Contrasting leaf transcriptomic responses to drought and heat stress in the desert CAM species Mesembryanthemum forsskalii

TL;DR

This study explores how the desert plant Mesembryanthemum forsskalii responds to drought and heat stress at the genetic level, revealing that heat stress triggers a much stronger gene response than drought.

Contribution

The study provides the first integrated transcriptomic and rhizosphere metagenomic resources for Mesembryanthemum forsskalii and identifies key heat-inducible transcription factors.

Findings

Heat stress induced 1,348 differentially expressed genes, compared to only 84 under drought stress.

Transcription factor families B3, bHLH, and bZIP showed significant upregulation under heat stress.

Rhizosphere metagenomics identified stress-tolerant archaeal and bacterial genomes associated with M. forsskalii.

Abstract

Dryland ecosystems are increasingly exposed to extreme heat and prolonged water limitation. Facultative crassulacean acid metabolism (CAM) enables certain desert plants to enhance water-use efficiency and adjust carbon assimilation under stress conditions. Mesembryanthemum forsskalii Hochst. ex Boiss. (Aizoaceae; locally known as Samh) is a hyper-arid adapted species native to Saudi Arabia, yet genomic and transcriptomic resources for this plant remain scarce. This study aimed to generate foundational genomic resources and characterize transcriptional responses to drought and heat stress.

We integrated rhizosphere metagenomics and leaf transcriptomics. A genome-resolved rhizosphere metagenome was generated from mature field-grown plants. In parallel, micropropagated plants were exposed under controlled conditions to progressive drought (17 days without irrigation) or acute heat shock (55 °C for 120 min), each compared with well-watered controls. RNA sequencing generated 123.77 Gb raw data and 121.96 Gb clean reads after quality filtering. Differential gene expression was identified using thresholds of |log2FC| ≥ 2 and FDR ≤ 0.05, followed by transcription factor profiling and KEGG pathway annotation.

Heat stress induced substantially broader transcriptional reprogramming than drought. A total of 1,348 genes were differentially expressed under heat stress, compared with 84 genes under drought. Heat exposure strongly increased the expression of transcription factor families including B3 (20.00-fold relative to drought), bHLH (22.65-fold), and bZIP (8.94-fold). KEGG pathway analysis revealed expanded representation of metabolic pathways under heat, including secondary metabolite biosynthesis, ribosome function, carbon metabolism, and endoplasmic reticulum protein processing. Rhizosphere binning recovered archaeal and bacterial genomes affiliated with stress-tolerant lineages, providing the first microbial genomic framework associated with M. forsskalii.

These results demonstrate a heat-dominant transcriptional response in M. forsskalii and provide the first integrated transcriptomic and rhizosphere metagenomic resources for this desert facultative CAM species. Heat-inducible transcription factors, particularly B3 and NAC families, emerge as promising targets for improving thermotolerance and water-use efficiency in crops.

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