Exploring untapped potential of Streptomyces spp. in Gurbantunggut Desert by use of highly selective culture strategy

Streptomycetes have been, for over 70 years, one of the most abundant sources for the discovery of new antibiotics and clinic drugs. However, in recent decades, it has been more and more difficult to obtain new phylotypes of the genus Streptomyces by using conventional samples and culture strategies. In this study, we combined culture-dependent and culture-independent approaches to better explore the Streptomyces communities in desert sandy soils. Moreover, two different culture strategies termed Conventional Culture Procedure (CCP) and Streptomycetes Culture Procedure (SCP) were employed to evaluate the isolation efficiency of Streptomyces spp. with different intensities of selectivity. The 16S rRNA gene amplicon analysis revealed a very low abundance (0.04–0.37%, average 0.22%) of Streptomyces in all the desert samples, conversely the percentage of Streptomyces spp. obtained by the culture-dependent method was very high (5.20–39.57%, average 27.76%), especially in the rhizospheric sand soils (38.40–39.57%, average 38.99%). Meanwhile, a total of 1589 pure cultures were isolated successfully, dominated by Streptomyces (29.52%), Microvirga (8.06%) and Bacillus (7.68%). In addition, 400 potential new species were obtained, 48 of which belonged to the genus Streptomyces. More importantly, our study demonstrated the SCP strategy which had highly selectivity could greatly expand the number and phylotypes of Streptomyces spp. by almost 4-fold than CCP strategy. These results provide insights on the diversity investigation of desert Streptomyces, and it could be reference for researchers to bring more novel actinobacteria strains from the environment into culture.