Large-scale microbial connectivity across ocean depth

Marine microbes play central roles in marine food webs, carbon cycling, and climate regulation. Yet our understanding of how dispersal and environmental gradients shape microbial community composition in different layers of the ocean is limited. Here, using samples collected during the Malaspina expedition, we analyze spatial variations in the community structure of marine prokaryotes and pico-eukaryotes, and contrast patterns observed in the surface and deep ocean (4000 m). We found that in both groups, community similarity is significantly higher in the surface ocean relative to deep sea. We also found that for both groups, at the surface and at depth, community similarity decreases with horizontal distance. The decay in community similarity with horizontal distance is greater than expected from the strength of horizontal environmental gradients alone. In contrast, strong environmental gradients in the vertical direction correlate with large changes in prokaryotic community structure. We speculate that horizontal variations in marine microbiome assembly are strongly influenced by dispersal, while variations in the vertical direction are driven largely by niche segregation