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  • A Guide to Reef Aquarium Cycling



    A Guide to Reef Aquarium Cycling

    This topic is almost as old as reef keeping itself.  But within the past decade, governments have placed restrictions on live rock collection, and there's been a shift to starting new reef tanks with dry rock.  In this guide, I'll discuss the nitrogen cycle, as well as methods to cycle both live and dry rock (something which every new hobbyist should be aware of).


    I'll be using the following definitions:

    • Bio-load noun - The wastes produced by the biological organisms in your tank

    • Biofilter noun - The nitrifying bacteria which make up the nitrogen cycle

    • Curing verb - The process of removing dead organics (an ammonia source) from your rock

    • Cycle noun - The nitrogen cycle

    • Cycle verb - To establish the nitrogen cycle

    And even if commonly used, I'll try to avoid using confusing terms like "cycle" to describe an ammonia spike.


    The Nitrogen Cycle

    The nitrogen cycle doesn't change, so I won't spend a lot of time on this well documented topic.  When it comes to the cycle, we are primarily concerned about nitrifying bacteria and ammonia.  However, nitrite and nitrate are also part of the nitrification process:

    • Ammonia is produced by animals, including the breakdown of dead organic matter by heterotrophic bacteria.
    • Nitrifying bacteria oxidizes the ammonia into nitrite (which isn't considered toxic in marine aquariums).
    • Then nitrite is oxidized into nitrate (a critical nutrient for all photosynthetic life).
    • Finally, excess nitrate can be exported via water changes.

    Nitrate can also be taken up by phytoplankton, macroalgae, seagrass, and animals with zooxanthellae (a symbiotic algae living within corals and other "photosynthetic" animals).  More advanced methods of nitrate reduction include: supporting consumption by dosing liquid carbon, and by providing anaerobic zones for denitrifying bacteria.


    Notes:  Nitrifying bacteria reside on the hard surfaces in your tank (like rocks, sand, equipment, and tank walls).  Therefore, water changes will not remove this critical bacteria.  In addition, you can transfer the biofilter from one tank to another tank by moving the rocks, filter media, etc.


    Cycling Live Rock

    Rock that has been taken from the ocean, or from another reef tank, is called live rock.  When you purchase it, the nitrifying bacteria get transferred along with the rock.  Plus, it usually contains more than just bacteria (including things like pods, worms, and coralline algae).  This biodiversity can often help prevent pests like dinoflagellates from taking over without biological competition.  For this type of rock, we should generally wait until total ammonia drops to a safe range (of 0.25 ppm or less) before adding livestock.


    Note:  Fully cured live rock will produce less ammonia than it can process, so it won't elevate ammonia levels.


    Uncured Live Rock

    Since collection restrictions have made it harder to acquire uncured live rock from the ocean, you might find aquacultured and maricultured rock to be acceptable alternatives.  To keep costs down, live rock is often shipped to you (or your local store) wet, but not submerged in water.  This usually results in some die off, which will produce ammonia.


    As the name suggests, uncured live rock has not gone through the curing process (where heterotrophic bacteria breaks down the dead organic compounds).  But generally, there's already enough nitrifying bacteria on these rocks, so it's just a matter of waiting until the dead organics are broken down and ammonia reaches safe levels (which could take a few weeks).  During this time, there are usually temporary spikes in both ammonia and nitrite. The following graph represents a typical cycle when using uncured live rock:


    Figure 2: Nitrogen Cycle With Ammonia Spike[1]



    Note:  Ammonia levels might remain slightly elevated following an ammonia spike. In addition (like in the ocean), tanks with livestock will always have some level of total ammonia, even if it's not detectable by our test kits.


    Cured Live Rock

    This rock has already been cured; so it has little to no die off, and is capable of processing more ammonia than it produces.  On the other hand, rock which hasn't been fully cured, or has experienced die off during transport, can produce elevated ammonia levels.  If it does, simply wait until total ammonia reaches a safe range (of 0.25 ppm or less) before slowly adding livestock.


    Cycling Dry Rock

    Dry rock is a term used for any reef rock which is currently dry.  It doesn't contain any marine life (including nitrifying bacteria to process ammonia).  This rock could have been manufactured or mined from the ground, or have come from someone else's tank or collected from the ocean (and then dried out).  Because of this, it might or might not have dead organic matter on it.


    If you have any question about whether or not your rock might contain dead organics, I recommend testing it, and curing it if necessary.  You can test it by soaking it in some water for a few days.  If the water becomes discolored or starts to smell, the organics are probably starting to break down (and ammonia is being produced).  You can test the water for ammonia to be certain.


    Curing Dry Rock

    If it turns out that your rock has dead organic matter on it, you should cure it like you would cycle uncured live rock.  When you are done, and depending on how much ammonia was produced, it should have a working biofilter capable of handling a light bio-load.


    Adding Nitrifying Bacteria

    You can use a bottled bacteria culture (such as Instant Ocean BIO-Spira) to introduce or add nitrifying bacteria strains to your dry rock.  The bacteria is immediately capable of processing ammonia, even when it's still free floating in the water column.  And within 5 days, the bacteria should colonize onto the hard surfaces in your tank; after this, water changes will no longer remove the newly added bacteria.  Uncured rock will produce ammonia; if it does, simply wait until the level of total ammonia reaches 0.25 ppm.


    If you stop there and slowly add livestock, your fish will usually be fine; although the ammonia levels could still become elevated until the the bacteria populations increase.  This is sometimes referred to as cycling with fish (where the ammonia from fish is used to help build up the biofilter).  However, if the ammonia level gets too high, it can be harmful to your fish.  So prior to adding livestock, I typically suggest using the following fishless cycling method to build up the nitrifying bacteria on dry rock; although you might not always have time for this step when setting up something like an emergency quarantine tank.


    Fishless Cycling

    spacer.pngThe idea behind fishless cycling is to use a clean source of ammonia to build up the biofilter on pre-cured dry rock prior to stocking your tank.  This can be done in your display tank, or in a separate container with a powerhead for flow (a heater or light isn't required).


    While fishless cycling can be done without adding bottled bacteria, dosing nitrifying bacteria beforehand is usually recommended to speed up the process.[2]  The ammonia source used, will feed the bacteria and promote its reproduction.


    Fishless cycling is a simple process of: dosing, waiting, and testing.  The number of days that it takes isn't important; simply wait until your rocks are ready for the next step before proceeding:

    1. Dose ammonium chloride or another clean source of ammonia, so that total ammonia is between 1 and 2 ppm (don't overdose).  If you accidentally dose too much, you can perform a water change to bring down the level of ammonia.
    2. Wait for total ammonia to drop to 0.25 ppm  (if the level of total ammonia goes up, your rocks weren't fully cured, which will add time to this step).
    3. Repeat until your rocks can process the dosed ammonia down to 0.25 ppm within 24 hours.

    When finished, your tank will have a working biofilter capable of handling a typical initial bio-load.


    Notes: Don't add ammonia or ammonium to rock containing non-bacterial life (like pods or other inverts).  If using a pure ammonia cleaner as your ammonia source, make sure that it doesn't contain scents, surfactants, detergents, or dyes.


    Ghost Feeding

    Ghost feeding is an alternative method for adding an ammonia source to build up a biofilter.  It involves adding fish food to a tank (without any fish in it) until the biofilter can process the ammonia being produced.  And while effective, it's harder to control the level of ammonia, and the rotting food adds organics and phosphate, which could lead to future problems like cyanobacteria.


    Cycling a Combination of Dry and Live Rock

    We can add live rock to dry rock in order to introduce biodiversity.  The longer that you keep the dry rock and live rock together, the more life (like pods, bacteria, and coralline) will spread to the dry rock.  However, if the dry rock is uncured, you might choose to cure it separately, so as not to expose this beneficial life to the ammonia that is produced.


    Post Cycling

    After cycling your rocks (but before adding livestock), you can adjust the water's nutrient levels by: performing water changes to export excess nutrients, or by dosing nutrients if they are too low.  If you won't be keeping corals, I'd change out enough water to reduce nitrate to less than 20 ppm.


    If you will be keeping coral and anemones, I recommend trying to maintain nitrate levels between 3 and 10 ppm (dosing up to 3 ppm, or exporting down to 10 ppm).  Likewise, I recommend trying to keep phosphate levels between 0.03 to 0.10 ppm (dosing up to 0.03 ppm, or exporting down to 0.10 ppm).


    Once the cycle is established, and after you've adjusted the tank water's nutrient levels, I recommend adding livestock in smaller groups (waiting at least a week between additions).  This will give the bacteria populations some time to adjust to the new bio-load before adding more livestock.



    1. https://www.bulkreefsupply.com/content/post/md-2019-01-how-to-cycle-a-saltwater-tank-tips-to-help-you-succeed-with-your-new-aquarium
    2. https://www.drtimsaquatics.com/resources/library/quick-guide-to-fishless-cycling-with-one-and-only/


    Also check out:  A Look at Ammonia.


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    Outstanding article to demonstrate establishing nitrogen cycle.  In a mature reef tank, there will be other cycles besides bacteria but nitrogen bacteria cycle is mandatory for processing ammonia to less harmful nitrite then nitrate.  Higher level organisms will feed directly on ammonia, this includes all macroalgae and most corals.

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