Spore forming Actinobacterial diversity of Cholistan Desert Pakistan: Polyphasic taxonomy, antimicrobial potential and chemical profiling

Abstract

Background: Actinobacteria are famous for the production of unique secondary metabolites that help in controlling the continuously emerging drug resistance all over the globe. This study aimed at the investigation of an extreme environment the Cholistan desert, located in southern Punjab, Pakistan, for actinobacterial diversity and their activity against methicillin resistant Staphylococcus aureus (MRSA). The Cholistan desert is a sub-tropical and arid ecosystem with harsh environment, limited rainfall and low humidity. The 20 soil and sand samples were collected from different locations in the desert and the actinobacterial strains were selectively isolated. The isolated strains were identified using a polyphasic taxonomic approach including morphological, biochemical, physiological characterization, scanning electron microscopy (SEM) and by 16S rRNA gene sequencing.

Results: A total of 110 desert actinobacterial strains were recovered, which were found to be belonging to 3 different families of the order Actinomycetales, including the family Streptomycetaceae, family Pseudonocardiaceae and the family Micrococcaceae. The most frequently isolated genus was Streptomyces along with the genera Pseudonocardia and Arthrobacter. The isolated strains exhibited promising antimicrobial activity against methicillin resistant Staphylococcus aureus (MRSA) with zone of inhibition in the range of 9-32 mm in antimicrobial screening assays. The chemical profiling by thin layer chromatography, HPLC-UV/Vis and LC-MS analysis depicted the presence of different structural classes of antibiotics.

Conclusion: The study revealed that Cholistan desert harbors immense actinobacterial diversity and most of the strains produce structurally diverse bioactive secondary metabolites, which are a promising source of novel antimicrobial drug candidates.

Keywords: 16S rRNA gene sequencing; Actinobacterial diversity; Cholistan desert; MRSA; Polyphasic taxonomy; Scanning electron microscopy (SEM).

Fig. 1

GIS Location map of Cholistan desert Pakistan, Islam et al. [1], (Map used with permission)

Fig. 2

Scanning electron microscope images of Cholistan desert actinobacteria under different magnifications: Strain AFD1 (a) 10.0 kx, (b) 25.0 kx; Strain AFD7 (c) 20.0 kx, (d) 25.0 kx; Strain AFD8 (e) 10.0 kx, (f) 25.0 kx; Strain AFD16 (g) 10.0 kx, (h) 20.0 kx; Strain AFD19 (i) 5.0 kx (j) 40.0 kx; Strain AFD26 (k) 10.0 kx (l) 50.0 kx

Fig. 3

Molecular Phylogenetic analysis by Neighbor Joining method. The tree showing the interrelationships of isolated actinobacterial strains along with their closely related taxa belonging to Streptomyces, Saccharothrix and Arthrobacter inferred from 16S rRNA gene sequence. Data with gaps were removed after alignment by CLUSTAL W. The rooted tree was constructed using Neighbor Joining method. The analysis involved 49 nucleotide sequences. Codon positions included were 1st + 2nd + 3rd + Noncoding. There were a total of 254 positions in the final dataset. Evolutionary analyses were conducted in MEGA6

Fig. 4

HPLC/UV analyses of the crude extracts produced by the actinobacterial strains AFD2, AFD4 and AFD7 (Detection wavelength 254 nm). For the full-expended versions of this figure, see Supplementary Information, Additional files 6, 8 and 7 (Figure S3, S5 and S7)