Microbial modulation of plant epigenetics: the role of miRNA and lncRNA in enhancing salt tolerance

Soil salinity is a major abiotic stress that severely affects crop productivity and global food security. Conventional breeding and genetic engineering approaches have had limited success in developing salt-tolerant crops due to the complexity of plant stress responses. Emerging evidence suggests that beneficial microbes play a crucial role in enhancing plant salt tolerance by modulating epigenetic mechanisms, particularly through microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). These regulatory molecules influence key stress-adaptive pathways, including reactive oxygen species (ROS) detoxification, ion homeostasis, chromatin remodeling, and hormone signaling. This review highlights the molecular interactions between plant-associated microbes and epigenetic regulators, emphasizing the role of Pseudomonas fluorescens, Bacillus subtilis, and other plant growth-promoting bacteria (PGPB) in regulating miRNA and lncRNA expression. Notably, miR398-mediated ROS scavenging and lncRNA973-associated NAC transcription factor modulation have been identified as critical mechanisms for salt stress adaptation. Additionally, microbial signals such as quorum sensing molecules and volatile organic compounds (VOCs) influence phytohormone pathways, further enhancing plant resilience. Despite these advances, significant knowledge gaps remain in understanding the precise molecular mechanisms of microbial–epigenetic interactions under salt stress. Future research should integrate multi-omics approaches and comparative studies between halophytes and glycophytes to identify conserved microbial–epigenetic strategies. Harnessing these insights for microbial-based bioformulations and breeding programs offers a sustainable, eco-friendly solution for mitigating the adverse effects of salinity in agriculture, paving the way for improved crop resilience and global food security.