Rare taxa and dark microbial matter: novel bioactive actinobacteria abound in Atacama Desert soils

Abstract

An "in house" taxonomic approach to drug discovery led to the isolation of diverse actinobacteria from hyper-arid, extreme hyper-arid and very high altitude Atacama Desert soils. A high proportion of the isolates were assigned to novel taxa, with many showing activity in standard antimicrobial plug assays. The application of more advanced taxonomic and screening strategies showed that strains classified as novel species of Lentzea and Streptomyces synthesised new specialised metabolites thereby underpinning the premise that the extreme abiotic conditions in the Atacama Desert favour the development of a unique actinobacterial diversity which is the basis of novel chemistry. Complementary metagenomic analyses showed that the soils encompassed an astonishing degree of actinobacterial 'dark matter', while rank-abundance analyses showed them to be highly diverse habitats mainly composed of rare taxa that have not been recovered using culture-dependent methods. The implications of these pioneering studies on future bioprospecting campaigns are discussed.

Extreme environments: microbiology leading to specialized metabolites

“…In particular, there are good reasons for believing that extremophilic and extremotolerant micro‐organisms will have pride of place in the provision of a new generation of clinically significant drugs thereby preventing a return to preantibiotic days of medicine. However, the success of future bioprospecting campaigns will depend upon access to extreme biomes, notably ones like the Atacama Desert, that are known to be reservoirs of gifted micro‐organisms, especially Actinobacteria and Cyanobacteria (Bull et al ; Goodfellow et al ; Bull and Goodfellow ). However, extreme habitats by their very nature are fragile and hence vulnerable to human activities such as mining and to climate breakdown, as shown by the decimation of microbial communities in hyperarid core areas in the Atacama Desert due to unprecedented rain (Azua‐Bustos et al ) and the melting of permafrost soils (Mackelprang et al ; Hultman et al ).…”

“…The recent discovery that filamentous actinobacteria with large genomes contain many NP‐biosynthetic gene clusters (NP‐BGCs) which express for unknown drug leads partly accounts for the increased focus on these micro‐organisms in bioprospecting campaigns (Bull and Goodfellow ). Especially gifted actinobacteria that have moderate or large genomes (~5·0–7·9 and >8·0 MB respectively) harbour many NP‐BGCs (20–19 and >30 respectively) (Baltz , ; Nouioui et al ) are at the premium in the search for new chemical leads using state‐of‐art‐technologies, such as genome mining (Harvey et al ; Goodfellow et al ). Other micro‐organisms with large genomes laden with NP‐BGCs include cyanobacteria (Vijayakumar and Menakha ), ktedonobacteria (Zheng et al ), myxobacteria (Hoffmann et al ) and fungi (Keller et al ).…”

Dark, rare and inspirational microbial matter in the extremobiosphere: 16 000 m of bioprospecting campaigns

“…The main efforts of our arid biome prospecting have focused on the Atacama Desert where actinobacteria are a dominant taxon in many habitats including those defined as extreme hyper-arid. Culture-based surveys of recent years have reported members of over 23 validly named genera and many new and putatively new species have been highlighted including ones belonging to the poorly studied genera Actinomadura, Cryptosporangium, Kribbela, Nonomuraea, Pseudonocardia and Saccharothrix [26,27]. However, it is only from the results of metagenomic surveys that the spectacular extent of actinobacterial diversity in Atacama habitats has been fully recognised [28,29].…”

Streptomyces spp. From the Marine Sponge Antho dichotoma: Analyses of Secondary Metabolite Biosynthesis Gene Clusters and Some of Their Products

“…Streptomyces are Gram-positive GC rich bacteria of the order Actinomycetales that are ubiquitous in nature and can be isolated from a variety of sources, including terrestrial (soil, insects, animals and plants), as well as marine (sediments, fish, corals and sponges) habitats (Goodfellow et al, 2018;Subramani and Sipkema, 2019). These bacteria remain of significant interest in terms of discovery of biologically active secondary metabolites that can potentially be developed into human medicines such as antimicrobial and anticancer agents, immunosuppressants etc.…”