Petroleum hydrocarbon contamination reshapes rhizosphere bacterial communities and root-associated metabolite profiles in two tropical grasses

Hydrocarbon contamination alters soil microbial communities and interferes with plant–microbe interactions essential for ecosystem functioning. In this study, we evaluated how this pollution influences rhizosphere bacterial communities and root-associated metabolite composition in two tropical grasses, Brachiaria decumbens and Megathyrsus maximus, during a six-month rhizoremediation experiment under controlled greenhouse conditions. Plants were grown in either Hydrocarbon-contaminated or uncontaminated soils. Using 16S rRNA gene amplicon sequencing and untargeted LC–MS-based metabolomics, we characterized bacterial diversity, community composition, and root-associated metabolite profiles. Contaminated soils exhibited higher bacterial alpha diversity than uncontaminated soils, as reflected by Shannon diversity (Welch’s t-test, p = 0.039; Cohen’s d = 1.00), and showed greater community heterogeneity. PERMANOVA showed that soil contamination was the primary driver of beta diversity (adonis2: R2 = 0.231, p = 0.001), whereas no statistically significant plant species effect was detected by PERMANOVA (p = 0.199). Polluted rhizospheres were enriched in taxa associated with hydrocarbon degradation, including Sphingomonas, Cellulomonas, Afipia, and members of Saccharimonadales, while oligotrophic and acidophilic taxa dominated uncontaminated soils. Metabolomic profiling revealed distinct root-associated chemical signatures under contamination, including increased relative abundance of malic acid in root-associated extracts and several putatively annotated boron-containing features. Overall, petroleum contamination restructured the rhizosphere at both microbial and metabolic levels, highlighting adaptive plant–microbe responses for rhizoremediation.