Plant root exudates drive changes in rhizobacterial gene expression: effects on hydrocarbon degradation and plant growth-promoting rhizobacteria traits in rhizoremediation

Purpose: Rhizoremediation leverages plant–microbe interactions to restore hydrocarbon-contaminated soils. However, the molecular mechanisms that mediate these interactions remain poorly understood. This study aimed to investigate how tropical grasses and their root exudates modulate rhizobacterial gene expression related to hydrocarbon degradation and plant growth promotion, providing functional insights to optimize rhizoremediation strategies. Materials and methods: A greenhouse pot experiment was conducted using petroleum-contaminated soil planted with Brachiaria decumbens and Megathyrsus maximus. Total petroleum hydrocarbon (TPH) removal and soil physicochemical parameters were evaluated after 3 months. Rhizospheric soil was analyzed for expression of six functional genes (alkB, alkB2, P450, rhlA, nifH, and gcd) by qRT-PCR. A complementary microcosm assay was performed to assess gene expression responses to individual and mixed root exudate analogs (sucrose, citric acid, oxalic acid, glutamic acid, flavanone, isoflavone) at days 7 and 15. Statistical comparisons were conducted using ANOVA or non-parametric equivalents, and integrative multivariate analyses were applied to explore associations between gene expression and soil quality indicators. Results and discussion: Megathyrsus maximus showed the highest TPH removal (41.47%) and improved soil properties, including pH, porosity, cation exchange capacity, and nutrient availability. Gene expression analyses revealed upregulation of alkB2 and P450 in vegetated soils, while alkB remained unchanged. Expression of PGPR-related genes nifH and gcd was also enhanced in planted treatments. In the microcosm assay, sucrose and the compound mix induced the highest alkB2 and P450 expression at day 7, with expression declining by day 15, suggesting transient microbial activation by labile exudates. Principal component analysis showed strong associations between gene expression, improved soil parameters, and vegetation. These findings highlight species-specific and compound-specific modulation of microbial functional activity in rhizoremediation contexts. Conclusions: Tropical grasses stimulate microbial gene expression linked to both hydrocarbon degradation and nutrient cycling, enhancing soil restoration. M. maximus outperformed B. decumbens in TPH removal and nitrogen cycling. The microcosm assay demonstrated that specific exudate compounds can transiently enhance microbial degradation potential. Overall, the study provides mechanistic evidence supporting the use of plant–microbe associations and exudate-informed biostimulation to improve the effectiveness of rhizoremediation in petroleum-contaminated soils.