Genome analysis of a salinity adapted Achromobacter xylosoxidans rhizobacteria from the date palm

Rhizospheric bacteria play an indispensable role in plant growth, development, and stress response in plants. This project aims to isolate and functionally characterize plant-growth-promoting rhizobacteria (PGPR) from date palm (Phoenix dactylifera L.) rhizosphere, to investigate its potential uses as a biofertilizer in date palm. Here, we report an Achromobacter xylosoxidans SQU-1 (SQU-1), as a rhizobacteria strain isolated from date palms grown under salinity. The strain was visualized using electron microscopy, identified using protein profiling and 16 S rRNA gene sequencing, functionally characterized, and its genome was sequenced, assembled, and annotated. The results showed that SQU-1 is a Gram-negative flagellated strain and possesses several plant-growth-promoting traits, including the ability to solubilize micronutrients such as zinc, potassium, phosphorus and to produce ammonia, iron siderophores, indole acetic acid (IAA) phytohormone, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. SQU-1 was also able to significantly enhance date palm seed germination and Arabidopsis growth under normal and saline conditions. Whole-genome sequencing of SQU-1 revealed a total of 6,441,875 bp reads that were assembled into 15 scaffolds. Genome sequence analysis indicated the presence of 5968 open reading frames (ORFs), including 5848 coding genes, 56 pseudogenes, and 64 rRNA DNA sequences. Sequence and cluster of orthologous groups (COG) analysis of SQU-1 enabled the identification of potential genes involved in plant growth-promoting characteristics such as ACC DEAMINASE (acdS), D-CYSTEINE DESULFHYDRASE, and various siderophore production and transporter genes. In conclusion, SQU-1 can be a good candidate for a sustainable agricultural system that aims at producing date fruits under saline conditions with minimal usage of chemical fertilizers.