Pseudonocardiaceae sp. TD-015 from the Thar Desert, India: Antimicrobial Activity and Identification of Antimicrobial Compounds

Background and objective: Isolate TD-015, obtained from the Thar Desert (India), was subjected to investigation for its antimicrobial activity and identification of the contributing compound(s). Method: TD-015 was isolated from the Thar Desert (India), identified by 16S rDNA sequencing and analyzed for the hyper-variable regions. Culture supernatant of TD-015 was tested for antimicrobial activity following organic solvents extraction of the metabolites. The bioactive compounds were extracted from the filtrate culture with ethyl acetate, purified and analyzed using thin layer chromatography and GC-MS procedures. In silico prediction of nearest identified compounds was carried out using the software Prediction of Activity of Spectra for Substances (PASS). Results: TD-015 was identified by 16S rDNA sequencing and analysis of variable region specific for members of Pseudonocardia. Based on 16S rDNA sequence data, isolate TD-015 was identified as belonging to the rare actinomycete genus Pseudonocardia with 91.86% similarity to Yuhushiella deserti. Analysis of the variable region showed that TD-015 was related to members of Pseudonocardiaceae, but formed a distinct clade. Aqueous and ethyl acetate extracts of culture supernatant showed antimicrobial activity against Staphylococcus epidermidis, Micrococcus luteus, Bacillus subtilis, Brevibacterium linens, Pseudomonas fluorescens and a clinical isolate of Escherichia coli (from urine). GC-MS data of the antimicrobial fractions showed nearest identity to two compounds, Dehydroabietic Acid (DHA) and Methyl Dehydroabietate (MD), which were predicted to have antimicrobial activity as per in silico analysis. However, combined analyses of the retention time (RT), similarity index (SI), mass ion spectra (MS) and retention indices (observed and calculated) of these two compounds suggests that they could be potentially novel. Conclusion: We conclude that understudied extreme habitats like Thar Desert continue to be important sources of novel actinomycetes and potential chemodiversity.