Tillage is a killer
Among the main reasons beneficial saprophytic and mycorrhizal fungi is so scarce in agricultural soils is intensive tillage. Along with their ability to mine fertility from the soil, they are also responsible for creating structure. Aerobic bacteria are very effective at creating microaggregates in soil. Fungi, with their vast mycelial networks, gather and bind these together to create macroaggregates and the overall structure that allows oxygen and water to infiltrate. Without fungi, there is no structure and without structure, erosion and anaerobic conditions persist in soil.
For this reason, deep cultivation with a ripper, sub-soiler or keyline plow is often necessary to break-up compacted soils so that air, water, roots and microorganisms can begin to penetrate and recreate the structure that once was. A guiding principal for annual crop farmers working toward a system of reduced tillage and productivity is that biology must be reintroduced every time a tillage event occurs.