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Liquid manure (slurry) storage facilities are important point sources of atmospheric pollution. Being point sources, containment of gaseous emissions via improved storage conditions may be possible, and permeable surface covers (natural crusts and artificial covers) are increasingly recognized for their capacity to reduce various gaseous emissions. Microbial transformations in permeable surface covers include bacterial-methane oxidation, but this interface between nitrogen-rich slurry and the atmosphere is also an environment with intense nitrogen turnover that can lead to nitrous oxide emissions. Both methane and nitrous oxide are greenhouse gases, and strategies to reduce environmental impact of slurry stores must consider the total greenhouse gas balance. In this paper, greenhouse gas mitigation options for manure storages are discussed with reference mainly to practical storage conditions in Europe and North America.