Hi helenf,
I don have any knowledge or experience in "El Natural", however I had a similar thing in an earlier tank of mine.
If its not air trapped under the substrate from the first setup, I am afraid it might be H2S (hydrogen sulphide) from the anaerobic bacteria. Thats what these bacteria produce when theres no O2 about.
If you are using regular pot soil you are more to come across this gas I think.
This gas is no harm to fish or the plants
only if you dont distrurb the substrate. The small bubbling wont be dangerous. However if you disturb the substrate and the deep soil you will have some pretty stressfull fish.
Hope this helps