Phenotypic and Genomic Analysis Deciphering Plant Growth Promotion and Oxidative Stress Alleviation of Stenotrophomonas sepilia ZH16 Isolated from Rice

A newly isolated Stenotrophomonas sepilia ZH16 from rice stems, highly resistant to oxidative stress in vitro, exhibited versatile plant-growth promoting activities including zinc and phosphate solubilization, production of extracellular polymeric substances (EPS) production, and indole-3-acetic acid (IAA) synthesis. Strain ZH16 also significantly promoted rice seedling growth in vivo in the pot experiments. To better understand the underlying mechanisms related to plant growth-promoting properties, the whole genome of strain ZH16 was sequenced and analyzed, yielding a circular chromosome of 4 533 553 bp with a G+C content of 66.5%, 4112 protein-coding sequences, 67 tRNAs, and 5 rRNAs. Both the 16S rRNA gene phylogeny and genome-based classification identified the isolate as Stenotrophomonas sepilia ZH16. Genome mining showed that S. sepilia ZH16 possessed an extensive set of genes responsible for phytohormone biosynthesis, solubilization of phosphate and zinc, fungal suppression, and EPS production, which contribute to plant growth promotion. Further analysis proved that the strain ZH16 was equipped with various genes encoding non-enzymatic and enzymatic antioxidants to withstand oxidative stress, among which glutathione and ergothioneine biosynthesis have not previously been reported in the genus Stenotrophomonas to date. This is the first report that sheds light on the plant growth-promoting potential of high oxidative stress tolerant S. sepilia, which lays the foundation to develop the bacterium as an inoculant biofertilizer beneficial for rice cultivation.