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Subantarctic Indian Ocean microbial gene duplications and their role in biogeochemical cycling
Dissertation (MSc (Genetics))--University of Pretoria, 2023.
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| Format: | Thesis |
| Language: | English |
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University of Pretoria
2023
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| _version_ | 1867613530842202112 |
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| access_status_str | Open Access |
| author2 | Makhalanyane, Thulani Peter |
| author_browse | Makhalanyane, Thulani Peter |
| author_facet | Makhalanyane, Thulani Peter |
| collection | Thesis |
| dc_rights_str_mv | © 2023 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. |
| description | Dissertation (MSc (Genetics))--University of Pretoria, 2023. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/91540 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:37:37.270Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | University of Pretoria |
| publisherStr | University of Pretoria |
| record_format | dspace |
| source_str | UPSpace — University of Pretoria Institutional Repository |
| spelling | oai:repository.up.ac.za:2263/91540 Subantarctic Indian Ocean microbial gene duplications and their role in biogeochemical cycling Makhalanyane, Thulani Peter u17035245@tuks.co.za Mogase, Oliver Fourie, Caitlyn Heather UCTD Marine microbiomes Biogeochemical cycling Subantarctic Indian Ocean Gene duplication Metagenomics Pangenome 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 2023-07-19T10:32:29Z 2023-07-19T10:32:29Z 2023-06 2023 Dissertation * S2023 http://hdl.handle.net/2263/91540 DOI: https://doi.org/10.25403/UPresearchdata.23690043.v1 10.25403/UPresearchdata.23690043 en © 2023 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. application/pdf application/pdf University of Pretoria |
| spellingShingle | UCTD Marine microbiomes Biogeochemical cycling Subantarctic Indian Ocean Gene duplication Metagenomics Pangenome Subantarctic Indian Ocean microbial gene duplications and their role in biogeochemical cycling |
| title | Subantarctic Indian Ocean microbial gene duplications and their role in biogeochemical cycling |
| title_full | Subantarctic Indian Ocean microbial gene duplications and their role in biogeochemical cycling |
| title_fullStr | Subantarctic Indian Ocean microbial gene duplications and their role in biogeochemical cycling |
| title_full_unstemmed | Subantarctic Indian Ocean microbial gene duplications and their role in biogeochemical cycling |
| title_short | Subantarctic Indian Ocean microbial gene duplications and their role in biogeochemical cycling |
| title_sort | subantarctic indian ocean microbial gene duplications and their role in biogeochemical cycling |
| topic | UCTD Marine microbiomes Biogeochemical cycling Subantarctic Indian Ocean Gene duplication Metagenomics Pangenome |
| url | http://hdl.handle.net/2263/91540 |