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GAIA Host Collective
I suspect fertilizer is the better use for it.
A. There needs to be large scale livestock farms so we might as well collect the waste and convert it to local energy.
OR
B. The best model is sustainable organic agriculture where crops and livestock co-exist or livestock is raised free range.
I prefer B. In that context, manure is not concentrated enough to make it's collection worthwhile.
My advice is to dont bother if A or B is best but make the equipment movable and recycleable if the site it was used on ends up being outcompeted.
I suspect you are right. The two most petroleum-dependent industries are transportation and agriculture. People seem willing to accept that transportation is going to have to change fundamentally, but not many think the same about agriculture.
C. The best model is to size farms such that energy from manure and other byproducts can be captured and the nutrients recycled. The actual division between grazing/feeding hay in barns is part of the determination of optimum size.
I beg to differ a bit. The die-off of pathogenic organisms depends on the HRT (hyrdraulic retention time) and temperature of digester operation. The most common are plug flow mesophilic systems operating at about 100F and pathogen reduction is only several logs. The thermophilic systems, operating at 140F or higher, essentially produce a sterile product.
With respect to reduction of nutrient content, the most important impact may be the potential reduction of soil carbon, which has an adverse impact on both soil productivity and atmospheric CO2 level. The impact on soil health and productivity is likely a major weak point of all non-food energy production schemes; some refer to these as "dirt burning".
Take a look at:
Building Soils for Better Crops http://www.sare.org/publications/soils.htm (in print and on-line)
The Soil Biology Primer http://soils.usda.gov/sqi/concepts/soil_biology/index.html
Glomalin: Hiding Place for a Third of the World's Stored Soil Carbon
http://www.ars.usda.gov/is/AR/archive/sep02/soil0902.htm
Soil Carbon Center
http://soilcarboncenter.k-state.edu/
Several blogs that cover topics in this area are Muck and Mystery http://www.garyjones.org/mt/ and Transect Points http://transectpoints.blogspot.com/