Genome sequence of the desert endophyte Pseudomonas granadensis R4-79 reveals potential for plant-growth promotion and disease suppression

Desert ecosystems are limited by resources and optimal climatic conditions to support cropping in different farming models. Recently, microbial applications have emerged as promising strategies to enhance plant survival and adaptation in such extreme environments. However, identifying beneficial microbes and understanding their functional roles and adaptation mechanisms remains underexplored. This study reports, for the first time, the isolation and characterization of the Pseudomonas sp. R4-79 strain from the arid environment of Wadi Rum, Jordan, associated with Ifloga spicata . The genome of Pseudomonas sp. R4-79, sequenced at 275× PacBio coverage, consists of a 6.18 Mbp chromosome encoding 5,445 proteins, including gene clusters for siderophores, phenazines, hydrogen cyanide, and phytohormones, as well as advanced secretion systems (T2SS, T4SS, T6SS, and TAT). Genomic and phenotypic analyses revealed that Pseudomonas sp. R4-79 belongs to the genus P. granadensis and exhibits plant growth-promoting attributes and substantial biocontrol potential. Pseudomonas sp. R4-79 effectively suppresses key phytopathogens, including the necrotrophic fungus Botrytis cinerea in vitro , as well as Pseudomonas syringae pv. tomato DC3000 and root-knot nematodes ( Meloidogyne incognita ) in vivo in Arabidopsis and tomato. This work suggests that P. granadensis R4-79 might be a good biocontrol agent to improve crop yield and ecological restoration in arid systems.