The root enrichment of bacteria is consistent across different stress-resistant plant species

Abstract

Bacteria, inhabiting around and in plant roots, confer many beneficial traits to promote plant growth and health. The secretion of root exudates modulates the nutritional state of the rhizosphere and root area, further selecting specific bacteria taxa and shaping the bacteria communities. Many studies of the rhizosphere effects have demonstrated that selection by the plant rhizosphere consistently enriches a set of bacteria taxa, and this is conserved across different plant species. Root selection effects are considered to be stronger than the rhizosphere selection effects, yet studies are limited. Here, we focus on the root selection effects across a group of 11 stress-resistant plant species. We found that the root selection consistently reduced the alpha diversity (represented by total number of observed species, Shannon's diversity, and phylogenetic diversity) and altered the structure and composition of bacteria communities. Furthermore, root selection tended to enrich for clusters of bacteria genera including Pantoea, Akkermansia, Blautia, Acinetobacter, Burkholderia-Paraburkholderia, Novosphingobium, Massilia, Pseudomonas, Chryseobacterium, and Stenotrophomonas. Our study offers some basic knowledge for understanding the microbial ecology of the plant root, and suggests that several bacteria genera are of interest for future studies.

Keywords: Abiotic stress; Amplicon sequencing; Bacteria; Microbial diversity; Microbial richness; Microbiota; Pantoea; Plant-microbe interaction; Rhizosphere community; Root.

Figure 1. The overall comparison of the bacteria communities among the bulk soil, the rhizosphere soil, and the root.

(A) The rarefaction curves of sequenced samples rarefied at 32,416 sequences. The number of observed species (B), Shannon’s diversity (C), and phylogenetic diversity (D); the principal component analysis of bacteria communities (E) and predicted genes (F) among the samples of the bulk soil, the rhizosphere soil, and the root. The p values from a Tukey comparison test are marked with “ns” for p ≥ 0.05, “*” for p < 0.05, “**” for p < 0.005, “***” for p < 0.0005.

Figure 2. The comparison of the number of observed species (A) Shannon’s diversity (B) and phylogenetic diversity (C) among the bulk soil, the rhizosphere soil, and the root by plant species.

The p values of the t-tests are marked with “ns” for p ≥ 0.05, “*” for p < 0.05, “**” for p < 0.005, “***” for p < 0.0005. The abbreviations of the plant species: CE, Casuarina equisetifolia; CI, Calophyllum inophyllum; FC, Fagraea ceilanica; GS, Guettarda speciosa; HL, Heritiera littoralis; HS, Hernandia sonora; MB, Melaleuca bracteata; PP, Pongamia pinnata; PPI, Portulaca pilosa; RB, Ruellia brittoniana; SS, Scaevola sericea.

Figure 3. The comparison of the first two principle components PCoA 1 (A) and PCoA 2 (B) among the bulk soil, the rhizosphere soil, and the root by plant species.

The p values of the t-tests are marked with “ns” for p ≥ 0.05, “*” for p < 0.05, “**” for p < 0.005, “***” for p < 0.0005. The abbreviations of the plant species are listed in Fig. 2.

Figure 4. Heatmaps show the log fold change of bacterial genera (A) and predicted genes (B) in root samples, either enriched (red) or decreased (blue), when compared against rhizosphere samples, plotted by plant species.

The root enrichment and depletion numbers are calculated as the Log₂ fold change of in the root by in the rhizosphere, and are represented by grid color. The p values (<0.05) of the t-tests are marked as asterisk (*) in the grid. The abbreviations of the plant species are listed in Fig. 2.

Figure 5. The comparison of the representative OTUs of the enriched bacteria genera among the bulk soil, the rhizosphere soil, and the root by plant species.

(A) OTU1 of the genus Pantoea, (B) OTU3 of the genus Pseudomonas, (C–F) OTU2, OTU4, OTU21 and OTU215 of the species complex Burkholderia-Paraburkholderia. The p values of the t-tests are marked with “ns” for p ≥ 0.05, “*” for p < 0.05, “**” for p < 0.005, “***” for p < 0.0005. The abbreviations of the plant species are listed in Fig. 2.

Figure 6. The comparison of the cellular pathways involving enriched genes among the bulk soil, the rhizosphere soil, and the root by plant species.

(A) amino acid metabolism, (B) biofilm formation, (C) carbohydrate metabolism, and (D) membrane transport. The p values of the t-tests are marked with “ns” for p ≥ 0.05, “*” for p < 0.05, “**” for p < 0.005, “***” for p < 0.0005. The abbreviations of the plant species are listed in Fig. 2.