Ammonia comes from decaying protein and urea. If you compost mostly brown stuff, for example autumn leaf litter and wood chips, then there is not much protein or nitrogen to be converted to ammonia. The more green vegetation you have, the more protein there is and that can give off ammonia as it composts. When you add animal manure to the mix, you jump to a whole new level of nitrogen availability, because now in addition to undigested protein that may be present in the manure, you also have urea, each molecule of which can give rise to two molecules of ammonia.
The more nitrogen you have in your compost pile, the hotter it can get (more nutrients available for the bacteria to grow on), and the more ammonia that it can give off. As your link describes, sometimes you err on the side of too much ammonia and it kills the plants. There are too many variables here to give you a simple answer; ambient temperature and air flow are two variables that you have under your control that you can use to manage your greenhouse. If it's too cool, you add more manure and the compost pile heats up. If it's getting too hot, you can increase the air flow during the day and maybe stop it at sundown to keep the heat in.
A simple temperature probe in the compost pile could help you arrive at a workable solution. You can get a cheapie indoor/outdoor digital thermometer and stick the outdoor probe in the middle of the compost pile and have the indoor read the ambient in the greenhouse. From those measurements, you can get an idea of how much heat (and indirectly how much ammonia) the compost pile is producing.
I think it depends on your feed stocks and if you are going to turn your pile. In our first year with a hughtunnel we put in a mix of chicken bedding and hay. It was going well until after a few weeks I turned the pile to mix it up a bit. There was way to much nitrogen in the mix and it off gassed to much Ammonia. All our leafy greens looked bleached and died backed. It was still mid fall so they were able to grow back. If you use bulkier material that will break down slower and add a nice layer of carbon 12inch on the outside you should be fine. Big composting operations use a layer of completed compost of woodchips to slow the ammonia from escaping.
Gilbert - another thing you might consider if keeping the hoop houses warm is your concern - try putting animals in there with them. Rabbits give off a lot of heat so having a hutch in the hoop house is beneficial. You can place the hutch over a bin of composting worms and let the rabbit poop drop right in. Then use the worm poop to make compost tea - or for a saleable product. The stacking functions possibilities are endless. Chickens would also work as long as you kept them away from your plants!
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In the New Alchemy Institute's research on the subject they concluded that a compost pile big enough to produce heat for a greenhouse produces CO2 at toxic levels for plants. That being said having composting in a greenhouse can be a great advantage. CO2 in limited amounts is great for plant growth and can help offset reduced airflow. Here is a link to the paper:
FWIW, it occurs to me that if say, the back wall of the greenhouse or coldframe, was solid and able to conduct heat easily, then a person could build a nice hot compost pile up against the wall. That way you'd get the benefit of the heating, W/O having it inside and mebbe hurting the plants. I use the "hot" composting method, so it'd only last 3 weeks for me.....
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