Transcriptomic, biochemical, and microbiome assessments into drought and salinity tolerance in durum wheat mediated by plant growth-promoting bacteria.

This study investigates the efficacy of plant growth-promoting bacteria (PGPB) in improving stress tolerance in plants by analyzing the molecular and biochemical bases in durum wheat grain. An experiment was conducted where soil and seeds were inoculated with PGPB, under drought and salinity stress. 16 S rRNA sequencing indicated no change in grain bacterial communities in response to biofertilizers and stress. However, a genome-wide analysis identified 153 up-regulated and 33 down-regulated plant genes in response to PGPB, predominantly enriched in stress-related biological processes. These genes specifically encode for proteins involved in metabolite interconversion enzyme, chaperone, protein modifying enzyme, and transporters, which are functionally related groups assisting protein folding in the cell under stress conditions. Moreover, pathway analysis confirmed related changes at the metabolite and enzyme activity levels. In this regard, PGPB-treated plants exhibited heightened activity of both enzymatic and non-enzymatic (e.g., thioredoxins, peroxiredoxins, etc.) antioxidants under stress, showcasing significant enhancements ranging from + 27% to + 283% and + 36% to + 266%, respectively. Further elucidation of biochemical pathways revealed alterations in the activation of non-antioxidant enzymes in PGPB-treated plants, exemplified by increased activities of glutamate synthase (40-44%) and decreased activities of protein-tyrosine-phosphatase (29-31%) under both stresses, as well as elevated activities of anthocyanidin reductase (91%) and lipoxygenases (18%) specifically under drought. Overall, the present research highlighted the potential of beneficial bacteria in improving plant stress tolerance, especially under drought, through shifting transcriptome expression of plant genes and employing multiple protective strategies which can complement each other. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-025-01686-z.