Screening and Characterization of Soil Microbes Producing Antimicrobial Compounds in Makkah Province, Saudi Arabia

Abstract

This study aimed to investigate a method to manage antimicrobial resistance (AMR) issues by exploring soil microorganisms that are capable of producing bioactive compounds. Eight different types of soil were selected from three locations to screen, isolate, and identify microorganisms that are capable of producing antimicrobial compounds. The multi-drug resistant strains are Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, and Candida albicans were selected for primary and secondary screening using the crowded plate method and the agar well diffusion method. Inhibition zones were measured, and data were assessed using statistical tests to check for normality and differences between parametric variables and nonparametric data. This was followed by biochemical characterization, DNA isolation, and polymerase chain reaction (PCR). Molecular identification was performed using 16S rRNA amplification and sequencing. Here, 86 isolates containing bacteria and fungi were successfully extracted from soil samples. Further, 49 of 86 microbes showed possible antimicrobial activity, but only 12 isolates resulted in distinct inhibition zones with the selected multi-drug resistant strains. The following different taxa were identified: Firmicutes (nine strains), Proteobacteria (one strain), Actinobacteria (one strain), and Azotobacter (one strain). Species are represented in a phylogenetic tree, which was constructed using the unweighted pair-group method with arithmetic mean (UPGMA) method. The evolutionary distances were computed using the Maximum Composite Likelihood method. The identified microorganisms showed antimicrobial activity, confirming that soil microorganisms have great potential to address AMR issues.