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A Short (and Long) Guide to Aquarium Cycling

Updated: Jul 19

[Updated 08/07/2022]

[Got questions about this blog post? Comment below.]

[Got general questions? Check out the forum!]

 

I am gonna start with a quick guide. If you already understand cycling but perhaps just want to try a new method, or simply just want to follow instructions to a tee and ensure your tank is cycled, follow the quick guide. To get a glossary of all these wonky 'fancy schmancy' words everybody keep throwing around, see the next section after. To get an in-depth cycling guide, well follow even further along. Enjoy!

Tada! Follow this guide and you will have no issues (I hope). Do let me know if you do though, I can help troubleshoot it.

 

Glossary (alphabetical):

  • Aerobic - something that respires ('breaths') using oxygen.

  • Ammonia - the product of fish waste, decomposition, and just general ammonification. Toxic to both freshwater and marine fish.

  • Ammonification - conversion of organic nitrogen into ammonium (ammonia). This is really as much as you need to know.

  • Bioload - The 'biological' limit that an aquarium can hold, generally measured as a combination of numbers of fish. That or effectively/more accurately, how much nitrogen is ultimately added to an aquarium over a day/week/etc. from feeding activities.

  • Biomedia - Anything that can be colonized by (beneficial) microorganisms. Technically anything with a surface, but probably better considered to be products specially designed or designated for settlement of beneficial microorganisms (bioballs, ceramic noodles, live rock, lava rock, etc.). If you need a recommendation, I'd suggest CerMedia MarinePure, best product I have tested, and I have tested a lot of biomedia.

  • Cycling - everyone defines this differently, but I define it as 'to establish enough nitrifiers in an aquarium to fully handle ammonia produced by a full bioload'.

  • Microorganism - small living things. Include bacteria, but also other living beings, such as algae, fungi, archaea, and so on. There is some debate amongst scientists about what can exactly be classified as a microorganism. Mostly irrelevant to the aquarium-keeping hobby, so don't worry too much about it.

  • Nitrification - The process in which ammonia is oxidized to nitrite then nitrate. Do not worry about what 'oxidized' means, you can use the term 'converted' instead. Not exactly important, but may be of interest: ammonia can actually be directly converted to nitrate, by microorganisms such as Nitrospira inopinata. This is called 'comammox', i.e. COmplete AMMonia OXidation.

  • Nitrifier - A microorganism that either converts ammonia to nitrite, or nitrite to nitrate (or ammonia to nitrate directly, see nitrification). Common genera ('groups') of nitrifiers are Nitrosomonas, Nitrosospira, and Nitrospira. In marine environments, certain nitrifying Thermoproteota species are also common, specifically from the genera Nitrosopumilus and Nitrososphaera.

  • Nitrate - The final product of nitrification. Nitrate can be consumed by certain organisms, including microorganisms in via varying processes, or by plants and algae. Nitrate toxicity varies greatly depending on live stock species, but generally not as much as ammonia or nitrite.

  • Nitrite - The product of ammonia oxidation, which is then oxidized to nitrate. Nitrite is very toxic to freshwater fish, but needs to be at very high concentrations to be toxic to marine fish. Toxicity varies between marine fish species, but probably around 100+ppm is enough to be lethal for some species, and higher for others. I would suggest nonetheless keeping nitrite below 25ppm for marine systems, as even if not lethal, higher concentrations of nitrite can still cause disease.

 

The goal of cycling

'But wait, did you not already state the goal of cycling above?'


Well yes, but also, I want to expand on this a bit. To me, everything is goal-driven, and what one does depend on the goal. I think this is also the reason why there are so many different methods to cycling out there. Some aquarists consider cycling a tank not only to involve establishing nitrifiers, but also going beyond that, like adding clean up crew (snails, etc.) or dealing with algae growth. However, I really want to focus on the 'nitrogen cycle' side of things, not only as that's the traditional definition, but also because this process in and of itself is important and already 'separate' enough from the other steps that it warrants dedication. For more information on all these different definitions of cycling, see here.


So what is my definition of 'cycling'?

"Cycling: to ensure there is enough nitrifiers to handle a full bioload."

Why this definition in particular? Let's take a step back. A lot of guides will say after the cycle, you have to stock with live stock slowly. Others will say go for it, just chuck everything in! Confused? I find it is just because of different contexts, boiling down to whether enough nitrifiers are established by the proposed cycling process to only handle a slow stocking process, or if there are so much more established that you can stock a lot more at once.


To me, cycling should result in enough nitrifiers to handle the ammonia production by a full bioload. Why? Two reasons.

  1. It is safer. Every time you add fish, you do not really want the nitrification capacity to then have to catch up, seeing some ammonia and/or nitrite that could turn into a spike. Additionally, if a fish dies (yes, sometimes they do, through no fault of your own), a more robustly cycled system can have extra nitrification capabilities to handle the ammonia produced by the fish death, at least for the short term. By the time you find out, it may be the difference between you taking that dead fish out before anything major happens (when the tank is cycled my way), and seeing an ammonia spike that could already start harming other fish (when to tank is cycled to a 'lower nitrification capacity').

  2. You have tested the nitrification capability of your aquarium. There are so many biomedia products on the market, not to consider nitrifiers can live on/in substrate (sand, gravel, etc.), rocks, decorations, and so on. Different nitrifying species have different nitrification rates too, so more or less nitrifiers may be needed depending on what species/strain actually grew. Sometimes you might not have enough surfaces in your aquarium, and so never be able to establish enough nitrifiers, likely a reason why some aquarists see their aquarium 'uncycle' after a certain point of adding fish, where no matter what, ammonia and/or nitrite just could never be fully processed. If you can determine that you do not have enough biomedia during the cycle, then that can be remedied before things go too awry.

If it is not clear by now, I am advocating for a fishless cycling process. It is not that I think fish-in cycling cannot work, or that it is even unethical. No, I just find the fish-in process a LOT of work, a 'last resort' if one needs to, but not the preferred option. I may write a fish-in cycling guide in the future, probably, but it can be so messy that I am quite lazy to do so.


So how do we satisfy this goal? Well, by ensuring an aquarium can convert 1, 2, or 4ppm ammonia to nitrate within 24 hours. Why these numbers?

  • 2ppm - the 'original' target, this is believed to be the maximum amount of ammonia produced from feeding fish a day with the highest bioload one can have. However, this was borne from cichlid-keeping, which often is where aquariums are 'overstocked' and hence there is a very high bioload. So if you want to have a very high stocking and feed a lot, aim for 2ppm.

  • 1ppm - feeding activities for most aquariums generally produce closer to 1ppm ammonia a day, even 'heavy feeding'. This is especially true if you keep say, one betta. Chances are it will not produce so much ammonia, but it also depends on the aquarium size as well. Remember, 'ppm' is a unit of concentration, so one better way to think about it is, the ammonia produced by fish will be more concentrated in a small aquarium than a large one. A betta in a 2.5 gallon tank (I am not judging this, it's just an example of situations that can and often do occur) will produce 4x higher concentrations of ammonia for example, compared to a betta in a 10 gallon tank.

  • 4ppm - a 'stretch goal' essentially. Some aquarists aim for 4ppm because they want to ensure the nitrification capability is beyond what is needed for a maximum bioload, so that if anything goes wrong, the nitrification capacity can handle it.

I would personally recommend 1ppm for most tanks. So therefore, to achieve our goal, i.e. to determine if an aquarium is cycled, we need to determine that:

"The aquarium can handle 1ppm ammonia a day. In other words, if one doses an aquarium with 1ppm ammonia, then 24 hours later both ammonia and nitrite should read 0."


Considerations during a cycle

Now that we know what the goal of cycling is, let's move on to how cycling actually works.


First thing's first. I would not recommend cycling with fish food, food from the deli, etc. Reasons:

  1. You cannot control the amount of ammonia produced. It can generate a lot of ammonia, or very little. Ammonia may also be produced over very different periods of time, again, making it hard to judge the progress.

  2. It can promote the growth of microorganisms that compete against the nitrifiers we want to grow. The nitrifiers we want are 'autotrophic', in other words capable of producing their own 'food' from carbon dioxide and water, therefore does not need to be 'fed'. By adding food, we are only really promoting the growth of 'heterotrophic' microorganisms, in other words microorganisms that can and do actually consume the food (or at least use it as a carbon source). They tend to grow faster than our nitrifiers, and so may outcompete our nitrifiers for space. For more information on the feeding habits of nitrifiers, see here.

This is also why we do not need to 'feed' our aquariums during a cycle. We only need to dose ammonia. However if you really want to use fish food ('ghostfeeding') or similar instead of dosing ammonia, then I have wrote a guide here. I must iterate though - if given the choice, between ammonia-dosing or ghostfeeding, I absolutely would not recommend ghostfeeding.

"Ammonia is all nitrifiers need to grow and reproduce."*

Because nitrifiers can produce their own 'food', they only need something to use for respiration ('breathing'). Okay this is not absolutely true, hence the asterisk - nitrifiers still need phosphorous, sulfur, and some other elements. The thing is, these are pretty readily available in the environment, they do not need to be significantly introduced from feeding.


For the most part, nitrifiers can keep producing their own 'food' and use that to grow and reproduce.


So where does ammonia come into play? Well, ammonia can be used by nitrifiers as a source of energy when they 'breath', in other words, they are 'lithotrophic'. What this means is that everyday, nitrifiers can consume a certain amount of ammonia, and that can keep going on day after day. This also mean of course, the more nitrifiers, the more ammonia can be consumed a day.


This is the gist of cycling - all we are doing is grow enough nitrifiers to handle more and more ammonia to a point where it satisfies our demand (2ppm a day or whatever).


Two things of note:

  1. Microorganisms generally do consume ammonia. However, most, specifically heterotrophs, are not 'lithotrophic' for ammonia, i.e. they do not consume ammonia as a source of energy. They incorporate the ammonia directly into compounds they need for growth, but there is a limit to this. At a certain point, these microorganisms will stop growing/reproducing as they reach a critical mass, and therefore any more ammonia in the environment will stay there. This is another reason why we want to focus on growing nitrifiers and not other microorganisms. This may also be why many aquarists can see ammonia initially drop as they get a 'bacterial bloom', and then the ammonia spike happens.

  2. Nitrifiers generally are found to go for a long period of time ammonia-starved. Like months on end. They either go dormant, or there are other mechanisms that allow them to persist. Though if they go for a long enough period of time, it does take some time for them to 'return to activity'. However, it definitely is not within the magnitude of days - so don't worry about starving your nitrifiers if you do not provide them with ammonia for some time.

With the above said, let's go into how to cycle.


My cycling method (what you have been waiting for)

Here's how to cycle:

  1. Detoxify your water. I.e. using a dechlorinator/water conditioner to remove/detoxify chlorine, chloramine, heavy metals, or whatever else that can kill microorganisms (or your fish). Do this every time you add water to the aquarium. I am using the term 'dechlorinator' and 'water conditioner' interchangeably, because while technically a dechlorinator is only a type of water conditioner, specifically designed to combat chlorine/chloramine, nowadays the two words are essentially synonymous. A good product is expected to detoxify chlorine, chloramine, heavy metals, and a whole host of other stuff. I am not a chemist, so this here is a bit beyond me how it works. XD Also, make sure the pH is where you want it to be. pH may swing a bit during the cycle, if so that is when you can do water changes or use other methods to buffer it. Different species of nitrifiers are adapted to different pH, so it is important that you cycle the tank at the intended pH - otherwise with a latter shift in pH you may find nitrification to not be as effective (whether going from low to high pH or vice versa). The nitrifiers in FritzZyme TurboStart 700 for example, exhibits nitrification optimally at a pH of 7.3 - 8.0.

  2. Dose a target amount of ammonia (1, 2, 4ppm, or whatever it is you prefer). This can and should be ammonium chloride. If you are a newbie or are unsure, just buy Dr. Tim's ammonium chloride. Just buy it. Yes other products work, etc. but this is not very expensive anyways, and it is proven, so why not. Well, unless you cannot get it, then get an alternative product - google helps. Otherwise, sorry I cannot help you. MEASURE ammonia. Make sure it is your target amount. If lower, dose more. If higher, well do not fret unless it is above 16ppm or so. If you do not want to own a test kit or measure parameters, sorry I cannot help you.

  3. Add nitrifiers. Whether transferred from established biomedia, from 'bottled bacteria' products, or whatever other method you fancy. You don't have to do this, technically. Yes nitrifiers can come along in tap water, or from the air, etc., but 1. you run the risk of establishing the 'wrong' type of nitrifier, or the cycle can take six months. Yes, there has been people who said their aquarium took six months to cycle this way. You may of course get lucky and it works out, but hey, if it was me, I would not be bothered spending a bit more money just for peace of mind. By the way, what are the 'wrong' type of nitrifier, you may ask? Well, different species/strains are adapted to different conditions and may not grow very well, or cannot engage in as much nitrification as we want them to in our aquarium. So it may take longer to cycle, or well, the tank may just never cycle. A lot of bottled bacteria products contain nitrifiers adapted to higher pH, so may be pointless to use in a low pH aquarium. Similarly, getting established biomedia from a high pH tank to add to a low pH aquarium (or vice versa) may not work out.

  4. Wait 24 hours, and measure ammonia and nitrite. If it is not 0 or close (0.25ppm for ammonia, because sometimes test kits can get a false positive reading), then measure again after 24 hours, and repeat until it reads 0, then dose the target amount of ammonia again. Yes, only re-dose ammonia when both ammonia and nitrite hit 0. DO NOT DOSE ammonia if your nitrite still read above 0. No, your nitrifiers will not die if you do not dose ammonia. That is a lie/misunderstanding. For a caveat, see the FAQ in the quick guide.

  5. When you can measure 0 ammonia and nitrite within 24 hours of dosing ammonia, congratulations, your aquarium is cycled.

Simple as that. Let's break down what would happen during this kind of cycle.


You dose ammonia, introducing an energy source. You add your nitrifiers. They will colonize surfaces, and start to use the ammonia as an energy source. They will start to reproduce, while ammonia is converted to nitrite. Then nitrifiers that can use nitrite as an energy source (in a similar way to the ones that use ammonia) will then use nitrite, converting it to nitrate. As this happens, the nitrifiers will grow and reproduce. As they reproduce, they can use up more and more ammonia and nitrite more quickly.


This is why you will start by seeing what seems like no change in ammonia, then it will decrease, and decrease faster over time. Same with nitrite.


Sometimes you will see nitrite increase before decreasing. In such case, there was not yet enough nitrite-oxidizers, and so nitrite builds up more than it is consumed, then it will plateau as the nitrite produced is equal to the nitrite consumed, and finally decrease when the nitrite consumed is more than nitrite produced.


Sometimes you will see no increase in nitrite, at all. That's fine. You just happen to have enough nitrifiers to consume all the nitrite produced from the very start.


Tada! Simple, right?


Frequently asked questions

  • If I do want to 'cheat' and dose ammonia when nitrite is still present, what is the highest nitrite you'd suggest I am still seeing before dosing ammonia?

  • I'd say 2ppm. Definitely not whatever the highest value in the chart is for whatever test you are using - because then you'd have no idea if things are changing or not.


  • So what IS the optimal pH for cycling?

  • It is whatever you want your pH to finally be. The thing is, while a lot of nitrifiers indeed prefer a higher pH (7 to 8 for example), especially sold commercially, the problem is... if you get them to establish at a high pH, and then eventually have to decrease the pH to suit your live stock, then these nitrifiers stop working well or in fact entirely in some cases - making your entire effort moot. The converse is also true - despite what a lot of articles may try to say otherwise. For example, Nitrosotalea devanaterra is an obligate acidophile, meaning it can only grow at a low pH (specifically 4 - 5.5), and that is also where it performs nitrification. Granted it is from soil and not water, but you get the idea. More relevant is for example Nitrotoga sp. HW29 found in freshwater systems that actual has a nitrification pH optimum of 6.8. So this species actually do best below a pH of 7.


  • Oh my god, my nitrate is through the roof!

  • The nitrate test kit works by converting a portion to nitrite, and then reading that as a proxy. So if you already have some nitrite, that can cause an artificially high nitrate reading. Crazy right? I only learnt about this recently. Check out this Marine Depot youtube video to learn more. So make sure nitrite is zero before checking nitrate, because it may not really be through the roof. Even if it is, it should not impact nitrification, but if you want to be sure just do a 100% water change.


  • Can I top up my aquarium with water if evaporation lowers the water level?

  • Yes, yes you can, any time.


  • Can I do a water change?

  • Yes, yes you can, but only if there is a reason why. For example, if nitrate starts to be too high. But make sure that is not a false reading because of the presence of nitrite. If you have 0 nitrite, then you can safely presume your nitrate reading is more or less correct. The reason why you generally should not do a water change during a cycle is because 1. there is no reason to, given that ammonia and nitrite and stuff is what you actually want to be there to let your nitrifiers grow, and 2. it makes it hard to track where your cycle is at, if you artificially lower ammonia and nitrite readings. If you need to do a water change, do it. But next time your ammonia and nitrite reads 0, add 2ppm ammonia again and go from there. For more information, see here.


  • It has been a week and there is no signs!

  • Different aquariums take different amounts of time to cycle. Unfortunately, a week is not long enough to know that your aquarium is cycling, but just very slowly, or if you do not have enough nitrifiers. So just have to wait it out, if you have followed the procedure correctly.


  • It has been a month and there is no signs!

  • Yeah okay this is taking some time now. While aquariums can cycle naturally given that nitrifiers can arrive from the air, if you purposefully introduced nitrifiers and there is no change after a month, that's a bad sign. Something went wrong. It is hard to say what the problem is, so best ask with as many details as possible. A lot of aquarists will jump in and say 'just be patient'. Ignore them and listen to people who actually want to help you (but do ask questions if anything does not make sense). Patience is definitely important in this hobby, but I see no value in letting problems persist if they can and should be fixed.



  • Should I add plants during the cycle?

  • No, it is preferred that you do not have plants during the cycle, at least when cycling by ammonia-dosing and the goal is to establish robust nitrification. The reason is because plants (and algae) also consumes ammonia, along with phosphates and other substrates, which means they can compete directly against the nitrifiers we want to establish. So while long term plants can be very helpful, it is preferable to add them after, rather than during, the cycle. On the same token, it is better to have lights off too to inhibit algae growth.


  • My question is not here!

  • Please do let me know! I will update this post with anything I find valuable, so if you have questions, definitely let me know!

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