Environmental drivers and ecological processes underlying microbial community zonation in deep-sea polymetallic...

Microbial communities are key drivers of ecosystem processes and biodiversity in the deep-sea. However, the mechanisms sustaining the composition and function of microbial communities remain poorly understood in deep-sea polymetallic nodule sediments. Here, we investigated the microbial populations, vertical distribution pattern, and environmental determinants at different depth of sediment cores from the Western Pacific polymetallic nodule region. 16S rRNA gene amplicon sequencing revealed a pronounced vertical stratification in prokaryotic diversity. Alpha diversity is highest in surface sediments and exhibited a marked decline with increasing depth, while significant differences in beta diversity were observed between distinct sediment layers. Surface sediments contained the greatest number of biomarkers and specialized taxa, and also exhibited more complex co-occurrence networks, with a higher proportion of negative associations (15.6%) compared to middle (2.7%) and deep layers (0.5%). Depth was the primary factor structuring prokaryotic communities, followed by TOC, TN, and heavy metals. Interestingly, a small core microbiota, dominated by Chloroflexi, Proteobacteria, Patescibacteria, and Acidobacteriota, was ubiquitous across all layers and constituted the majority (76.4%) of the total community, underscoring the vertical dominance of a few ubiquitous taxa. With increasing depth, microbial systems shift adaptively: their co-occurrence networks become more cooperative and modular while their assembly mechanisms transition from deterministic to stochastic dominance, highlighting a profound ecological shift along the depth gradient. Our findings offer critical baseline insights into microbial communities in polymetallic nodule sediments, informing future environmental impact assessment and ecological restoration of deep-sea mining.