The second major group of mycorrhizae are the endomycorrhizae that grow within the root cells and are commonly associated with grasses, row crops, vegetables, and shrubs. Ericoid mycorrhizal fungi can by either ecto- or endomycorrhizal. The third group of fungi, pathogens or parasites , cause reduced production or death when they colonize roots and other organisms. Root-pathogenic fungi, such as Verticillium , Pythium , and Rhizoctonia , cause major economic losses in agriculture each year. Many fungi help control diseases.
Saprophytic fungi are commonly active around woody plant residue.
Fungal hyphae have advantages over bacteria in some soil environments. Under dry conditions, fungi can bridge gaps between pockets of moisture and continue to survive and grow, even when soil moisture is too low for most bacteria to be active. Fungi are able to use nitrogen up from the soil, allowing them to decompose surface residue which is often low in nitrogen. Fungi are aerobic organisms. Soil which becomes anaerobic for significant periods generally loses its fungal component.