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The increased dependence of farmers on chemical fertilizers poses a risk to soil fertility and ecosystem stability. Plant growth‐promoting rhizobacteria (PGPR) are at the forefront of sustainable agriculture, providing multiple benefits for the enhancement of crop production and soil health. Bacillus subtilis is a common PGPR in soil that plays a key role in conferring biotic and abiotic stress tolerance to plants by induced systemic resistance (ISR), biofilm formation and lipopeptide production. As a part of bioremediating technologies, Bacillus spp. can purify metal contaminated soil. It acts as a potent denitrifying agent in agroecosystems while improving the carbon sequestration process when applied in a regulated concentration. Although it harbours several antibiotic resistance genes (ARGs), it can reduce the horizontal transfer of ARGs during manure composting by modifying the genetic makeup of existing microbiota. In some instances, it affects the beneficial microbes of the rhizosphere. External inoculation of B. subtilis has both positive and negative impacts on the endophytic and semi‐synthetic microbial community. Soil texture, type, pH and bacterial concentration play a crucial role in the regulation of all these processes. Soil amendments and microbial consortia of Bacillus produced by microbial engineering could be used to lessen the negative effect on soil microbial diversity. The complex plant–microbe interactions could be decoded using transcriptomics, proteomics, metabolomics and epigenomics strategies which would be beneficial for both crop productivity and the well‐being of soil microbiota. Bacillus subtilis has more positive attributes similar to the character of Dr. Jekyll and some negative attributes on plant growth, soil health and the environment akin to the character of Mr. Hyde.

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Aims The aim of this study was to identify the best combination of plant growth promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF) for biofortification and enhancing yield in wheat as well as improve soil health under field conditions. Another aim was to get insights into metabolite dynamics in plants treated with PGPB and AMF. Methods and Results Different combinations of PGPB and AMF that gave good results in greenhouse study were used in a field study. The combined application of Bacillus subtilis CP4 (native PGPB) and AMF gave the best results with a significant increase in biomass, macronutrient and micronutrient content in wheat grains and improvement in yield‐related parameters relative to the untreated control. PGPB and AMF treatment increased antioxidant enzymes and compounds and decreased the level of an oxidation marker. Metabolite profiling performed using Gas Chromatography–Mass Spectrometry (GC‐MS) showed significant upregulation of specific organic acids, amino acids, sugars and sugar alcohols in plants treated with CP4 and AMF. The altered pathways due to CP4 and AMF inoculation mainly belong to carbohydrate and amino acid metabolism. A positive correlation was observed between some organic acids, sugars and amino acids with wheat growth and yield parameters. The activities of soil enzymes increased significantly with the best results shown by native PGPB and AMF combination. Conclusions A native bacterial isolate Bacillus subtilis CP4 in combination with AMF showed exceptional ability for biofortification and yield enhancement under field conditions. The upregulation of a number of metabolites showed correlation plant growth promotion and nutrients. Significance and Impact of the Study The combined application of native B. subtilis CP4 and AMF could offer a more sustainable approach for the development of a biofertilizer to enhance wheat nutrient content and production and soil health thereby advancing agriculture.