Nitrosopumilus maritimus is a key ammonia-oxidizing archaeon in the global nitrogen cycle. This study reveals the structure of its surface layer (S-layer), which is crucial for trapping and channeling ammonium ions to the cell membrane. Using electron cryotomography and subtomogram averaging, researchers determined the in situ structure of the S-layer, which is composed of the NmSLP protein. The S-layer is arranged in a hexagonal pattern and is heavily glycosylated, contributing to its negative charge. This charge facilitates the binding and concentration of ammonium ions on the cell surface, acting as a multichannel sieve. Biochemical analyses confirmed the strong ammonium binding by the cell surface, which was lost after S-layer disassembly. Molecular simulations and structural data showed that the S-layer can bind ammonium ions, enabling their transport to the cell membrane for oxidation. The S-layer's structure and function are conserved among many ammonia-oxidizing archaea, highlighting its role in the nitrogen cycle. The study also identified the presence of similar S-layers in other ammonia-oxidizing archaea, suggesting a common mechanism for ammonium binding and transport. The findings provide insights into the biogeochemical processes essential for marine microbial communities and the global nitrogen cycle.Nitrosopumilus maritimus is a key ammonia-oxidizing archaeon in the global nitrogen cycle. This study reveals the structure of its surface layer (S-layer), which is crucial for trapping and channeling ammonium ions to the cell membrane. Using electron cryotomography and subtomogram averaging, researchers determined the in situ structure of the S-layer, which is composed of the NmSLP protein. The S-layer is arranged in a hexagonal pattern and is heavily glycosylated, contributing to its negative charge. This charge facilitates the binding and concentration of ammonium ions on the cell surface, acting as a multichannel sieve. Biochemical analyses confirmed the strong ammonium binding by the cell surface, which was lost after S-layer disassembly. Molecular simulations and structural data showed that the S-layer can bind ammonium ions, enabling their transport to the cell membrane for oxidation. The S-layer's structure and function are conserved among many ammonia-oxidizing archaea, highlighting its role in the nitrogen cycle. The study also identified the presence of similar S-layers in other ammonia-oxidizing archaea, suggesting a common mechanism for ammonium binding and transport. The findings provide insights into the biogeochemical processes essential for marine microbial communities and the global nitrogen cycle.