There's 2 seperate issues here--Genetically altered food is what's causing labeling confusion for the FDA, whether corn came, for instance, from a genetically altered strain or a "natural" one. Fertilizer, whether naturally or artificially produced, contains the same molecules to enable plant growth. The difference is how each is created. In the case of organic fertilizer, it's created from compost. In the case of manufactured fertilizer, it's created from oil. Most of US crop production has relied on manufactured fertilizer for decades, but with the end of cheap oil, the mass production of organic fertilizer will become economically viable.
The whole point of organic food is to not use any type of fertilizer other than what is produced by nature itself. Organic fertilizers are made of natural herbs, plants, animal wastes, and composts. A synthetic fertilizer would contain chemicals or artificial ingredients that will alter the state of organic foods and cause numerous labeling confusion and validity issues that the Food and Drug Administration may have difficulty approving. This in itself I believe would deter the growth of a synthetic fertilizer industry.
All plants that grow food need many nutrients that they obtain from the soil in which these are planted. The soils contain these nutrients naturally, and the fertility of any soil is directly related to the type and quantities of nutrients present in it.
Because of intensive farming, the nutrients present in the soil get depleted at a rate much higher than the rate at which these get replenished by natural processes of the nature. As a result the soil becomes less fertile and it becomes necessary to replenish the nutrients manually. This can be done by adding fertilizers to the soil, which are material containing some or all of the nutrients needed to restore the soil fertility.
These fertilizers are broadly classified in two categories - synthetic fertilizers and organic fertilizers. Synthetic fertilizers are manufactured by chemical processes. These are comparatively cheaper, have very high concentration of the nutrients, and can be manufactured in large quantities. But the range of nutrients contained in them is very limited. In general the synthetic fertilizers are very good source for supplying three basic nutrients nitrogen, phosphorus and potassium. However the synthetic fertilizers do not many other nutrients, called micro-nutrients, which are required by soils in very small quantities, but are very important for maintaining the nutritional and other qualities of food produced by plants. As a result, though the use of synthetic fertilizers has enabled increasing the total yield of food that can be grown from a given area of land, the quality of food has declined.
Organic fertilizers are made using the material naturally available on farms and using natural processes for its manufacture. These fertilizers contain all different types of nutrients including nitrogen, phosphorus and potassium as well as the micro-nutrients. Therefore, use of such fertilizers increase yield and the same time maintain quality of food produced. However it is not possible to produce these types of fertilizers in very large quantities to match the volume of synthetic fertilizers.
Now the problem facing the mankind is to find ways of grow enough food for the population of the world, and at the same time maintain the quality of food. Increasing production and use of organic fertilizers, is just one of the many different actions that will be required to solve these problems. Perhaps, it will be essential to find ways of producing the micro-nutrients also more economically in sufficient quantities to supplement the nitrogen, phosphorus and potassium provided by synthetic fertilizers currently. Efforts in this direction have already been made and some progress has been made, but still there is a long way to go.