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Cycling A Tank / Nitrogen Cycle


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The NitrogenCycle

The final step in setting up an Aquarium before adding livestock, Also the main step a lot of new comers seem to miss.

I thought I'd write up a thread explaining what it is, why it's important etc.

Commonly referred to as; Cycling, Nitrification, Biological Cycle, Breaking in. For this thread we will refer to it as "Cycling"

In simple terms;

A cycle is a process in which chemical reactions take place to convert Ammonia into Nitrite which is then converted into Nitrates.

This is the primary and MOST IMPORTANT part of your filter. Many new comers have the idea a filter is there to catch particles floating around the tank, While this is true it's not the main reason nor most important function of your filter. Your filter is there to preform a biological filtration which is what the "Cycle" process is kick starting.

This is a VERY simple explanation, And I will go more in depth about the process below.

The Cycle Explanation.

Initial Stage;

The initial stage begins with the introduction of Ammonia this can either be ionized or unionized.

Ionized Form: Represented as - NH4 - "N(Nitrogen)H(Hydrogen)" and is referred to as "Ammonium" and is generally present in Aquariumswith a pH value below 7.0.

Unionized Form: Represented as - NH3 and is referred to as "Ammonia" and is generally present in Aquariums with a pH value above 7.0

Sources of Ammonia: Uneaten Foods, Fish/Shrimp Waste, Decomposing Organic Materials.

Second Stage;

This is where our " Beneficial Bacteria" come in to play, And are the main reason and need for a well cycled Aquarium. These beneficial bacterias will colonize themselves within your filter on the noodles, rocks, balls, substrate, ornaments or what ever biological media your filter is using.

The bacteria in the second stage are referred to as "Nitrosomonas Bacteria" And are used to "Oxidize" the Ammonia.

By Oxidizing the Ammonia they eliminate it, However a by-product of this is "Nitrites"

Third Stage;

The bacteria in the third stage are referred to as "Nitrobacter Bacteria" And are used to convert "Nitrites" into "Nitrates"

So now that you know the 3 stages in the biological filtration of theAquarium, I will elaborate more on each step, and process.

During the cycle process we can use our water test kits to check where the cycle is at and where it's up too. Each step of the process takes several days to complete (There are ways to speed up this process which will be discussed more below).

Initial Step:


Sources; Fish/Shrimp Waste, Decomposing organic matter, Uneaten foods.

Any traces of Ammonia are bad for shrimp, Which is why the cycle process is so important. Adding shrimp during the cycle process esp at the initial stage will result in shrimp deaths which in turn leads to more Ammonia being introduced to the Aquarium.

Unlike Fish Aquariums, Most Shrimp keepers will not cycle their tank with any livestock in the tank and tend to cycle more with what's called a "Fish-less Cycle".

A fish less cycle is basically a method in which a tank is cycled with no livestock in the tank at all (Pretty obvious right?) to do this we still need to find a way to introduce Ammonia into the tank to kick start the cycle. Without any initial traces of Ammonia our filters will not begin to develop the "Nitrosomonas Bacteria" we need to oxidize the ammonia and convert it into "nitrites", and in turn not begin the cycle process.

There are several ways to introduce Ammonia into our Aquariums, Different people use different methods but they will all work if done correctly and all have the same primary princible... To add a source of Ammonia into our Aquariums.

Ways to introduce Ammonia into the Aquarium;

- Feed the empty tank small amounts of food each day. Seems strange to 'feed' an empty Aquarium, however the idea behind this is to allow the food to break down and decay in the Aquarium which like over feeding a tank will lead to Ammonia being introduced to the tank.

- Use water from an 'established' tank. an 'established tank' means any tank that's already completed the cycle process and has water which contains all 3 elements to the cycle process, Ammonia, Nitrites & nitrates. It will also contain small amounts of the beneficial bacterias we need (Nitrosomonas & Nitrobacter).

The best time/place to obtain water from an established tank to do this is when you preform a "gravel vac" of the established tank as the dirty water obtained from the substrate will contain more of the two bacterias we need than water from the "Water Column" itself as the bacteria will establish themselves on the substrate surfaces.

- Ammonia sold in the shops as a cleaning agent. You want to read the label however for the ingredients list and ensure the brand you purchase is free of any additives such as colouring or perfumes. You want to find a brand that's simple plain Ammonia. These are usually the no-brand cheaper ones (Score!)

I personally think that adding raw ammonia in a liquid form is something that new keepers should prob keep away from. It's just too easy to add a little too much and should really be used by more experienced Aquarium keepers. For newbies I'd recommend using established water in conjunction with the feeding method. If you don't have access to cycled aquarium water using the feeding method alone will work fine. It will simply take a little longer to begin and complete the cycle thats all.

The beneficial bacteria stages (Stages 2 & 3)

The next step from the Ammonia stage in the cycle process is getting the beneficial bacteria we need that convert this toxic substance into Nitrites which are then turned intro Nitrates. There are also a few ways we can increase or speed up this step. A few different methods are;

- Using sources from an established tank. Good sources to use from an established tank are;

-- Filter Materials, a small piece of filter wool from an established filter or a few noodles, ceramic balls etc.

-- Gravel or Substrates from an established tank.

-- Any other ornaments - Decorations, Rocks, Driftwoods.

-- Water obtained from gravel vacuuming an established tank.

- The gunk from an established filter, Commonly referred to as "Filter Mud". Squeezing some of the gunk from an established filter is a very good way to introduce beneficial bacteria into your new Aquarium as this is where the bacteria will colonize and 'hang out'.

- Seeding your new filter in an established tank. This is basically placing your new filter in an established tank for a week or two to allow the established tank to establish bacteria in your new filter. Important to note that you should still run your original filter on the established tank while seeding the new filter. Basically running the two filters together.

- Adding liveplants to your tanks. This is not only a good way to help increase the cycle rate but also to help with the water quality of an already established tank as the plants will uptake NH4 (Ammonium) and Nitrates etc. It's also a great food source for your shrimps as they feed off the micro-organisms that find their way to the plants leaves. The faster growing the plants the more uptake of Nitrates etc they will consume. Most 'floating' plants are very good for this and plants such as horn wort, wisteria, water sprite.

- Commercially sold products to speed up the process. There are a few available but I have had personal success using "Nutrafin - Cycle" but any additive that contains beneficial bacteria will do the same thing. It's pretty much just Dependant on what is available to you.

Cycle Results;

We use our tests to see what stages the cycle is at. The first stage "Ammonia stage" you will get results that look a little something like this;

Ammonia: 4.0 ppm ( or more, or less the amount isn't important. It's the presence we're looking for at the moment )

Nitrite: 0.0 ppm

Nitrate: 0.0ppm

We can see with the above results that our tank has begun the first stage of the cycle as Ammonia is present. However since there is no traces of Nitrites we know that the beneficial bacteria needed for stage two to convert Ammonia into Nitrites are not yet present. So we can assume our cycle is in "Stage 1"

The Nitrite stage, Or stage Two our results should look a little something like this;

Ammonia: 2.0 ppm (Once again the amount isn't important, It's the presence we're looking for at the moment)

Nitrites: 2.0 ppm (Once again the amount isn't important, It's the presence we're looking for at the moment)

Nitrates: 0.0 ppm

We can see with these results that our tank is now in the second stage of cycle known as the "Nitrite stage". Basically we can see that there is still ammonia present so we are yet to have enough beneficial bacteria to convert the Ammonia into nitrites fast enough to keep the Aquarium at a 'safe' level.

However since we now have the presence of Nitrites we know that these bacterias are starting to colonize and do their job converting the Ammonia into Nitrites.

The Nitrate stage, Or stage Three our results should look a little something like this;

Ammonia: 0.0 ppm

Nitrites: 1.0 ppm

Nitrates: 80ppm

We can see with these results that our tank is now in stage Three. We no longer have any Ammonia in an amount our tests can trace meaning that the bacteria needed in stage 1 to convert Ammonia into Nitrites are really kicked in and doing their job exactly as we need them too. We can also see that the presence of nitrates mean that we are starting to develop the beneficial bacteria needed to convert Nitrites into Nitrates. So from these 3 points we can see we're at stage 2.

And the final stage, A Cycled aquarium should look a little something like this;

Ammonia: 0.0 ppm

Nitrites: 0.0ppm

Nitrates: 5.0ppm

We can see with these results that our tank is now completely cycled.

- Our beneficial bacteria from stage two are keeping up with the amount of ammonia being introduced into the aquarium from stage 1 and are keeping the Nitrites at an untraceable level.

- We can see that the beneficial bacteria from stage three are keeping up with the amount of Nitrites being introduced and are doing so fast enough to keep our Nitrates at acceptable levels.

Now it's just a matter of balancing and managing the aquarium to ensure all 3 stages are balanced enough to work with each other.

A few things that can throw this balance out of whack are;

- Over feeding; Over feeding can cause an Ammonia spike as the food decays and since it's been introduced at such a fast rate the beneficial bacteria are unable to consume enough to keep the Ammonia level stable.

- Over stocking, Or introducing too much livestock at once; Just like above this increases the Ammonia and bio-load too fast for the beneficial bacteria to consume fast enough to keep the levels stable.

- Over cleaning an aquarium; Many new aquarium keepers like to keep their tanks as 'clean' as possible. While this is a noble approach cleaning your filters and or substrate too much or too often can mean that you're removing too much beneficial bacteria from the filter or substrate resulting in declined bacteria meaning increase in Ammonia as there isn't enough bacteria left to keep the balance in check.

Things to help and ensure good water quality;

- Ensure your filter is an acceptable size for your tank and livestock. Under filtration will result in a lack of beneficial bacteria to keep up with the intake of Ammonia

- Ensure your tank isn't over stocked. It doesn't matter what you do, If you have far more livestock than what a filter or tank capacity can handle you will never get it balanced.

- Add livestock slowly and over time. Don't go rushing in and add all your livestock too fast once your tank is cycled as the newly formed beneficial bacteria are in limited numbers and will be unable to cope with the sudden increases of Ammonia.

- Add live plants; Live plants can help consume some of the NH4 and nitrates and help the filters beneficial bacteria to keep levels lower.

Remember, All 3 stages work in balance with each other. I personally like to view it as;

1.Fish eat food, Which in turns creates it into "Ammonia"

2. The Ammonia is then a food source for the Nitrosomonas Bacteria whom then create "Nitrites" from their waste.

3. Nitrite waste is a food source for Nitrobacter Bacteria who eat the Nitrite and create "Nitrates" from their waste.

4. Nitrates are a food source for Plants which in turn give off oxygen which is taken up by your fish. Who then eat. And the cycle begins again!

This is of course a simplistic view of the cycle process. However if you view it as food sources it's easier to see why increasing 1 particular thing can be damaging to the next as they're unable to consume or eat it at a fast enough rate to keep the Aquarium balanced.

I hope this article helps, Any questions or anything please ask icon_e_smile.gif

Good luck with your tank and cycle process!

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TRIGGS!!! fantastic write up mate... thank you for taking the time and putting in such an effort to write such a great in-depth article mate.

im sure this will be of great use and benefit to many readers.

what would make it absolutely perfect would be a nice diagram showing the process you just explained??

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@Dean - I Can handle that. Glad you like my write up :-D Thanks!

@Sprae - Sounds like a brilliant idea, Thanks for the kind words also!

@SUSS8 - Cheers Buddy, Never understood why people make things more complicated than need be.

@Jess - Thanks Heaps! :D

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Great work! I've read similar threads on many boards but never seen it written so well!

Impressd :)

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Great work! I've read similar threads on many boards but never seen it written so well!

Impressd :)

:) Thank you very much. Your kind words mean a lot and are greatly appreciated.

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  • 8 months later...

Hey Triggs,

good write up. However, I'd like to add a few things to the list based on my experience with cycling tanks.

I will assume people are observing the Fishless/Shrimpless cycle procedure since this is less stressful to livestock.

Firstly, when trying to establish a beneficial bacteria colony either by adding mature filter material from an established tank or from scratch by introducing an ammonia source (eg raw prawn) .... HEAT plays a big role in the speed the bacteria will multiply and propagate on the surfaces of substrate and filter media. Again, assuming you are following a fishless cycle procedure ... turn up the heat to 28 - 30 deg C. However, if you have fish or shrimp in the tank, turn the heat up as high as the tank inhabitants are capable of handling.

Second, ALWAYS monitor the parameters of the tank. As mentioned already, Ammonia, Nitrite and Nitrate monitoring is important. However, you also need to monitor pH levels in a cycling tank. The ideal pH is above 7.0 for a cycling tank.

However, the conversion of Ammonia into nitrites and nitrates causes the pH to drop naturally, if your tank water isn't buffered. So try to keep the pH above 7.0.

The nitrifying bacteria (Nitrosomonas and Nitrobacter) might go dormant (slow down in multiplying and converting ammonia) at a pH lower than 6, and might die if the pH continues to drop much lower than 5.0pH.

During the cycling process, your pH will fluctuate wildly, but this should stabilise once your tank has completed it's cycle.

If the pH drops too much (< 6.0) you could adjust it with baking soda and/or Potassium sulfate. Add it slowly to bring the pH back up to around 7. Again, you shouldn't need to worry about livestock since you followed the fishless cycle process ? Potassium sulfate (Potash) raises pH and KH, which buffers the water preventing the pH from dropping. A little K2SO4 here can increase pH be a lot, so add it a little at a time depending on the size of your aquarium.

Note: if pH rises above 7, don't worry, you don't need to take any action, it won't harm the nitrifying bacteria.

Thirdly, do not assume your tap water is free from ammonia. Recently with the heavy rains and floods in certain parts of Australia, the councils have been dosing our tap water with additional Chloramines. Chloramine breaks down into ammonia. I have tested my tap water in Sydney (June 2013) and it has shown between 0.25 - 0.50 readings of ammonia. This is great when you are starting a tank cycle. All you need to do is change a small percentage of water to add a source of ammonia. However, be careful to treat it with a good quality water conditioner first.

Water changes in a mature tank needs to be done cautiously as well knowing that there is ammonia in tap water. A large water change could introduce too much ammonia into a tank and cause livestock to perish. Test your tap water for ammonia first, treat it with a water conditioner (double dose if needed), leave it for at least 1 hour (or better overnight), before adding to your tank.


if it wasn't clear, if you had followed a fishless cycle process, you DO NOT need to change the water during the cycling period. Not unless, your pH drops below 5.5 or if you need to add additional ammonia from tapwater (as mentioned above Sydney water has ammonia in it). Even if Ammonia readings go off the charts to 8.0, water changes aren't strictly necessary during the cycling period.

If you are cycling with fish, then do what you need to to with water changes to ensure the fish don't suffer.


once your tank is completely cycled, do a 50% water change before adding any new livestock. This dilutes any baking soda or Potassium sulfate you added during the cycling process, as well as Nitrates. Continue to monitor pH, and Ammonia after these water changes, especially if you use Sydney tap water (which has a bit of ammonia in it). Ammonia readings should go back to 0 after 24 hours.



Edited by jayc
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Thanks jayc that might explain the difficulty I have had cycling my 30" tank the PH has been around 5 because of the thick layer of benibachi soil I have.

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Great write up jayc. However im not sure all that fiddling with pH will work with the buffering shrimp soils we use. In my head, i'd be a constant battle to try and keep the ph up and it could potentially ruin your soil? This is unless you cycle before adding the soil..

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Great write up jayc. However im not sure all that fiddling with pH will work with the buffering shrimp soils we use. In my head' date=' i'd be a constant battle to try and keep the ph up and it could potentially ruin your soil? This is unless you cycle before adding the soil..[/quote']

Shrimp soils will buffer the pH, probably around 6.5 (ish) depending on the brand. That's still ok for nitrifying bacteria. pH will drop as ammonia is converted to nitrite and nitrates, there is no doubt about it. However if the pH falls much further, your cycling will stall. Your shrimp soils will not stop pH from falling further.

Raising the pH with baking soda and/or buffering the GH & KH with Epsom salts is safer than pH UP products. It will not damage or ruin your substrate soils. Alternatively you could use products like Mosura Mineral Plus or Salty Shrimp Mineral GH+ to help buffer the water from falling further. But you'd still need to adjust pH back to around 7.

Epsom salts is essentially just Magnesium sulfate MgS04. This is essentially a fertiliser and it helps with the buffering. Win-win.

Sodium bicarbonate (NaHCO3), commonly known as baking soda will increase pH, and again is quite safe for aquariums. Just don't go crazy adding more than necessary. A little pinch will raise the pH by 1 point in 20 litres of water.

Don't forget, raising the pH is not something I am recommending to do constantly. It is only for the duration of the cycling period.

As I mentioned in my post, the pH will stabilise once the cycling is completed. Addition of baking soda or epsom salts should be stopped after that. Water changes and the continued nitrifying action in the tank will bring your pH to a balance.

It's the lesser of two evils scenario here. You want to cycle your tank. But if the pH drops too low, your cycle stalls. What are you to do?

Sea shells and crushed corals will raise you pH ... slowly, over a long time. It's too slow for the cycle process.

Also depending on your location, you might have hard or soft water. People with softer water will find pH dropping fast during a cycle. Especially if you use rain water or RO water. These are the people that need to monitor and maintain their pH around 7.

At the end of the day, my suggestion is mainly to highlight the monitoring of pH while cycling a tank. How you increase it during your cycling period is totally up to you.

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Thanks for that :) I've always had no issue with tank cycling as I've used mature filter media, but this must be why Ineke's tank too so long :encouragement:

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yes it completely makes sense but I've put shrimp in now and will just see how we go as long as the ammonia doesn't rise we should get there. If it rises I will catch out the shrimp and buffer the PH .thanks again it is a relief to know that there may actually be a reason for my cycling problem.

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Yep, definitely sounds like Ineke's problem with her tank cycle.

Combination of Benibachi soil lowering pH and the nitrifying process lowering pH even more.

If your test kit's lower limit is 5, your actual pH could be lower than that! Not good for the colonisation of bacteria.

If you have shrimp in there, be careful raising the pH and changing GH/KH (impacting TDS) too quickly.

I'm sure you know the detriments of raising pH/TDS too quickly on livestock ;)

Edited by jayc
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I would catch them out first but the ammonia is just green not quite yellow and nitrates back down to 5 shrimp seem ok so hopefully it will continue to finish it's cycle it is soooo close.

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Sounds like you are close.

How long has the cycling been going for?

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Six weeks well six and a half now I did a write up on my missing nitrite cycle but Dean said you don't get the nitrites with Benibachi. The tank had a new canister seeded with old material plus plants and driftwood, sponges etc from other cycled tanks but it is a very deep 30" tank and I thought that might be the the new canister and lots of water. As I said though the ammonia is just green but still not yellow.

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  • 2 weeks later...

Whoah, hold on here. I'm using Benibachi soil and it's buffered my pH down like crazy to below 6.0. Therefore the cycling of my tank isn't going to happen because the bacteria don't like that pH. How can I raise the pH to allow the bacteria to grow? I'm even using the recommended amount of Benibachi soil and it's making my water really acidic!!

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Whoah' date=' hold on here. I'm using Benibachi soil and it's buffered my pH down like crazy to below 6.0. Therefore the cycling of my tank isn't going to happen because the bacteria don't like that pH. How can I raise the pH to allow the bacteria to grow? I'm even using the recommended amount of Benibachi soil and it's making my water really acidic!![/quote']

You are freaking out over nothing...many many members are using benibachi soil and have no problems with it cycling.

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Yeah no need to panic just yet.

if you have no livestock in the tank, raise the pH slightly.

pH below 6 will slow cycling down, it doesn't necessarily stop.

Just don't let it drop much further. The problem is our test kits only go down to 5 while the pH might actually be lower.

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If you are worried or would like it to go faster raise the temp and add some live bacteria like cycle...or some old filter material from an established filter, I chuck in gross looking brown filter floss and sponges from my cycled filters.

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Mine is fine now ,Ihad a new canister which can take 6 weeks to cycle anyway and I have a very deep layer of soil. week 8 i have my mishlings and TBM babies in there and all is well. I hate to say it but patience is the key. My shrimp are fine the ph is 5.1 they are all doing very well. Don't worry it will cycle and the shrimp will be all the better for it:encouragement:

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