Abstract

The impact of agroclimatic conditions on worldwide agricultural food crops has become increasingly severe. Plant growth-promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF) consortia offer sustainable solutions for enhancing crop productivity. This study investigated the possible molecular mechanisms underlying the enhancement in yield and other agronomical traits of wheat through proteomic and metabolomic analysis of grain and root tissues of field-grown wheat (HD3086) inoculated with native PGPB (Bacillus spp. CP4), non-native PGPB (Bacillus spp. AHP3), and AMF in the 2nd year of a 2-year field trial. Four treatments were compared: CP4, AMF, CP4+AMF (bipartite), and CP4+AHP3+AMF (tripartite) against uninoculated controls. Tripartite inoculation resulted in 88 significantly upregulated proteins in grain tissue. These included seed storage proteins (avenins and gliadins), stress-response proteins (heat shock proteins and defensins), zinc (Zn) homeostasis (EC protein I/II), energy-production enzymes (adenosine triphosphate synthases), nucleic acid-processing enzymes (helicases), and redox homeostasis regulators. Metabolomic profiling revealed 31 and 35 significantly altered metabolites in grain and root tissues, respectively. The tripartite treatment showed maximum upregulation of sugars (trehalose, maltose, and sucrose), amino acids, and signaling molecules like jasmonic acid. Kyoto encyclopedia of genes and genomes pathway analysis identified significant modulation of glyoxylate and dicarboxylate metabolism, aminoacyl-tRNA biosynthesis, amino acid metabolism, and galactose metabolism. Molecular docking analysis revealed strong protein–metabolite interactions, particularly between seed storage proteins and disaccharides, with helicase-sucrose complexes exhibiting the highest binding affinity (−7.8 Kcal/mol). The integrated proteo-metabolomic approach provided molecular insights into enhanced growth, grain yield, and micronutrient biofortification mechanisms. Our findings suggest that microbial consortia treatment differentially regulates wheat HD3086 metabolism toward improved stress tolerance, energy production, and nutrient accumulation. This study provides a molecular toolkit that can be employed in wheat improvement and supports the application of beneficial microbial consortia in sustainable agricultural practices.

Key words: Plant growth-promoting bacteria, Wheat, Grain proteomics, Metabolomics, Molecular docking, Microbial consortia