Plant invasion alters rhizosphere microbial communities across temperate ecosystems

Invasive plants threaten ecosystems, and their management remains a challenge in ecological restoration. Control and replanting outcomes can vary considerably, with restoration sites often experiencing re-invasion, secondary invasion, or failed native plant establishment. While impacts are often focused above ground, plant invasion can also alter rhizosphere microbial communities in ways that may inhibit recovery. This study characterized bacterial and fungal communities of native and invasive shrub-layer plants across three British Columbia ecosystems (coastal forest, riparian forest, and coastal wetland) and tested whether invasion-associated taxonomic shifts corresponded with differences in predicted microbial functions and ecological guilds. Rhizosphere soils were sequenced for 16S rRNA and ITS2 markers and analyzed in QIIME2 using weighted UniFrac and PERMANOVA. Functional potential (PICRUSt2 MetaCyc pathways) and fungal guilds (FUNGuild) were compared using Bray-Curtis dissimilarities and PERMANOVA. Microbial communities differed significantly by plant species and invasion status in the riparian site, by plant species in the coastal forest site, and showed no significant differences with lower amplicon sequence variant (ASV) richness at the coastal wetland site. Predicted functional composition differed among plant species in coastal forest bacterial MetaCyc profiles, while fungal functional groups differed by both plant species and invasion status at the riparian site, where invasive Japanese knotweed showed a predicted shift from ectomycorrhizal toward saprotrophic fungi. Responses were strongly context-dependent across ecosystems. These findings highlight the importance of belowground microbial variation in invasion ecology and support further investigation on whether targeted soil interventions, such as inoculation or soil transfer, can improve restoration outcomes.