Comparative analysis reveals distinct microbial community profiles and assembly mechanisms in sediments of coastal wetland ecosystems.

UNLABELLED: Coastal wetland ecosystems (CWEs), including mangroves, saltmarshes, and seagrasses, support vital biogeochemical cycles mediated by microbes, yet their global microbial diversity, distribution, and potential functions remain elusive. Thus, we analyzed 1,381 16S rRNA gene amplicon data sets targeting the V3-V4 and V4 regions to examine microbial diversity and assembly processes across these habitats. Results revealed significant differences in microbial diversity and composition among these ecosystems, with mangroves exhibiting the highest richness and diversity. The habitat-specific indicator taxa were Rhodothermia, Anaerolineaceae, and SBR1031 in mangroves, Flavobacteriaceae, Burkholderiales, and Woeseiaceae in saltmarshes, and Desulfosarcinaceae, Pseudomonadaceae, Firmicutes, and Bacillales in seagrasses through linear discriminant analysis effect size (LEfSe) and random forest analyses. Co-occurrence network analysis revealed a robust structure comprising 1,521 nodes and 64,463 edges, dominated by Gammaproteobacteria, Desulfobacteria, Bacteroidia, and Desulfobulbia. KEGG-based functional prediction revealed distinct functional profiles across CWEs. Mangrove communities exhibited higher predicted potentials for carbon fixation and complex hydrocarbon metabolism, whereas seagrass communities showed higher potentials for sulfate metabolism. Saltmarsh communities were enriched in predicted functions related to the degradation of certain aromatic compounds. Using iCAMP, drift was most pronounced in seagrass communities (63.10%), whereas its contribution was lower but remained substantial in mangroves and saltmarshes. Deterministic processes also contributed considerably to community assemblies in mangroves (43.04%) and saltmarshes (44.42%). This underscores the dependence of dominant assembly processes on local environmental contexts. Our findings establish a basis for elucidating the structure and function of microbial communities in CWEs, offering insights for future hypothesis-driven research and enhancing predictive capacity amid growing anthropogenic and climatic pressures. IMPORTANCE: Coastal wetlands, including mangroves, saltmarshes, and seagrasses, protect shorelines and play a critical role in regulating the global climate. Microbial communities maintain the stability and essential functions of these ecosystems. This study provided the first comprehensive global map of microbial communities in the three ecosystems. By analyzing over 1,381 samples, the results revealed that different habitats relied on different diversity, composition, and dominant taxa. Mangroves showed the highest richness and diversity. KEGG-based functional predictions suggested that microbial communities in the CWEs shared core predicted metabolic functions but differed in their predicted functional potentials. The null model revealed that the assembly process of the three habitats is mainly shaped by stochastic ecological drift. However, deterministic selection also played a significant role in structuring saltmarsh and mangrove communities, suggesting that environmental factors commonly influenced the community assembly. Understanding these patterns is crucial for conservation because it allows scientists to better predict how coastal protection and carbon storage face increasing pressure from human activity.