The main focus of this research was to study in detail the selected plant growth promoting bacteria (PGPR) from Bacillus group. PGPR have been described as possible solution to the negative effects of chemicals fertilizers experienced by human beings, other living organisms and the environment through reducing or replacing the use of chemical fertilizers and pesticides. The work aimed at finding plant promotion and plant protection activity of selected PGPR species. Different bioassays were performed in the laboratory and greenhouse to find if the selected bacteria promote plant growth and protect plants through inhibiting pathogens, or protect them during drought conditions. RNA sequencing technology was carried out to study gene expression regulation of a Bacillus atrophaeus UCMB-5137. The selected bacteria showed some plant growth promotion and protection abilities. Bacillus atrophaeus UCMB-5137 and Bacillus amyloliquefaciens ssp. plantarum UCMB-5007 actively promoted wheat growth. All strains showed some pathogen inhibition, while some strains induced drought tolerance abilities. Genes responsible for plant colonization of the Bacillus atrophaeus UCMB-5137 and transcription factors regulating gene expression were identified. This work will create a basis for the possible development of industrially potential biofertilizers and biopesticides for agricultural practices.