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Wind driven ammonia fuels and fertilizes the corn crop. You're right that ammonia is bad for soil organisms ... I think urea is kinder. We used to rotate corn and soy so the legume would have a chance to fix nitrogen, but now they're doing corn on corn ... madness, I think, and we'll see how long it lasts.
Ethanol needs heat, wind driven ammonia produces it. Ethanol produces distiller's grain ... and a feed lot can use the protein. Corn oil should be fractionated for biodiesel first. Note that I am only considering ethanol EROI and not global food security concerns - this is the environment in which I have to work.
The feed lot waste can produce either methane or ammonia. We hear that biological methods are going to be better/faster/stronger than any other renewable ... but I wonder how that works if they don't have the feed for the animals to produce the waste. I think they'll be complementary - we need every bit of every renewable source we can lay our hands on. E3 in Mead, Nebraska was powering their ethanol production with feedlot waste generated methane. The plant had a design fault and it blew up ... but it was working well until that time.
I just hope we get a chance to address these things before everything lets go with a bang. I think we will see/hear bangs before we get it - Pakistan being the name that comes to mind first.
I am surprised to see the monocropping and the farmers are a bit befuddled by it all as well. We always had corn/soy in rotation until just a few years ago and corn/soy/alfalfa(unharvested) would be even better. I suppose we'll have to see some ort of systemic failure before it changes - crop failure due to things you describe, or ethanol plant failure due to policy changes related to global food security, etc.
Interesting times in which we live ...