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A biofilter for use in treating contaminated gasses is provided with a container having a layer of particulate rubber, which serves as a filter media. One preferred source of the rubber particulate is recycled tires. Smaller containers may be provided with apertures in their bottom walls and a cover for the top of the container, so that the containers can be incorporated within municipal sewage systems as manhole covers. Another embodiment floats the layer of rubber particulate on a layer of water or sludge. Various systems are provided for the delivery of gaseous, liquid or solid waste to the container. The rubber particulate provides a platform for the growth and maintenance of a microbial ecosystem that substantially treats the contaminated gases emanating from the waste.