Halophilic bacteria and archaea in salinity-resilient agriculture: mechanisms and multi-omics perspectives

Soil salinization due to anthropogenic activity and climate change is a bottleneck to the global agricultural yield and food security. Conventional approaches for mitigating salt stress, including utilization of chemical fertilizers, have shown limited success, and the use of genetically engineered microbes as bioinoculants or salt-tolerant crop varieties against abiotic salinity stress often faces regulatory challenges with extended timelines. Contrary to the existing approaches, employment of halophilic bacteria and archaea offers a promising platform for eco-friendly and sustainable crop cultivation under salt-affected soils. These unique salt-loving microbes can thrive in hypersaline ecosystems and exhibit physiological features for tolerating salt stress along with plant growth-promoting traits. They have distinctive adaptations in homeostasis, biosynthesis, and accumulation of compatible solutes like glycine betaines and amino acids, production of Volatile Organic Compounds (VOCs) as osmo-protectants, and exopolysaccharide (EPS) formation. Apart from salt tolerance, plant growth-promoting bacteria and Halobacteria (PGP-HB) exhibit direct and indirect mechanisms. Direct mechanisms involve 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, phytohormone production, siderophore production, nutrient solubilization, and biological nitrogen fixation, whereas indirect mechanisms involve the production of lytic enzymes, hydrogen cyanide (HCN), and antimicrobial production, as well as induced systemic resistance. Biochar and Nano-encapsulated halophilic plant growth-promoting rhizobacteria (HT-PGPR) together are an effective strategy for plant growth promotion. This review highlights the importance of halobacteria and halotolerant PGPR with an integrated omics approach to potentiate molecular mechanisms underlying adaptations and plant growth promotion in salt-affected soils. The focal point of this review is to explore the possibilities of exploiting halophilic bacteria and archaea in mitigating the negative impact of salt stress on crop production. It emphasizes solutions to current challenges, limitations, prospects of exploiting halophiles, and provides a translational route of eco-friendly bioformualtion production for sustainable agriculture with food security and is aligned with Sustainable Development Goal 2 (SDG 2).