Genomic features of a plant growth-promoting endophytic Enterobacter cancerogenus JY65 dominant in microbiota of halophyte Suaeda salsa

Amis Plant growth-promoting bacteria (PGPB) are beneficial organisms that promote plant growth and increase plant tolerance to abiotic stresses. Many halophytes attract and recruit salt-tolerant microorganisms to enhance salt tolerance. However, little is known about the composition and ecological function of bacterial microbiota of Suaeda salsa.Methods Here, using a culture-dependent technique, we characterized the bacterial communities in the roots, stems, leaves, the rhizosphere, and bulk soils of S. salsa.Results We identified 71 representative bacterial strains belonging to 13 genera, with Enterobacter as the most dominant genus. All isolates produce indole-3-acetic acid (IAA) although the yields vary, have similar tolerance to alkaline pH up to 12 but varied salt tolerance. One strain JY65 isolated from the leaves showed the highest tolerance to salt stress. Addition of JY65 promoted growth of rice under NaCl stress with significantly increased plant biomass, plant height and root length. Up-regulated Na+ homeostasis-related gene expression and accumulation of antioxidant compounds was found in rice inoculated with JY65 strain. The strain was named as Enterobacter cancerogenus JY65 based on phylogenetic analysis. Genomic analysis of JY65 revealed existence of many PGP related genes such as IAA production, siderophore, nutrient uptake, and antimicrobial compounds. In addition, genes involved in adaptation to the harsh environment, including antioxidant enzyme, exopolysaccharide, osmoprotectant accumulation, ion homeostasis, were identified in JY65 genome.Conclusions These results provide novel insights into the composition of microbiota associated with halophyte S. salsa and revealed the mechanisms underlying the plant growth promotion of E. cancerogenus JY65.