Nitrification primer:


The four primary processes of the N cycle that control movement of N are nitrogen fixation, ammonification, denitrification, and nitrification (Figure and Pidwirny, M.), all of which are predominantly facilitated by microorganisms. Nitrifying bacteria participate in the nitrogen cycle by catalyzing the dissimilatory oxidation of reduced nitrogen (ammonia or ammonium) to oxidized nitrogen (nitrite, nitrate, and gaseous N oxides). Under aerobic conditions, two groups of bacteria mediate this process. The ammonia-oxidizing bacteria (AOB) carry out the oxidation of ammonia to nitrite. The nitrite-oxidizing bacteria (NOB) carry out the oxidation of nitrite to nitrate. In both cases, the bacteria carry out these oxidations to obtain an energy and reductant source for their growth and maintenance. Furthermore, both groups also use carbon dioxide predominantly as their carbon source. As such, these bacteria are examples of chemolithoautotrophs that obtain energy and reductant from the oxidation of inorganic compounds and obtain their carbon for biomass production from carbon dioxide. Representatives of the AOB and the NOB are typically found together in ecosystems and, consequently, nitrite accumulation is rare.

Nitrification and nitrifying bacteria play key roles in controlling the availability of nitrogen for plant productivity. As such, nitrification influences the carbon cycle and the potential of plants for sequestration of carbon dioxide from the atmosphere.

Nitrifying bacteria are also of interest because of their unusual metabolisms. Neither ammonia nor nitrite is a particularly good substrate for growth from a thermodynamic standpoint. Nonetheless, these bacteria have developed metabolisms that rely almost exclusively on the use of these substrates for growth and maintenance. AOB require ammonia, carbon dioxide, sulfate, phosphate and some trace elements for growth, and from this they synthesize all the biochemical constituents required for life. Three enzymes are key to this unusual metabolism (see Nitrification). The AOB use ammonia monooxygenase (AMO) to initiate the catabolism of ammonia, which is oxidized to hydroxylamine. Hydroxylamine oxidoreductase (HAO)then catalyzes the transformation of hydroxylamine to nitrite. The electrons released in the second step are partitioned back to ammonia monooxygenase, to an electron transport chain coupled to production of a proton gradient, and to reverse electron flow to produce NAD(P)H for biosynthesis. In the NOB, a single enzyme, nitrite oxidoreductase (NXR), catalyzes the oxidation of nitrite to nitrate.


Nitrification is a microbial process that involves the transformation of ammonia* to nitrate. This process is found wherever free ammonia is formed (predominantly from degradation of organic matter) or introduced (N fertilization of croplands) and includes environments such as soils, sediments, wastewaters, and surface waters (including oceans). Nitrification is a critical step in the biochemical nitrogen (N) cycle. When unbalanced by anthropogenic activities, rapid nitrification overwhelms denitrification in the N cycle leading to the accumulation of nitrate and resulting in the contamination of ground waters and eutrophication of lakes. On the other hand, rapid nitrification is desired in wastewater reclamation, where removal of ammonia is required.

Nitrification in aerobic environments is carried out by two groups of bacteria in a two-step process (Arp et al., 2002) (Figure). First, ammonia-oxidizing bacteria (or AOB; e.g. by N. europaea or Nitrosococcus oceani) convert ammonia to nitrite and second, nitrite-oxidizing bacteria (or NOB; e.g by Nitrobacter winogradsky) convert nitrite to nitrate. Recently, a role for crenarchaeota (AOA) in ammonia oxidation was identified. Current research is establishing the extent to which AOA contribute to nitrification (Nicol and Schleper, 2006, Treusch et al. 2005). In anaerobic environments,nitrite and ammonia can combine to form nitrogen gas in the anammox process (Op de Camp, 2006, Strous, 2006). Among the aerobic ammonia-oxidizing bacteria, Nitrosomonas europaea is the best studied. As a chemolithoautotroph, N. europaea can derive all of its energy and reductant for growth from the oxidation of ammonia to nitrite and meet its requirements for carbon from the fixation of carbon dioxide (Arp et al., 2002). Given the thermodynamically low energy yield of ammonia, the obligate dependence of nitrifiers on ammonia as an energy source is enigmatic.

*Ammonia in aqueous solutions is in equilibrium with ammonium, which dominates the equilibrium at neutral pH (pK=9). For simplicity, here we refer to ammonia, the actual substrate for ammonia-oxidizing bacteria.

Nitrogen Cycle Imbalancing:

The anthropogenic influence on the N cycle is greater than on any of the other biogeochemical cycles. Total nitrogen loading to the global landmass has nearly doubled since the pre-industrial era from about 111 Tg yr-1 to 223 Tg yr-1 due to human related activities (Frink CR, et al.). This relatively new input (anthropogenic nitrogen fixation, agricultural and fossil fuel sources primarily) to the cycle has a myriad of effects on waters, soils, and the atmosphere. While a portion of this increase is stored in biomass, soil organic matter and agricultural products, a significant flux of reactive N is mobilized to surface waters as nitrate. Nitrate travels through rivers and results in large areas of eutrophication at the outlets of major river systems. Large dead-zones such as that formed in the Gulf of Mexico at the Mississippi delta are increasing evidence that N pollution has reached a global level of impact.