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Life cycle assessment (LCA) methodology was used to compare the environmental loads from wastewater systems with different technical solutions. This study compared proposed conventional wastewater systems, both large and small scale, with separation systems: one in which urine is handled separately and one in which black water is treated in a liquid composting process. The study showed that large economies of scale, in environmental terms, could be gained both for the operation and for the construction phase. The separation systems outperformed the conventional systems by showing lower emissions to water and more efficient recycling of nutrients to agriculture, especially of nitrogen but also of phosphorus. This implies that the use of separation systems could significantly reduce the need for, and hence the production of, mineral fertilizers and thus reduce the overall use of energy and phosphate minerals. The combination of large-scale wastewater treatment and urine separation was found to be especially advantageous in these respects. It is concluded that some of the most important environmental advantages of separation systems emerge only when models of wastewater systems are expanded to also include potential effects on the production of fertilizers.