© 2022, The Author(s), under exclusive licence to Springer Nature B.V.Abstract: An endophytic beneficial bacterium was isolated and characterized from in vitro grown microshoots of Fraser’s Photinia (Photinia × fraseri Dress.) in our previous studies. This bacterium, which is nominated as PGB_invit and determined as a member of Pseudorhodoplanes sp., has ability to fix nitrogen and produce plant growth promoting regulators such as indole acetic acid and gibberellic acid. Due to its beneficial traits, this specific bacterium promotes in vitro proliferation of Fraser’s Photinia microshoots and enables microshoots to be conserved at 25 ± 2ºC for up to 16 months without requiring periodic subculture. Thus, the aim of the study is to identify physiological, biochemical and molecular influences of this bacterium together with determination of its localization in plant tissues. Our results showed that the optimum inoculum concentration of PGB_invit is 106 cfu ml− 1 and the optimum incubation period is 60 days. Also, this study provides clear microscopic evidence of the endopyhtic bacterial colonization of GFP-labeled bacteria detected by confocal microscopy in Fraser’s Photinia. Proline content was significantly enhanced in response to bacterial treatment whereas cellular H2O2 content was decreased. An increase in catalase activity was also detected, indicating that the results were consistent with the decrease in H2O2 content. Moreover, RNA sequencing (RNA-Seq) was also used to assess gene expression patterns and differential expression of five genes (predicted “MID1-Complementing Activity 1”, Ubiquitin-conjugating enzyme E2, predicted “E3 ubiquitin-protein ligase RHA1B-like”, 4-coumarate–CoA ligase-like 9, and methionine aminopeptidase 2B-like) between active and inactive form of the bacterium was confirmed by qRT-PCR. Among them, ubiquitin-conjugating enzyme E2 and predicted “E3 ubiquitin-protein ligase RHA1B-like genes which play important roles in plant immunity and stress were down-regulated in plant samples inoculated with bacteria which may demostrate that PGB_invit does not evoke plant immune system and has a positive effect on reducing stress on Fraser’s Photinia. Key message: PGB_invit (Pseudorhodoplanes sp.) has a positive impact on plants growth and development with several mechanisms. Besides its shown that PGB_invit is not act as a stress factor, as it does not cause a severe oxidative stress and thus can be used as a biofertilizer.