Uncovering the potential of novel micromonosporae isolated from an extreme hyper-arid Atacama Desert soil

Abstract

The taxonomic status, biotechnological and ecological potential of several Micromonospora strains isolated from an extreme hyper arid Atacama Desert soil were determined. Initially, a polyphasic study was undertaken to clarify the taxonomic status of five micromonosporae, strains LB4, LB19, LB32^T, LB39^T and LB41, isolated from an extreme hyper-arid soil collected from one of the driest regions of the Atacama Desert. All of the isolates were found to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Micromonospora. Isolates LB32^T and LB39^T were distinguished from their nearest phylogenetic neighbours and proposed as new species, namely as Micromonospora arida sp. nov. and Micromonospora inaquosa sp. nov., respectively. Eluted methanol extracts of all of the isolates showed activity against a panel of bacterial and fungal indicator strains, notably against multi-drug resistant Klebsiella pneumoniae ATCC 700603 while isolates LB4 and LB41 showed pronounced anti-tumour activity against HepG2 cells. Draft genomes generated for the isolates revealed a rich source of novel biosynthetic gene clusters, some of which were unique to individual strains thereby opening up the prospect of selecting especially gifted micromonosporae for natural product discovery. Key stress-related genes detected in the genomes of all of the isolates provided an insight into how micromonosporae adapt to the harsh environmental conditions that prevail in extreme hyper-arid Atacama Desert soils.

Figure 1

Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showing relationships between the isolates and between them and closely related Micromonospora type strains. The numbers at the nodes indicate bootstrap values ≥50%. Asterisks indicate branches of the tree that were also recovered in the maximum-likelihood tree. Bar, 0.005 substitutions per nucleotide position.

Figure 2

Neighbour-joining phylogenetic tree based on multilocus sequence alignment of 16S rRNA, gyrB, rpoB, atpD, and recA gene sequences showing relationships between the isolates and between them and Micromonospora type strains. The numbers at the nodes are bootstrap support values when ≥50%. Asterisks indicate branches of the tree that were also recovered in the maximum-likelihood tree. Catellatospora koreensis DSM 44566^T was used as the outgroup. Bar, 0.02 substitutions per nucleotide position.

Figure 3

Biosynthetic gene clusters found in the genomes of isolates LB4, LB19, LB32^T, LB39^T, and LB41 using antiSMASH 4.0.