Karakum Desert: A Unique Source of Cultivable Novel and Rare Actinomycetes with a Remarkable Biosynthetic Potential

Abstract

A culture-based strategy was used to isolate and screen representative actinomycetes from six sampling sites in the Karakum Desert, Turkmenistan. A total of 459 actinomycete isolates were obtained using 16 selective media, and 270 representative strains were subjected to 16 S rRNA gene sequencing. Comparative 16 S rRNA gene sequence analyses on colour-group representatives led to their assignment to 17 genera with validly published names which included many isolates assigned to novel or putatively novel species including ones belonging to rare genera, such as Actinocorallia, Actinomadura, Jiangella and Nonomuraea. Mining of whole-genome sequences of 32 isolates which formed distinct lineages in phylogenomic trees revealed biosynthetic gene clusters predicted to encode for many novel specialized metabolites, notably antibiotics. The genomes of most of these isolates included genes associated with the promotion of plant growth while bioinformatic analyses of stress-related genes provided on insight into how filamentous actinomycetes have adapted to harsh environmental conditions in the Karakum Desert. This extensive bioprospecting campaign shows that the Karakum Desert is a unique source of novel, rare and gifted filamentous actinomycetes with the ability to synthesise new specialized metabolites needed to address key existential issues facing humankind, especially, the urgent need to find a new generation of therapeutic antibiotics to control multidrug-resistant microbial pathogens and compounds that protect and promote plant growth.