Novel actinobacterial diversity in arid Atacama Desert soils as a source of new drug leads

Abstract

The search for new specialised metabolites, notably antibiotics, that can be developed for healthcare has steadily shifted towards the isolation and screening of rare and novel actinobacteria from extreme habitats on the premise that such habitats give rise to unique biodiversity that is the basis of novel chemistry. To this end, a taxonomic approach to bioprospecting for bioactive compounds was used to selectively isolate, dereplicate and classify actinobacteria from hyper-arid and extreme hyper-arid areas of the Atacama Desert in northwest Chile, namely from the Salar de Atacama and Yungay regions, respectively. Sample pretreatment and selective isolation strategies enabled the recovery of actinobacteria from each of these habitats and while population sizes were small, taxonomic diversity was high. Relatively large numbers of Amycolatopsis and Streptomyces strains were isolated from the hyper-arid Salar de Atacama soil, as were smaller numbers of Actinomadura, Kribbella, Lechevalieria, Nonomuraea and Saccharothrix strains. In contrast, Modestobacter and Streptomyces isolates predominated in the extreme hyper-arid Yungay soil, the latter also contained smaller numbers of Blastococcus, Couchioplanes, Geodermatophilus and Pseudonocardia strains. With few exceptions representatives of these genera formed distinct phyletic lines in 16S rRNA gene trees. Polyphasic studies carried out on strains of ecological and biotechnological interest showed that isolates assigned to the genera Modestobacter and Streptomyces belonged to putative new species, as exemplified by the proposal for Streptomyces leeuwenhoekii sp. nov. for strains that formed a distinct branch in the Streptomyces 16S rRNA gene tree. In contrast, representatives of the genus Amycolatopsis were assigned to known species, albeit ones classified in a rare taxon, the Amycolatopsis 16S rRNA gene clade. Most of the representative isolates examined in standard plug assays inhibited the growth of one or more of a panel of five wild type microorganisms. In addition, some of the representative streptomycetes from the hyper-arid Salar de Atacama soil were found to inhibit cell envelope, cell wall, fatty acid and RNA synthesis in assays based on the use of Bacillus subtilis reporter genes. The results of this project demonstrate for the first time that hyper-arid and extreme hyper-arid Atacama Desert soils are rich reservoirs of cultivable rare and novel actinobacteria with the capacity to produce a broad range of bioactive compounds that can be developed as drug leads for medicine. Indeed, microorganisms, unlike plants and animals, have overcome the prevailing harsh conditions of the Desert. Life abounds in the Atacama Desert, but most of it is microbial!