I would stir up the litter very well with a rake, and put a couple of fresh bags of pine shavings on top. Ammonia can cause respiratory infections as well as cause cataracts and eye problems.Have a 2 year old 4 lb Araucana and she has frothy white bubbles in both eyes. I have 26 chickens and so far she is the only one with this. I have had High levels of ammonia as the days are now getting warmer. And wondering if I should use tylan as a precaution. She is now in the house isolated from the other chickens. Would also want to know how other chicken caregivers in MI are able to keep ammonia levels down. We are ventilated well but the litter in the coop has to come out but the weather is still to cold to do a total clean out.