1 Vol.:(0123456789) Scientific RepoRtS | (2020) 10:14857 | https://doi.org/10.1038/s41598-020-71652-0 www.nature.com/scientificreports plant growth promoting rhizobacteria isolated from halophytes and drought‑tolerant plants: genomic characterisation and exploration of phyto‑benefcial traits Kleopatra Leontidou 1,7 , Savvas Genitsaris 2,3,7 , Anastasia Papadopoulou 1 , nathalie Kamou 1 , Irene Bosmali 4 , Theodora Matsi 5 , Panagiotis Madesis 4 , Despoina Vokou 3 , Katerina Karamanoli 1* & Ifgeneia Mellidou 1,6* Plant growth promoting rhizobacteria (PGPR) are able to provide cross‑protection against multiple stress factors and facilitate growth of their plant symbionts in many ways. the aim of this study was to isolate and characterize rhizobacterial strains under natural conditions, associated with naturally occurring representatives of wild plant species and a local tomato cultivar, growing in diferently stressed Mediterranean ecosystems. A total of 85 morphologically diferent rhizospheric strains were isolated; twenty‑fve exhibited multiple in vitro PGP‑associated traits, including phosphate solubilization, indole‑3‑acetic acid production, and 1‑aminocyclopropane‑1‑carboxylate deaminase activity. Whole genome analysis was applied to eight selected strains for their PGP potential and assigned seven strains to Gammaproteobacteria, and one to Bacteroidetes. The genomes harboured numerous genes involved in plant growth promotion and stress regulation. They also support the notion that the presence of gene clusters with potential PGP functions is afrmative but not necessary for a strain to promote plant growth under abiotic stress conditions. the selected strains were further tested for their ability to stimulate growth under stress. This initial screening led to the identifcation of some strains as potential PGPR for increasing crop production in a sustainable manner. Environmental stresses can severely injure the majority of plant species and are among the major constraints to plant growth and crop production worldwide 1–3 . Plants can actively engage microorganisms from the sur- rounding environment, whereas plant rhizosphere is considered as a hot-spot of microbial activity harboring a wide range of bacteria, many of them exerting positive efects on plants performance and stress resilience 4,5 . Te identifcation of rhizospheric bacterial strains with the potential of enhancing plant growth, denoted as Plant open 1 Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece. 2 International Hellenic University, 57001 Thermi, Greece. 3 Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece. 4 Institute of Applied Biosciences, CERTH, 57001 Thessaloniki, Greece. 5 Soil Science Laboratory, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece. 6 Institute of Plant Breeding and Genetic Resources, HAO, 57001 Thermi, Thessaloniki, Greece. 7 These authors contributed equally: Kleopatra Leontidou and Savvas Genitsaris. * email: katkar@agro.auth.gr; ifmellidou@gmail.com