Unseen, Underestimated, Misdiagnosed.
Crop yields go down with continuous crop monoculture because of increased damage from root diseases and not because the soil is depleted of nutrients. Growing the same crop in the same field year after year leads to the build-up of root pathogens of that crop. It can also lead to the buildup on natural enemies of the pathogens of that crop, resulting in disease decline and return to higher yields after many years of continuous crop monoculture.
Claims of allelopathy in response to plowed-down cover crops more often than not are unrecognized root disease where the pathogen uses the plowed-down crop as a food base to increase its inoculum potential. Pythium species in particular are ubiquitous in the top few inches of virally change to virtually all agricultural and garden soils, have the ability to use fresh plant material as a food base, and are noted for their ability to strip away root hairs and fine rootlets. The result is a greatly reduced ability of the plant to explore the soil for nutrients, especially the relatively immobile nutrients such as phosphorus. The resulting symptoms of nutrient deficiency are due to lack of healthy roots and not depletion of soil nutrients. Other root pathogens attack and sever the larger roots, disconnecting entire roots from the tops. Still others such as vascular pathogens use root infections to access upper parts of the plant.
Apart from the natural soil sanitization achieved with crop rotation, soil disinfestation usually requires the use of a heat treatment or soil fumigation.