Mycelium (vegetative part of a fungus) digest numerous kinds of organic debris, and this characteristic can be useful to filter microorganisms (especially pathogenic ones such as protozoa, bacteria, and viruses), pollutants, and silt . We can choose mushroom species that target specific bacteria, to customize the desired effect on a particular site. For example, farms often have toxic levels of zinc and copper, which are byproducts of manure. It was found that the mycelium of fungus Aspergillus niger was able to remove 91% of copper and 70% of zinc in the environment .
In addition, mycelium is useful in farming, where it stops erosion, replenishes soil with nutrients and water, and reduces need for fertilizers .
Shiitake is a good candidate for mycofiltration, as it is effective against several microbes, many of which are pathogens. The list includes, Candida albicans, Listeria monocytogenes, Mycobacterium tuberculosis, Staphylococcus aureus, Streptococcus pneumoniae, and Streptococcus pyogenes. 
Brazilian mushrooms are also natural at mycofiltration, as they are good at filtering and recycling farm wastes. They abosrb cadmium, copper, lead, and mercury, and is even a consumer of Escherichia coli.