Efficacious use of Micrococcus yunnanensis GKSM13 for the growth of rice seedlings under copper stress with elucidation into genomic traits

Rice is widely cultivated worldwide, and beneficial bactrial colonization are particularly desirable for sustainable agriculture because they promote growth and production by preventing excessive heavy metal contamination. The present study was conducted with the aim of improving the growth of rice seedlings (MTU1010 variety) under copper (Cu) stress by using Cu-tolerant plant growth promoting bacteria (PGPB) Micrococcus yunnanensis GKSM13. Strain GKSM13 was able to produce plant growth promoting factors (PGPFs) such as indole-3-acetic acid (IAA), gibberellin A3 (GA₃) and ammonia, accumulate proline, fix N₂, and inhibit 2,2-Diphenyl-1-picrylhydrazyl (DPPH). Rice seedlings treated with Cu²⁺ and co-inoculated with GKSM13 significantly improved their growth in morphological and biochemical aspects. When analysed by field emission scanning electron microscope (FE-SEM), GKSM13 was found to be associated with the root cells in the form of large number of coccoid cells. The uptake of Cu²⁺ in rice seedlings was reduced to 57.5% in the presence of GKSM13. Strain GKSM13 treatment also reduced Cu-induced oxidative stress of rice seedlings by activating antioxidant enzymes including superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APOX) and glutathione peroxidase (GPOX), which was supported by DPPH inhibition and reduction of malondialdehyde (MDA) accumulation. Insight into the genome of strain GKSM13 reveals the presence of tryptophan (trp), ent-kaurene, cyanase (cyn), phosphate-specific transport (pst), major facilitator superfamily transporter (MFS), sulphate transporter (cys), proline (pro) and SOD (sod) genes, which are responsible for promoting plant growth and alleviating Cu²⁺ stress. Therefore, the application of strain M. yunnanensis GKSM13 could provide a sustainable agricultural solution for Cu-affected mining areas.