In contrast to toxicology, which deals with the effects of contaminants on individual organisms, ecotoxicology is concerned with the effects of contaminants on complex and interacting ecosystems. This implies that ecotoxicology not only considers direct effects on individual organisms but also pathways and processes through which contaminants affect other organisms and ecosystem functions. Since ecotoxicology considers ecosystem level effects, detrimental effects on individual organisms or species can be of less importance than effects on certain pathways or the development of an ecosystem. These can be very important ecotoxicological processes, even if they do not necessarily involve killing individual organisms. This is of specific interest when considering the ecotoxicological effects of nitrogen, since nitrogen is an essential nutrient and many ecosystems are nitrogen limited. Although increased nitrogen levels can increase the growth of some species, this can lead to adverse effects on other species, on characteristic species assemblages, and on ecosystem function.

For a clear understanding of the ecotoxicological effects of nitrogen in all its different forms, an understanding of nitrogen sources and cycling is essential.

Nitrogen and nitrogen compounds cycle, like any other element, through the air, water, and soil. Although nitrogen in its inert, molecular, form (N2) is the most common gas in the Earth's atmosphere, most organisms require nitrogen to be in a reactive form (bound to hydrogen, oxygen, or carbon), to be able to use it. The most common of these reactive forms are organic nitrogen compounds, nitrogen oxides (NO^,), nitrate (NO^), and ammonium (NH^) and ammonia (NH3), together often referred to as NHX. It is the oxidized and reduced forms of reactive nitrogen that are the most toxic forms to organisms.

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