The Impact of Soybean Genotypes on Rhizosphere Microbial Dynamics and Nodulation Efficiency

Abstract

Rhizosphere microbiome exerts a significant role in plant health, influencing nutrient availability, disease resistance, and overall plant growth. Establishing a robust and efficient nodulation process is essential for optimal nitrogen fixation in legumes like soybeans. Different soybean genotypes exhibit variations in their rhizosphere microbiome, potentially impacting nitrogen fixation through nodulation. However, a detailed understanding of how specific soybean genotypes influence rhizosphere microbial communities and nodulation patterns remains limited. Our study aims to investigate the relationship between rhizosphere microbial abundance and plant growth in four soybean genotypes. We evaluated plant growth parameters, including biomass, leaf area, and stomatal conductance, and identified significant genotypic differences in nodulation. Specifically, genotypes PI 458505 and PI 603490 exhibited high levels of nodulation, while PI 605839A and PI 548400 displayed low nodulation. 16S rRNA gene amplicon sequencing revealed diverse bacterial communities in the rhizosphere, with Proteobacteria as the dominant phylum. High-nodulation genotypes harbored more diverse microbial communities enriched with Actinobacteria and Acidobacteriota, while low-nodulation genotypes showed higher abundances of Firmicutes and Planctomycetota. Alpha and beta diversity analyses confirmed distinct microbial community structures between high- and low-nodulation groups. Our findings suggest that the rhizosphere microbiome significantly influences soybean growth and nodulation, highlighting the potential for genotype-driven strategies to enhance plant-microbe interactions and improve soybean productivity.

Keywords: alpha diversity; amplicon sequencing; beta diversity; microbiome; stomata; taxonomic abundance.

Figure 1

Plant physiological responses of four soybean genotypes (PI 458505, PI 603490, PI 605839 A, and PI 548400) under control growth conditions. (a) Stomatal conductance. (b) Number of nodules. (c) Nodule fresh weight. (d) Leaf area. (e) Shoot biomass. (f) Root biomass. The bars represent the mean ± standard error (SE) of five biological replicates. Statistical significance was determined using a one-sample t-test and the Wilcoxon test. Asterisks above the bars indicate statistical significance with the following p-value thresholds: * p < 0.05, ** p < 0.005, *** p < 0.0005, and **** p < 0.00005. ‘ns’ indicates non-significant differences (p ≥ 0.05).

Figure 2

Relative abundance of bacterial communities in soybean rhizosphere samples. Bar graphs illustrate the microbial composition across four soybean rhizosphere samples (SY105, SY107, SY112, and SY209) at different taxonomic levels: (a) phylum, (b) family, and (c) genus. The y-axis represents the relative abundance (%) of each bacterial group. Each bar represents a sample, with different colors indicating different bacterial taxa. The phylum-level graph (a) shows the overall distribution of major bacterial groups. The family-level graph (b) provides a more detailed view of the microbial community composition, and the genus-level graph (c) presents the relative abundance of bacterial genera, illustrating the variations in microbial community structure and richness among the different soybean genotypes.

Figure 3

Comparative analysis of bacterial communities across soybean genotypes. (a) Bacterial Phyla Relative Abundance: Heatmap depicts the relative abundance of bacterial phyla in the rhizosphere of four soybean genotypes (SY105, SY107, SY112, SY209), categorized into two groups, G1 (SY105, SY107) and G2 (SY112, SY209). The color gradient indicates the differential abundance of each phylum, with darker red representing higher relative abundance and darker blue representing lower relative abundance. The phyla are listed on the left, and the samples are shown across the top. (b) Shared and unique OTUs: Venn diagram illustrates the overlap and unique operational taxonomic units (OTUs) among the rhizosphere microbiomes of the four soybean genotypes. The numbers within each section represent the quantity of shared or unique OTUs, providing a visual representation of community similarity and uniqueness. (c) Phylum relative abundance and (d) family relative abundance: Donut plots illustrating the relative abundance of major bacterial phyla and families, respectively, in the rhizosphere of G1 and G2. Each segment of the donut plot represents a phylum (c) and family (d), with the size of the segment corresponding to its relative abundance percentage. The legend below the plot indicates the phyla and families associated with each color.

Figure 4

Differences in rhizosphere microbial community diversity. (a) Alpha diversity: Box plots illustrating the alpha diversity indices (ACE, Chao1, Observed OTUs, and Shannon) of the rhizosphere microbiomes associated with the two soybean groups, G1 (SY105, SY107) and G2 (SY112, SY209). Each box represents the interquartile range (IQR) of the data, with the median value indicated by a horizontal line. Outliers are represented by individual dots. Different colors represent each group. Asterisks (**) indicate statistically significant differences between groups, and ‘ns’ indicates non-significant differences (p ≥ 0.05). (b) Beta diversity: Principal coordinates analysis (PCoA) plot illustrating the beta diversity, or community dissimilarity, between the rhizosphere microbiomes of G1 and G2. Each point represents a single rhizosphere sample, colored by its corresponding group (G1 or G2) and shaped by its soybean genotype (SY105, SY107, SY112, SY209). Proximity of points indicates greater community similarity. (c) Shared and unique OTUs: Venn diagram illustrates the overlap and unique OTUs between the rhizosphere microbiomes of G1 and G2. Numbers within each section represent the number of shared or unique OTUs, providing a visual representation of community similarity and uniqueness.