Denitrifying prokaryotes

Abstract

Denitrification is the dissimilatory reduction of nitrate to nitrogen gas. This respiratory process requires four enzymes that produce three obligatory intermediates prior to production of the terminal product. Denitrification is found in diverse array of microbes including members of both bacteria and archaea. However, no bacterium has been described that solely depends on denitrification as a form of energy generation. All denitrifiers, with one exception, are aerobes. Genome sequencing has provided a better appreciation of the distribution of denitrification genes among microbes. Complete denitrification, the reduction of nitrate to N 2, is less frequent than partial denitrification among sequenced bacteria. Partial denitrification chains of nearly all possible arrangments have been found. This includes chains with only a single enzyme or discontinuous chains of two or more enzymes. Nitrate reductase catalyzes the reduction of nitrate to nitrite and is used in a number of pathways other than denitrification; therefore, its distribution has not been a focus of this chapter. Nitrite reductase catalyzes the reduction of nitrite to nitric oxide and is the defining reaction of denitrification since it is the first step to produce a gaseous nitrogen oxide. There are two unrelated types of nitrite reductase, one of which has copper cofactors while the other contains heme-bound iron. The copper form has several different subtypes with N- and C-terminal extensions containing metal-binding sites. Some members of the Actinobacteria have a particularly large copper nitrite reductase with a membrane-bound domain of unknown function. Nitric oxide reductase catalyzes the reduction of nitric oxide to nitrous oxide. This enzyme is membrane bound and occurs in two subtypes referred to as cNor and qNor. The former receives electrons from cytochrome c while the latter carries an N-terminal extension allowing it to oxidize quinol. Nitrous oxide reductase is a soluble copper-containing enzyme with one of the copper centers, designated the CuZ center, being unique to this enzyme. While most model denitrifiers use denitrification to support growth when oxygen is limiting, this may not be the case in all bacteria that contain genes encoding denitrification-associated nitrogen oxide reductases. Bacteria with partial chains consisting of a single enzyme may use that enzyme for alternative functions. For example, some Staphylococcus aureus subspecies aureus strains only contain nitric oxide reductase which is likely used for detoxification of nitric oxide. There are a number of bacteria which only contain nitrite reductase and the function of this enzyme is unclear in these organisms since its turnover will produce nitric oxide, which is toxic due to its reactivity with metal centers and other compounds. Environmental studies have found denitrification genes are nearly universal in environments that receive some exposure to oxygen. Quantitative studies have found that the genes for nitrous oxide reductase are frequently underrepresented compared to other denitrification genes. While common in soil and aquatic environments, denitrifiers are also found in association with humans. Sequencing of both skin and oral microbiomes has revealed a significant number of denitrifiers, consistent with the occurrence of both nitrate and nitrite in these areas.