Long-term per- and polyfluoroalkyl substances (PFAS) exposure causes selective changes in the rhizosphere bacterial community

Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants, yet their impact on soil microbial diversity, function, and plant-microbe interactions remain poorly understood. This study investigates the effects of short-term (3 months, high concentration) and long-term (>30 years, low concentration) PFAS exposure on rhizosphere bacterial communities, incorporating plant interactions and functional gene profiling. Using 16S rRNA amplicon sequencing, selective microbial shifts were observed, where Firmicutes, Bacteroidetes and Gemmatimonadetes were enriched, while Actinobacteria and Acidobacteria declined in PFAS-contaminated soils. LEfSe biomarker analysis identified 33 genera including Nitrosospira , Nakamurella , Gemmatimonas , Nitrosomonas , Nordella and Pseudonocardia present in long-term exposed soils but were absent in short-term exposure, highlighting adaptive microbial responses over time. Functional predictions revealed enrichment of genes associated with xenobiotic degradation, lipid metabolism, and redox processes, inferring possible microbial metabolic adaptations to PFAS. Plant-specific effects further shaped microbial communities, with willow promoting Bacteroidetes and poplar reducing Actinobacteria, emphasizing their potential role in phytoremediation strategies. Overall, this study provides insight into potential microbial biomarkers and functional redundancy associated with PFAS exposure and features the long-term impact of PFAS on rhizoshpere microbial ecosystems, informing strategies for bioremediation and ecosystem recovery. • Long-term PFAS exposure induces selective shifts in rhizosphere bacterial communities. • Short-term high-concentration PFAS exposure showed transient microbial changes. • Bacteroidetes, Gemmatimonadetes and Acidobacteria are affected by PFAS exposure • Nitrosospira , Nakamurella and Gemmatimonas are the top 3 biomarkers of long term PFAS exposure. • PFAS influences genes linked to microbial metabolic adaptation