Abstract Marine ammonia-oxidizing archaea (AOA) play an important role in the global nitrogen cycle by obtaining energy for biomass production from CO2 via oxidation of ammonium. The isolation of Candidatus “Nitrosopumilus maritimus” strain SCM1, which represents the globally distributed AOA in the ocean, provided an opportunity for uncovering the contributions of those AOA to carbon and nitrogen cycles in ocean. Although several ammonia oxidation pathways have been proposed for SCM1, little is known about its ATP production efficiency. Here, based on the published genome of Nitrosopumilus maritimus SCM1, a genome-scale metabolic model named NmrFL413 was reconstructed. Based on the model NmrFL413, the estimated ATP/NH4 + yield (0.149–0.276 ATP/NH4 +) is tenfold lower than the calculated theoretical yield of the proposed ammonia oxidation pathways in marine AOA (1.5–1.75 ATP/NH4 +), indicating a low energy production efficiency of SCM1. Our model also suggested the minor contribution of marine AOA to carbon cycle comparing with their significant contribution to nitrogen cycle in the ocean.
