Aquarium Fish-in Cycling

2.5. Aquarium Fish-in Cycling

If one has fish in the aquarium during cycling the tank, this is called “fish-in cycling”. I don’t recommend fish-in cycling. There is simply no reason to do it. The only benefit is that doing it in its simplest form is very easy (doing it in its more complicated form is very difficult). But often one has no choice but to do fish-in cycling.

Reasons not to do fish-in cycling:

  • It typically takes longer than other methods
  • There is a small chance of damaging or even killing the fish put in the aquarium, especially for a beginner who overstocks and/or overfeeds their fish.
  • Normally the water isn’t crystal clear at the end of the cycling.
  • You cannot add much fish at the end of the cycling as it doesn’t produce a lot of beneficial bacteria.
  • The fish will not have an established filter. Established filters have been proven to prevent fatal ich outbreaks. So doing a fish-in cycle significantly increases the risk of fatal ich outbreaks.

But fish-in cycling is easy and reasonably safe if one remembers the two cardinal rules to feed very lightly and stock very lightly. Prophylactic ich treatments are also in order (Ich-X and other formalin/malachite green medications do not kill beneficial bacteria, per actual scientific university research).

Fish-in cycling can be frustrating in that it can take many months to get up to a decent stocking of decent sized fish. So I’ve come up with “milk jug sponge filter cycling” as a “work around” for this problem. This is gone into in this link:

2.5.2. Rapid Fish-in Cycling

We will explain fish-in cycling in two layers. The simplest method will be given first, with a second and more complicated method after that. Both work fine.

Melanochromis loriae Chizumulu
Melanochromis loriae Chizumulu

Level #1, Simple Fish in cycling

The simple way to do fish-in cycling is to simply only feed the fish the amount of one eyeballs every two days for two weeks, then up the food level to one eyeball a day for two weeks. Then up the feeding to a permanent level of two eyeballs per day. If you have six fish that will be the amount of dry fish food equal to the volume of their twelve eyes combined. Do not change out the water, even if it gets cloudy. Do nothing other than light feeding. And in six to eight weeks your aquarium will be “cycled”. Easy! Just be sure not to clean or change out the filters unless they plug up (the brown gunk is the beneficial bacteria) and the fish will be fine.

This is what we did fifty years ago and it worked just fine. This simplicity is why experts like Cory of Aquarium Co-op recommend this way of cycling.

Petrochromis red bulu
Petrochromis red bulu

Level #2, Complex Fish-in Cycling

To maximize the safety factor for the fish used in fish-in cycling one needs to get pretty complex. Again, we do not recommend this method. But if one has a tank with fish in it and one wants to be as safe as possible when doing the fish-in cycling this method works the best.

The safest way to do fish-in cycling is to buy two different ammonia test kits. First off buy the “Seachem Ammonia Alert”, a test that mounts on the side of the aquarium.

Seachem ammonia alert
Seachem ammonia alert

This test measures the free ammonia gas (NH3) that is in the water. This is the poisonous ammonia compound. The goal during fish-in cycling is to keep this color the dull green of the “Alert 0.05 ppm” range. If the color changes to blue (the “Alarm 0.2 ppm”) then a 50% water change needs to be done to protect the fish. If the color stays in the yellow range then the aquarium won’t cycle as there is no food for the beneficial bacteria.

OB Peacock Marmalade
OB Peacock Marmalade

The second test is the “Total Ammonia Test”. This is commonly an API liquid test. It measures largely the relatively harmless ammonium (NH4+) in the water. When it goes to 0.25 ppm or less (yellow or very light yellow-green) 24 hours after adding food then the fish-in cycling is normally pretty complete.

API ammonia test kit
API ammonia test kit

During fish-in cycling, the total ammonia will typically only rise to 0.5 to 1.0 ppm.  Then nitrite will rise to 1 or 2 ppm (sometimes this doesn’t happen, the cycle commonly skips the nitrite phase). Then the nitrate may rise to 5 to 10 ppm (sometimes there is no nitrate because bacteria can absorb nitrate and/or the food loading is just inadequate to give any readable nitrates). Normally hobbyists do water changes to keep nitrate down to 40 or 80 ppm. When the ammonia goes down to 0.25 or less and the nitrite (if there is any) has hit zero, the tank is considered “cycled”.

Many people are quite “successful” putting fish in the tank and doing a “fish-in” cycle. Fish poop sometimes has some amounts of beneficial bacteria in it and can “cycle” a tank in as little as fourteen days. But most of the fish-in cycles I did “way back when” took four to six weeks to “cycle”.

The problem with this “fish-in” cycling is the definition of cycling. Many consider cycling “done” when there is no longer any ammonia in the water of a fish-in cycled aquarium. Since a few fish only put out tiny amounts of ammonia this can happen quite rapidly. But “way back when” I considered an aquarium cycled when the water cleared. And clear water takes much longer. I recommend that anyone doing fish-in cycling define the cycle as complete when the water clears.

Melanochromis chipokae male
Melanochromis chipokae male

Pointers to doing Any Cycling

“Cycling” is the cultivation of colonies of very slow-growing bacteria which convert semi-poisonous fish pee (ammonia) to a non-poisonous compound (nitrate). These colonies grow on the surface of the media in the filter. The following is what one needs to do when you have fish in an aquarium being started and being cycled:

  • Simply turn on the filter and leave it on. Do not clean the filter or change the cartridge and/or the filter media until the filter plugs or falls apart. Changing cartridges or media in a filter is just a big money-making scheme for filter manufacturers. The beneficial bacteria colonies which are grown by the cycling process over weeks reside in the filter cartridge or the filter media. If you change or thoroughly clean the cartridge or filter media once a month you restart the whole cycling process.
  • First and foremost measure the acidity of the water. This is called the “pH”. It can be measured with a test kit. If the pH is less than 6.5 in water that has been aerated for at least one day, you need to bring it up to 7.5. This is because beneficial bacteria don’t work at less than 6.5 pH. This requirement was confirmed by testing. The processes needed to raise pH are explained in this link:

4.4.5. Raising pH

  • If the pH is greater than 8.5 in water that has been being aerated for at least one day, it needs to be brought down with acid. This is because above 8.6 the ammonia fish produce is somewhat more poisonous. Anything greater than 2 ammonia is poisonous to fish at greater than 8.5 pH. In addition, the beneficial bacteria slow down above 8.6 pH. Lowering pH is covered in this link:

4.4.4. Lowering pH

Melanochromis johanni
Melanochromis johanni
  • Try and get some “gunk” (brown biomedia) from an established aquarium filter to “seed” the new filter. One can also use the soil around potted plants from the LFS or black garden soil from the garden as “seeds” of beneficial bacteria. Note commercial soil mixes from the garden store do NOT work because they are sterilized. Compost is often enriched with large amounts of ammonia so this cannot be used with fish in the tank.
  • Just wash and squeeze the filter media, soil, or compost into the water in the new tank. Then throw the inoculate into the water. The water will cloud up but it will clear in a few days. Click the following for more information:

2.11. Inoculate for Cycling

  • Don’t buy “instant start” bacteria in a bottle like Seachem Stability. The common “bacteria-in-a-bottle” were tested and none of them worked.  Hit the following link for more information:

2.8. Bacteria-in-a-bottle

  • Don’t add any chemicals. The “ammonia detoxifying” chemicals that supposedly let one instantly cycle a tank, such as Prime, Safe, and Amquel, are also a big scam and don’t work. Testing showed that the combination of Stability and Prime recommended by Seachem made cycling take an average of 15 days longer. Prime is a reducing agent and ammonia is oxidized by beneficial bacteria. Reduction is the opposite of oxidation. So Prime interferes with the beneficial bacteria. Hit the following link for more information:

2.9. “Instant Cycling” Chemicals

Otopharynx lithobates Off 3 Peaks
Otopharynx lithobates Off 3 Peaks
  • Add as much aeration (either wavemaker creating choppy waves at the surface or multiple air stones) as possible. Beneficial bacteria require lots of oxygen.
  • Feed the fish one eyeball of dry commercial fish food every other day for two weeks. Then do one eyeball every day for two weeks. Then go to two eyeballs per day as the permanent level of feeding (double this for juveniles).
  • Plants remove ammonia, nitrite, and nitrate from the water. Since ammonia and nitrite are required during cycling to feed the beneficial bacterial growth, adding plants to the aquarium during cycling will prevent the tank from cycling.
  • Add one teaspoon of table salt or aquarium salt for every 10 gallons of water to reduce nitrite toxicity.
  • It is recommended to always keep the pH above 7.0 by adding baking soda when the pH drops during cycling

This is not a critical process. You do not HAVE to do ANY of these things. These things will just give the fish the best chance to survive with no long-term damage.

Melanotaenia boesemani, Boesemani rainbowfish
Melanotaenia boesemani, Boesemani rainbowfish

The Biggest Error in Fish-in Cycling

While doing this process one must not panic when the ammonia or nitrite goes to 0.5, 1, or even 2 ppm and do water changes (see the chart above). Beneficial bacteria colonies need ammonia and nitrite as their food source. If you do water changes there will be little growth of the beneficial bacteria colonies and the aquarium will take a very long time to become cycled.

But ammonia levels over 4 ppm with food as the source of the ammonia can get one in trouble. This is not because of ammonia. Rather it is the bacteria that are feeding on the food and feces in the water column. These bacteria are very bad for the fish and can cause diseases to pop up. So we recommend 50% water changes when the API ammonia test hits 4.0 with fish-in cycling, regardless of pH.

Just keep going with no water changes unless gaseous ammonia (Seachem Alert test) hits 0.2 ppm, ammonia and ammonium (API test) hit 4, or nitrite hits 2 ppm (at 7.6 pH). Remember, cycling requires three things:

Patience, Patience, and Patience.

Note that if one has feeder goldfish, “fair prize goldfish”, common goldfish, or comet goldfish and is doing fish-in cycling the levels of ammonia and nitrite which can be safely breached are very high. That is because the goldfish has been raised in small earthenware basins and ceramic bowls for close to one thousand years in China. And these Chinese had no idea what cycling or the nitrogen cycle is. So “unintentional genetic selection” has taken place and these fish are amazing as to the levels of contamination they will thrive in.

Albino Pundamilia nyererei
Albino Pundamilia nyererei

Also, note it is common for the water to become cloudy or even green. Don’t panic when this happens. It TYPICALLY won’t hurt the fish. The cloudiness or green color will clear in a few weeks and the fish will survive just fine the vast majority of the time. Note that if you start changing the water with cloudy or green water you will just make things worse, and the cloudiness can persist for months. Remember, cycling requires three things: patience, patience, and patience.

Parathelphusa ferruginea Gold Leg Matano Crab
Parathelphusa ferruginea Gold Leg Matano Crab

Deliberate Fish-in Cycling with Cheap Fish

This topic is bound to raise huge howls of protest from the PETA “save the fish” group. But using cheap feeder fish to set up an aquarium is perfectly acceptable. Feeder goldfish are especially useful for this process as they have been “inadvertently selectively bred” to take huge amounts of waste in the water with no effect.

If I were to do feeder fish fish-in cycling I would add one feeder goldfish per twenty gallons and feed them for one week three times a day an amount they can eat in five minutes (that is a LOT of food!). After the first week, I would add one more feeder goldfish per twenty gallons. After the second week, I would add one more feeder goldfish per twenty gallons.

Then, after six weeks of NO water changes and NO cleaning of anything, I would transfer the feeder goldfish to a pond and let the tank just run for two weeks. These two weeks of running without fish are to allow the levels of any fish pathogens to drop to negligible/non-pathogenic levels. That is, if the goldfish were asymptomatic carriers of something, after 2 weeks without a host, a pathogen would most likely fall to levels that normally a fish’s immune system would shrug off. In addition, these two weeks just let things “settle out” and for all the beneficial organisms in the brown gunk to reach healthy populations. The more “mature” an aquarium is the healthier the fish and the fewer problems one sees. Note this is not “necessary” in any way, shape, or means.

This will give you a very mature, well-cycled 20-gallon tank capable of handling any amount of fish you want to put in it. If the tank is say 75 gallons I would add four feeder goldfish initially and two feeder goldfish every week for two weeks. That being said this is NOT how I cycle a tank. I use the “How I Cycle” method of fishless cycling with ammonia and food

2.3. How I Cycle

Placidochromis milomo Super VC10
Placidochromis milomo Super VC10

Fish-in Cycling Science

For an even more in-depth analysis of fish-in cycling one can go to this link:

2.5.1. Fish-in Cycling Science

Fast Fish-in Cycling

One problem many get into is how to reasonably make a fish-in cycle work to add a decent number of fish in three to six weeks. If one does fish-in cycling properly, you only lightly feed a small number of fish. So how does one get up to a decent number of fish in less than four to six months? Several commentators on this website have asked this very question. So I’ve come up with “milk jug sponge filter cycling”. This is gone into in this link:

2.5.2. Rapid Fish-in Cycling

Belief Perseverance Effect

Now there is a psychological phenomenon called the “belief perseverance effect” which is very strong. “Belief perseverance effect,” says that if someone believes that small amounts of ammonia can kill fish overnight and fish-in cycling is cruel to fish, they will rationalize and support that belief no matter what. There is no way any amount of logic can penetrate the brick walls that the belief perseverance effect puts up in the mind. So we won’t try.

“Nothing dies harder than a lie that people want to believe”


Startpage Aquariumscience

Source: – David Bogert

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