4.0 ammonia is deadly to fish, but just fine for raising bacteria.
Here is how I would have handled this project. (For anyone else who is reading this post to find out 'how to')
How to handle the nitrogen cycle when doing a full substrate change:
The filter media holds roughly half the nitrifying bacteria. Clean it a week or more before starting the substrate swap so the bacteria can recover. Remember to clean the media in water removed from the tank.
You can start a fishless cycle in a bucket with some bio balls, poret or other bio media. This takes 3 weeks if you start with no Nitrospira, or can go a lot faster if you add some used filter media to the bucket to jump start the bacteria population. I have added the fishless cycle at the bottom of this post.
If you do not want to do the fishless cycle, then look for a bottled bacteria product that contains Nitrospira species of bacteria. Do not waste your money on anything else.
I would submerge the soil before hand too. Test for ammonia, nitrite and nitrate. Some soils, when submerged will go through a bit of a cycle themselves. The microorganisms that live in the soil may not like being under water, and some will die off (creating ammonia) and others will love it and reproduce. This adjustment can take several weeks to a month. If the soil you are using produces any ammonia, then you could put it through its cycle in a bucket, but a more open, shallower container might be better. Perhaps a plastic storage bin? Do lots of water changes. When the tests show no more ammonia or nitrite then the soil is ready.
If you will be changing any other equipment have that on hand, too.
Read through these instructions and get whatever tools you need.
If you prepare your tank water ahead of time make enough for more than 100% water change. Make sure the new water matches the old for GH, KH, TDS.
The day of the change:
Turn off, unplug all equipment.
Put the filter media in a bucket with some water and an air stone. These bacteria need oxygen more than anything else.
Drain off some of the best water into as many buckets as you need to hold fish and plants. Keep aggressive species separate. Keep Loaches separate. Keep schooling fish together unless there are too many of them to fit in one bucket. Cover the buckets. You could put all the fish into a large plastic storage bin and run the filter on it. Put them in a place where the temperature will be stable. Option: Add an air stone into each bucket. Pretty gentle- several stones off one pump for example.
Other things like large stones, driftwood or ceramic merpeople can be kept moist by placing them in a garbage bag.
Option: If the plants have a lot of algae you might want to treat them at this time. Depending on the algae you could add hydrogen peroxide, Excel, potassium permanganate or bleach to the buckets, then thoroughly rinse the plants before putting them back in the tank. Do some research about whichever product you want to use so you get the dose and duration correct. If you do this then any bacteria on the leaves is probably dead, and the stress to the plants might make them slower to get started removing ammonia from the new set up. Make sure of the nitrogen bacteria population by following at least one of the suggestions about adding more.
Drain the remaining water. I use this as an excuse to do a really thorough gravel vac. Some day you may want to use the substrate, or you may want to sell it.
The maximum bacteria population lives in the top layer of the substrate. There is too little oxygen lower down. One way to conserve the bacteria is to skim that top 1/4" or so and set it aside.
Scoop out the substrate.
Add the new substrate. It should be wet.
Sculpt it into hills and valleys, add the driftwood and stone accents. If you want to use fertilizer tablets add them as deep as you can under the substrate.
Plant, misting often.
Put a plate or plastic bag over the substrate and fill the tank with water very slowly, allowing the new water to run over the sides of the plate and seep into the substrate.
As the tank is filling you can be installing the equipment.
If you did a fishless cycle in some bio media, add that to the filter if there is room.
If you saved the top layer of substrate put that in several bags, perhaps nylon stockings. Hang these in the tank where there is a lot of water movement. You can also do this with extra cycled bio media from the fishless cycle.
If you bought bottled bacteria add it according to the label directions.
When the tank is full turn on the equipment and make sure it all works.
Scoop the fish out of the buckets. Do not add the bucket water to the tank. Fish under stress add excess ammonia and stress hormones to the water.
The rest of the day: Lights out. Feed lightly, and only if the fish are behaving normally. If the fish are accustomed to pressurized CO2 you might turn it on about half or less the normal rate.
The next day: lights on, feed lightly. Test for ammonia, nitrite, nitrate. Be ready to do a water change if needed. (However, if you added bottled bacteria do not do a water change. These bacteria take a day or two to settle onto surfaces, and a water change would remove too many of them) If the fish are accustomed to pressurized CO2 you could start adjusting it back up to what they were used to. This might take a few days to dial it in just right. Let it take time, small changes are better.
The next few days: Continue monitoring the water for ammonia, nitrite and nitrate. Fine tune the CO2.
Cycle: To grow the beneficial bacteria that remove ammonia and nitrite from the aquarium.
Fish-In Cycle: To expose fish to toxins while using them as the source of ammonia to grow nitrogen cycle bacteria. Exposure to ammonia burns the gills and other soft tissue, stresses the fish and lowers their immunity. Exposure to nitrite makes the blood unable to carry oxygen. Research methemglobinemia for details.
Fishless Cycle: The safe way to grow more bacteria, faster, in an aquarium, pond or riparium.
The method I give here was developed by 2 scientists who wanted to quickly grow enough bacteria to fully stock a tank all at one time, with no plants helping, and overstock it as is common with Rift Lake Cichlid tanks.
1a) Set up the tank and all the equipment. You can plant if you want. Include the proper dose of dechlorinator with the water.
Optimum water chemistry:
GH and KH above 3 German degrees of hardness. A lot harder is just fine.
pH above 7, and into the mid 8s is just fine.
Temperature in the upper 70s F (mid 20s C) is good. Higher is OK if the water is well aerated.
A trace of other minerals may help. Usually this comes in with the water, but if you have a pinch of KH2PO4, that may be helpful.
High oxygen level. Make sure the filter and power heads are running well. Plenty of water circulation.
No toxins in the tank. If you washed the tank, or any part of the system with any sort of cleanser, soap, detergent, bleach or anything else make sure it is well rinsed. Do not put your hands in the tank when you are wearing any sort of cosmetics, perfume or hand lotion. No fish medicines of any sort.
A trace of salt (sodium chloride) is OK, but not required.
This method of growing bacteria will work in a marine system, too. The species of bacteria are different.
1b) Optional: Add any source of the bacteria that you are growing to seed the tank. Cycled media from a healthy tank is good. Decor or some gravel from a cycled tank is OK. Live plants or plastic are OK. Bottled bacteria is great, but only if it contains Nitrospira species of bacteria. Read the label and do not waste your money on anything else.
At the time this was written the right species could be found in:
Dr. Tims One and Only
Tetra Safe Start
Microbe Lift Nite Out II
...and perhaps others.
You do not have to jump start the cycle. The right species of bacteria are all around, and will find the tank pretty fast.
2) Add ammonia until the test reads 5 ppm. This ammonia is the cheapest you can find. No surfactants, no perfumes. Read the fine print. This is often found at discount stores like Dollar Tree, or hardware stores like Ace. You could also use a dead shrimp form the grocery store, or fish food. Protein breaks down to become ammonia. You do not have good control over the ammonia level, though.
Some substrates release ammonia when they are submerged for the first time. Monitor the level and do enough water changes to keep the ammonia at the levels detailed below.
3) Test daily. For the first few days not much will happen, but the bacteria that remove ammonia are getting started. Finally the ammonia starts to drop. Add a little more, once a day, to test 5 ppm.
4) Test for nitrite. A day or so after the ammonia starts to drop the nitrite will show up. When it does allow the ammonia to drop to 3 ppm.
5) Test daily. Add ammonia to 3 ppm once a day. If the nitrite or ammonia go to 5 ppm do a water change to get these lower. The ammonia removing species and the nitrite removing species (Nitrospira) do not do well when the ammonia or nitrite are over 5 ppm.
6) When the ammonia and nitrite both hit zero 24 hours after you have added the ammonia the cycle is done. You can challenge the bacteria by adding a bit more than 3 ppm ammonia, and it should be able to handle that, too, within 24 hours.
7) Now test the nitrate. Probably sky high!
Do as big a water change as needed to lower the nitrate until it is safe for fish. Certainly well under 20, and a lot lower is better. This may call for more than one water change, and up to 100% water change is not a problem. Remember the dechlor!
If you will be stocking right away (within 24 hours) no need to add more ammonia. If stocking will be delayed keep feeding the bacteria by adding ammonia to 3 ppm once a day. You will need to do another water change right before adding the fish.
A) You can run a fishless cycle in a bucket to grow bacteria on almost any filter media like bio balls, sponges, ceramic bio noodles, lava rock or Matala mats. Simply set up any sort of water circulation such as a fountain pump or air bubbler and add the media to the bucket. Follow the directions for the fishless cycle. When the cycle is done add the media to the filter. I have run a canister filter in a bucket and done the fishless cycle.
B) The nitrogen cycle bacteria will live under a wide range of conditions and bounce back from minor set backs. By following the set up suggestions in part 1b) you are setting up optimum conditions for fastest reproduction and growth.
GH and KH can be as low as 1 degree, but watch it! These bacteria use the carbon in carbonates, and if it is all used up (KH = 0) the bacteria may die off.
pH as low as 6.5 is OK, but by 6.0 the bacteria are not going to be doing very well. They are still there, and will recover pretty well when conditions get better.
Temperature almost to freezing is OK, but they must not freeze, and they are not very active at all. They do survive in a pond, but they are slow to warm up and get going in the spring. This is where you might need to grow some in a bucket in a warm place and supplement the pond population. Too warm is not good, either. Tropical or room temperature tank temperatures are best. (68 to 85*F or 20 to 28*C)
Moderate oxygen can be tolerated for a while. However, to remove lots of ammonia and nitrite these bacteria must have oxygen. They turn one into the other by adding oxygen. If you must stop running the filter for an hour or so, no problem. If longer, remove the media and keep it where it will get more oxygen.
Once the bacteria are established they can tolerate some fish medicines. This is because they live in a complex film called Bio film on all the surfaces in the filter and the tank. Medicines do not enter the bio film well.
These bacteria do not need to live under water. They do just fine in a humid location. They live in healthy garden soil, as well as wet locations.
C) Planted tanks may not tolerate 3 ppm or 5 ppm ammonia. It is possible to cycle the tank at lower levels of ammonia so the plants do not get ammonia burn. Add ammonia to only 1 ppm, but test twice a day, and add ammonia as needed to keep it at 1 ppm. The plants are also part of the bio filter, and you may be able to add the fish sooner, if the plants are thriving.