The decomposing crop residue from prior years is another source of fertility. Though not strictly considered "fertilizer", the distinction seems more a matter of words than reality.
Some ambiguity in the usage of the term 'organic' exists because some of synthetic fertilizers, such as urea and urea formaldehyde, are fully organic in the sense of organic chemistry. In fact, it would be difficult to chemically distinguish between urea of biological origin and that produced synthetically. On the other hand, some fertilizer materials commonly approved for organic agriculture, such as powdered limestone, diatomaceous earth, and Chilean saltpeter, are inorganic in the use of the term by chemistry.
Although the density of nutrients in organic material is comparatively modest, they have some advantages. For one thing organic growers typically produce some or all of their fertilizer on-site, thus lowering operating costs considerably. Then there is the matter of how effective they are at promoting plant growth, chemical soil test results aside. The answers are encouraging. Since the majority of nitrogen supplying organic fertilizers contain insoluble nitrogen and are slow release fertilizers their effectiveness can be greater than conventional nitrogen fertilzers.
Implicit in modern theories of organic agriculture is the idea that the pendulum has swung the other way to some extent in thinking about plant nutrition. While admitting the obvious success of Leibig's theory, they stress that there are serious limitations to the current methods of implementing it via chemical fertilization. They re-emphasize the role of humus and other organic components of soil, which are believed to play several important roles:
Organics also have the advantage of avoiding certain long-term problems associated with the regular heavy use of artificial fertilizers;
Organic fertilizers also have their disadvantages. As acknowledged above, they are typically a dilute source of nutrients compared to inorganic fertilizers, and where significant amounts of nutrients are required for profitable yields, very large amounts of organic fertilisers must be applied. This results in prohibitive transportation and application costs, especially where the agriculture is practiced a long distance from the source of the organic fertilizer. The composition of organic fertilizers tends to be highly variable, so that accurate application of nutrients to match plant production is difficult. Hence, large-scale agriculture tends to rely on inorganic fertilizers while organic fertilizers are cost-effective on small-scale horticultural or domestic gardens. Finally, some organic fertilizers such as manures can contain bacteria or heavy metals harmful to human health.
In practice a compromise between the use of artificial and organic fertilizers is common, typically by using inorganic fertilizers supplemented with the application of organics that are readily available such as the return of crop residues or the application of manure.
It is important to differentiate between what we mean by organic fertilizers and fertilizers approved for use in organic farming and organic gardening by organizations and authorities who provide organic certification services. Some approved fertilizers may be inorganic, naturally occurring chemical compounds, e.g. minerals.
Over-application of chemical fertilizers, or application of chemical fertilizers at a time when the ground is waterlogged or the crop is not able to use the chemicals, can lead to surface runoff (particularly phosphorus) or leaching into groundwater (particularly nitrates). Excessive surface runoff of easily soluable nutrients often pollutes lakes and streams, in a process called eutrophication. This can lead to algal blooms which are destructive and even deadly to wildlife.
It is also possible to over-apply organic fertilizers. However: their nutrient content, their solubility, and their release rates are typically much lower than chemical fertilizers, partially because by their nature, most organic fertilizers also provide increased physical and biological storage mechanisms to soils.
The problem of over-fertilization is primarily associated with the use of artificial fertilizers, because of the massive quantities applied and the destructive nature of chemical fertilizers on soil nutrient holding structures. The high solubilities of chemical fertilizers also contribute to their tendancy to rapidly pollute ecosystems.
Storage and application of some fertilizers in some weather or soil conditions can cause emissions of the greenhouse gas nitrous oxide (N2O). Ammonia gas (NH3) may be emitted following application of inorganic fertilizers, or manure or slurry. Besides supplying nitrogen, ammonia can also increase soil acidity (lower pH, or "souring").
For these reasons, it is recommended that knowledge of the nutrient content of the soil and nutrient requirements of the crop are carefully balanced with application of nutrients in inorganic fertiliser especially. This process is called nutrient budgeting. By careful monitoring of soil conditions, farmers can avoid wasting expensive fertilizers, and also avoid the potential costs of cleaning up any pollution created as a byproduct of their farming.
The concentration of up to 100 mg/kg of Cadmium in phosphate minerals (for example Nauru[2] and the Christmas islands [3]) increases the contamination of soil with Cadmium, for example in New Zealand.[4] Uranium is an other example for impurities of fertilizers