The diversity of polyketides in the South Atlantic and Southern Ocean

Abstract

Nature has long provided valuable pharmaceuticals, with many effective antibiotics originating from soil and plants. Yet, rising antibiotic resistance and repeated rediscovery of known compounds have redirected natural product drug discovery toward the ocean. Previous studies have shown that the extreme and oligotrophic environment substantially produce novel compounds. The significant pharmaceutical value of polyketides has sparked extensive research into their biosynthesis. The bulk of these studies have focused on the diversity of polyketides in an oligotrophic ocean, limited in iron and nitrogen, interpreting and understanding their role to the microbial community, by harnessing the available metagenomic tools. The knowledge deficit is especially true of South Atlantic Ocean (SAO) and Southern Ocean (SO), given that they are largely under sampled and pristine respectively. To reduce this knowledge deficit, we established a broad scale analysis of the SAO euphotic zone. We thereafter assessed the diversity of polyketide in the euphotic zone of SAO. We further assessed the role viruses play in the propagation of polyketides. The analysis was carried out using the contextualize approach designed due to the continuous increase of metadata in databases. We further assessed the efficacy of the approach. Our analysis revealed there is high diversity of polyketides in the euphotic zone of SAO, with the majority encoding arylpolyene pathway suggesting its role in photo-protection. Most of the identified polyketides had low similarity to known BGCs, suggesting substantial functional novelty. The result also suggested virus may be playing a role in the propagation of the abundant polyketide type. To elucidate the biosynthetic potential across the ocean depths, samples were taken from the epipelagic, mesopelagic and bathypelagic zones of the SO, in two seasons (Spring and Winter). Using metagenome-assembled genome approach, a total of 21 BGC types were recovered with at least 8 different types of BGC in each zone. The highest diversity was observed in the bathypelagic zones of the two seasons. We observed terpene and PUFA to be the most abundant in the environment and are thought to play important roles in the ecosystem function. Interestingly, we discovered SAR324 as the most biosynthetically diverse microbe in SO. Taken together, our findings substantially broaden insights regarding the diversity of polyketides in SAO and SO communities. We reveal how the continuous increase in metadata in databases can be harnessed for prospecting. These analyses demonstrate that the bathypelagic zone of SO harbours more diverse BGC types. The insights generated from the study provide an important basis for prospective researchers about the SAO and SO’s biosynthetic potentials and ability to produce different specialized metabolites in different zones. In addition, the MAGs generated will fill some phylogenetic gaps in the available genome collection, making them useful for inferring details about microbial phylogenetic relationships.