Plant and soil transcriptomics reveal the consequences of bioaugmentation of co-contaminated soil with Pseudomonas qingdaonensis ZCR6 during bacteria-assisted phytoremediation

Our study evaluated the bioaugmentation potential of the Pseudomonas qingdaonensis ZCR6 strain to support the phytoremediation of multicontaminated soil. This metal-resistant strain expresses several plant growth-promoting features and petroleum hydrocarbon degradative potential in biochemical tests. A microcosm experiment with maize (Zea mays) treated with a suspension of live or thermally inactivated ZCR6 cells was performed (representing a scenario of unsuccessful bioaugmentation). Although the ZCR6 colonized the rhizosphere and plant tissues, its application did not impact the removal of hydrocarbons compared to the control (17.4% vs. 19.6%, respectively). In contrast, treatment of soil with thermally inactivated bacterial biomass significantly increased hydrocarbon removal efficiency by approximately 8%, compared to the nontreated control. The Zn accumulation in the roots of maize treated with either live or thermally inactivated cells of ZCR6 was about 30% higher compared to the control. The soil transcriptomic analysis revealed downregulation of bacterial genes involved in hydrocarbon degradation after soil inoculation with live ZCR6, whereas plants showed upregulation of stress-related genes. No increase in the expression of bacterial genes encoding plant growth-promoting mechanisms was observed in any of the treatments. Our research has shown that the utility of each strain considered for bioaugmentation must be properly verified prior to in situ application. This should also include testing scenarios assuming a lack of survival and/or activity of the introduced strain and assessing its actual impact on the metabolic activity of plants and soil microorganisms by applying advanced transcriptomic approaches. KEY POINTS: • Bioaugmentation significantly downregulated bacterial genes of degrading pathways. • Soil inoculation increased transcription of genes involved in maize stress response. • Treatments didn't increase the expression of genes crucial for phytoremediation.