Elucidating key plant growth–promoting (PGPR) traits in Burkholderia sp. Nafp2/4‐1b (=SARCC‐3049) using gnotobiotic assays and whole‐genome‐sequence analysis

Burkholderia sp. Nafp2/4‐1b (=SARCC‐3049) is a plant growth–promoting rhizobacteria (PGPR) initially isolated from the rhizosphere of pristine grassland in South Africa, and its ability to enhance growth was previously evaluated on maize (Zea mays L.). Here, the bacterium was tested with the aim of investigating its role in improving the nodulation and growth of the forage legume lucerne (Medicago sativa L.) when it is co‐inoculated with the rhizobial symbionts of this legume in the glasshouse. When the co‐inoculation resulted in a statistically significant (P = 0·05) increase in the number of nodules and improved plant biomass compared with single inoculation, we sequenced and analysed its genome to gain a better understanding of the genetic determinants responsible for the observed PGPR traits. The Illumina HiSeq 2500‐sequenced genome resulted in 92 scaffolds, with an N50 of 322 407 bp, a total draft genome size of 7 788 045 bp and GC content of 66·2%. Analysis of the genome sequence confirmed the presence of a number of essential genes that code for various PGPR traits. The main plant beneficial genes associated with PGPR traits in Burkholderia sp. Nafp2/4‐1b include pyoverdine siderophores biosynthesis gene (PvdF); acdS that codes for 1‐aminocyclopropane‐1‐carboxylate (ACC) deaminase; the tryptophan synthase genes involved in auxin biosynthesis (TSA1, TSB1) and the pqqABCDE operon related to phosphate solubilization. This study generated valuable information on the potential of the PGPR Burkholderia sp. strain Nafp2/4‐1b as an effective commercial inoculant, which warrants further formulation and field application studies before developing it into a low cost, environmentally safe and effective biofertilizer. Significance and Impact of the StudyWith increasing negative impacts posed by the prolonged usage of external inputs such as chemical fertilizers as well as the adverse effects of abiotic stresses on both soil health and crop productivity, the need arises to look for sustainable means of mitigating these problems. This study investigates the plant growth–promoting traits in Burkholderia sp. Nafp2/4‐1b and its impacts on the nodulation of the legume Medicago sativa L. when co‐inoculated with Rhizobium spp. The findings provide baseline information in the development Burkholderia sp. Nafp2/4‐1b as a commercial inoculant for use in the sustainable production of essential crops.