Influence of genotype, nodule position, and edaphic factors on microbial diversity and assembly of pigeonpea (Cajanus cajan) root nodules in Indian soils

Abstract

Background: Pigeonpea (Cajanus cajan) is an important legume crop in semi-arid regions with multiple uses. The microbial diversity within its root nodules in Indian soils remains poorly explored. We investigated the bacterial diversity of pigeonpea root nodules across different genotypes and soil types to identify the factors driving their assembly. Using a metagenomic approach and high-throughput sequencing of the 16S rRNA gene, we analyzed the nodule microbiomes of three pigeonpea genotypes (Asha, Durga, and Mannem Konda Kandi) grown in three different soil types (Alfisol, Vertisol, and Inceptisol) and wild pigeonpea (C. scarabaeoides) in its native soil.

Results: Our results indicated that pigeonpea nodules harbor diverse rhizobial and non-rhizobial endophytes and that host genotype, nodule position, soil type, and other edaphic factors influence significant variation in the microbial community structure. The core nodule microbiome was dominated by Proteobacteria and Bacteroidetes. Bradyrhizobium and Ensifer were predominant among the rhizobial taxa, and non-rhizobial genera such as Pseudomonas, Chitinophaga, and Limnobacter were also abundant. Edaphic factors, particularly soil type, pH, and nutrient availability, had a stronger influence on the nodule bacterial community composition than the host genotype. Although bulk soil exhibited higher bacterial diversity, nodule microbiomes were less diverse but more specialized, indicating host-mediated selection. A comparison of the nodule microbiomes of wild and cultivated pigeonpea revealed distinct differences, with the core nodule microbiome of wild pigeonpea dominated by Bradyrhizobium, while that of cultivated pigeonpea exhibited a diverse bacterial community.

Conclusions: These findings demonstrate that soil properties play a more critical role than host genetics in shaping the pigeonpea nodule microbiome, emphasizing the importance of environmental conditions in symbiotic interactions. The differences between wild and cultivated genotypes suggest that domestication has altered microbial recruitment strategies. This study provides foundational insights into the factors driving microbial assembly in pigeonpea nodules, with implications for improving crop productivity through targeted microbial management. Future research should explore the functional roles of these microbial communities to optimize their use in sustainable agriculture.

Keywords: Edaphic factors; Genotype influence; Nodule microbiome; Non-rhizobial endophytes; Pigeonpea; Rhizobia; Soil type.

Fig. 1

Heatmaps representing the core nodule microbiome of pigeonpea across diverse soils at the (A) phylum and (B) genus levels. The Y-axis represents the prevalence level of core bacterial taxa across the detection threshold (relative abundance) range on the X-axis. The variation in the prevalence of each phylum/genus is indicated by a color gradient from blue (decreased) to red (increased). The ‘Uncultured_’ taxa label in the figure represents unclassified bacterial taxa

Fig. 2

PERMANOVA output measuring the influence of different factors on the pigeonpea nodule microbiota using the pseudo-F values as proxies. (A) Edaphic factors, (B) Soil macronutrients, (C) Soil micronutrients, (D) Agricultural factors, (E) Geoclimatic factors, and (F) Host factors. * p < 0.05; ** p < 0.01; *** p < 0.001; ns p > 0.05

Fig. 3

Schematic representation of analysis of similarities (ANOSIM) between the pigeonpea nodule microbial communities across the three different genotypes. Numerals represent the percentage of variance in the nodule microbial community composition explained by the analyzed factors based on ANOSIM R values. The dotted lines in black represent the differences between nodule positions within each genotype, while the red dotted lines represent the overall variation in nodule microbial communities between the genotypes. Higher percentages indicate a stronger influence of the respective factor (nodule position or genotype) on the microbial community composition. The distances depicted by the dotted lines are representative and do not correspond to actual spatial distances in relation to the percentage variations

Fig. 4

The core microbiome of wild pigeonpea nodules at the (A) phylum and (B) genus levels. The Y-axis represents the prevalence level of core bacterial taxa across the detection threshold (relative abundance) range on the X-axis. The variation in the prevalence of each phylum/genus is indicated by a color gradient from blue (increased) to yellow (decreased). The ‘Not_assigned/Uncultured_’ taxa label in the figure represents unclassified bacterial taxa

Fig. 5

Principal coordinate analysis for the wild vs. cultivated pigeonpea nodule microbiome. The samples were transformed by the square root and distance matrix constructed with the Bray‒Curtis similarity metric. Total variations of 28.2% (X-axis) and 11.9% (Y-axis) were observed with principal coordinate analysis