Antimicrobial potential of the endophytic actinobacteria isolated from Harpagophytum procumbens: A southern African medicinal plant

Endophytic actinobacteria associated with ethnobotanical medicinal plants are key reservoirs for the discovery of novel biomolecules and enzyme activities. The knowledge of such endophytic actinobacteria in the Southern Africa arid regions remains scanty. This study was designed to isolate and investigate the antimicrobial activity and determine the taxonomic diversity of endophytic actinobacteria from the Devil's claw (Harpagophytum procumbens), a well-known Kalahari Desert plant with indigenous pharmaceutical uses. The antimicrobial activity was evaluated using perpendicular screening, culture filtrate extracts disk diffusion and minimum inhibitory concentration (MIC) methods. Amongst the various extracts (ethyl acetate, chloroform and methanol) tested, ethyl acetate disc diffusion fraction exhibited a broad-spectrum antimicrobial activity against test organisms and significantly higher zone of inhibition and lower MIC values (p = 0.000) as compared to other extracts. Further, greater inhibitory activities against gram-negative than gram-positive bacteria were observed. Antimicrobial analysis coupled with the results of amplifying gene clusters coding for polyketide synthetase I (PKS-I) and nonribosomal peptide synthetase (NRPS) demonstrated a significant broad-spectrum potential against all the test organisms except C. albicans. The subsequent 16S rRNA gene partial sequence analysis of the 23 isolates revealed 6 families affiliated to 7 genera that included the dominant Streptomyces genus (53%) whereas rare genera (Agromyces, Nocardiopsis, Rubrobacter, Patulibacter, Rhodococcus, Curtobacterium) and 3 unidentified strains accounted for 43%. A total of 23 volatile compounds were identified in the three extracts using gas chromatography – mass spectrometry (GC–MS). Extracts B12, B44 and A65 contained 10, 9 and 14 compounds, respectively. These volatile compounds include long chain alkanes, alkenes/alcohols, esters and amides. This study suggests that the endophytic actinobacteria isolated from H. procumbens are diverse and promising sources of bioactive antimicrobial compounds.