Cool that you brought up fungi. It seems to be a very poorly understood field of study. I think it was an accepted part of the ecosystem for ancient farm technologies, however our modern world of compartmentalizing, nutrients, minerals, pests, etc is missing many of the inter locked natural systems. There have been interesting studies in the last 15-20 years revealing more and more about the micro life in soil. The interplay of bacteria, fungus, nutrients, biology and chemistry, can be quite fragile and using mono crops, selected fertilizers, selected pesticides can screw up that ecosystem. Think about old farmers spreading cow shit everywhere in the garden, composting with other animal manure, which all came from animals fed a wide range of food stuffs.