The presence of soil-borne disease infection is not correlated to the presence of an infectious organism, but to the absence of suppressive microbes.
Here is an example from Paul Syltie1 on wheat take-all disease:
It is well documented that the fungus responsible for the take all of wheat Gaeumannomyces graminis var. tritici is attacked by soil bacteria, in particular by the bacteria in what are called take-all suppressive soils. These soils are unique in that the severity of the disease becomes progressively less as the cropping season continues. In some cases the disease may not even express itself whatsoever despite being present.
It is concluded by soil microbiologists that most soils express some degree of natural pathogen suppression. This occurs generally in soils by the mass of beneficial organisms overwhelming the pathogens at a critical time in their life cycle, robbing critical nutrients from them. Specific suppression occurs when select species or groups of beneficial organisms antagonize the pathogen at some stage of its life cycle.
Take-all in wheat or barley becomes less and less of a problem if the crop is grown in consecutive years. Both fungi and bacteria, such as friendly saprophytic Fusarium species, reduce pathogen numbers by competing for food supplies, and at the same time specific antagonistic microbes like fluorescent pseudomonads attack the G. graminis. The pseudomonads are especially effective when ammonium rather than nitrate fertilizer is used, resulting in a lower rhizosphere pH. This suppression likely occurs mostly in the rhizosphere, but also throughout the soil mass.