Subantarctic Indian Ocean microbial gene duplications and their role in biogeochemical cycling

Dissertation (MSc (Genetics))--University of Pretoria, 2023.

The Southern Ocean represents an important carbon sink, and recent studies suggest that microbial communities contribute substantially to ecosystem functions via the biological pump. There is some evidence that microbial communities within the vicinity of the Prince Edward Islands (PEIs) are shaped by factors such as depth and the availability of nutrients. However, we lack a clear mechanistic understanding regarding the interplay between these environmental variables and their effects on microbial communities. Gene duplication is a known source of genetic variation in both macrofauna and microorganisms. Duplication events contribute to the evolution of genomes by providing additional genetic material for natural selection or neutral genetic drift to act on, causing evolution at a molecular level. Previous studies on suggest that gene duplications may be mechanisms used by microbial communities to adapt to extreme conditions. However, few studies have investigated gene duplications in marine microbiota, and we lack empirical insights regarding evolutionary dynamics. Little is known about the role gene duplication events play in biogeochemical cycling. There are no reports from the Southern Ocean focused on paralogs responsible for these cycles in critical locations such as the PEIs and surrounding waters. This thesis aims to examine the extent and potential function of gene duplicates in marine microbial communities from the subantarctic Indian Ocean (SIO), specifically in waters surrounding the PEIs. We lack insights regarding the factors that influence microbial communities in these locations, and even less regarding the factors influencing gene duplications in these environments. The extent and putative functions of gene duplications in these microbial communities was evaluated, using shotgun metagenomic approaches. These findings were correlated with extracellular enzymatic activity assays and nutrient analyses to determine the potential function of the paralogs, as well as the factors which determine their relative abundance. The results revealed several gene duplication events within the PEIs marine microbial communities. Duplications varied significantly (statistical test and P value) across eleven bacterial and archaeal phyla, where Proteobacteria, Actinobacteria and Verrucomicrobiota genomes showed the highest levels of duplications. Paralogs with the genomic potential for carbon, nitrogen, and phosphorous metabolism, as well as methanogenesis were observed in our data. Previous studies of the PEIs and surrounding waters have revealed the remarkable capacity for biogeochemical cycling in the region, and several mechanisms linked to the cycling of carbon and nitrogen. Our data suggests that gene paralogs may play an important role in mediating these cycles, as well as in the cycling of phosphorous in the SIO. This study provides the first insights regarding the extent of gene duplications in SIO microbial communities. The data provide insights regarding the factors which potentially influence the rate of gene duplication events in these environments. For the first time, we provide a clear understanding regarding the potential function of the gene paralogs observed in these microbial communities and their putative roles.

AtlantECO

National Research Foundation

Genetics

MSc (Genetics)

Unrestricted