in acidic soils (pH < 5.5)
• Engineered systems achieving ammonia oxidation at pH 2.5

pH Thresholds and Species Variation​

Critical pH Ranges

Research has identified several critical pH thresholds for different aspects of ammonia oxidation:

• pH 5.8-6.0: This represents a critical transition zone where conventional ammonia-oxidizing bacteria like Nitrosomonas europaea begin to lose activity
• pH 5.4: This is identified as a typical pH limit for the N. europaea lineage, below which acid-tolerant species may take over
• pH 4.35-5.36: Some studies have demonstrated stable ammonia oxidation in engineered systems at these extremely low pH values

Microbial Community Shifts

The ability of ammonia oxidation to continue below pH 6.0 often involves shifts in the microbial community:

At pH 6.0 and above, Nitrosomonas europaea typically dominates. As pH decreases below this threshold, more acid-tolerant species become active:

• Candidatus Nitrosoglobus: Becomes dominant at pH 4.35
• Candidatus Nitrosacidococcus urinae: Can grow at pH as low as 2.2
• Novel gammaproteobacterial species: Some can oxidize ammonia at pH 2.5
• Nitrosospira species: Show tolerance to pH levels as low as 4.5

Environmental and Operational Factors​

Biofilm vs. Planktonic Growth

Attached populations in biofilms can maintain ammonia oxidation at lower pH values than suspended cells. This is attributed to localized pH buffering at attachment surfaces and microenvironmental conditions that differ from bulk solution pH.

Substrate Concentrations and Alkalinity

The relationship between pH and ammonia oxidation is influenced by:

• Ammonia concentration in the medium
• Alkalinity of the system
• Presence of buffering compounds
• Oxygen availability

Practical Implications

For wastewater treatment applications, stable nitrification without nitrite accumulation typically occurs within a narrow pH range of 5.8-6.7. Outside this range, either traditional nitrifiers become inhibited or acid-tolerant species take over, potentially leading to process instability and production of harmful nitrogen oxide gases.

Conclusion​

While ammonia oxidation by conventional microbial species is severely limited or stops below pH 6.0, the process does not completely cease in all systems. The continuation of ammonia oxidation below this pH threshold depends on the presence of specialized acid-tolerant microorganisms and specific environmental conditions. The traditional pH limit of 6.0 applies primarily to conventional ammonia-oxidizing bacteria in pure culture laboratory conditions, but natural and engineered systems can harbor diverse microbial communities capable of ammonia oxidation at much lower pH values, sometimes as low as pH 2.5.

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