Revision of N<sub>2</sub>O-Producing Pathways in the Ammonia-Oxidizing Bacterium Nitrosomonas europaea ATCC 19718

Kozlowski, Jessica A.; Price, Jennifer L.; Stein, Lisa Y.

doi:10.1128/aem.01061-14

Cited by 135 publications

(104 citation statements)

References 35 publications

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“…NirK generally functions to reduce NO 2 -to NO in denitrification or nitrifier denitrification pathways. NirK deletion variants of N. europaea show no disruption in N 2 O production under anaerobic conditions, which suggests that NirK is unnecessary for nitrifier denitrification in these organisms (37,38). However, these variant strains exhibit considerably decreased NO 2 -production.…”

Section: Hao Stoichiometrically Oxidizes Nh 2 Oh To No Under Anaerobicmentioning

confidence: 98%

Nitric oxide is an obligate bacterial nitrification intermediate produced by hydroxylamine oxidoreductase

Caranto

Lancaster

2017

Proc. Natl. Acad. Sci. U.S.A.

350

274

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Ammonia (NH 3 )-oxidizing bacteria (AOB) emit substantial amounts of nitric oxide (NO) and nitrous oxide (N 2 O), both of which contribute to the harmful environmental side effects of large-scale agriculture. The currently accepted model for AOB metabolism involves NH 3 oxidation to nitrite (NO 2 -) via a single obligate intermediate, hydroxylamine (NH 2 OH). Within this model, the multiheme enzyme hydroxylamine oxidoreductase (HAO) catalyzes the four-electron oxidation of NH 2 OH to NO 2 -. We provide evidence that HAO oxidizes NH 2 OH by only three electrons to NO under both anaerobic and aerobic conditions. NO 2 -observed in HAO activity assays is a nonenzymatic product resulting from the oxidation of NO by O 2 under aerobic conditions. Our present study implies that aerobic NH 3 oxidation by AOB occurs via two obligate intermediates, NH 2 OH and NO, necessitating a mediator of the third enzymatic step.nitrification | nitric oxide | enzymology | bioinorganic chemistry S ynthetic nitrogenous fertilizers are necessary in agriculture to sustain the growing human population, but their use causes significant imbalance in the biogeochemical nitrogen cycle (1). The application of ammonia (NH 3 )-based fertilizers increases concentrations of nitrite (NO 2 -) and nitrate (NO 3 -) in the water table. These species pollute drinking water and drive the eutrophication of lakes and estuaries. Moreover, elevated NH 3 concentrations in soil have been linked to nitrous oxide (N 2 O) and nitric oxide (NO) emissions. N 2 O is an ozone-depleting greenhouse gas with a global warming potential ∼300× greater than that of carbon dioxide (2), and NO contributes to the production of ground-level ozone and acid rain (3, 4). Balancing human needs with environmental impact requires an intimate understanding of the biological pathways that produce these pollutants (5).Biological sources of NO and N 2 O include NH 3 -oxidizing bacteria (AOB), which mediate the oxidation of NH 3 to NO 2 -. The prevailing view of NH 3 oxidation, based largely on studies of the model AOB Nitrosomonas europaea, is that it occurs via a two-step enzymatic process (6):An integral membrane metalloenzyme, NH 3 monooxygenase (AMO), catalyzes the dioxygen (O 2 )-dependent hydroxylation of NH 3 to hydroxylamine (NH 2 OH; Eq. 1). Two electrons are required to turn over AMO. NH 2 OH is then oxidized by four electrons to NO 2 -(Eq. 2) by a multiheme enzyme, hydroxylamine oxidoreductase (HAO). Two of these electrons return to AMO, leaving two net electrons to enter the respiratory electron transport chain using O 2 as the terminal electron acceptor. Under anaerobic conditions, AOB carry out nitrifier denitrification, in which O 2 is substituted by NO 2 -as the terminal electron acceptor and is reduced to N 2 O or dinitrogen (7). The obligate intermediates of nitrifier denitrification are NO and N 2 O, both of which can escape from cells and into the atmosphere. Emissions of NO and N 2 O have also been linked to aerobic NH 3 oxidation (4, 8), which suggests that alternate ...

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Section: Hao Stoichiometrically Oxidizes Nh 2 Oh To No Under Anaerobicmentioning

confidence: 98%

Nitric oxide is an obligate bacterial nitrification intermediate produced by hydroxylamine oxidoreductase

Caranto

Lancaster

2017

Proc. Natl. Acad. Sci. U.S.A.

350

274

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“…Is79 and N. europaea (20,66). During ammonia oxidation, NirK is hypothesized to act as an electron sink and prevent the buildup of the toxic intermediate hydroxylamine in AOB (67,68). NirK has been shown to be essential for efficient ammonia oxidation in N. europaea, with ammonia oxidation rates decreasing in nirK mutants compared to the rate in the wild type (68).…”

Section: Discussionmentioning

confidence: 99%

“…During ammonia oxidation, NirK is hypothesized to act as an electron sink and prevent the buildup of the toxic intermediate hydroxylamine in AOB (67,68). NirK has been shown to be essential for efficient ammonia oxidation in N. europaea, with ammonia oxidation rates decreasing in nirK mutants compared to the rate in the wild type (68). Since the NO 2 Ϫ concentration in the chemostats decreased from 4,653 M in the absence of N. winogradskyi to below 15 M when N. winogradskyi was present (see Table S3 in the supplemental material), our results suggest that NirK in Nitrosomonas sp.…”

Section: Discussionmentioning

confidence: 99%

Effects of Bacterial Community Members on the Proteome of the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain Is79

Sedlacek

Nielsen

Greis

et al. 2016

Appl Environ Microbiol

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Microorganisms in the environment do not exist as the often-studied pure cultures but as members of complex microbial communities. Characterizing the interactions within microbial communities is essential to understand their function in both natural and engineered environments. In this study, we investigated how the presence of a nitrite-oxidizing bacterium (NOB) and heterotrophic bacteria affect the growth and proteome of the chemolithoautotrophic ammonia-oxidizing bacterium (AOB) Nitrosomonas sp. strain Is79. We investigated Nitrosomonas sp. Is79 in co-culture with Nitrobacter winogradskyi, in co-cultures with selected heterotrophic bacteria, and as a member of the nitrifying enrichment culture G5-7. In batch culture, N. winogradskyi and heterotrophic bacteria had positive effects on the growth of Nitrosomonas sp. Is79. An isobaric tag for relative and absolute quantification (iTRAQ) liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was used to investigate the effect of N. winogradskyi and the co-cultured heterotrophic bacteria from G5-7 on the proteome of Nitrosomonas sp. Is79. In co-culture with N. winogradskyi, several Nitrosomonas sp. Is79 oxidative stress response proteins changed in abundance, with periplasmic proteins increasing and cytoplasmic proteins decreasing in abundance. In the presence of heterotrophic bacteria, the abundance of proteins directly related to the ammonia oxidation pathway increased, while the abundance of proteins related to amino acid synthesis and metabolism decreased. In summary, the proteome of Nitrosomonas sp. Is79 was differentially influenced by the presence of either N. winogradskyi or heterotrophic bacteria. Together, N. winogradskyi and heterotrophic bacteria reduced the oxidative stress for Nitrosomonas sp. Is79, which resulted in more efficient metabolism. IMPORTANCEAerobic ammonia-oxidizing microorganisms play an important role in the global nitrogen cycle, converting ammonia to nitrite. In their natural environment, they coexist and interact with nitrite oxidizers, which convert nitrite to nitrate, and with heterotrophic microorganisms. The presence of nitrite oxidizers and heterotrophic bacteria has a positive influence on the growth of the ammonia oxidizers. Here, we present a study investigating the effect of nitrite oxidizers and heterotrophic bacteria on the proteome of a selected ammonia oxidizer in a defined culture to elucidate how these two groups improve the performance of the ammonia oxidizer. The results show that the presence of a nitrite oxidizer and heterotrophic bacteria reduced the stress for the ammonia oxidizer and resulted in more efficient energy generation. This study contributes to our understanding of microbemicrobe interactions, in particular between ammonia oxidizers and their neighboring microbial community.

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“…As a consequence, gene expression data reported by Jiang et al represented transitional and not steadystate conditions (6). Other studies have suggested that N 2 O is produced via reduction of nitric oxide (NO) formed either by reduction of NO 2 Ϫ or by incomplete oxidation of NH 2 OH (15)(16)(17). N 2 O production by AOB has traditionally been associated with high NH 4 ϩ /NH 3 and NO 2 Ϫ concentrations and with low oxygen conditions (18)(19)(20), and further studies are needed to confirm the mechanism of N 2 O production under IC-limiting conditions.…”

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confidence: 99%

Steady-State Growth under Inorganic Carbon Limitation Conditions Increases Energy Consumption for Maintenance and Enhances Nitrous Oxide Production in Nitrosomonas europaea

Mellbye

Giguere

Chaplen

et al. 2016

Appl Environ Microbiol

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Nitrosomonas europaea is a chemolithoautotrophic bacterium that oxidizes ammonia (NH 3 ) to obtain energy for growth on carbon dioxide (CO 2 ) and can also produce nitrous oxide (N 2 O), a greenhouse gas. We interrogated the growth, physiological, and transcriptome responses of N. europaea to conditions of replete (>5.2 mM) and limited inorganic carbon (IC) provided by either 1.0 mM or 0.2 mM sodium carbonate (Na 2 CO 3 ) supplemented with atmospheric CO 2 . IC-limited cultures oxidized 25 to 58% of available NH 3 to nitrite, depending on the dilution rate and Na 2 CO 3 concentration. IC limitation resulted in a 2.3-fold increase in cellular maintenance energy requirements compared to those for NH 3 -limited cultures. Rates of N 2 O production increased 2.5-and 6.3-fold under the two IC-limited conditions, increasing the percentage of oxidized NH 3 -N that was transformed to N 2 O-N from 0.5% (replete) up to 4.4% (0.2 mM Na 2 CO 3 ). Transcriptome analysis showed differential expression (P < 0.05) of 488 genes (20% of inventory) between replete and IC-limited conditions, but few differences were detected between the two IC-limiting treatments. IC-limited conditions resulted in a decreased expression of ammonium/ ammonia transporter and ammonia monooxygenase subunits and increased the expression of genes involved in C 1 metabolism, including the genes for RuBisCO (cbb gene cluster), carbonic anhydrase, folate-linked metabolism of C 1 moieties, and putative C salvage due to oxygenase activity of RuBisCO. Increased expression of nitrite reductase (gene cluster NE0924 to NE0927) correlated with increased production of N 2 O. Together, these data suggest that N. europaea adapts physiologically during IC-limited steady-state growth, which leads to the uncoupling of NH 3 oxidation from growth and increased N 2 O production. IMPORTANCENitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is an important process in the global nitrogen cycle. This process is generally dependent on ammonia-oxidizing microorganisms and nitrite-oxidizing bacteria. Most nitrifiers are chemolithoautotrophs that fix inorganic carbon (CO 2 ) for growth. Here, we investigate how inorganic carbon limitation modifies the physiology and transcriptome of Nitrosomonas europaea, a model ammonia-oxidizing bacterium, and report on increased production of N 2 O, a potent greenhouse gas. This study, along with previous work, suggests that inorganic carbon limitation may be an important factor in controlling N 2 O emissions from nitrification in soils and wastewater treatment. During nitrification in aerobic environments, ammonia (NH 3 ) oxidation to nitrite (NO 2 Ϫ ) is initiated by ammonia-oxidizing bacteria (AOB) and archaea (1). These microorganisms are predominantly chemolithoautotrophs that derive energy for growth from NH 3 and meet their carbon (C) needs by fixing carbon dioxide (CO 2 ) (1). All known AOB fix CO 2 via the CalvinBenson-Bassham (CBB) cycle for growth, utilizing ribulose bisphosphate carboxylase/oxygenase (RuB...

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Revision of N₂O-Producing Pathways in the Ammonia-Oxidizing Bacterium Nitrosomonas europaea ATCC 19718

Cited by 135 publications

References 35 publications

Nitric oxide is an obligate bacterial nitrification intermediate produced by hydroxylamine oxidoreductase

Nitric oxide is an obligate bacterial nitrification intermediate produced by hydroxylamine oxidoreductase

Effects of Bacterial Community Members on the Proteome of the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain Is79

Steady-State Growth under Inorganic Carbon Limitation Conditions Increases Energy Consumption for Maintenance and Enhances Nitrous Oxide Production in Nitrosomonas europaea

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Revision of N2O-Producing Pathways in the Ammonia-Oxidizing Bacterium Nitrosomonas europaea ATCC 19718

Cited by 135 publications

References 35 publications

Nitric oxide is an obligate bacterial nitrification intermediate produced by hydroxylamine oxidoreductase

Nitric oxide is an obligate bacterial nitrification intermediate produced by hydroxylamine oxidoreductase

Effects of Bacterial Community Members on the Proteome of the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain Is79

Steady-State Growth under Inorganic Carbon Limitation Conditions Increases Energy Consumption for Maintenance and Enhances Nitrous Oxide Production in Nitrosomonas europaea

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Revision of N₂O-Producing Pathways in the Ammonia-Oxidizing Bacterium Nitrosomonas europaea ATCC 19718