Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of <italic toggle="yes">Nitrosomonas europaea</italic> and <italic toggle="yes">Nitrobacter winogradskyi</italic>

ABSTRACT Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, emits nitrogen (N) oxide gases (NO, NO2, and N2O), which are potentially hazardous compounds that contribute to global warming. To better understand the dynamics of nitrification-derived N oxide production, we conducted...

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Autores principales:	Brett L. Mellbye, Andrew T. Giguere, Ganti S. Murthy, Peter J. Bottomley, Luis A. Sayavedra-Soto, Frank W. R. Chaplen
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	Nitrobacter winogradskyi Nitrosomonas europaea genome-scale hydroxylamine metabolic modeling nitric oxide Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/47d0085cab5148b58dcc6dcb738ebe6f
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spelling	oai:doaj.org-article:47d0085cab5148b58dcc6dcb738ebe6f2021-12-02T18:39:16ZGenome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of <italic toggle="yes">Nitrosomonas europaea</italic> and <italic toggle="yes">Nitrobacter winogradskyi</italic>10.1128/mSystems.00170-172379-5077https://doaj.org/article/47d0085cab5148b58dcc6dcb738ebe6f2018-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00170-17https://doaj.org/toc/2379-5077ABSTRACT Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, emits nitrogen (N) oxide gases (NO, NO2, and N2O), which are potentially hazardous compounds that contribute to global warming. To better understand the dynamics of nitrification-derived N oxide production, we conducted culturing experiments and used an integrative genome-scale, constraint-based approach to model N oxide gas sources and sinks during complete nitrification in an aerobic coculture of two model nitrifying bacteria, the ammonia-oxidizing bacterium Nitrosomonas europaea and the nitrite-oxidizing bacterium Nitrobacter winogradskyi. The model includes biotic genome-scale metabolic models (iFC578 and iFC579) for each nitrifier and abiotic N oxide reactions. Modeling suggested both biotic and abiotic reactions are important sources and sinks of N oxides, particularly under microaerobic conditions predicted to occur in coculture. In particular, integrative modeling suggested that previous models might have underestimated gross NO production during nitrification due to not taking into account its rapid oxidation in both aqueous and gas phases. The integrative model may be found at https://github.com/chaplenf/microBiome-v2.1. IMPORTANCE Modern agriculture is sustained by application of inorganic nitrogen (N) fertilizer in the form of ammonium (NH4+). Up to 60% of NH4+-based fertilizer can be lost through leaching of nitrifier-derived nitrate (NO3−), and through the emission of N oxide gases (i.e., nitric oxide [NO], N dioxide [NO2], and nitrous oxide [N2O] gases), the latter being a potent greenhouse gas. Our approach to modeling of nitrification suggests that both biotic and abiotic mechanisms function as important sources and sinks of N oxides during microaerobic conditions and that previous models might have underestimated gross NO production during nitrification.Brett L. MellbyeAndrew T. GiguereGanti S. MurthyPeter J. BottomleyLuis A. Sayavedra-SotoFrank W. R. ChaplenAmerican Society for MicrobiologyarticleNitrobacter winogradskyiNitrosomonas europaeagenome-scalehydroxylaminemetabolic modelingnitric oxideMicrobiologyQR1-502ENmSystems, Vol 3, Iss 3 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Nitrobacter winogradskyi Nitrosomonas europaea genome-scale hydroxylamine metabolic modeling nitric oxide Microbiology QR1-502
spellingShingle	Nitrobacter winogradskyi Nitrosomonas europaea genome-scale hydroxylamine metabolic modeling nitric oxide Microbiology QR1-502 Brett L. Mellbye Andrew T. Giguere Ganti S. Murthy Peter J. Bottomley Luis A. Sayavedra-Soto Frank W. R. Chaplen Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of <italic toggle="yes">Nitrosomonas europaea</italic> and <italic toggle="yes">Nitrobacter winogradskyi</italic>
description	ABSTRACT Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, emits nitrogen (N) oxide gases (NO, NO2, and N2O), which are potentially hazardous compounds that contribute to global warming. To better understand the dynamics of nitrification-derived N oxide production, we conducted culturing experiments and used an integrative genome-scale, constraint-based approach to model N oxide gas sources and sinks during complete nitrification in an aerobic coculture of two model nitrifying bacteria, the ammonia-oxidizing bacterium Nitrosomonas europaea and the nitrite-oxidizing bacterium Nitrobacter winogradskyi. The model includes biotic genome-scale metabolic models (iFC578 and iFC579) for each nitrifier and abiotic N oxide reactions. Modeling suggested both biotic and abiotic reactions are important sources and sinks of N oxides, particularly under microaerobic conditions predicted to occur in coculture. In particular, integrative modeling suggested that previous models might have underestimated gross NO production during nitrification due to not taking into account its rapid oxidation in both aqueous and gas phases. The integrative model may be found at https://github.com/chaplenf/microBiome-v2.1. IMPORTANCE Modern agriculture is sustained by application of inorganic nitrogen (N) fertilizer in the form of ammonium (NH4+). Up to 60% of NH4+-based fertilizer can be lost through leaching of nitrifier-derived nitrate (NO3−), and through the emission of N oxide gases (i.e., nitric oxide [NO], N dioxide [NO2], and nitrous oxide [N2O] gases), the latter being a potent greenhouse gas. Our approach to modeling of nitrification suggests that both biotic and abiotic mechanisms function as important sources and sinks of N oxides during microaerobic conditions and that previous models might have underestimated gross NO production during nitrification.
format	article
author	Brett L. Mellbye Andrew T. Giguere Ganti S. Murthy Peter J. Bottomley Luis A. Sayavedra-Soto Frank W. R. Chaplen
author_facet	Brett L. Mellbye Andrew T. Giguere Ganti S. Murthy Peter J. Bottomley Luis A. Sayavedra-Soto Frank W. R. Chaplen
author_sort	Brett L. Mellbye
title	Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of <italic toggle="yes">Nitrosomonas europaea</italic> and <italic toggle="yes">Nitrobacter winogradskyi</italic>
title_short	Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of <italic toggle="yes">Nitrosomonas europaea</italic> and <italic toggle="yes">Nitrobacter winogradskyi</italic>
title_full	Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of <italic toggle="yes">Nitrosomonas europaea</italic> and <italic toggle="yes">Nitrobacter winogradskyi</italic>
title_fullStr	Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of <italic toggle="yes">Nitrosomonas europaea</italic> and <italic toggle="yes">Nitrobacter winogradskyi</italic>
title_full_unstemmed	Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of <italic toggle="yes">Nitrosomonas europaea</italic> and <italic toggle="yes">Nitrobacter winogradskyi</italic>
title_sort	genome-scale, constraint-based modeling of nitrogen oxide fluxes during coculture of <italic toggle="yes">nitrosomonas europaea</italic> and <italic toggle="yes">nitrobacter winogradskyi</italic>
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/47d0085cab5148b58dcc6dcb738ebe6f
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Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of <italic toggle="yes">Nitrosomonas europaea</italic> and <italic toggle="yes">Nitrobacter winogradskyi</italic>

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