Comparative Analysis Unveils Distinct Functional Profiles and Assembly Mechanisms of Microbiomes in Global Coastal Wetland Ecosystems

Coastal wetland ecosystems (CWEs), including mangroves, saltmarshes, and seagrasses, deliver vital ecosystem services at the land-ocean interface, where microbial communities act as key agents of biogeochemical cycles by mediating energy flow and material transformation. Yet, a comprehensive understanding of their global-scale diversity, distribution, and functional attributes remains elusive. To elucidate these aspects, we analyzed 1,384 high-throughput sequencing samples to examine microbial diversity and assembly processes across these global habitats. Our results revealed significant differences in microbial diversity and function among these ecosystems (p < 0.001), with mangroves exhibiting the highest richness and diversity. The habitat-specific keystone taxa were Rhodothermia, Anaerolineaceae, and SBR1031 in mangroves, Flavobacteriaceae, Burkholderiales, and Woeseiaceae in saltmarshes, and Desulfosarcinaceae, Pseudomonadaceae, Firmicutes, and Bacillales in seagrasses through LEfSe and Random Forest model analysis. Co-occurrence network analysis revealed a robust structure comprising 1521 nodes and 64,463 edges, dominated by Gammaproteobacteria, Desulfobacteria, Bacteroidia, and Desulfobulbia. KEGG-based functional profiling showed that mangroves were distinguished by a high abundance of microbial functions related to nitrogen cycling and sulfate metabolism. Seagrasses showed a higher abundance of taxa involved in the methane metabolism and saltmarsh communities were dominated by functions related to aromatic hydrocarbon metabolism. Using iCAMP, we found that deterministic selection governed community assembly in saltmarshes (44.42%), whereas ecological drift was the major contributor in seagrass (63.1%) and mangrove (43.17%) ecosystems. 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.