Reconstruction And Analysis Of Genome-scale Metabolic Models For Microbes In Ammonia Oxidation

Ammonia oxidation is the rate-limiting step of nitrification,which plays an important role in the nitrogen cycle.Ammonia oxidation are mostly completed by ammonia-oxidizing archaea?AOA?and ammonia-oxidizing bacteria?AOB?.In this study,three genome-scale metabolic models for one AOA?Nitrosopumilus maritimus SCM1?and two AOB?Nitrosomonas eutropha C91,Nitrosomonas europaea ATCC19718?were reconstructed based on bioinformatics database and automatic metabolic modeling platforms.We also did manual refinement of these three models based on KEGG,Meta Cyc database and literature.After doing quality control,we got three high-quality genome-scale metabolic models.Using these models,we analyzed the ammonia oxidation efficiency of AOA and AOB,and also estimated the contribution of AOA towards the nitrogen cycle.Marine ammonia-oxidizing archaea?AOA?play an important role in the global nitrogen cycle which obtain energy for biomass production by oxidation of ammonium.Although several ammonia oxidation pathways have been proposed for AOA,little is known about the real ATP production efficiency of the pathways.Here,we presented a reconstructed genome-scale metabolic model of an important marine AOA Nitrosopumilus maritimus SCM1.We calculated the ATP equivalent cost for biomass production using the model and then obtained the real ATP/NH₄⁺yield of the ammonia oxidation pathway by making use of the published experimental data on biomass/NH₄⁺yield.The results indicated that the real energy yield from ammonium oxidation was far less than the theoretical maximum.The results also suggested that although marine ammonia-oxidizing archaea play a significant role in global nitrogen cycle,their contribution in global carbon cycle may be low.Ammonia-oxidizing bacteria?AOB?are also widely distributed in the natural ecosystems,and also paly an important part in the nitrogen cycle.We have reconstructed the genome-scale metabolic models for two AOB strains Nitrosomonas eutropha C91 and Nitrosomonas europaea ATCC 19718.We calculated the ATP equivalent cost for biomass production using the model,and compared with the value from the SCM1 model.We verified our model using published experiment data on growth rates and ammonium uptake rates,and also confirmed these models can be used to predict the anaerobic growth and chemorganic growth.