Acknowledgements: This work was supported by the Medical Research Council, as part of UK Research and Innovation (programme MC_UP_1201/31 to T.A.M.B., U105184326 to J.L.). T.A.M.B. thanks the Human Frontier Science Program (grant RGY0074/2021), the Vallee Research Foundation, the European Molecular Biology Organization, the Leverhulme Trust and the Lister Institute for Preventative Medicine for support; V.A. thanks A. Lupas for continued support and the Human Frontier Science Program (grant RGY0074/2021); C.K.C. thanks P. Zhang and M. S. P. Sansom for their support as well as funding through the ERC AdG Program (grant 101021133) and a faculty start-up package from the University of Missouri-Columbia Department of Physics. We thank F. Elling and A. Pearson for the gift of a running N. maritimus cell culture; R. Rachel, S. H. W. Scheres and J. Zivanov for advice; and T. Darling, J. Grimmett, I. Clayson and J. J. E. Caesar for help with high-performance computing. One dataset for cryo-ET was acquired at the cryo-electron microscopy platform of the European Molecular Biology Laboratory (EMBL) in Heidelberg. This work was partly supported by institutional funds of the Max Planck Society; iNEXT, project number 653706, funded by the Horizon 2020 program of the European Union; and the MRC Laboratory of Molecular Biology Electron Microscopy Facility and Central Oxford Structural Molecular Imaging Centre (COSMIC). Simulations were performed on computational resources provided by HECBioSim, the UK High End Computing Consortium for Biomolecular Simulation, which is supported by the EPSRC (EP/L000253/1), as well as by the Research Computing Support Services division at the University of Missouri-Columbia, which is supported in part by the National Science Foundation (grant CNS-14229294). For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright license to any Author Accepted Manuscript version arising.Nitrosopumilus maritimus is an ammonia-oxidizing archaeon that is crucial to the global nitrogen cycle1,2. A critical step for nitrogen oxidation is the entrapment of ammonium ions from a dilute marine environment at the cell surface and their subsequent channelling to the cell membrane of N. maritimus. Here we elucidate the structure of the molecular machinery responsible for this process, comprising the surface layer (S-layer), using electron cryotomography and subtomogram averaging from cells. We supplemented our in situ structure of the ammonium-binding S-layer array with a single-particle electron cryomicroscopy structure, revealing detailed features of this immunoglobulin-rich and glycan-decorated S-layer. Biochemical analyses showed strong ammonium binding by the cell surface, which was lost after S-layer disassembly. Sensitive bioinformatic analyses identified similar S-layers in many ammonia-oxidizing archaea, with conserved sequence and structural characteristics. Moreover, molecular simulations and structure determination of ammonium-enriched specimens enabled us to examine the cation-binding properties of the S-layer, revealing how it concentrates ammonium ions on its cell-facing side, effectively acting as a multichannel sieve on the cell membrane. This in situ structural study illuminates the biogeochemically essential process of ammonium binding and channelling, common to many marine microorganisms that are fundamental to the nitrogen cycle
