As the report, Moove that Manure, in Scientific American describes, manure from large farm animal operations can overwhelm the systems meant to contain or dilute it. The result is often contaminated surface waters and groundwater. This is but one symptom of the unsustainable system of agriculture we are growing in America and many other countries around the world.
In the farms of yesteryear, manure was not simply a waste product, but essential fertilizer. It enriched the soil for the next growing season, and helped prevent erosion and the depletion of soil fertility. The smaller and more diverse farms of that day could optimize their use of everything because they did not depend on the mass production of any one product.
But we don't have to return farming to what it was 50 or 100 years ago to make it once again sustainable. We may have to change our conception of a reasonable size for a farming operation, establish incentives that promote diverse agricultural businesses, and remove barriers that make it difficult for small farms to thrive. But we can do those things while still taking advantage of new technologies such as genetic engineering.