Metagenomic and Metabolomic Perspectives on the Drought Tolerance of Broomcorn Millet (Panicum miliaceum L.)

Abstract

Drought stress is an important abiotic stress factor restricting crop production. Broomcorn millet (Panicum miliaceum L.) has become an ideal material for analyzing the stress adaptation mechanisms of crops due to its strong stress resistance. However, the functional characteristics of its rhizosphere microorganisms in response to drought remain unclear. In this study, metagenomics and metabolomics techniques were employed to systematically analyze the compositional characteristics of the microbial community, functional properties, and changes in metabolites in the rhizosphere soil of broomcorn millet under drought stress. On this basis, an analysis was conducted in combination with the differences in functional pathways. The results showed that the drought treatment during the flowering stage significantly altered the species composition of the rhizosphere microorganisms of broomcorn millet. Among them, the relative abundances of beneficial microorganisms such as Nitrosospira, Coniochaeta, Diversispora, Gigaspora, Glomus, and Rhizophagus increased significantly. Drought stress significantly affects the metabolic pathways of rhizosphere microorganisms. The relative abundances of genes associated with prokaryotes, glycolysis/gluconeogenesis, and other metabolic process (e.g., ribosome biosynthesis, amino sugar and nucleotide sugar metabolism, and fructose and mannose metabolism) increased significantly. Additionally, the expression levels of functional genes involved in the phosphorus cycle were markedly upregulated. Drought stress also significantly alters the content of specific rhizosphere soil metabolites (e.g., trehalose, proline). Under drought conditions, broomcorn millet may stabilize the rhizosphere microbial community by inducing its restructuring and recruiting beneficial fungal groups. These community-level changes can enhance element cycling efficiency, optimize symbiotic interactions between broomcorn millet and rhizosphere microorganisms, and ultimately improve the crop's drought adaptability. Furthermore, the soil metabolome (e.g., trehalose and proline) functions as a pivotal interfacial mediator, orchestrating the interaction network between broomcorn millet and rhizosphere microorganisms, thereby enhancing plant stress tolerance. This study sheds new light on the functional traits of rhizosphere microbiota under drought stress and their mechanistic interactions with host plants.

Keywords: broomcorn millet; drought stress; metabolomics; metagenomics; rhizosphere microorganisms.

Figure 1

Analysis of rhizosphere microbial communities in broomcorn millet under drought stress. (a) Alpha and beta diversity indices; (b) principal component analysis (PCA) plot. (c) Species abundance clustering analysis. Relative abundance of rhizosphere bacteria at the (e) phylum and (f) genus levels, and fungi at the (g) phylum and (h) genus levels. (d) LEfSe analysis of differentially abundant taxa at the genus level between treatments. p < 0.05. HD: Drought stress treatment; HCK: Control treatment.

Figure 1

Analysis of rhizosphere microbial communities in broomcorn millet under drought stress. (a) Alpha and beta diversity indices; (b) principal component analysis (PCA) plot. (c) Species abundance clustering analysis. Relative abundance of rhizosphere bacteria at the (e) phylum and (f) genus levels, and fungi at the (g) phylum and (h) genus levels. (d) LEfSe analysis of differentially abundant taxa at the genus level between treatments. p < 0.05. HD: Drought stress treatment; HCK: Control treatment.

Figure 2

Metabolic functional analysis of the rhizosphere microorganisms of broomcorn millet. (a) Principal Component Analysis (PCA) plot. (b) Clustering heatmap. HD: Drought stress treatment; HCK: Control treatment.

Figure 3

Heatmap of drought-responsive genes and functional genes.

Figure 4

Metabolomic analysis. (a) PCA of metabolites from both treatment groups, (b) OPLS-DA score plot comparing drought-stressed and control soils. (c) Relative abundance of functional metabolite classes.

Figure 5

Classification and differential analysis of metabolites under drought stress. (a) Pie chart of differential metabolite categories: the percentages depicted represent the proportion of metabolites within each chemical class relative to the total number of identified metabolites. (b) Volcano plot of metabolite differences between groups: The x-axis illustrates the log₂ (fold change), while the y-axis represents -log₁₀ (p-value). Each dot symbolizes a metabolite, and the colors are indicative of regulation, where red denotes upregulated metabolites (“up”), green indicates downregulated metabolites (“down”), and gray signifies metabolites with no significant difference (“nosig”). The size of the dots corresponds to the VIP (Variable Importance in the Projection) value of the metabolite. (c) Specific metabolites and cluster analysis in drought-stressed soil: the colored blocks indicate the relative expression levels of metabolites at various positions. Specifically, red represents high expression, and blue represents low expression.

Figure 6

A heatmap illustrating the correlations between the soil metabolites affected by drought and the relative abundances of bacterial genera (a), bacterial species (b), fungal genera (c), and fungal species (d).

Figure 6

A heatmap illustrating the correlations between the soil metabolites affected by drought and the relative abundances of bacterial genera (a), bacterial species (b), fungal genera (c), and fungal species (d).

Figure 7

Heatmap of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in enriched pathways. Each grid represents the expression levels of genes and metabolites. The orange boxes indicate upregulated genes, while the green boxes indicate downregulated genes (EC: Enzyme Commission number). The red boxes represent upregulated metabolites, and the blue boxes represent downregulated metabolites.

Figure 8

Schematic illustration of the symbiotic functional unit composed of the rhizosphere of broomcorn millet, soil metabolites, and rhizosphere microorganisms.