What can kill a bio filter?

The question is a good one and I have lot's of experience gained from working retail LFS trying to troubleshoot tank problems for the goldfish killers.

Number one reason for a dead or disfunctional bio-filter is adding medicine. Sad part is, lotsa time the symptoms they're treating actually result from already compromised filtration. The anti-biotics or random snake oil, often pushed unethically by sales clerks on comission, finish off the already taxed bacteria in the filter. Surprisingly, feeding medicated food DOES tend to hurt the good bugs, prolly cause people tend to overfeed and the filter is sucking in uneaten medicated food.

Cleaning the filter media is another common cause of spikes.
Long term chronic problems are usually from overstocking, over feeding and under filtrating.

If you have high ammonia and zero nitrite, you have zero biofiltration whtsoever. Your water would stink and your fish would be gasping and scratching or worse.
I'm totally in agreement with those who say your test is bogus. Take a fresh sample to a decent LFS and have them test it.

having said that, if I had to speculate on a problem based on your brief description, the word "SOIL" jumped off the screen to me. Where'd you get it? How sure are you about the content of the soil?

I did another test last night and I have an explanation but don't understand it. I get the ammonia only reading when I empty out the tank in to the bucket for a water change and test the water from the bucket. If I test it straight from the tank I get very minimal readings of ammonia and nitrites and a low reading on nitrates.