Assessment of nitric oxide (NO) redox reactions contribution to nitrous oxide (N₂O) formation during nitrification using a multispecies metabolic network model

Abstract

Over the coming decades nitrous oxide (N2O) is expected to become a dominant greenhouse gas and atmospheric ozone depleting substance. In wastewater treatment systems, N2O is majorly produced by nitrifying microbes through biochemical reduction of nitrite (NO2(-)) and nitric oxide (NO). However it is unknown if the amount of N2O formed is affected by alternative NO redox reactions catalyzed by oxidative nitrite oxidoreductase (NirK), cytochromes (i.e., P460 [CytP460] and 554 [Cyt554 ]) and flavohemoglobins (Hmp) in ammonia- and nitrite-oxidizing bacteria (AOB and NOB, respectively). In this study, a mathematical model is developed to assess how N2O formation is affected by such alternative nitrogen redox transformations. The developed multispecies metabolic network model captures the nitrogen respiratory pathways inferred from genomes of eight AOB and NOB species. The performance of model variants, obtained as different combinations of active NO redox reactions, was assessed against nine experimental datasets for nitrifying cultures producing N2O at different concentration of electron donor and acceptor. Model predicted metabolic fluxes show that only variants that included NO oxidation to NO2(-) by CytP460 and Hmp in AOB gave statistically similar estimates to observed production rates of N2O, NO, NO2(-) and nitrate (NO3(-)), together with fractions of AOB and NOB species in biomass. Simulations showed that NO oxidation to NO2(-) decreased N2O formation by 60% without changing culture's NO2(-) production rate. Model variants including NO reduction to N2O by Cyt554 and cNor in NOB did not improve the accuracy of experimental datasets estimates, suggesting null N2O production by NOB during nitrification. Finally, the analysis shows that in nitrifying cultures transitioning from dissolved oxygen levels above 3.8 ± 0.38 to <1.5 ± 0.8 mg/L, NOB cells can oxidize the NO produced by AOB through reactions catalyzed by oxidative NirK.

Quorum Quenching of Nitrobacter winogradskyi Suggests that Quorum Sensing Regulates Fluxes of Nitrogen Oxide(s) during Nitrification

“…NO x gas measurements were made from such suspensions of concentrated QS-proficient or -deficient N. winogradskyi cells during 24 h of NO 2 − oxidation. We predicted that an increase in expression of the nirK cluster genes under QS-proficient conditions would either increase NO x production as earlier studies have suggested (32–34) or decrease NO x production by consuming NO as previously reported (34–36). …”

Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of Nitrosomonas europaea and Nitrobacter winogradskyi

“…To date, most genome-scale and metabolic models of nitrification have focused on biotic reactions (17, 22, 23, 36). While this approach simplifies the construction of models, it neglects the importance of abiotic chemistry in the N cycle (13).…”

“…Among AOB, the genus Nitrosospira is usually most numerous in soils, and genomic data are available for assembly into genome-scale metabolic models (52–54). Perez-Garcia et al (17) constructed a stoichiometric metabolic model of several AOB and NOB based on genomic data and published studies of nitrifying mixed cultures in wastewater treatment, but specific kinetic information and genome-scale models of many species are still lacking. Before genome-scale metabolic models of these microorganisms can be fully completed, growth and energy yield parameters and nutrient and O 2 affinity data are needed.…”

“…Representatives of the AOB, AOA, and NOB have the capacity to produce NO and N 2 O, but the exact mechanisms and overall contributions by each group of organisms are not well characterized (4, 13–17). The magnitude of nitrifier-derived emissions of N oxides generated by nitrification from soils and engineered environments are extremely variable and depend on a variety of environmental conditions such as the rate of nitrification, pH, temperature, and oxygen (O 2 ), among other factors (4, 13, 18–21).…”

“…The magnitude of nitrifier-derived emissions of N oxides generated by nitrification from soils and engineered environments are extremely variable and depend on a variety of environmental conditions such as the rate of nitrification, pH, temperature, and oxygen (O 2 ), among other factors (4, 13, 18–21). Recent modeling efforts by Perez-Garcia et al and others have sought to understand conditions that generate N oxides through single and multispecies metabolic network models of wastewater treatment systems (17, 22–24). Modeling N oxide production by simplified communities of model nitrifiers in both single culture and coculture, including abiotic reactions, can expand on previous work to better explain the mechanisms and conditions that affect N oxide gas emissions.…”