In the United States, there are approximately one million farms with livestock, of which about 212,000 confine animals and are defined as animal feeding operations (AFOs) under current regulations (USEPA, 2012a). A facility is an AFO if animals are stabled or confined and fed or maintained for 45 days or more within any 12-month period, and crops, vegetation, forage growth, or post-harvest residues are not sustained in the normal growing season over any portion of the lot or facility. Approximately 20,000 of these are large enough to be classified as concentrated animal feeding operations (CAFOs) which, under previous definitions, were generally considered to be operations with more than 1,000 animal units (USEPA, 2012a). AFOs generate approximately 500 million tons of manure each year which must be properly treated and disposed or utilized to prevent contamination of soil, air, and water (USEPA, 2003). Animal manure is a valuable source of nutrients and has been used as fertilizer to enhance production of agricultural crops and forage. However, there have been substantial changes in the U.S. animal production industry over the past several decades. Although the total number of operations has decreased, overall production has increased. As a result, CAFOs are increasing in size and generating considerably more waste requiring disposal over an increasingly limited area. As livestock production has become more spatially concentrated, the amount of available manure nutrients often exceeds the assimilative capacity of the land on the farms, especially in high production areas, and studies have shown that this problem is becoming much more widespread (Kellogg et al., 2000). The problem is not just limited to nutrients, and the industrialization of livestock production in the U.S. over the past three decades has not been accompanied by either improvements in waste treatment technologies or the corresponding changes in environmental regulations necessary to protect public health.