Soil organic matter and salinity as critical factors affecting the bacterial community and function of Phragmites australis dominated riparian and coastal wetlands.

Soil salinization poses a great threat to the natural ecosystem and interferes with the structure and function of the biological community, resulting in different vegetation distributions. However, little attention is paid to the changes in microbial community in different wetland types with the same vegetation. In this study, the Yellow River Delta was used as a model because of its typical and extensive distribution of Phragmites australis-dominated saltwater and freshwater wetlands. We investigated the differences in the structure and function of bacterial communities, as well as their relationships with soil properties in coastal (Zone A) and riparian (Zone B) wetlands. Results showed higher salinity and pH in Zone A than Zone B (p < 0.05), whereas TN (p < 0.05) and SOM were lower than those in Zone B. Significant differences existed in microbial community composition between Zones A and B. The nitrifying-bacteria Nitrospira and norank_f_Nitrosomonadaceae had high abundance in Zones A and B. Alcanivorax, Halomonas, and Marinobacter were extensively distributed in Zone A, whereas Flavobacterium and Pseudomonas were dominant in Zone B, indicating the diversity characteristics of denitrifying bacteria. Conversely, methane-oxidizing bacteria Methylophaga were significantly higher in Zone A than in Zone B (p < 0.05), indicating that high salinity was conducive to aerobic methane oxidation and that the genetic diversity at strain level endowed it with a certain denitrification potential. Salinity and SOM played important roles in shaping microbial community at phylum and genus levels. The gene abundances related to xenobiotics metabolism and repair were high in Zone A, whereas the genes encoding energy metabolism and signal transduction were relatively high in Zone B. Denitrification was more favored for the low-salinity Zone B, whereas methane oxidation was enriched in the high-salinity Zone A. Therefore, our study emphasized the importance of an in-depth understanding of the microbial-community structure and function in Phragmites australis-dominated saltwater and freshwater wetlands.