Ok, so I have just recently setup a 55 Gallon tank at the beginning of November, It is dirted with Miracle gro organic choice potting mix. It is capped with Vigoro Pea pebbles from Home depot. Everything was going good in my tank besides all of my wisteria has pretty much melted away but it is still new so plants arent lookin too good yet anyways. Just this last Saturday I noticed 2 of my Boesemani's were dead, they showed no signs earlier that day when i fed them of being sick. Because of the deaths I decided to do about a 50% water change. The next morning I noticed that 2 more Boesemani's where dead as can be. Now i was worried, few hours later my 5/6 boeses were dead. I also noticed that my one small Angelfish wasn't acting right as well, but the other was fine. The next morning the angel died as well, I quickely took out the rest of my 2 turquoise, 1 boesemani and 1 angelfish and put them in my 20 long. The only fish left in the 55 are 3 Zebra Danios which as of now are still alive. I have 2 ideas of what the problem could be but I need some input on to let me know if one of these could be right. I had put a rug down on the concrete floor where the tank is and I sprayed it down with quite a lot of air freshener, and i heard this could get into the water somehow even though i sprayed it at the ground. My second idea was Hydrogen sulfide or whatever is caused by air pockets under dirt which I have seen a lot of as of late. When i push down on gravel I get a lot of bubbles. If one of these 2 could more likely be the problem please let me know you opinion, thanks.

My guess would be either contaminate entering the tank, and or possibly ammonia spike possibly caused by organic's leaching from the miracle grow, possibly combined with excess food we sometimes accidentally offer.
No info on water parameter's,temp's,how long fish have been in the tank,filtration,water change schedule,Medication's or chemical's used recently,new fishes added recently,plant's uprooted recently.

Its probably not the air freshener if you didnt loose all the fish in the tank. Same goes for the idea of anaerobic substrate conditions. You should however be poking around in that substrate every so often to make sure those gas pockets get released and dont grow too large.

You mentioned this was a newly setup tank. Did you attempt to cycle it in anyway prior to adding fish? Have you been testing your water and do you know the ammonia, nitrite and nitrate readings?

I bought the Vigoro 'river rocks' from Home Depot and found out they are not inert (would raise pH). Might not be the problem, but thought I'd mention.
Some of those "river rocks" even had cement/concrete on them! (quite a bit too, no, no concrete on the bag, it was inside hardened to some rocks). There was many different types of stone and I'm no rock expert so I don't know which ones would be inert/safe.

It is said that the Hydrogen Sulfide pockets in anaerobic substrates are "instantly" "safe/nontoxic" as soon as they rise up into the aerobic/oxygenated water. I guess that is scientifically proven to be true, but I for one still believe there is something deadly that can build up under the substrate, some others agree as well, especially for those that have experienced or seen these events, but no one is 100% sure what it is. Some say disturbing the substrate can kick up decomposing organic matter and cause ammonia spikes. This is a whole big subject that I've been meaning to ask around on in hopes to finally get scientific answers as to possible reasons of sudden fish deaths when disturbing anaerobic substrates.

Do test your water as mentioned above. Even if you had to, take a cup of water from your tank and have your LFS test the water (some good LFS use the API liquid test kits, which is preferred over test strips). Knowing could possibly help identify what may be the cause of death.

Surely there must be some signs/symptoms leading to the fishes' death. Even if it was ammonia/nitrite poisoning, disease or even chemical poisoning, there would be some sort of exhibited signs before they die.

idk about ammonia, my seachem ammonia alert says my ammonia is @ 0

Bump: Cycling was done by running Whisper 60 on 20 gallon (that is an established tank) for about 5-7 days and then putting it on the 55, letting it run on 55 for 2-3 days, then getting zebra danios and letting them live in there for about a week before adding 2 rainbows.

Bump: Yeah nitrites + nitrates are 0 Ammonia is 0 as well. Since the deaths began I have done 2- 50% water changes and 2 80-90% water changes,

The way you cycled it is not a great way to grow plenty of bacteria, but as long as the ammonia and nitrite tests showed 0ppm of either, then I think the plants are doing almost all the ammonia removal.

Soils, from bags or the garden, can contain microorganisms that may be happy in the soil as long as they can get plenty of oxygen from the air, but die when that soil is placed underwater. This is why it is generally recommended to run the tank for about a month before adding livestock. The microorganisms can get adjusted to life under water, and any that are going to die will do so, and get decomposed by the ones that live. You can also do the fishless cycle in this time.

I am not sure what else the soils can release in this time, usually all you hear about are ammonia, nitrite and nitrate.

If your water was testing fine for ammonia etc. when this occurred I'm wondering about some type of contamination. Did you start using any new equipment, heater or anything else that went in the tank or the water came in contact with? Perform any maintenance or change anything in or around the tank? I don't know if you're running any carbon in the filter but if not it would help remove a lot of various "bad things", at least for a while to remove anything it can.

Test all parameters, use a new test kit, do not rely on alerts.

Test results of 0 across the board usually indicate a non cycled tank. Yes you want 0 ammonia and 0 nitrite; but I doubt your plants are really consuming 100% of the nitrate that gets produced leading to a test result of 0.

Not quite sure what ammonia alert is; but unless its a liquid test kit I wouldn't fully trust it. What are you using to do your tests?

I have similar size tank and substrate. But with high light + CO2 and fluval 4 at max speed. My 40(+) fishes (20+ rainbows) are happy than ever. No problem if I skip water change two weeks. My starting cycling was about 3 days. I think filtration is very important. Over power is always better than under power.

I have never really been a fan of testing water, I have always had success in smaller tanks, but now a 55 is the largest I have dealt with, Tank has been running for almost 2 months now with fish in it and just added a canister filter along with the Whisper 60 about 2 weeks ago. Seachem Ammonia Alert (Look it up) is the only ammonia test i have. The only thing i ever test in my water in the PH.

LOL so how did you come to tell us that you have 0 nitrite and 0 nitrate? Cant really help you if you're not willing to help us help you. Good luck