Integrated Omics Analysis of PGPR and AMF Effects on Soil Microbiota and Root Metabolites in Isatis indigotica

Shuai Yang¹Ting Yuan²Tingting Duan³Huimin Zhu³Xiaoxia Zhang³Haihong Zhang³Junjie Jiang³Jun Yang³Lichuan Hu³Yu Yu³Lijun Zhang³Zhaodi Yuan^3*

• ¹Tongren Academy of Agricultural Sciences, Tongren, 554200, Guizhou, China, Tongren, China
• ²School of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China, Guiyang, China
• ³Mianyang Normal University, Mianyang, China

The intensive use of chemical fertilizers and pesticides in modern agriculture has led to severe soil degradation and environmental pollution, which threatens the sustainable production of crops. Plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) are promising biofertilizers which can enhance plant growth and improve soil health. However, their combined effects on medicinal plants like Isatis indigotica remain unclear. We isolated six PGPR strains (Acinetobacter sp. and Bacillus albus) from the rhizosphere of Isatis indigotica, all of which demonstrated multiple growth-promoting traits, including the ability to solubilize phosphate, fix nitrogen, produce indole-3-acetic acid (IAA) and deaminate 1-aminocyclopropane-1-carboxylate (ACC). A pot experiment demonstrated that inoculations with PGPR and AMF+PGPR significantly improved plant height, root length while enhancing soil organic carbon (SOC), total nitrogen (TN) and available phosphorus (AP). Rhizosphere microbiome analysis showed a shift toward beneficial taxa, including Proteobacteria and Ascomycota, indicating microbial recruitment by inoculated strains. Metabolomic profiling revealed elevated concentrations of key bioactive compounds, such as flavonoids, lipids and amino acids, which enhance a plant's tolerance to stress and its medicinal properties. Furthermore, analysis of the RDA revealed strong correlations between dominant microbial genera (e.g. Acinetobacter, Pedobacter and Botryotrichum) and the accumulation of different root metabolites (e.g. benzenesulfonic acids, carbohydrates and fatty acids). PGPR and AMF alter the composition of the rhizosphere microbiome and root metabolism, thereby enhancing the uptake of nutrients and the synthesis of secondary metabolites in Isatis indigotica. These findings support their use as biofertilizers for sustainable cultivation of medicinal plants.