ABSTRACT The Mariana Trench, a stable marine ecosystem minimally impacted by human activities, has the greatest vertical depth in the ocean. Depth gradients profoundly influence the physical, chemical, and biotic conditions in the deep oceans. Therefore, elucidating the depth-related effects on microbiome assembly and interaction is integral to understanding marine hadal ecosystems. In this study, eight samples were collected along vertical gradients to compare the assembly and associations of bacteria, archaea, and microeukaryotes, in the Marina Trench using high-throughput sequencing. There is no significant difference in the niche breadth occupied by bacteria, archaea, and microeukaryotes, indicating that microorganisms from the surface to the hadal water of the trench are well adapted to this environment. Stochastic processes significantly influenced the distribution of bacteria and microeukaryotes as well as archaea when the phylogenetic distance was considered. Although diversities of all three microbial domains were consistent across depth, distinct bacterial and archaeal community structures occurred between hadal waters (3,699–8,727 m) and upper bathypelagic waters (≤1,000 m). Bacteria and archaea in upper bathypelagic zones were more affected by a random process and exhibited higher phylogenetic distance than those in hadal waters. In contrast, stochasticity in assembly and phylogenetic distance of microeukaryotes remained unchanged. Bacteria made vital contributions to the stability of trench microbiomes, while consistent community stability was observed between the upper bathypelagic and hadal zones. Our results reveal the complexity of community assembly and associations of multi-domain microbiomes in hadal ecosystems and also highlight the differential adaptations and contributions of prokaryotes vs. microeukaryotes to microbiome community stability and robustness. IMPORTANCE Exploring microbial interactions and their stability/resilience from the surface to the hadal ocean is critical for further understanding of the microbiome structure and ecosystem function in the Mariana Trench. Vertical gradients did not destabilize microbial communities after long-term evolution and adaption. The uniform niche breadth, diversity, community complexity, and stability of microbiomes in both upper bathypelagic and hadal waters suggest the consistent roles of microbiomes in elemental cycling and adaptive strategies to overcome extreme environmental conditions. Compared with microeukaryotes, bacteria and archaea play a pivotal role in shaping the stability of the hadal microbiome. The consistent co-occurrence stability of microbiomes across vertical gradients was observed in the Mariana Trench. These results illuminate a key principle of microbiomes inhabiting the deepest trench: although distinct microbial communities occupy specific habitats, the interactions within microbial communities remain consistently stable from the upper bathypelagic to the hadal waters.
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