Characterizing rhizosphere microbiota of peanut (Arachis hypogaea L.) from pre-sowing to post-harvest of crop under field conditions

Abstract

The rhizosphere, a narrow zone of soil near plant roots, is a hot spot for microbial activity. Rhizosphere microbiota directly or indirectly benefit plants by supplementing nutrients, producing beneficial chemicals, or suppressing pathogens. Plants attract and modulate bacteria within the rhizosphere by releasing exudates. Plants also tend to select the rhizosphere microbiota based on their needs; a phenomenon termed as "rhizosphere effect". In this study, we characterized the rhizosphere microbiota of peanut plants across the crop development cycle from pre-sowing of seeds to post-harvest of crop under field conditions. The rhizosphere and bulk soil samples from different crop developmental stages were also compared. The composition of bulk soil microbiota resembled microbiota of pre-sowing and post-harvest soil and was markedly different from rhizosphere soil samples. Rhizosphere samples were enriched with multiple organisms mostly from the Proteobacteria, Firmicutes and Bacteroidota phyla. Differences in diversity were observed among the rhizosphere samples but not in bulk soil across different crop development stages. Pseudomonas_M indica was highly enriched during the germination of seeds. Furthermore, Plant Growth Promoting (PGP) bacteria like Bacillus were enriched during the middle stages of crop development but there was a decline in PGP organisms in the matured crop stage. We also observed a significant association of pH and Electrical Conductivity (EC) with the profiles of microbial community. Overall, this study portrayed the changes in rhizosphere microbiota of peanut during different developmental stages of crop and may help to design stage specific bio-strategies such as bio-fertilizer to improve crop yield.

Figure 1

Alpha diversity measures Observed ASVs (top), and Shannon Index (bottom) plotted against sample groups. p-value from Wilcoxon-test between groups are given by bracket pointing to groups. p-value from Kruskal–Wallis test among four types/groups of samples is mentioned on the top. Second line mentions p-value from Kruskal–Wallis test of all groups (as plotted), all rhizosphere sample groups/collections and bulk soil sample groups/collections.

Figure 2

Taxonomic distribution at (A) phylum level and (B) Genus level. Only the top taxa are plotted for both levels. Sample names are coloured by type of sample.

Figure 3

NMDS plot of Bray–Curtis distance calculated from (A) all samples and (B) Rhizosphere samples only. Collection number of each sample is used as shape to denote the sample. Environment fit vectors representing physical parameters and nutrient concentrations are shown as arrows. Vectors with significant associations are shown in red coloured arrow.

Figure 4

Plot representing core microbiome from rhizosphere samples. The plot compares prevalence of genus in samples across varying levels of abundance. Only the genera with minimum prevalence of 0.4 at 0.001 abundance are plotted.

Figure 5

Correlation plot among genera from core microbiome. Only the significant (p-value < 0.05) correlations are plotted.