Ultrastructural Insights Into Cellular Organization, Energy Storage And Ribosomal Dynamics Of An Ammonia-oxidizing Archaeon From Oligotrophic Oceans

Introduction: Nitrososphaeria, formerly known as Thaumarchaeota, constitute a diverse and widespread group of ammonia-oxidizing archaea (AOA) inhabiting ubiquitously in marine and terrestrial environments, playing a pivotal role in global nitrogen cycling. Despite their importance in Earth’s ecosystems, the cellular organization of AOA remains largely unexplored, leading to a significant unanswered question of how the machinery of these organisms underpins metabolic functions.

Methods: In this study, we combined spherical-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 Nitrososphaeria.

Results and Discussion: Our tomograms show the native ultrastructural morphology of SCM1 and one to several dense storage granules in the cytoplasm. STEM-EDS analysis identifies two types of storage granules: one type is possibly composed of polyphosphate and the other polyhydroxyalkanoate. With precise measurements using cryo-ET, we observed low quantity and density of ribosomes in SCM1 cells, which are in alignment with the documented slow growth of AOA in laboratory cultures. Collectively, these findings provide visual evidence supporting the resilience of AOA in the vast oligotrophic marine environment.

Observation of cell division in Nitrosopumilus maritimus SCM1. (A,C,E) Tomographic slices (13.6 Å in thickness) of SCM1 cells in the exponential phase. (B,D,F) 3D segmentation of (A,C,E). S-layer (dark blue), cell membrane (orange); cytoplasm (light blue); nucleoid (purple); ribosomes (yellow); high-density region (red). (G) The average length of SCM1 at different time points. SCM1 cells were analyzed every 4 h for 48 h period in the late exponential phase (n = 40). — Frontiers in Microbiology

Ultrastructural insights into cellular organization, energy storage and ribosomal dynamics of an ammonia-oxidizing archaeon from oligotrophic oceans, Frontiers in Microbiology (open access)

Astrobiology