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Background  The present study aims to study the effects of biofertilizers potential of Arbuscular Mycorrhizal Fungi (AMF) and  Bradyrhizobium japonicum  ( B. japonicum ) strains on yield and growth of drought stressed soybean (Giza 111) plants at early pod stage (50 days from sowing, R3) and seed development stage (90 days from sowing, R5).    Results  Highest plant biomass, leaf chlorophyll content, nodulation, and grain yield were observed in the unstressed plants as compared with water stressed-plants at R3 and R5 stages. At soil rhizosphere level, AMF and  B. japonicum  treatments improved bacterial counts and the activities of the enzymes (dehydrogenase and phosphatase) under well-watered and drought stress conditions. Irrespective of the drought effects, AMF and  B. japonicum  treatments improved the growth and yield of soybean under both drought (restrained irrigation) and adequately-watered conditions as compared with untreated plants. The current study revealed that AMF and  B. japonicum  improved catalase (CAT) and peroxidase (POD) in the seeds, and a reverse trend was observed in case of malonaldehyde (MDA) and proline under drought stress. The relative expression of the  CAT  and  POD  genes was up-regulated by the application of biofertilizers treatments under drought stress condition. Interestingly a reverse trend was observed in the case of the relative expression of the genes involved in the proline metabolism such as  P5CS ,  P5CR ,  PDH,  and  P5CDH  under the same conditions. The present study suggests that biofertilizers diminished the inhibitory effect of drought stress on cell development and resulted in a shorter time for DNA accumulation and the cycle of cell division. There were notable changes in the activities of enzymes involved in the secondary metabolism and expression levels of  GmSPS1 ,  GmSuSy,  and  GmC-INV  in the plants treated with biofertilizers and exposed to the drought stress at both R3 and R5 stages. These changes in the activities of secondary metabolism and their transcriptional levels caused by biofertilizers may contribute to increasing soybean tolerance to drought stress.    Conclusions  The results of this study suggest that application of biofertilizers to soybean plants is a promising approach to alleviate drought stress effects on growth performance of soybean plants. The integrated application of biofertilizers may help to obtain improved resilience of the agro ecosystems to adverse impacts of climate change and help to improve soil fertility and plant growth under drought stress.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-02949-z.

Physiological and biochemical responses of soybean plants inoculated with Arbuscular mycorrhizal fungi and Bradyrhizobium under drought stress