Bacterial natural product gene biomining in polar desert soils

• Main Author: Benaud, Nicole
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: UNSW, Sydney 2019
• Subjects: Genome; Antarctic bacteria; Natural products; Long-read sequencing; Polyketide synthase; Non-ribosomal peptide synthetase; Arctic; Antarctic; Antarc*; polar desert
• Online Access: http://hdl.handle.net/1959.4/64912; https://unsworks.unsw.edu.au/bitstreams/c6f936f0-cb7a-45f2-9afc-b917ae610c08/download; https://doi.org/10.26190/unsworks/21598

New antimicrobial agents are urgently required to address a global antibiotic resistance crisis. Natural products, biosynthesised through secondary metabolite pathways, remain at the forefront of drug discovery. Extreme environments are attractive targets for microbial biomining, due to their potential as reservoirs for novel metabolites. In polar regions, environmental conditions are some of Earth's most severe, and microbes dominate the biosphere. Moreover, arid polar soils comprise high relative abundances of Actinobacteria and Proteobacteria, prolific producers of natural products. This research had three main objectives: to identify polar soil bacterial communities with novel biosynthetic potential; to establish a culture collection of Antarctic isolates with demonstrated bioactive capabilities; and to perform whole genome sequencing (WGS) on biotechnologically promising isolates for biosynthetic gene cluster (BGC) mining. Third generation long-read PacBio sequencing was employed to survey > 200 Antarctic and high Arctic soils for non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) domain amplicons. Significant negative relationships were observed between natural product genes and soil fertility factors carbon, nitrogen and moisture. Sequences primarily aligned to domains encoding antifungal, antitumour and antimicrobial/surfactant compounds, but with low sequence similarity (< 70%) to known genes. Using novel culturing approaches, 19 bacterial genera across 4 phyla were isolated from Antarctic soils, including 32 Actinomycetales species. Extended oligotrophic incubation times were related to the recovery of novel and rare strains. In in situ antimicrobial assays, Streptomyces was the only genus to produce measurable activity. WGS was performed for 17 Antarctic isolates using PacBio technology. Genomes predominantly returned high-quality assemblies, and BGC analysis revealed an abundance of terpene, NRPS, PKS, bacteriocin and siderophore clusters, with minimal gene similarity (< ...