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The intriguing picture emerging is of a coherent soil-world in which the diversity of life, especially the microbial forms, prevent, and sometimes cure, diseases. In this subterranean world, pathogens exist but are crowded out by the sheer variety of life around them. Plant roots orchestrate a consortium of friendly microbes around and within themselves. The soil, thus, not only provides a non-specific immune-system for the plants, but also forms an evolving protection against specific pathogens which are remembered in future years if the same pathogen emerges again.
Human efforts to engineer soil immunity by adding 'key' microbes have met with very limited success: the simple, single-pronged attack just isn't stable or comprehensive or intelligent enough.
In the soil-world, agri-chemicals poison the living immune-system, leaving a gap in which pathogens flourish. The biotech industry 'answer' to pesticide-induced pests, is, of course, more pesticides.
Current science for sustainable management of plant disease suggests that we should change the way we farm: add organic matter to they soil to feed the diversity of microbes, and breed plants for they ability to summon the microbes they need instead of for yield and appearance alone.
The biggest hurdle is probably not that these techniques are difficult or expensive, but that they're not lucrative for the agri-industry.
Bt insecticidal and glyphosate-tolerant monocultures account for almost all commercial GM crops.
Science has shown that 'Bt' insecticide-generating GM crops are deficient in their ability to summon the friendly soil microbes they need . Glyphosate herbicide, used on herbicide-tolerant GM crops, is able to damage soil-life diversity by several mechanisms . This sounds like a lose-lose situation for soil health.
Are any other GM plants able to orchestrate their environment to make it supportive to their health? No one's testing.
The best reason yet to change the way we farm:
A recent report by the International panel of experts on sustainable food systems (IPES-Food) has concluded the solution is to diversify agriculture and re-orient it around ecological practices.
We need to ditch our dependence on agri-chemicals, intensification, global markets, and dominance of our food supply by a handful of corporations. What we will gain is carbon in the ground instead of in the air, biodiversity around us, fertile soil in the fields, sustainable yields from our crops, secure farm livelihoods, a diverse diet, and improved health. 
 FUNGI DON'T LIKE Bt CROPS - September 2016
 GLYPHOSATE DAMAGES SOIL - September 2016
 THE ILLUSION OF SAFER SUBSTITUTION - July 2016
- Carl Zimmer, Scientists Hope to Cultivate an Immune System for Crops, New York Times, 16.06.16
- Jos M. Raaijmakers and Mark Mazzola, Soil immune responses, Science Magazine, 17.06.16