Molecular Basis of Endophytic Bacillus megaterium-induced Growth Promotion in Arabidopsis thaliana: Revelation by Microarray-based Gene Expression Analysis

Black pepper root endophytic Bacillus megaterium BP17 (BmBP17) displayed excellent antagonistic activity against diverse plant pathogens. BmBP17 endophytically colonized plantlets of Arabidopsis with significant growth promotion as exemplified by increased root and shoot length. To elucidate the molecular basis of growth promotion, microarray-based gene expression profiling was performed on interactome of Arabidopsis-BmBP17. A total of 150 genes were found differentially expressed which represented 80 up-regulated and 70 down-regulated plant genes. Key up-regulated Arabidopsis genes were (i) NIR1, AMT1-5, TIP2-3, and SULTR1-2 participating in the transport of nutrients through transmembranes; (ii) SHV3, MMP, RLP44, PROPEP4, AGL42, SCPL30, ANAC010, and KNAT7 involved in cell organization, biogenesis, and transcription; (iii) SRO5, ANNAT7, and DDF1 associated with abiotic stress tolerance like salt stress and water deprivation; and (iv) MYB7, MYB4, MYB49, WRR4, ATHCHIB, and ATOSM34 involved in defense against biotic stress. Strikingly, most of the genes participating in growth and development were up-regulated in diverse plant tissues right from root to seed. The up-regulation of nutrient mobilization and uptake-related genes could be attributed to plant growth promotion. The regulation of endogenous population of BmBP17 could be due to the activation of biotic stress defense-associated genes. The bacterial colonization triggered down-regulation of genes coding for transcription factors of ethylene-responsive genes such as ERF5, ERF71, ERF104, ERF105, TEM1, and RAP2.6 and salicylic acid and jasmonic acid-responsive gene such as BAP1, SIB1, BT4, MKK9, and PLA2A. Our study showed that the plant growth promotion as observed in Arabidopsis thaliana Col 0 could be attributed to the up-regulation of nutrient uptake-associated genes and down-regulation of genes coding for transcription factors of ethylene-responsive genes.