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, LB32T, LB39T 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 LB32T and LB39T 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.

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

“…Genomes of members of the family Geodermatophilaceae isolated from extreme hyper-arid soils were relatively small (3.89-5.51 Mb) but contained a high proportion of genes related to environmental stress response including heat and cold shock responses, osmotic stress, carbon starvation and stress factors that give rise to reactive oxygen species [28,29,49]. Perhaps surprising is the high capacity of these bacteria to synthesis specialized metabolites, a feature also noted in novel species of Micromonospora isolated from extreme hyper-arid Lomas Bayas soil [52], the assumption being that competitive success in extreme, sparsely populated ecosystems might be more likely determined by stress resistance rather than by antibiosis. The genomes of all the Atacama actinobacteria included in Table 4 contained large numbers [35-46, 49, 52, 56-71] of biosynthetic gene clusters (BGCs), a fact that promises well for bioprospecting action.…”

Marine Sediment Recovered Salinispora sp. Inhibits the Growth of Emerging Bacterial Pathogens and other Multi-Drug-Resistant Bacteria

“…All media were prepared with artificial seawater (Instant Ocean, USA). These media have been used to characterize and isolate members of the family Micromonosporaceae ( Wiese et al 2008 ; Maldonado et al 2009 ; Maldonado and Quintana 2015 ; Carro et al 2019 ). Isolation plates were incubated at 30°C (IncuMax TM IC-320 Incubator, Amerex Instruments, Inc., USA) for at least eight weeks.…”

Biotechnological and Ecological Potential of Micromonospora provocatoris sp. nov., a Gifted Strain Isolated from the Challenger Deep of the Mariana Trench

“…Novel filamentous actinobacteria isolated from marine sediments are a prolific source of new specialized metabolites [ 1 , 2 , 3 ], as examplified by the discovery of the abyssomicins, a new family of polyketides [ 4 ] produced by Micromonospora (formerly Verrucosispora ) maris [ 5 ] and the proximicins, novel aminofuran antibiotics and anticancer compounds isolated from Micromonospora ( Verrucosispora ) fiedleri [ 6 , 7 ]. Novel micromonosporae have large genomes (6.1–7.9 Mbp) which contain strain, species and clade specific biosynthetic gene clusters (BGCs) with the potential to express new bioactives [ 8 , 9 , 10 ] needed to counter multi-drug resistant pathogens [ 11 ]. These developments provide an objective way of prioritizing novel micromonosporae for genome mining and natural product discovery [ 8 , 9 , 10 ].…”