Phragmites australis invasions linked to shifts in soil microbial community composition and functional potential in a Northeastern U.S. salt marsh

Coastal salt marshes of the northeastern United States are increasingly affected by invasion of the non-native lineage of Phragmites australis , which can alter sediment characteristics, nutrient dynamics, and belowground microbial communities. However, the extent to which these vegetation-associated changes influence microbial community composition and predicted ecological functions remains incompletely understood. We compared soils associated with invasive Phragmites australis and native Sporobolus alterniflorus (formerly Spartina alterniflora ) in a brackish salt marsh at the mouth of the Quinnipiac River, Connecticut. Soil physicochemical properties were quantified, bacterial communities were characterized using high throughput 16S rRNA amplicon sequencing and an amplicon sequence variant (ASV) workflow, and predicted microbial functions were evaluated using FAPROTAX. Total nitrogen and soil organic carbon stocks (SOC) did not differ significantly between vegetation types, whereas Phragmites soils exhibited higher bulk density, while pH differed between vegetation and seasons. Sporobolus soils had higher C:N ratios. Alpha diversity (Observed richness, Shannon and Simpson indices) was similar between vegetation types; however, microbial community composition differed significantly based on Bray–Curtis dissimilarity (PERMANOVA, p < 0.001). The two vegetation types shared only 6,104 ASVs (15.2% of the total community), while 15,452 ASVs (38.4%) were unique to Phragmites soils and 18,674 ASVs (46.4%) were unique to Sporobolus soils. Multivariate ordination further demonstrated that community structure was significantly associated with vegetation type and measured soil physicochemical gradients, particularly pH, bulk density, C:N ratio, soil carbon, and total nitrogen. Predicted functional annotation analysis indicated significantly greater relative abundance of nitrification-associated taxa in Phragmites soils, whereas sulfate respiration-associated taxa were significantly more abundant in Sporobolus soils. No significant differences were detected for cellulolysis, fermentation, methanogenesis, or nitrogen fixation. Although invasion by Phragmites australis was not associated with changes in overall bacterial alpha diversity or bulk soil carbon and nitrogen stocks, our analysis suggests it was associated with substantial shifts in microbial community composition and predicted functional potential. These findings suggest that plant invasions may play a role in restructuring belowground microbial assemblages in northeastern US salt marshes but not necessarily impact microbial diversity. The functional analysis further suggested implications for nitrogen and sulfur cycling in northeastern salt marshes. Future studies integrating metagenomics, functional gene quantification, direct measurements of biogeochemical process rates, and long-term environmental monitoring are needed to determine whether these predicted functional differences translate into measurable changes in ecosystem functioning.