Microbial biodiversity as an indicator of health : a focus on selected peatlands of the Southern Cape, South Africa

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.