Nitrification

Any chemical reaction requires substrate molecules, which in the case of nitrification is ammonium. The most important natural source of this substrate is ammonium released from decaying organic matter through the microbial process of ammonification, during which this ion is produced as a waste product of the oxidation of various forms of organic nitrogen such as proteins. There are also inputs of ammonium from the atmosphere, both dissolved in precipitation and through the dry deposition of gas. The biological fixation of atmospheric dinitrogen (or nitrogen gas, N₂) into ammonia can be another important source of input, especially when legumes are cultivated in agriculture as well as in some natural ecosystems, for example, sites dominated by alders (Alnus spp.). Ammonium may also be added to agricultural soils in large quantities when inorganic fertilizers are used or when manure or sludges are spread on fields.

The genera of bacteria that are responsible for nitrification are highly sensitive to acidity, so this process does not occur at significant rates in acidic soil or water, especially in those with pH less than 5.5. Plants that grow in acidic habitats such as bogs and some forests must be capable of utilizing ammonium as their source of nitrogen nutrition because nitrate is not available in those habitats. Because Nitrobacter is somewhat more sensitive to acidity and some other stresses than Nitrosomonas, nitrite can accumulate under some conditions.

Interestingly, nitrification is a process that actually generates acidity, equivalent to two H⁺ ions for every ion of NO₃^– produced by the oxidation of NH ⁺ 4 . However, the ammonification of organic nitrogen to ammonium consumes one H⁺, as does the uptake of nitrate from soil by plant roots. Therefore, nitrification only acidifies soils if the ammonium substrate is added directly, for example through fertilization or by atmospheric deposition, or if the nitrate is not taken up by plants and leaches from the soil.

The nitrifying bacteria are also very sensitive to high temperatures. Their populations are substantially reduced by exposures to temperatures of 212°F (100°C), and they are virtually eliminated at temperatures hotter than 284°F (140°C). As a result, nitrifying bacteria are often uncommon after a ground fire. The rates of nitrification are correspondingly small, even if there is an abundant substrate of ammonium.

The rate of nitrification is known to decline during some ecological successions. This is probably caused by an increasing acidification of the ecosystem and perhaps also by the presence of organic chemicals that inhibit the nitrifying bacteria. Decreasing nitrification has been observed during the succession of abandoned pastures into old-field conifer forests in eastern North America as well as in conifer forest successions elsewhere. A potential benefit of decreasing nitrification during succession is that this causes the major form of soluble, inorganic nitrogen to become ammonium, an ion that is bound readily by soils and is not easily leached. However, nitrification does not always decrease during succession; it is known to increase when some abandoned farmlands develop into an angiosperm forest which tends not to acidify soils as much as most conifer forests.