Global biogeography of mangrove sediment microbiomes is structured by a conserved core and environmental selection

Abstract

Mangrove sediments are globally important biogeochemical hotspots, yet the large-scale organization and assembly of their microbiomes remain poorly resolved. Here, we compiled and analysed 390 shotgun metagenomes from mangrove sediments across 43 sites worldwide to quantify how diversity, spatial turnover, and ecological processes structure microbial communities across environmental and geographic gradients. We identify a striking dual architecture in mangrove sediment microbiomes. A remarkably small and ubiquitous taxonomic core, representing a minor fraction of total richness but dominating community abundance, persists across continents, climatic regimes, and marine realms. This core is composed primarily of anaerobic microbial lineages associated with carbon, nitrogen, and sulfur cycling and shows limited spatial and environmental turnover. In contrast, the non-core fraction is highly diverse, responds strongly to climatic and edaphic gradients, and drives most biogeographic differentiation. Assembly-process modelling reveals that deterministic selection dominates global taxonomic turnover, with homogeneous selection stabilizing shared community components and heterogeneous selection promoting regional differentiation, while dispersal limitation plays a secondary role. Network analyses further show that core taxa occupy structurally central positions in microbial co-occurrence networks, supporting overall connectivity despite pronounced regional variation in peripheral community composition. Together, these results demonstrate that mangrove sediment microbiomes combine a conserved functional backbone with an environmentally responsive periphery. This organization reconciles global functional continuity with strong regional differentiation and provides a basis for anticipating microbiome responses to environmental change in mangrove ecosystems.