Long-term environmental stability promotes reproducible, depth-structured sediment microbiomes

Long-term environmental stability is widely assumed to erode microbial diversity by limiting dispersal and connectivity. However, its effects on sediment microbial organization remain insufficiently characterized. Here, we used rare inland relict mangroves from the San Pedro Mártir River (Mexico), isolated more than 170 km from the coast since the Last Interglacial, as a natural experiment to examine how sustained environmental stability shapes sediment microbiome organization. Using depth-resolved 16S rRNA gene profiling, we showed that inland relict sediments harbor highly cohesive microbial communities characterized by large resident core microbiomes, low compositional dispersion and consistent vertical stratification across sites and sediment depths. Contrary to expectations of diversity loss under isolation, microbial richness is maintained or even accumulates with sediment depth, coupled with coherent taxonomic turnover and inferred functional stratification. In contrast, natural and hydrologically impaired coastal mangroves exhibit high variability, reduced diversity at depth, and erosion of the resident cores. Together, these findings indicate that long-term environmental stability enables predictable, depth-structured modes of microbial community organization, providing a foundational framework for interpreting microbiome variability across dynamic, restored, and disturbed coastal ecosystems.