Healthy soils are essential for progressive agronomic activities. Organic fertilization positively affects agro-ecosystems by stimulating plant growth, enhancing crop productivity and fruit quality and improving soil fertility. Soil health and food security are the key elements of Organic Agriculture 3.0. Landfilling and/or open-dumping of animal wastes produced from slaughtering cause environmental pollution by releasing toxic substances, leachate and greenhouse gases. Direct application of animal carcasses to agricultural fields can adversely affect soil microbiota. Effective waste management technologies such as thermal drying, composting, vermicomposting and anaerobic digestion transform animal wastes, making them suitable for soil application by supplying soil high in organic carbon and total nitrogen. Recent agronomic practices applied recycled animal wastes as organic fertilizer in crop production. However, plants may not survive at a high fertilization rate due to the presence of labile carbon fraction in animal wastes. Therefore, dose calculation and determination of fertilizer application frequency are crucial for agronomists. Long-term animal waste-derived organic supplementation promotes copiotrophic microbial abundance due to enhanced substrate affinity, provides micronutrients to soils and protects crops from soil-borne pathogens owing to formation of plant-beneficial microbial consortia. Animal waste-derived organically fertilized soils possess higher urease and acid phosphatase activities. Furthermore, waste to fertilizer conversion is a low-energy requiring process that promotes circular bio-economy. Thus, considering the promotion of soil fertility, microbial abundance, disease protection and economic considerations application of animal-waste-derived organic fertilizer should be the mainstay for sustainable agriculture.

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Although organic standards do not refer directly to soil health, organic agriculture has the potential to improve soil health and environmental services by promoting soil conservation and reducing greenhouse gases. This chapter presents findings from a field experiment which continuously monitored the soil health of an organically managed production system from 2003 to 2014. The experiments focus on intensive organic vegetable crop production systems typical of experienced fresh market growers. The research sought to evaluate short- and long-term effects of various different management systems, including crop rotations, cover crops and animal amendments. We discuss the impact of these measures in terms of nutrient release, soil health, greenhouse gas emissions and ecosystem structure and function.