Ectomycorrhizal fungi dominate the humus layers of boreal forests. They depend on carbohydrates that are translocated through roots, via fungal mycelium to microsites in the soil, wherein they forage for nutrients. Mycorrhizal fungi are therefore sensitive to disruptive disturbances that may restrict their carbon supply. By disrupting root connections, we induced a sudden decline in mycorrhizal mycelial abundance and studied the consequent effects on growth and activity of free living, saprotrophic fungi and bacteria in pine forest humus, using molecular community analyses in combination with enzyme activity measurements. Ectomycorrhizal fungi had decreased in abundance 14 days after root severing, but the abundance of certain free-living ascomycetes was three times higher within 5 days of the disturbance compared with undisturbed controls. Root disruption also increased laccase production by an order of magnitude and cellulase production by a factor of 5. In contrast, bacterial populations seemed little affected. The results indicate that access to an external carbon source enables mycorrhizal fungi to monopolise the humus, but disturbances may induce rapid growth of opportunistic saprotrophic fungi that presumably use the dying mycorrhizal mycelium. Studies of such functional shifts in fungal communities, induced by disturbance, may shed light on mechanisms behind nutrient retention and release in boreal forests. The results also highlight the fundamental problems associated with methods that study microbial processes in soil samples that have been isolated from living roots.