Plant growth promotion and pathogen protection by the desert endophyte Pseudomonas grandensis R4-79

Desert ecosystems have limited resources and harsh climatic conditions and cannot support cropping in most farming models. Recently, microbial applications have emerged as promising strategies to enhance plant survival and adaptation in such extreme environments. However, the beneficial microbes and our understanding of their functional roles and adaptation mechanisms in desert ecosystems remain underexplored. This study reports the isolation and characterization of the Pseudomonas sp. R4-79 strain from the arid environment of Wadi Rum, Jordan, associated with the desert plant 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 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 suppressed 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 could represent an effective biocontrol agent to improve crop yield in sustainable agriculture.