Background: New antimicrobial agents are urgently required to address a global antibiotic resistance crisis. Bacterial natural products (NPs), biosynthesised through secondary metabolite pathways, remain at the forefront of drug discovery. Actinobacteriota are important producers of NPs, and this ubiquitous soil phyla are remarkably dominant in the arid soils of Antarctica, where metabolic adaptations influence survival under extreme conditions. Biosynthetic gene clusters (BGCs) which encode NPs, are typically long and repetitious high G + C regions difficult to sequence with short-read technologies.
Methods: We sequenced 10 Antarctic soil Actinobacteriota from multi-genome libraries, employing the long-read PacBio platform to optimise capture of complete BGCs and facilitate a comprehensive analysis of their NP capacity. Comparative genome analysis was used to map BGC variation between closest related strains from geographically distant environments.
Results: Antarctic BGCs exhibited low similarity to known compound BGCs (av. 31%), with an abundance of terpene, non-ribosomal peptide and polyketide-encoding clusters. Similarities to BGCs encoding antitumour, antifungal, antibacterial and biosurfactant compounds were identified. Compared with their closest related genomes, two strains displayed the greatest biosynthetic differences, a Streptomyces finlayi strain cultured under psychrophilic conditions, and a 'rare' Actinobacteriota strain, Kribbella qitaiheensis. Phylogenetic analysis of BGC domain sequences indicated that short-read sequenced genomes are susceptible to inflated BGC counts, with comparative genomes displaying domains from the same BGC fragmented across multiple genomic regions.
Conclusion: These findings show the advantages of long-read sequencing for NP gene discovery, and indicate that cold-adapted and rare Actinobacteriota from Antarctic desert soils are excellent candidates for novel natural product bioprospecting.