Biogeography, biodiversity, and barcodes: accounting for seagrass associated biodiversity along the South African coastline
Date
2022-04
Authors
Journal Title
Journal ISSN
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Publisher
Stellenbosch : Stellenbosch University
Abstract
ENGLISH ABSTRACT: Environmental DNA metabarcoding is gaining momentum for global biodiversity studies. Many studies
have demonstrated the ability of metabarcoding to characterize communities for biodiversity surveys,
biogeographical analyses, and impact assessments. However, few studies have been performed
along the complex coastline of South Africa, which is influenced by two current systems that shape
three highly diverse biogeographic regions (the subtropical and warm temperate regions on the east
coast, and cool temperate region on the west coast); especially in highly variable estuarine systems.
Given the important ecological and economic services that estuaries, their seagrasses and their
associated biodiversity provide, it is important that metabarcoding is assessed as a tool for
biodiversity studies in South African estuaries. Yet there are still many unknowns surrounding
metabarcoding in estuaries, such as the effect of sampling substrate choice on the communities
returned, and the ability of metabarcoding to capture biogeographical variation. As such, this study
aimed to investigate metabarcoding using a partial fragment of the mitochondrial cytochrome oxidase
1 (CO1) gene in six estuaries containing the seagrass, Zostera capensis, along the coastline of South
Africa, with two estuaries per biogeographic region. Broadly, this project compared the multicellular,
eukaryotic communities returned by different sampling substrates (water and three different sediment
samples, including intertidal vegetated and unvegetated sediments, and subtidal vegetated sediment).
There were some differences in community composition from water and sediment samples, likely due
to the different communities harboured by the environments. It was expected that sediment substrates
from different environments (intertidal and subtidal, and vegetated and unvegetated seagrass beds)
would also capture different communities, yet there was no difference between them, which may likely
reflect patchiness and insufficient sampling replication. This study further aimed to explore whether
eDNA metabarcoding would capture the biogeographical signals associated with the South African
coastline. Indeed, this approach was sufficient to detect variation in communities along the coastline
to delineate biogeographic regions. The communities returned by regions were significantly different,
with the strongest biogeographic differentiation between the east and west coast sites. Furthermore,
species richness was found to be greatest in the warm temperate region as has been shown by
previous studies. Finally, a redundancy analysis was used to explore the environmental variables that
could explain the variation in communities between regions, which showed that nitrate, mean sea
surface temperate and water quality were the three most powerful explanatory variables. In all, this
study showed that selection of sampling substrate is critical for determining community structuring,
and that overall metabarcoding is a useful tool to provide insights into biogeographical structuring of
communities.
AFRIKAANSE OPSOMMING: Geen opsomming beskikbaar.
AFRIKAANSE OPSOMMING: Geen opsomming beskikbaar.
Description
Thesis (MSc)--Stellenbosch University, 2022.
Keywords
Biodiversity -- South Africa, DNA metabarcoding, Seagrass, Biogeography -- South Africa, Sampling substrates, Cytochrome oxidase -- Genetic aspects, Mitochondrial DNA, UCTD