High-resolution ultrastructure and morphology of marine ammonia-oxidizing archaea Nitrosopumilus maritimus SCM1 revealed by Cryo-ET and STEM-EDS

Nitrososphaerota, formerly known as Thaumarchaeota, constitutes a diverse and ubiquitous group of ammonia-oxidizing archaea (AOA) inhabiting ubiquitously in marine and terrestrial environments, playing a pivotal role in global nitrogen cycling. Despite their significance in Earth's ecosystems, the cellular organization of AOA remains largely unexplored, leading to a significant question unanswered of how the machinery of these organisms underpins metabolic functions. In this study, we combined chromatic-aberration-corrected cryo-electron tomography (Cryo-ET), scanning transmission electron microscopy (STEM), and energy dispersive X-ray spectroscopy (EDS) to unveil the cellular organization and elemental composition of Nitrosopumilus maritimus SCM1, a representative member of marine Nitrososphaerota. Our tomograms show the native ultrastructural morphology of SCM1 and find each cell contains one to several dense storage granules in the cytoplasm. STEM-EDS analysis identifies two types of storage granules with one type of granule being dominated by possibly polyphosphate and the other type being dominated by polyhydroxyalkanoate. The quantity of ribosomes in SCM1 are apparently an order of magnitude lower than that in eukaryotes and bacteria, supporting the slow growth of AOA commonly observed in the laboratory culture. Collectively, these findings provide visual evidence for the resilience of AOA in the vast oligotrophic marine environment. ### Competing Interest Statement The authors have declared no competing interest.