Microbial nitrate respiration – Genes, enzymes and environmental distribution
Introduction
Nitrate is one of the essential environmental components in the biosphere. It serves as nutrient for plants and microorganisms, and is used as an electron acceptor by many bacteria, archaea and also by several eukaryotes (Hayatsu et al., 2008, Zumft, 1997). Because of the wide distribution of nitrate respiration and the phylogenetic pattern of the involved enzymes, it has been argued that nitrate respiration was a common process in microorganisms already before the increasing concentration of oxygen in the atmosphere led to the development of oxygen respiration (Castresana and Saraste, 1995, Ducluzeau et al., 2009).
Several microbial processes compete for nitrate, such as denitrification, dissimilatory nitrate reduction to ammonium and anaerobic ammonium oxidation. As evidence for the widespread existence of these processes accumulated in the past two decades it became obvious that the so-called nitrogen cycle is in fact a network of pathways (Fig. 1). One of the key reactions of this network is the reduction of nitrate to nitrite, since this reaction is always the first step in the use of nitrate. Depending on the microbial community and environmental conditions nitrite is then either released or further reduced in different ways.
Current human impact on the global nitrogen cycling is substantial (Galloway et al., 2008, Schlesinger, 2009). The use of nitrogen as fertilizer in agriculture often causes changes in the adjacent habitats, mostly due to nitrite pollution or rapid eutrophication (Vitousek et al., 1997). Intense agricultural fertilization may lead to increased concentrations of nitrate in the groundwater (Almasri and Kaluarachchi, 2004). This constitutes a risk for public health, given that groundwater is an important drinking-water supply (Ward et al., 2005).
Increased input of fixed nitrogen has also demonstrated impacts on more distant terrestrial (Brooks, 2003, Clark and Tilman, 2008) and marine ecosystems (Duce et al., 2008), where fixed inorganic nitrogen, one of the key nutrients, often is a limiting factor for primary productivity (Arrigo, 2005). Furthermore, fertilization increases the atmospheric concentrations of methane and nitrous oxide and thus contributes to global warming (reviewed by Hanke and Strous, 2010). In waste water treatment plants the conversion of nitrate to gaseous nitrogen and thus the loss of fixed nitrogen from the water is the aim. Complete denitrification to N2 and anammox are usually the desired processes (Kartal et al., 2010, Kumar and Lin, 2010, Strous et al., 1997).
Although a fair amount of studies on pure cultures have been performed, little is known about how the natural microbial communities of terrestrial and aqueous habitats react to changing nitrate concentrations and nitrogen speciation. Application of high throughput tools for DNA, RNA and protein analysis showed that only a small fraction of the entire natural microbial diversity has been discovered and described so far (Pace, 2009, Rappe and Giovannoni, 2003). All known processes of microbial nitrate and nitrite reduction appear to be globally widespread and it is likely that most microbial communities in nature are able to use different nitrogen compounds in different ways. This interaction of nitrogen reaction pathways will probably be affected as a whole as soon as the concentration or fluxes of one of the involved compounds changes. The same might hold true for the composition of the affected microbial community, more precisely, for the presence of specific genes and enzymes.
This review summarizes the current view on the network of respiratory nitrate reduction pathways and the enzymes involved, as well as their environmental distribution and impact.
Section snippets
Denitrification
Among the different pathways of microbial nitrate reduction, bacterial denitrification is most extensively described and numerous studies have been undertaken to elucidate this pathway. A number of comprehensive reviews have been published during the last years discussing bacterial and archaeal denitrification and the influencing factors and enzymes involved (Berks et al., 1995, Cabello et al., 2004, Hermann et al., 2000, Moura and Moura, 2001, Philippot, 2002, Shapleigh, 2006, Wallenstein et
Dissimilatory nitrate reduction to ammonium (DNRA)
In contrast to denitrification, dissimilatory nitrate reduction to ammonium (DNRA) is assumed to occur when nitrate in comparison to organic carbon is limiting (Cole and Brown, 1980). In DNRA nitrite is reduced to ammonium and eight electrons are transferred. The reduction of nitrate to nitrite is assumed to mostly being catalyzed by the periplasmic nitrate reductase complex NapAB (Fig. 2c). However, a membrane-bound nitrate reductase, NarGHI (Fig. 2a), may also be present in the same organism (
Anaerobic ammonium oxidation (anammox)
Under anoxic conditions, anammox bacteria are able to gain energy by the formation of nitrogen gas from nitrite and ammonium (Jetten et al., 2005, Mulder et al., 1995, Richards, 1965, Strous et al., 1999, van de Graaf et al., 1995, van de Graaf et al., 1997).
Since their identification by Strous et al. (1999), several bacteria that were found to be able to perform the anammox pathway have been characterized. They all belong to the order of Planctomycetales. They form a monophyletic order
Nitrite reduction drives methane oxidation
Recently, microbes that couple dinitrogen formation to methane oxidation were enriched (Ettwig et al., 2009, Hu et al., 2009) which let to the discovery of a new dinitrogen forming pathway. ‘Candidatus Methylomirabilis oxyfera’, the dominant organism of enrichment cultures from different drainage ditch sediments, is capable of oxidizing methane under anoxic conditions, using oxygen originating from nitric oxide (Ettwig et al., 2010). The pathway was deduced from metagenomic data followed by
Conclusions
Regarding the numerous biochemical pathways starting from nitrate and their interactions it is obvious that the nitrogen cycle is a complex network rather than a cycle. This network provides a great variety of ecological niches that bacteria and other (micro-)organisms can occupy and linkings between the different pathways add even more complexity to the network. For instance, W. succinogenes known for carrying out DNRA also reduces nitrous oxide to dinitrogen and thus carries out the last step
Acknowledgements
We wish to thank two anonymous reviewers for their helpful comments on the manuscript. Beate Kraft, Marc Strous and Halina Tegetmeyer are supported by the European Research Council (ERC) Starting Grant ‘MASEM’ (242635) and the Federal State of Nordrhein-Westfalen.
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