Microbial survival strategies in desiccated roots of Myrothamnus flabellifolia

Abstract

Introduction: Root-associated microbiomes are critical to plant vigor, particularly under drought stress. The spatial dynamics of microbial community diversity and composition are strongly influenced by plant root and environmental factors. While the desiccation tolerance of the resurrection plant Myrothamnus flabellifolia using leaf tissue has been previously investigated, the transcriptional responses of its root-associated microbiomes under desiccation remain completely unexplored.

Methods: Here, we conducted metatranscriptome sequencing on root samples of M. flabellifolia collected in the field across four states: dry, desiccated, partially hydrated, and fully hydrated.

Results: Bacterial transcripts dominated the root metatranscriptome across all conditions. Desiccated roots exhibited a significant increase in transcripts from Actinomycetota, whereas fully hydrated roots showed an enrichment of Pseudomonadota. Under desiccation, root-associated bacteria upregulated genes involved in antioxidant systems, trehalose biosynthesis, and hormonal regulation.

Discussion: These findings highlight microbial adaptive mechanisms to withstand extreme water loss. In contrast, the bacterial transcriptional response in hydrated roots was characterized by genes linked to peptidoglycan biosynthesis, sugar transporters, and chemotaxis. Taken together, our findings indicate that root-associated bacteria deploy defense mechanisms analogous to those of their host plant to adapt to extreme drought stress, highlighting their crucial role in plant resilience.

Keywords: Myrothamnus flabellifolia; desiccation; metatranscriptomics; microbiomes; plant growth-promoting bacteria; resurrection plants; rhizosphere.

Figure 1

(A) Geographical distribution of Myrothamnus flabellifolia. (B) Natural habitat of M. flabellifolia at the SwebeSwebe field site. (C) Root anatomy of M. flabellifolia showing root hairs under desiccated conditions.

Figure 2

(A) Kingdom-level taxonomic affiliation of the transcripts retrieved from all samples (S1-S5) across different conditions excluding unknown transcripts. (B) Principal component analysis (PCA) of bacterial transcripts showing taxonomic abundance and (C) total gene expression. Dehydrated conditions include partially dehydrated (PD) and desiccated (D). Rehydrated samples were labeled as partially rehydrated (PR) and fully rehydrated (FR).

Figure 3

Effects of dehydration and rehydration on the relative water content (RWC) of leaf and root tissues of Myrothamnus flabellifolia in Swebeswebe field site. Plants were sampled at four-time points during the process of dehydration and rehydration.

Figure 4

(A) Bacterial taxonomic profiling of transcripts at phylum level across four-time points. (B) Differentially abundant transcripts of associated bacterial species under dehydrated (partially dry and desiccated) and rehydrated (partially and fully rehydrated) conditions.

Figure 5

Venn diagram shows the unique and shared transcripts across four conditions (A). Differentially abundant transcripts (DATs), significantly transcripts are highlighted in red with an application of adjusted p-value <0.05 and log fold change cut-off = 2 (B). Heatmap of the top 25 DATs of bacteria in roots of Myrothamnus flabellifolia, DA1-DA4 represent dehydrated and RB6-RA5 is rehydrated condition (C). Functional assignment of bacterial transcripts associated with roots under dehydration (red) and rehydration (cyan) conditions (D).

Figure 6

Summary diagram of key findings of functional role(s) of the root-associated microbiome, bacteria in particular, of Myrothamnus flabellifolia. The abundance of sucrose in M. flabellifolia roots under drought stress may be secreted into the rhizosphere via apoplastic or symplastic pathways, potentially acting as a chemoattractant for the microbial community (Tebele, 2024). (1) Metatranscriptomic analysis identified predominant bacterial communities in M. flabellifolia roots under desiccated conditions (<10% RWC). This is consistent with findings from Tebele et al. (2024), which utilized amplicon-based metagenomics to quantify similar microbiomes in bulk soil, rhizosphere, and endosphere compartments. (2) The rhizosphere soil of M. flabellifolia exhibited enhanced physicochemical properties and nutrient availability compared to bulk soil, potentially attributed to the activity of the microbiome during desiccation stress (Tebele et al., 2024). (3) Differentially abundant transcripts (DATs) in bacterial cells under desiccation stress were associated with drought response mechanisms. Key pathways included the activation of sigma factors for extracellular stress detection, upregulation of drought-responsive genes (e.g., molecular chaperones such as DnaK and HSP20), ATP synthase, antioxidant enzymes, protein kinases, and carbohydrate biosynthesis to mitigate reactive oxygen species (ROS). (4) Biological processes enriched within root-associated bacterial cells under desiccation included respiration, stress responses, and photosynthesis. Notably, photosynthetic bacteria, such as Cyanobacteria spp., were implicated in these functions. (5) Upon rehydration, bacterial molecular responses showed upregulation of DATs associated with plant-microbe interactions, including genes involved in chemotaxis and exopolysaccharide biosynthesis. (6) Favorable conditions also enhanced the abundance of plant growth-promoting genes, including those related to nutrient recycling, sugar and amino acid transport, and the regulation of metabolite flux in bacterial cells. DATs under rehydration were further linked to biological processes such as protein biosynthesis (e.g., amino acid transporters) and carbohydrate metabolism (e.g., exopolysaccharide synthesis, trehalose utilization), underscoring the role of the microbiome in promoting resilience and recovery of M. flabellifolia after desiccation stress.