Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to Withstand Salinity

Abstract

Root microbiota is a crucial determinant of plant productivity and stress tolerance. Here, we hypothesize that the superior halo-tolerance of seepweed Suaeda salsa is tightly linked to a specialized belowground microbiome. To test this hypothesis, we performed a phylogenetic trait-based framework analysis based on bacterial 16S rRNA gene and fungal nuclear rRNA internal transcribed spacer profiling. Data showed that the dominant α-proteobacteria and γ-proteobacteria communities in bulk soil and root endosphere tend to be phylogenetically clustered and at the same time exhibit phylogenetic over-dispersion in rhizosphere. Likewise, the dominant fungal genera occurred at high phylogenetic redundancy. Interestingly, we found the genomes of rhizospheric and endophytic bacteria associated with S. salsa to be enriched in genes contributing to salt stress acclimatization, nutrient solubilization and competitive root colonization. A wide diversity of rhizobacteria with similarity to known halotolerant taxa further supported this interpretation. These findings suggest that an ecological patterned root-microbial interaction strategy has been adopted in S. salsa system to confront soil salinity. We also demonstrated that the potential core microbiome members improve non-host plants growth and salt tolerance. This work provides a platform to improve plant fitness with halophytes-microbial associates and novel insights into the functions of plant microbiome under salinity.

Figure 1. Phylogeny of diverse well-known halotolerant bacterial MOTUs found in belowground microbiome of S. salsa (classified into four classes: γ-proteobacteria, α-proteobacteria, Bacteroidetes and Verrucomicrobia) and their relative abundance in the root endosphere, rhizosphere soil and bulk soil habitats (R = root endosphere, RS = rhizosphere soil, BS = bulk soil).

Figure 2. An unrooted phylogenetic tree of closely related MOTUs based on ITS1 sequences showing the infrageneric genetic diversity within Monosporascus genus.

Percentages of the total Monosporascus members in the BS, RS and R habitats are indicated with pie charts. The relative abundance of each MOTU is presented with bar charts. R = root endosphere, RS = rhizosphere soil, BS = bulk soil.

Figure 3. A heatmap showing the hierarchical clustering of the predicted KEGG Orthologs (KOs) functional profiles of bacterial microbiota across all samples.

The color bar on top shows the relative abundance of selected genes.

Figure 4. Beneficial effects of a root endophytic Montagnulaceae sp. on plant growth and salt tolerance.

(a) endophyte-mediated plant (rice seedlings) salt tolerance. (b) endophytic colonization on plant biomass accumulation under salt stress conditions. (c) endophytic colonization on chlorophyll content of leaves under salt stress conditions. (d) the number of pyrosequencing reads of Montagnulaceae sp. detected in the R, RS and BS habitats. (e,f) endophytic colonization on plant growth when the nitrogen source occurs in both organic (valine) and inorganic (NaNO₃) forms in the media. (g,h) colonization of Montagnulaceae sp. on root surface (H: hyphae) and aggregation of sclerotium-like (S) structures in root cortical cells. (i) alignment of partial ITS1 sequences of Montagnulaceae sp. derived from pyrosequencing data and pure cultures. EI: endophyte-infected; EF: endophyte-free.

Figure 5. Beneficial effects of a single bacterial culture and a mixed bacterial cultures (MBC) on plant growth and salt tolerance.

(a) bacterial composition of three replicated MBC using a pyrosequencing approach. (b,c) MBC-mediated plant growth and salt tolerance (cucumber seedlings). (d,e) a rhizospheric strain, Pseudomonas sp. RS1, rescued rice seedlings when exposed to salinity stress.

Figure 6. Conceptual illustration of the microbial community assembly and functional traits in the bulk soil (BS), rhizosphere soil (RS) and root endosphere (R).

A rapid loss of diversity from soil (pedoshere) to the root endosphere (phytosphere) indicates the presence of a biotic filter at the root-soil interface (e.g., host genotype and root exudates). The dominant α-proteobacteria and γ-proteobacteria communities in BS and R showed patterns of phylogenetical clustering, suggesting the microbial response to environmental extremes; there were over-dispersion trends in RS. In all habitats, a group of closely related MOTUs assigned to the same microbial lineages (at the genus level) indicated some degree of phylogenetic redundancy, a known buffering mechanism against stresses. The representative abundant functional genes predicted by PICRUSt in each habitat were presented. These genes were often related to bacterial salinity tolerance and improved plant performance. Re-colonization and salt stress assays (a bottom-up approach) confirmed the extended phytobeneficial traits of some core culturable members on non-host plants.