What Can a Dissimilatory Nitrate Reduction to Ammonium Organism Do

Nitrogen Cycling in Coastal Sediments

Samantha B. Joye , Iris C. Anderson , in Nitrogen in the Marine Environment (Second Edition), 2008

5.five Dissimilatory nitrate reduction to ammonium

Measuring rates of DNRA requires a ^xvN tracer approach (Binnerup et al., 1992; Koike and Hattori, 1978); otherwise it is incommunicable to distinguish NH₄ ⁺ generated from organic matter mineralization from that derived from NO₃ ⁻. Relative to DNF, DNRA rates are poorly constrained but DNRA activeness can be comparable to DNF activity in coastal sediments (An and Gardner, 2002; Binnerup et al., 1992; Jørgensen, 1989). The full general approach for estimating DNRA is to add ^xvN-NO_iii ⁻ and rail the production of ^xvN-NH₄ ⁺ over time. Because ¹⁵N-NH_four ⁺ tin can rapidly adsorb onto particles, it is important to quantify both dissolved and solid stage ^xvN-NH_iv ⁺ pools. Often, only the pore water or overlying h2o ¹⁵N-NH₄ ⁺ pool is quantified, which can lead to significant underestimates of DNRA rates. The isotopic signature of ¹⁵Due north-NH_four ⁺ tin be estimated by high operation liquid chromatography (Gardner et al., 1995) or by isotope ratio mass spectrometry (Holmes et al., 1998).

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Population Diversity Groupings of Soybean Bradyrhizobia

Jeffry J. Fuhrmann , in Advances in Agronomy, 1993

3 Relationship to Dna Homology Groupings

Possible relationships betwixt DNR activity and DNA homology have not been specifically addressed. However, based on reported correlations betwixt DNR and serological phenotypes (van Berkum and Keyser, 1985) it is possible to infer that a reasonably strong human relationship exists between DNR and genetic groupings. In general, strains in serogroups associated with DNA homology grouping I/Ia were able to denitrify, whereas those identified with grouping II exhibited nitrate respiration. A small number of exceptions to the correlation between DNR and serogroup were noted past van Berkum and Keyser (1985). Additionally, strains in serogroup 135 were uniformly deficient in DNR, merely these strains are of uncertain Deoxyribonucleic acid homology.

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The Dissimilatory Reduction of Nitrate to Ammonia past Anaerobic Bacteria

Sudesh B. Mohan , Jeff A. Cole , in Biology of the Nitrogen Bike, 2007

7.one Dissimilatory nitrate reduction to ammonia, a process distinct from denitrification and nitrate assimilation

Nitrate reduction to NO ₂ ⁻ is the showtime step of three major biological processes, NO_iii ⁻ assimilation, denitrification and the dissimilatory reduction of NO_iii ⁻ to ammonia. This brief review is concerned with the 3rd of these processes that, because information technology bypasses denitrification and Northward₂ fixation, has been chosen the short circuit of the biological N-cycle [1, 2]. Like NO_three ⁻ assimilation, information technology is a two-step process involving NO₃ ⁻ reduction to NO₂ ⁻ followed past NO_ii ⁻ reduction to NH₄ ⁺. Information technology is strictly an anaerobic process that dominates NO₃ ⁻ and NO₂ ⁻ reduction in reductant-rich environments such as anaerobic marine sediments [iii] and S^2–-rich thermal vents [4], the human gastrointestinal tract [5] and the bodies of warm-blooded animals. There is an obvious caption for this. Electron acceptors are by definition scarce in an environs where reductants are abundant, so optimal use must be made of any available oxidant to regenerate NAD⁺ from NADH and hence sustain substrate oxidation and growth. It is therefore beneficial for bacteria to exploit this process rather than denitrification because NO_two ⁻ reduction to NH₄ ⁺ consumes 6 electrons compared with just two or 3 electrons consumed when NO₂ ⁻ is reduced via NirS or NirK to N₂O or N_ii.

Diverse names take been given to the process, including the ugly term, NO_three ⁻ ammonification, respiratory reduction of NO₃ ⁻ to NH₄ ⁺, and the championship used in this commodity. All of them emphasize – exaggerate – i aspect of the process. Genes required for NO_two ⁻ reduction to NH₄ ⁺ are oft misannotated as encoding assimilatory NO₂ ⁻ reductases with NAD(P)H designated every bit the electron donor, so it is important to begin by noting criteria that distinguish it from denitrification or NO₃ ⁻ assimilation (Table 7-1). Beginning, it is an anaerobic process that, unlike denitrification in some leaner, has no aerobic analogue. In facultative anaerobes like Escherichia coli and Staphylococcus carnosus, expression of the NO₃ ⁻ and NO₂ ⁻ reductase genes is tightly repressed in the presence of O_ii, induced during anaerobic growth and farther regulated by the availability of NO_three ⁻ and NO_two ⁻. A disquisitional point is that gene expression requires the housekeeping sigma factor, σ⁷⁰, rather than the specialized sigma factor, σ⁵⁴. NH_iv ⁺ does not repress cistron expression, which, different NO_iii ⁻ absorption in all bacteria so far studied in detail, is insensitive to the general N-control circuit mediated past NtrB–NtrC 2-component regulatory system (Table 7-1). Unlike NO₃ ⁻ assimilation, which is ever a cytoplasmic process, it can occur in the cytoplasm, or in the periplasm, or both, depending on the bacterial species and growth weather.

Table 7-one. Differences between denitrification, nitrate absorption and dissimilatory reduction of nitrate to ammonia.

Process	Enzymes involved	Regulation by				Location of the active site
		Oii	NH4 +	σ70	σ54
Nitrate assimilation	Nas; Nir	None	Repressed	No	Yeah	Cytoplasm
Denitrification	Nar, Nap, NirK, NirS	Repressed	None	Yes	No	Cytoplasm/periplasm
Dissimilation to ammonia	Nar, Nir	Repressed	None	Yes	No	Cytoplasm
Dissimilation to ammonia	Nap, Nrf	Repressed	None	Yes	No	Periplasm

Nas, assimilatory nitrate reductase; Nir, siroheme-dependent nitrite reductase; Nar, membrane-associated nitrate reductase; Nap, periplasmic nitrate reductase; NirK, copper-containing nitrite reductase; NirS, cytochrome cd ₁ nitrite reductase; Nrf, cytochrome c nitrite reductase.

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Nitrate assimilation is essential for the synthesis of organic matter

Hans-Walter Heldt , Birgit Piechulla , in Plant Biochemistry (Fourth Edition), 2011

Nitrate is reduced to nitrite in the cytosol

Nitrate reduction uses more often than not NADH as reductant, although some plants incorporate a nitrate reductase reacting with NADPH likewise as with NADH. The nitrate reductase of higher plants consists of two identical subunits. The molecular mass of each subunit varies from 99 to 104   kDa, depending on the species. Each subunit comprises an electron transport concatenation (Fig. 10.2) consisting of one flavin adenine dinucleotide molecule (FAD), one heme of the cytochrome- b blazon (cyt-b ₅₅₇), and one cofactor containing molybdenum (Fig. ten.3). The latter is a pterin with a side chain to which the molybdenum is attached by two sulfur bonds and is called the molybdenum cofactor, abbreviated MoCo. The bound Mo atom probably changes between oxidation states +4 and +Vi. The 3 redox carriers of nitrate reductase are each covalently jump to the subunit of the enzyme. The protein concatenation of the subunit can be cleaved by limited proteolysis into iii domains, each of which contains but one of the redox carriers. These separated domains, besides as the holoenzyme, are able to catalyze via their redox carriers electron transport to bogus electron acceptors (due east.thousand., from NADPH to Fe⁺⁺⁺ ions via the FAD domain or from reduced methylviologen (Fig. iii.39) to nitrate via the Mo domain). Moreover, nitrate reductase reduces chlorate (ClO₃ ⁻) to chlorite (ClO_ii ⁻). The latter is a very potent oxidant and therefore highly toxic to constitute cells. In the by chlorate was used as an cheap nonselective herbicide for keeping railway tracks free of vegetation.

Figure 10.2. A. Nitrate reductase transfers electrons from NADH to nitrate. B. The enzyme contains 3 domains where FAD, heme, and the molybdenum cofactor (MoCo) are bound.

Figure ten.3. The molybdenum cofactor (MoCo).

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Nitrate Assimilation Is Essential for the Biosynthesis of Organic Matter

Hans-Walter Heldt , Birgit Piechulla , in Plant Biochemistry (5th Edition), 2021

Nitrate is reduced to nitrite in the cytosol

Nitrate reduction uses mostly NADH equally reductant, although some plants incorporate a NR reacting with nicotinamide adenine dinucleotide phosphate (NADPH) as well every bit with NADH. The NR of higher plants consists of 2 identical subunits. The molecular mass of each subunit varies from 99 to 104   kDa, depending on the species. Each subunit comprises an electron ship chain (Fig. 10.3) consisting of one flavin adenine dinucleotide molecule (FAD), one heme of the cytochrome b type (cyt b ₅₅₇), and one cofactor containing molybdenum (Fig. x.four). The latter is a pterin with a side chain to which the molybdenum atom is attached by 2 sulfur bonds and is called the molybdenum cofactor (MoCo). The spring molybdenum cantlet changes between oxidation states +4 and +6. The three redox carriers of NR are each covalently bound to the subunit of the enzyme. The protein chain of the subunit can exist broken by limited proteolysis into 3 domains, each of which contains only ane of the redox carriers. These separated domains, also every bit the holoenzyme, are able to catalyze via their redox carriers electron transport to artificial electron acceptors [due east.1000., from NADPH to Fe³⁺ ions via the FAD domain or from reduced methylviologen (Fig. iii.19) to nitrate via the molybdenum domain]. Moreover, NR reduces the artificial substrate chlorate ( ${\mathrm{ClO}}_{{\mathrm{iii}}^{-}}$ ) to chlorite ( ${\mathrm{ClO}}_{2^{-}}$ ). Chlorate can exist taken up past some root nitrate transporters. Since it is a very strong oxidant, it is highly toxic to plant cells. In the past, chlorate was used as an inexpensive non-selective herbicide to keep railway tracks free of vegetation.

Figure 10.3. (A) Nitrate reductase transfers electrons from NADH to nitrate. (B) The enzyme contains three domains where FAD, heme, and the molybdenum cofactor (MoCo) are spring. FAD, flavin adenine dinucleotide.

Figure x.4. The molybdenum cofactor (MoCo).

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Nitrogen cycling during wastewater treatment

Dawn E. Holmes , ... Jessica A. Smith , in Advances in Applied Microbiology, 2019

4.2 Dissimilatory nitrate reduction to ammonia

Dissimilatory nitrate reduction to ammonia (DNRA) appears to outcompete denitrification in environments with loftier carbon-to-nitrogen ratios ( Strohm, Griffin, Zumft, & Schink, 2007; Tiedje, 1988; Tiedje, Sextone, Myrold, & Robinson, 1982; Yin, Chen, Chen, & Edis, 2002), loftier sulfide concentrations (An & Gardner, 2002; Brunet & GarciaGil, 1996; Shao et al., 2010), depression iron concentrations (Edwards, Kuesel, Drake, & Kostka, 2007; Weber, Urrutia, Churchill, Kukkadapu, & Roden, 2006), and high temperatures (Behrendt, de Beer, & Stief, 2013; Dong et al., 2011; Jorgensen, 1989; Ogilvie, Rutter, & Nedwell, 1997). These conditions tin exist found in a plant's rhizosphere (Burger & Jackson, 2005; Li, Rui, et al., 2014), an animal'due south rumen (Kaspar & Tiedje, 1981; Lewis, 1951), anaerobic sludge digestors (Kaspar, Tiedje, & Firestone, 1981; Ruiz, Jeison, & Chamy, 2006), estuaries (An & Gardner, 2002; Behrendt et al., 2013; Kelly-Gerreyn, Trimmer, & Hydes, 2001), littoral sediments (Giblin et al., 2013), aquaculture systems (Christensen, Rysgaard, Sloth, Dalsgaard, & Schwaerter, 2000; Gilbert, Souchu, Bianchi, & Bonin, 1997), salt marshes (Koop-Jakobsen & Giblin, 2010), and freshwater sediments (Brunet & GarciaGil, 1996; Nogaro & Burgin, 2014).

During the process of DNRA, microorganisms first reduce nitrate to nitrite and so to ammonium:

${{\mathrm{NO}}_3}^{-}\to {{\mathrm{NO}}_2}^{-}\to {{\mathrm{NH}}_{\mathrm{four}}}^{+}$

A diversity of microorganisms are capable of this metabolism and it can either be a heterotrophic (Tiedje, 1988) or an autotrophic process (Devol, 2015) (Table eight). More often than not, DNRA activity is highest in carbon-rich environments like those impacted past aquaculture (Christensen et al., 2000).

Table viii. Microorganisms known to be capable of DNRA.

Commonly, the first step in the DNRA pathway involves reduction of nitrate to nitrite by a periplasmic nitrate reductase circuitous (NapAB) (Giblin et al., 2013). The six electron reduction from nitrite to ammonia is and then usually catalyzed past cytochrome c nitrite reductase (NrfAB) (Einsle et al., 1999). Non all of the microorganisms that have been shown to be capable of DNRA accept homologs for these genes. Therefore, other pathways are also probable to catalyze the DNRA procedure.

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Nitrogen in Soils/Cycle☆

Hanna Poffenbarger , ... Wilbur West. Frye , in Reference Module in Earth Systems and Environmental Sciences, 2018

Dissimilatory nitrate reduction to ammonium (DNRA)

The ${{\mathrm{NH}}_{\mathrm{iv}}}^{+}$ produced during DNRA is non assimilated but is excreted into the surround (Eq. 16). The bacteria that perform DNRA are singled-out from denitrifiers. These leaner predominate in environments that are continuously saturated, anaerobic, and take high concentrations for C relative to ${{\mathrm{NO}}_{\mathrm{iii}}}^{-}$ :

(16) ${{\mathrm{NO}}_3}^{-}\to {{\mathrm{NO}}_2}^{-}\to {{\mathrm{NH}}_4}^{+}$

In the presence of ${{\mathrm{NO}}_3}^{-}$ , anammox bacteria in anaerobic biosolids handling systems are able to combine DNRA with ${{\mathrm{NH}}_4}^{+}$ oxidation to produce N₂ as the concluding product.

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Nitrogen Wheel

P. Cabello , ... C. Moreno-Vivián , in Encyclopedia of Microbiology (Third Edition), 2009

Dissimilatory Reduction of Nitrate to Ammonium (Nitrate Ammonification)

The dissimilatory nitrate reduction to ammonium (DNRA) or nitrate ammonification is an anaerobic process in which nitrate reduction to nitrite is followed by the six-electron reduction of nitrite to ammonium. This strictly anaerobic procedure occurs in reductant-rich environments like anaerobic marine sediments, sulfide-thermal vents, and gastrointestinal tracts of animals. There are ii types of DNRA: a periplasmic energy-conserving (respiratory) nitrate ammonification, which uses the pentaheme cytochrome c nitrite reductase Nrf to catalyze electron transfer from formate or H₂ to nitrite, and a cytoplasmic dissimilatory system that acts as electron sink and detoxifies nitrite formed in nitrate respiration, which uses the siroheme NADH-dependent Nir to reduce nitrite ( Tabular array 1 ). Therefore, DNRA is catalyzed by different enzymes (Nap–Nrf and Nar–Nir), occurs in dissimilar subcellular compartment (periplasm and cytoplasm), and plays unlike functions (ATP generation, dissipation of excess reducing ability, and nitrite detoxification), depending on the organism. Although ammonium formed in the anaerobic DNRA process may be potentially assimilated, this is not its primary office. Therefore, regulation of this process is completely dissimilar from assimilatory nitrate reduction but similar to denitrification since information technology is repressed past oxygen and unaffected past ammonium.

In respiratory ammonification, nitrate reduction is usually performed by the Nap and nitrite reduction to ammonium is catalyzed by the Nrf using nonfermentable substrates (formate or H₂) as reductants. This periplasmic system allows nitrate ammonification without nitrate/nitrite transport beyond the membrane and generates protonmotive force by coupling nitrite reduction to formate dehydrogenase or hydrogenase. Nrf is found in proteobacteria of the groups γ (E. coli), δ (Desulfovibrio), and ɛ (Wolinella), but not in α- and β-proteobacteria, which are mainly aerobic or facultative bacteria able to denitrify. In δ- and ɛ-proteobacteria, the pentaheme catalytic subunit NrfA (threescore   kDa) is located at the periplasmic side, anchored to the membrane past the NrfH protein, a 22   kDa tetraheme c cytochrome that oxidizes menaquinol and mediates electron transfer to NrfA. In γ-proteobacteria, NrfH protein is replaced by the nrfBCD gene products. NrfB is a pentaheme cytochrome c that reduces the NrfA catalytic subunit, and NrfCD are integral membrane proteins with quinol oxidase activeness. Information technology has been proposed that NrfA plays a role in nitrosative stress defense force since NO is substrate of this enzyme, which also produces North_twoO under certain weather. Denitrification and nitrate ammonification allow ATP generation under anaerobic conditions, but these processes do not occur in the same bacterium. Energy yield per reduced nitrate is slightly higher for respiratory nitrate ammonification than for denitrification, and probably for this reason, leaner living in environments with nitrate limitation prefer nitrate ammonification over denitrification.

Some bacteria use nitrite every bit electron sink to consume excess of reductant in anaerobic environments, assuasive regeneration of oxidized redox coenzymes (NAD⁺) to sustain an optimal growth. This nitrite reduction to ammonium also serves to detoxify nitrite formed in nitrate respiration in nondenitrifying facultative anaerobes, like Due east. coli. The Nir involved in this process, which in contrast to NrfA should be considered dissimilatory rather than respiratory, is the siroheme-containing Nir protein. The Eastward. coli enzyme has a large catalytic subunit (NirB) and a small-scale subunit (NirD) that is like to the C-termini of monomeric Nir of Klebsiella (NasB) and fungi. It should be emphasized that E. coli NirBD is non a proper assimilatory enzyme, although it uses NADH as reductant and shows the biochemical characteristics of assimilatory siroheme-containing Nir. In contrast to assimilatory enzymes, the E. coli ammonifying Nir is merely induced under anoxia and is not repressed by ammonium. Although nitrite ammonification by Nir is not coupled to free energy conservation, facultative bacteria obtain ATP in anaerobiosis by nitrate respiration through membrane-bound Nar. In addition, when fermentative bacteria reduce nitrite with the Nir enzyme, this compound is not only detoxified only also used as electron sink replacing intermediates of fermentation that would be reduced in the absence of nitrite. Thus, as acetate rather than ethanol is the final production of the C metabolism, boosted ATP is generated by substrate-level phosphorylation.

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METABOLIC PATHWAYS | Nitrogen Metabolism

R. Jeannotte , in Encyclopedia of Food Microbiology (Second Edition), 2014

Dissimilatory Nitrate Reduction to Ammonia (DNRA)

In some ecosystems, DNRA could be a ascendant process of nitrate consumption. It takes identify but nether anoxic conditions when carbon is available.

${{\text{NO}}_3}^{-}+\mathrm{two}{\text{H}}^{+}+4{\text{H}}_2\to {{\text{NH}}_{\mathrm{four}}}^{+}+3{\text{H}}_2\text{O}$

Nitrate is used every bit electron acceptor. DNRA is referred to as a 'brusk circuit in the biological N cycle' considering it directly transfers NO₃ ⁻ and NO_two ⁻ to NH₄, bypassing denitrification and N₂ fixation. Information technology was studied in many model organisms, such as Paracoccus denitrificans, Pseudomonas stutzeri, Escherichia coli, and Wolinella succinogene. The DRNA process widely occurs in the Bacillus species.

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Membrane-Associated Energy Transduction in Bacteria and Archaea

One thousand. Schäfer , in Encyclopedia of Biological Chemical science (Second Edition), 2013

Fumarate Respiration

In Wolinella , nitrate reduction can be achieved with molecular hydrogen or with formate as electron donors. It involves fumarate respiration ( Figure 2 ), as an alternative mechanism to generate a proton-motive strength. H⁺ is released at the outer side of the membrane by oxidation of hydrogen or formate, whereas proton uptake and reduction of fumarate occur at the inner side. The dehydrogenases as electron donors and the fumarate reductase as acceptor are interacting via b-type cytochromes and the menaquinone pool in the membrane (Due east′₀  =   −100   mV). The reduction of fumarate to succinate is catalyzed by an enzyme similar to nitrate reductase, but molybdopterin is replaced by flavine-adenine-dinucleotide (FAD). The enzyme is structurally and evolutionarily related closely to succinate dehydrogenases of aerobic organisms which catalyze the reverse reaction using ubiquinone (East′₀  =   +threescore   mV), or in thermoacidophilic archaea caldariella quinone (East′₀  =   +106   mV), equally primary electron acceptor.

Figure 2. Scheme of an anaerobic respiration. Fumarate respiration is taken as an example with two possible electron-donating systems. The type of energy conservation corresponds to principle A in Effigy one . MQ, menaquinone; P, periplasm; C, cytosol.

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