Antimicrobial activity of bacteria associated with the rhizosphere and phyllosphere of Avena fatua and Brachiaria reptans

Environmental pollution especially heavy metal-contaminated soils adversely affects the microbial communities associated with the rhizosphere and phyllosphere of plants growing in these areas. In the current study, we identified and characterized the rhizospheric and phyllospheric bacterial strains from Avena fatua and Brachiaria reptans with the potential for antimicrobial activity and heavy metal resistance. A total of 18 bacterial strains from the rhizosphere and phyllosphere of A. fatua and 19 bacterial strains from the rhizosphere and phyllosphere of B. reptans were identified based on 16S rRNA sequence analysis. Bacterial genera, including Bacillus, Staphylococcus, Pseudomonas, and Enterobacter were dominant in the rhizosphere and phyllosphere of A. fatua and Bacillus, Marinobacter, Pseudomonas, Enterobacter, and Kocuria, were the dominating bacterial genera from the rhizosphere and phyllosphere of B. reptans. Most of the bacterial strains were resistant to heavy metals (Cd, Pb, and Cr) and showed antimicrobial activity against different pathogenic bacterial strains. The whole-genome sequence analysis of Pseudomonas putida BR-PH17, a strain isolated from the phyllosphere of B. reptans, was performed by using the Illumina sequencing approach. The BR-PH17 genome contained a chromosome with a size of 5774330 bp and a plasmid DNA with 80360 bp. In this genome, about 5368 predicted protein-coding sequences with 5539 total genes, 22 rRNAs, and 75 tRNA genes were identified. Functional analysis of chromosomal and plasmid DNA revealed a variety of enzymes and proteins involved in antibiotic resistance and biodegradation of complex organic pollutants. These results indicated that bacterial strains identified in this study could be utilized for bioremediation of heavy metal-contaminated soils and as a novel source of antimicrobial drugs.