Vertically stratified microbial diversity and keystone species driving element cycling in the Magellan seamount sediments

Deep-sea polymetallic nodules, rich in cobalt, nickel and titanium, are valuable for electronics, aerospace and energy industries. However, the vertical distribution and ecological functions of prokaryotic communities in sediments beneath nodules from the Magellan seamounts, a unique microbial habitat characterized by ultra-slow sedimentation rates (0.4-4 mm ky^-1) and heterogeneous metal gradients, remain poorly characterized. In our research, 16S rRNA gene amplicon sequencing and metagenomic analyses of sediment cores (0-20 cm) from the western Pacific polymetallic nodule province revealed statistically significant decreases in prokaryotic diversity (Shannon index: 9.446 to 2.288; <i>P</i><0.001). <i>Proteobacteria</i>, <i>Crenarchaeota</i>, <i>Chloroflexi</i> and <i>Bacteroidota</i> were the dominant taxa. The microbial co-occurrence network in the surface layer had a longer mean path length (2.11 vs 1 in the bottom layer) and a larger network diameter (11 vs 1), indicating a loose community structure and greater resistance to disturbance, while the bottom microbial network had a higher density (0.037 vs 0.01) and clustering coefficient (0.32 vs 1), suggesting tight microbial interactions. The concentrations of MnO (6.96-9.41 µg g^-1) and P₂O₅ (2.55-3.89 µg g^-1) gradually decreased with increasing depth. The concentrations of Co and Pb were relatively high in the surface sediments (0-8 cm) but decreased significantly below 8 cm. In contrast, the concentrations of Fe₂O₃ and As increased with depth. The environmental factors depth, MnO, Fe₂O₃ and heavy metals (Cr, Zn and Cu) were found to be the main drivers of the microbial community structure. We assembled 122 metagenome-assembled genomes from the metagenomic data. Gene abundance analysis revealed that sox genes (<i>soxB</i>/<i>C</i>/<i>D</i>/<i>X</i>/<i>Y</i>/<i>Z</i>) and assimilatory sulphate reduction genes (<i>cysC</i> and <i>cysH</i>) were highly abundant in the surface sediment, whereas the abundance of dissimilatory sulphate reduction genes (<i>dsrA</i> and <i>dsrB</i>) was enhanced in the bottom layer, reflecting a hierarchical adaptive strategy for sulphur metabolism. Our study expands current knowledge on the vertical variations of microbial diversity and microbially driven biogeochemical cycling in deep-sea settings underneath polymetallic nodules. Characterizing the microbial community underneath those nodules may provide insights into microbial resilience in extreme oligotrophic environments and valuable insights for future deep-sea mining activities.