Utilising metagenomics to investigate presumptive novel actinomycete spp. isolated from the Great Salt Plains, Oklahoma

Actinomycetes have historically provided mankind with secondary metabolites that have led to the development of the majority of our antimicrobial agents, with Rifampicin and Streptomycin to name a few. The increased requirement for the discovery of new therapeutic and commercially significant antimicrobial agents has stimulated the need for the selective isolation of novel actinomycetes. In the present study, the 645 isolates (previously obtained from soil environments within the Great Salt Plains) were subjected to BOX PCR (a repetitive sequence-based polymerase chain reaction) to group isolates according to strain differentiation, where 58 isolates were shown to be of interest within 10 distinct clades. The strains were evaluated for their ability to produce bioactive compounds against known pathogens using a modified agar plug diffusion assay.

The 58 dereplicated isolates were subjected to 16S rRNA gene sequencing to ascertain their identity and novelty within the taxonomic family, Actinomycetales. Results included singular isolates of Rhodococcus, Micromonospera, Microbacterium, Sphingomonas and Pseudomonas with the majority being Streptomyces. The resulting phylogenetic tree showed that 18 of the 53 Streptomyces isolated were presumptive novel isolates as the percentage similarity was below 98.65 but also where they branched on the tree. The pH and salt tolerance of these presumptive novel isolates were tested at pH7, pH8 and pH9 with potassium chloride and sodium chloride ranging from 0% to 15%. It was evident that some of the presumptive novel isolates tolerated a higher potassium content (up to 15%) than sodium content (up to 11%).