Biocontrol Potential of Rhizospheric Soil Bacteria, Including Streptomyces and Comamonas Species, Against Aflatoxigenic Aspergillus flavus

Abstract

After decades of extensive exploration of bioactive compounds from Streptomyces spp., the discovery of new bioactive chemicals from routinely studied strains has been declining progressively. To tackle this challenge, recent studies have focused on Actinobacteria from under-explored ecological niches with significant microbial diversity. The present study aimed to assess the possible antifungal activity of Streptomyces spp. isolated from rhizospheric soils of Karura Forest, Nairobi, Kenya, against Aspergillus flavus (A. flavus), a fungal species known to produce aflatoxin. A total of 236 bacteria were isolated through in vitro cultures and characterized using macroscopic, microscopic, and biochemical tests to identify Streptomyces-like isolates, which were identified by dry, powdery colonies, filamentous branching hyphae, aerial mycelia, and the formation of spore chains, with Gram staining carried out later on isolates advanced through dual culture screening for antifungal activity. Dual culture assays, with A. flavus grown alone as the negative control, were performed to select the promising candidates for further extraction, gas chromatography-mass spectrometry (GC-MS) metabolite profiling, and antifungal testing by the disc diffusion method against PBS and nystatin as the negative and positive controls, respectively. The selected isolates also underwent molecular identification by PCR amplification and Sanger sequencing of the 16S rRNA gene. The analysis revealed that 190 isolates exhibited Streptomyces-like characteristics. Dual culture assays revealed that certain isolates inhibited the mycelial growth of A. flavus, and GC-MS profiling of the corresponding extracts confirmed the presence of bioactive metabolite classes. The pellet crude extracts of the six selected isolates (SA18, SD102, SD109, SD110, SE143, and SE194), exhibited the highest antifungal efficacy, with inhibitory zones of up to 31.60 ± 2.80 mm, relative to the positive control (nystatin); five of the isolates belonged to the genus Streptomyces, while SE143 was identified as Comamonas. Supernatant extracts and crude filtrates revealed lower and more variable inhibition across most of the isolates. The present findings indicated that rhizosphere-derived Streptomyces and Comamonas isolates from Karura Forest are potential natural candidates for biological control of A. flavus.