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Using eDNA metabarcoding as a tool to account for underexplored mangrove and seagrass associated biodiversity in South African estuaries
Thesis (MSc)--Stellenbosch University, 2025.
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| Language: | English |
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Stellenbosch : Stellenbosch University
2025
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| _version_ | 1867614024626077696 |
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| access_status_str | Open Access |
| author | Rossouw, Emma |
| author2 | Peer, Nasreen |
| author_browse | Peer, Nasreen Rossouw, Emma |
| author_facet | Peer, Nasreen Rossouw, Emma |
| author_sort | Rossouw, Emma |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MSc)--Stellenbosch University, 2025. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/132457 |
| institution | Stellenbosch University (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:45:27.799Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/132457 Using eDNA metabarcoding as a tool to account for underexplored mangrove and seagrass associated biodiversity in South African estuaries Rossouw, Emma Peer, Nasreen Von der Heyden, Sophie Stellenbosch University. Faculty of Science. Dept. of Botany & Zoology. Estuaries -- South Africa -- Management Environmental monitoring -- Data processing Mangrove forests -- Ecology Seagrasses -- Habitat eDNA metabarcoding -- Data processing Mitochondrial DNA UCTD Thesis (MSc)--Stellenbosch University, 2025. Rossouw, E. 2025. Using eDNA metabarcoding as a tool to account for underexplored mangrove and seagrass associated biodiversity in South African estuaries. Unpublished masters thesis. Stellenbosch: Stellenbosch University [online]. Available: https://scholar.sun.ac.za/items/b8d0a20e-e946-4887-9a1c-2dc5840b61db ENGLISH ABSRACT: Globally, mangroves and seagrasses provide crucial ecosystem services underscored by diverse faunal communities. In South Africa, fragmented mangrove forests and patchy seagrass meadows often co-occur in estuarine systems, supporting rich, often endemic biodiversity that remains understudied. Given the degrading effects of anthropogenic pressures, there is an urgent need to document the spatial and temporal diversity in these habitats. Current survey methods are inefficient and costly, which prohibit the detection of contemporary species patterns and ecosystem changes. Metabarcoding of environmental DNA has the potential to overcome the challenges associated with surveying estuarine habitats but remains underutilized in South African coastal ecosystems. There is a scope to develop this as a tool within an African context. As such, this thesis aimed to contribute to the development of rapid, inexpensive, high resolution methods for monitoring and conservation of coastal vegetation in estuarine ecosystems and exploring the spatial and temporal ecology of understudied mangroves and seagrass in southern Africa. This was done by targeting ichthyofaunal communities using the MiFish metabarcoding assay, and mangrove-associated invertebrates using a partial fragment of the mitochondrial cytochrome oxidase I (COI) gene. Environmental DNA samples were collected in mangrove and seagrass habitats from three estuaries along the east coast of South Africa in February 2023. To capture temporal variation, the same mangrove habitats were re-sampled in August 2023. Broadly, eDNA metabarcoding detected a total of 324 operational taxonomic units (OTUs) representing a wide range of ichthyofaunal and invertebrate diversity. However, taxonomic resolution was low for both taxonomic groups (~15 % for fish and ~1 % for invertebrates resolved to species level), highlighting that many species are unaccounted for on global reference libraries. I report that aquatic eDNA samples detected 97 % of the total ichthyofaunal diversity, with only 3 % of the diversity exclusively detected in sedimentary eDNA samples. This suggest that aquatic rather than sedimentary eDNA is an efficient substrate to resolve ichthyofaunal diversity. Moreover, the ichthyofaunal eDNA signals detected from the cooccurring mangrove and seagrass habitats were homogeneous. This results likely reflecting the combined influence of water movement between these habitats, that were only separated by approximately 10 meters, and insufficient sampling replication. In contrast, the communities found in estuaries were significantly different from one another, highlighting the structured nature of ichthyofaunal communities across large spatial scales that span different biogeographical regions. This study further aimed to explore whether eDNA metabarcoding would be useful tool to capture invertebrate communities from mangrove habitats across space and time. Indeed, this approach was sufficient to detect variation in communities along the coast, demonstrating that a limited number of eDNA samples is required to showcase the unique biodiverse communities supported by estuaries. Furthermore, localised eDNA signals suggest that communities supported in co-occurring mangrove and seagrass habitats are unique. However, this result requires further investigation with more replication as highlighted by the temporal differences detected. While the drivers of temporal variation in estuarine invertebrate communities remain poorly understood, there were significant differences in diversity among invertebrates observed across different months. Overall, this thesis provides novel insights regarding mangrove and seagrass associated biodiversity while contributing to the standardisation and optimisation of eDNA metabarcoding as a monitoring tool in South Africa. The results suggest that a structured fine-scale sampling design together with long-term replication will recover diverse estuarine fauna. Importantly, this thesis showcases eDNA metabarcoding as a useful method to explore highly understudied ecosystems and uncover ecological knowledge gaps that are crucial to guide future research efforts. With growing reference libraries, eDNA metabarcoding studies can become foundational to support conservation and management of estuarine biodiversity. AFRIKAANSE OPSOMMING: Geen opsomming beskikbaar. Masters 2025-06-09T08:41:30Z 2025-06-09T08:41:30Z 2025-03 Thesis https://scholar.sun.ac.za/handle/10019.1/132457 en Stellenbosch University 116 pages : illustrations, maps application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Estuaries -- South Africa -- Management Environmental monitoring -- Data processing Mangrove forests -- Ecology Seagrasses -- Habitat eDNA metabarcoding -- Data processing Mitochondrial DNA UCTD Rossouw, Emma Using eDNA metabarcoding as a tool to account for underexplored mangrove and seagrass associated biodiversity in South African estuaries |
| title | Using eDNA metabarcoding as a tool to account for underexplored mangrove and seagrass associated biodiversity in South African estuaries |
| title_full | Using eDNA metabarcoding as a tool to account for underexplored mangrove and seagrass associated biodiversity in South African estuaries |
| title_fullStr | Using eDNA metabarcoding as a tool to account for underexplored mangrove and seagrass associated biodiversity in South African estuaries |
| title_full_unstemmed | Using eDNA metabarcoding as a tool to account for underexplored mangrove and seagrass associated biodiversity in South African estuaries |
| title_short | Using eDNA metabarcoding as a tool to account for underexplored mangrove and seagrass associated biodiversity in South African estuaries |
| title_sort | using edna metabarcoding as a tool to account for underexplored mangrove and seagrass associated biodiversity in south african estuaries |
| topic | Estuaries -- South Africa -- Management Environmental monitoring -- Data processing Mangrove forests -- Ecology Seagrasses -- Habitat eDNA metabarcoding -- Data processing Mitochondrial DNA UCTD |
| url | https://scholar.sun.ac.za/handle/10019.1/132457 |
| work_keys_str_mv | AT rossouwemma usingednametabarcodingasatooltoaccountforunderexploredmangroveandseagrassassociatedbiodiversityinsouthafricanestuaries |