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Microbial biodiversity as an indicator of health : a focus on selected peatlands of the Southern Cape, South Africa
Author(s)
Weels, Shandre Sharnize Lavern
Date Issued
2022
Type
Thesis
Publisher
Cape Peninsula University of Technology
Abstract
South Africa has around 497 peatlands, 308 of which are located in KwaZulu-Natal (1% of the
global total). Compared to many peatlands found in the northern hemisphere, South African
peatlands are generally not of sphagnum-origin but are rather composed of the decaying
material of reeds, sedges, and grass. In the northern hemisphere extensive research has been
performed on the microbial diversity of peatlands, including actinobacterial diversity, and how
it is linked to the ‘health’ of the peatland. This study is the first of its kind in South Africa,
focusing on the microbial biodiversity associated with selected peatlands and how this can be
related to their health status.
In this study, we compared three different peatlands (with different health statuses) and looked
at their physicochemical and molecular data in order to assess their ‘health’ status. Peat
samples were collected from Vankervelsvlei (unimpacted and well-preserved peatlands),
Goukou River (impacted by agricultural wastewater and has exposed deposits), and
Springfield Farm (developing and impacted by agricultural wastewater). The physicochemical
analysis performed on the samples included measuring the pH, humification, loss-on-ignition
(LOI), and analysis of the major elements present in the samples. The molecular analysis
included terminal restriction fragment length polymorphism (T-RFLP) to look at bacterial
population similarity among the three sites, and next generation sequencing (NGS) to look at
the actinobacterial, and fungal diversity of the selected sites. In addition, selective isolation
techniques were applied in order to isolate and identify several actinobacterial strains from the
Vankervelsvlei and Goukou River samples.
As expected, the physicochemical data indicated that there were many similarities and
differences between the three selected sites, specifically Goukou River and the other two sites.
This is because Goukou River, similar to Vankervelsvlei is a well-developed peatland, but also
as is the case with Springfield Farm is affected by agricultural wastewater run-off which has
resulted in exposed peat deposits. The only similarity between Goukou River and
Vankervelsvlei was their pH levels, which were both acidic. While the pH of Springfield Farm
is basic. Humification, organic matter (OM), and elements including carbon (C), and nitrogen
(N), of Vankervelsvlei were high, while Goukou River and Vankervelsvlei had similar values.
The T-RFLP data showed that the microbial communities present in the three sites were
closely related, however different communities were found at different depths. A variety of
actinobacterial and fungal orders were detected in the different sites using NGS.
Actinobacteria such as the members of Acidimicrobiales, Actinomycetales and
Solirubrobacterales were abundant in Goukou River and Springfield Farm. Bifidobacteriales were abundant in Vankervelsvlei, whereas Micrococalles, Euzebyales, Nitriliruptorales, and
Rubrobacterales were only detected in Springfield Farm. BEST analysis (linking microbial
diversity patterns to environmental variables) showed that N, aluminium (Al), calcium (Ca),
phosphorus (P), and titanium (Ti) were the most significant physicochemical drivers of
actinobacterial community structure. Twenty-six actinobacterial strains were isolated and
identified from Goukou River and Vankervelsvlei, which included Nocardia africana,
Kitasatospora albolonga, and a variety of strains from the genus of Streptomyces. Fungi such
as Ascomycota and Basidiomycota are abundant in all three sites. However, Ascomycota are
abundant in Goukou River, Basidiomycota are abundant in Vankervelsvlei, while
Glomeromycota are abundant in Springfield Farm. BEST analysis confirmed that sulphur (S),
aluminium (Al), calcium (Ca), potassium (K), phosphor (P), titanium (Ti), silicon (Si),
magnesium (Mg), iron (Fe), humification, and pH were the environmental parameters that
affected the fungal communities the most. An overview of all the data obtained highlighted the
fact that the Vankervelsvlei peatland represented a ‘healthy’ peatland, having all the ‘typical’
features of an unimpacted peatland. Both the impacted (Goukou River) and the developing
(Springfield Farm) peatlands exhibited ‘typical’ features of ‘unhealthy’/impacted peatlands,
which is highlighted in the conclusion section of this thesis.
global total). Compared to many peatlands found in the northern hemisphere, South African
peatlands are generally not of sphagnum-origin but are rather composed of the decaying
material of reeds, sedges, and grass. In the northern hemisphere extensive research has been
performed on the microbial diversity of peatlands, including actinobacterial diversity, and how
it is linked to the ‘health’ of the peatland. This study is the first of its kind in South Africa,
focusing on the microbial biodiversity associated with selected peatlands and how this can be
related to their health status.
In this study, we compared three different peatlands (with different health statuses) and looked
at their physicochemical and molecular data in order to assess their ‘health’ status. Peat
samples were collected from Vankervelsvlei (unimpacted and well-preserved peatlands),
Goukou River (impacted by agricultural wastewater and has exposed deposits), and
Springfield Farm (developing and impacted by agricultural wastewater). The physicochemical
analysis performed on the samples included measuring the pH, humification, loss-on-ignition
(LOI), and analysis of the major elements present in the samples. The molecular analysis
included terminal restriction fragment length polymorphism (T-RFLP) to look at bacterial
population similarity among the three sites, and next generation sequencing (NGS) to look at
the actinobacterial, and fungal diversity of the selected sites. In addition, selective isolation
techniques were applied in order to isolate and identify several actinobacterial strains from the
Vankervelsvlei and Goukou River samples.
As expected, the physicochemical data indicated that there were many similarities and
differences between the three selected sites, specifically Goukou River and the other two sites.
This is because Goukou River, similar to Vankervelsvlei is a well-developed peatland, but also
as is the case with Springfield Farm is affected by agricultural wastewater run-off which has
resulted in exposed peat deposits. The only similarity between Goukou River and
Vankervelsvlei was their pH levels, which were both acidic. While the pH of Springfield Farm
is basic. Humification, organic matter (OM), and elements including carbon (C), and nitrogen
(N), of Vankervelsvlei were high, while Goukou River and Vankervelsvlei had similar values.
The T-RFLP data showed that the microbial communities present in the three sites were
closely related, however different communities were found at different depths. A variety of
actinobacterial and fungal orders were detected in the different sites using NGS.
Actinobacteria such as the members of Acidimicrobiales, Actinomycetales and
Solirubrobacterales were abundant in Goukou River and Springfield Farm. Bifidobacteriales were abundant in Vankervelsvlei, whereas Micrococalles, Euzebyales, Nitriliruptorales, and
Rubrobacterales were only detected in Springfield Farm. BEST analysis (linking microbial
diversity patterns to environmental variables) showed that N, aluminium (Al), calcium (Ca),
phosphorus (P), and titanium (Ti) were the most significant physicochemical drivers of
actinobacterial community structure. Twenty-six actinobacterial strains were isolated and
identified from Goukou River and Vankervelsvlei, which included Nocardia africana,
Kitasatospora albolonga, and a variety of strains from the genus of Streptomyces. Fungi such
as Ascomycota and Basidiomycota are abundant in all three sites. However, Ascomycota are
abundant in Goukou River, Basidiomycota are abundant in Vankervelsvlei, while
Glomeromycota are abundant in Springfield Farm. BEST analysis confirmed that sulphur (S),
aluminium (Al), calcium (Ca), potassium (K), phosphor (P), titanium (Ti), silicon (Si),
magnesium (Mg), iron (Fe), humification, and pH were the environmental parameters that
affected the fungal communities the most. An overview of all the data obtained highlighted the
fact that the Vankervelsvlei peatland represented a ‘healthy’ peatland, having all the ‘typical’
features of an unimpacted peatland. Both the impacted (Goukou River) and the developing
(Springfield Farm) peatlands exhibited ‘typical’ features of ‘unhealthy’/impacted peatlands,
which is highlighted in the conclusion section of this thesis.
Additional information
Thesis (Master of Environmental Health)--Cape Peninsula University of Technology, 2022
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