Department of Microbiology

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Browsing Department of Microbiology by browse.metadata.advisor "Bester, Elanna"

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    The effect of conventional herbicides, used for the control of alien vegetation on microbial communities within freshwater biofilms
    (Stellenbosch : Stellenbosch University, 2017-12) Van Wyk, Armand Jacobus; Jacobs, Karin; Slabbert, Etienne; Jacobs, Shayne Martin; Bester, Elanna; Stellenbosch University. Faculty of Science. Dept. of Microbiology.
    ENGLISH ABSTRACT: Freshwater streams in South Africa are heavily permeated with invasive plant species. These invasive plant species pose a major threat to native vegetations by competing for available ecosystem resources. A common method used for the removal of these species, is herbicide application. The overuse of these chemicals and the surface runoff into the nearby rivers, has become problematic. The effect of these chemicals on the freshwater biofilms, which consists of various microbial communities, is, however, still unknown. Microbial communities play an important role in the functioning of riparian ecosystems especially in biogeochemical cycling. Biofilms are mostly beneficial to their surrounding environment and the microbial communities change depending on the exposure to external factors. These factors are mostly abiotic factors and also include exposure to chemicals. These chemicals can either be harmful or beneficial to the microbial community. Some microbial species are able to break down these chemicals and utilise it as a nutrient source. In this study, the effect of three conventional herbicides, Springbok, Garlon and Plenum, on freshwater biofilms was investigated. The Berg River in the Western Cape was chosen based on the fact that it flows through herbicide applied zones. An optimized herbicide detection method using liquid chromatography coupled to mass spectrometry (LC-MS) was developed and used to determine the current levels of herbicide active ingredients present in the river system. A preliminary study was done to determine the effect of glyphosate on freshwater biofilms. This study showed that a significant microbial community shift occurs after the application of the herbicide. A physical disruption of the biofilm was also observed at the concentrations that were applied. In a follow-up study, river water collected from the Berg River which was used to set up a laboratory-scale artificial river system. Flow cells were used to cultivate the biofilms, using the river water as the natural inoculum. The biofilms were allowed to establish for 10 days after which the herbicide and the active ingredient were applied. The flow cells were then used for fluorescent microscopy and DNA extractions. Garlon, Plenum and Springbok were found to decrease the biofilm biomass significantly (p<0.05) for all treatments analysed. Finally, the DNA of the biofilm was extracted from the flow-cells using the standard DNA extraction protocol. The DNA was then used for PCR amplification with bacterial and fungal specific primers. Automated ribosomal intergenic spacer analysis (ARISA) primer sets were used. Significant shifts (p<0.05) were found for the herbicides, Springbok (glyphosate) and Plenum (fluroxypyr and picloram). The Shannon diversity index showed a decrease in diversity for both these treatments. This suggest that some species tend to dominate the biofilm because they can tolerate the environmental change. The hypothesis for this study which states that conventional herbicides influence the growth of microbial communities within freshwater biofilms, is not rejected. This is supported by the significant (p<0.05) decrease in biofilm biomass that was seen after herbicide application and also a microbial community shift occurred after herbicide application.