Why Is My Tank Cycling From Scratch?

It is now known that there is a substantial proportion of the bacteria in the substrate so you would have removed a lot of them, unfortunately.

How high does the ammonia level reach? Goldies are very messy fish so if your ammonia is not going off the top of the scale on a daily basis, you do have a lot of bacteria left.

Assuming you have some of both types of bacteria left, just not as many as you used to have, the roadblock will be at the ammonia stage. Insufficient ammonia eaters will cause ammonia to build up. But the ones that are left will be converting ammonia to nitrite and the nitrite eaters that are left will be able to cope with the reduced amount of nitrite being made.
I know goldies and plants aren't usually good tank mates but if you could throw in a bunch of elodea and leave it floating that would help as the plant would use some ammonia as food.

The nitrate is another things though because even a trickle of nitrite being converted should end up as nitrate unless you have live floating plants or plants attached to decor - I realise you can't have anything planted in the substrate if there isn't any.

Did you do anything to the filter at the same time as removing the substrate? Such as wash any media or replace any media?

I would just keep up with the water changes, easing off as the ammonia decreases but keep an eye on that and nitrite for several days.

Have you come across the ammonia calculator? Ammonia exists in water in 2 forms, toxic ammonia and less toxic ammonium, but our kits measure the two combined. The amount in each form depends on the pH and temperature and it is possibly to calculate how much of any given reading is in the toxic form. This is the calculator I use. Just enter your data, setting salinity to zero, and click calculate. The figure you want is the lower one, NH3 concentration.

Ammonium still burn the fish so the tester reading needs to be kept under 2ppm. The result from the calculator can be as high as 0.05 for a day or two but longer than that it should be kept below 0.02.


If you find nitrite begins to read over zero, you can use salt to mitigate its effects; goldies should be OK with that. If you do get that problem, I'll give the the equation to work out the dosage.

It is pssible depending on what your ammonia reading is and your pH and temp. If you want me to check, can you tell me your pH and temp and I'll tell you the highest safe reading with the tester.

If I were you I'd get some Seachem Safe or Seachem Prime

Safe™ converts ammonia into a safe, non-toxic form that is readily removed by the tank’s biofilter. Safe™ may be used during tank cycling to alleviate ammonia/nitrite toxicity. Safe™ detoxifies nitrite and nitrate, allowing the biofilter to more efficiently remove them. Safe™ is non-acidic and will not impact pH.

...

Safe™ is the dry version of Prime® and shares all of it’s advantages; however, Safe™ is even more concentrated than Prime®.
 

I'd use the Safe for it's detoxifying properties but still continue with the frequent water changes.

Since Seachem admit they don't know how Prime detoxifies nitrite, it is difficult to say 

With your pH being so low, almost all your ammonia is in the less toxic form. You can let it stay at 2ppm as long as you like. Any higher than 2ppm, the less toxic form will start to have an effect though - it is less toxic not non-toxic.

Has your pH always been this low or has it fallen recently (ie since you removed the substrate)? I ask because the filter bacteria multiply faster with a high pH.

if I used this would it not stop the natural cycle?

I've used Seachem Prime for many years, including in situations such as setting up a hospital/quarantine tank with a combination of mature filter media plus new filter media in the filter and also in the main/established tank where some of the filter media has been removed for use in the hospital/quarantine tank's filter, and so a mini/partial cycle might be happening. It doesn't seem to have posed any problem at all - as I understand it (Sue may correct me if I'm wrong), it doesn't affect the ammonia/nitrates/nitrites levels but instead converts them to a less toxic form.

Incidentally, like your water, mine is also very soft.

I'm a lot like Sue in regards being very cautious about adding chemicals unnecessarily, however I once found myself in a situation (self inflicted) which warranted drastic action.

I added too many fish at once, and the bacterial colony couldn't cope with the extra bio-load.

So I researched the Seachem products and read a lot of testimonials all over the internet and decided that I'd risk it.

So, whilst I was suffering a mini cycle, I used Seachem Safe to detoxify.
I also continued with the frequent water changes but, testing every other day,  Ammonia and Nitrite was still present and I was very concerned that without the Safe product I would have been harming my livestock.

The cycle continued as normal and I lost no fish and so, after about 12 days or so I stopped using the Safe and let the bacteria take over.

I might not have lost fish anyway, and perhaps the Safe was unnecessary, but it gave peace of mind and helped stop some sleepless nights.

I've also used Safe successfully since when setting up a quarantine tank, before the filter had completed its cycle.