Doctoral Degrees (Microbiology)

Permanent URI for this collection

https://scholar.sun.ac.za/handle/10019.1/3627

Browse

Browsing Doctoral Degrees (Microbiology) by browse.metadata.advisor "Botes, Marelize"

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    Antibiotic resistance in surface waters and biofilm-response to environmental contaminants
    (Stellenbosch : Stellenbosch University, 2021-12) Tucker, Keira; Wolfaardt, Gideon M.; Botes, Marelize; Feil, Edward; Stellenbosch University. Faculty of Science. Dept. of Microbiology.
    ENGLISH ABSTRACT: Ensuring water security for the future has become important due to rapid urbanisation and diminishing freshwater resources. South Africa’s water resources are scarce and as a result, reclamation of alternative freshwater resources such as treated wastewater is being investigated. There is growing evidence that drinking and wastewater treatment is either non- compliant to quality standards or lacking in certain communities. In areas with no infrastructure for wastewater removal, open sewers create a health risk for humans, animals, and the environment. Poor antimicrobial stewardship, over-use and incorrect disposal has led to increased resistance to antibiotics, rendering some bacterial infections untreatable. There is a concern that sub- inhibitory concentrations of antibiotics create a selection pressure that promotes horizontal gene transfer and emergence of bacterial communities that are resistant to antibiotics. Antibiotics, antibiotic resistant bacteria (ARB), as well as other contaminants that have been shown to promote antimicrobial resistance (AMR) such as heavy metals, enter surface waters and wastewater treatment works (WWTW) in trace concentrations via multiple pathways. As a result, WWTW are deemed hotspots for the emergence and dissemination of AMR. In addition, environmental waters are home to various matrices, including biofilms that are especially problematic in a clinical setting due to their antibiotic resistant and persistent nature. The research presented in this dissertation aimed to contribute to the knowledge surrounding the abundance of ARB in WWTW and surface waters in a South African context. Although ARB and antibiotic resistance genes (ARG) were detected in WWTW effluent, the abundance of both were reduced compared to the influent, suggesting that WWTW played a role in reducing AMR in receiving waters, while exposure to sub-inhibitory concentrations of antibiotics did not result in a significant change in the number of target ARG in isolates selected as representatives of a cultured population. This was emphasised in an expanded study that monitored various regions over a year. In addition, it was shown that surface waters, biofilms and sediments influenced by anthropogenic activities from residential and industrial sectors had higher prevalence of ARB compared to samples influenced by agricultural activity. Metagenomic analysis revealed that ARG relating to efflux pumps were the most common compared to those specific for target antibiotics. Due to heavy-metals and antibiotics being present in the environment in trace concentrations, exposure of mixed-community biofilms to sub-inhibitory concentrations of these contaminants was investigated. AMR in the biofilms did not increase, but it was suggested that the sub-inhibitory exposure promoted the development of persistent mixed community biofilms. Treatment interventions are crucial for removing pollutants and AMR already present in the environment. However, with due recognition of the complexity involved when considering humans, animals, the environment and a diverse pool of contaminants, this dissertation argues the need to expand the approach for mitigation of emergence or dissemination of AMR in the environment by incorporating greater emphasis on antibiotic stewardship, policies around antibiotic usage in all sectors, and overall public awareness.
  • Thumbnail Image
    Item
    Exploring a rumen-modelled carboxylate platform for the conversion of agricultural wastes to green chemicals and fuels in South Africa
    (Stellenbosch : Stellenbosch University, 2021-03) Njokweni, Sesethu Gift; Van Zyl, Willem Heber; Botes, Marelize; Stellenbosch University. Faculty of Science. Dept. of Microbiology.
    ENGLISH ABSTRACT: The notion of a “biobased economy” in the context of a developing country such as South Africa (SA) necessitates research and development of technologies that i) utilize sustainable feedstocks ii) have simple and robust operation iii) could work at small scale and iv) produces a variety of valuable bioproducts, fitting the biorefinery concept. One of the technologies that have been gaining increased global interest is the carboxylate platform based on ruminants. This platform uses mixed/undefined anaerobic co-cultures of rumen microorganisms to convert a variety of organic biomass to volatile fatty acids (VFA). VFA are short-chain fatty acids with two to four carbon atoms, which include acetic acid (C2), propionic acid (C3) and butyric acid (C4). These fatty acids have a wide variety of applications including the production of hydrocarbon fuels through electrolysis. Technological modelling has shown that each VFA corresponds to the production of a mixture of alkane hydrocarbons when using Kolbe electrolysis that may range from methane to octane depending on the average chain length and yield of alkyl groups in the produced VFA. Therefore, in order to produce higher alkanes, there is a need to produce VFA with higher yields of alkyl groups. In turn, these yields depend on a variety of operational aspects and input feedstocks used that need to be optimized to make the process economically feasible. Some of the operational challenges that need to be addressed include directing the microbiome into the desired products; Optimization of fermentation parameters and developing strategies for the preservation of the core microbiome involved in the production of the VFA. This study aimed to assess the feasibility of utilizing the ruminal carboxylate platform in SA to convert locally abundant sustainable organic feedstocks to VFA towards hydrocarbon fuel production. The study was separated into two research chapters: 1) Optimisation of the in-vitro anaerobic rumen fermentation conditions and selection of ideal SA organic waste products including fruit wastes (apple, grape and citrus pomace) and invasive plants (Prosopis juliflora) in terms of degradability, VFA yield and utility to serve as substrates for electrochemical conversion to hydrocarbons. 2) Examine the potential of preserving the core ruminal microbiome involved in VFA production using the two most common cryogenic agents (glycerol and dimethyl sulfoxide) and analyze population dynamics to determine any shifts using β-diversity distance metrics. It was shown that all organic waste products have the potential to serve as substrates for electrochemical conversion with citrus pomace showing the highest utility with 136 mM concentration of VFA (fractional yield of 0.52 out of a possible 0.75) and 12.16 mmol alkyl.g-1 present for conversion. Comparison of fresh rumen with glycerol preserved rumen showed Similarity index (β-diversity scale of 0 to 0.8, with 0.8 being the most diverse) with unweighted unifrac between the communities was 0.359 while the comparison of fresh rumen and DMSO cryo-preserved rumen was 0.250. This showed that both glycerol and DMSO cryo-preserved the rumen fluid without dramatic shifts in the community but the DMSO cryo-preserved community better resembled the core microbiome on the fresh rumen inoculum. This was further supported by analysis of VFA production and digestibility of pomace substrates with the preserved microbiome showing significantly similar yields to the fresh rumen inoculum. The results of this study further highlighted the potential of using a rumen-based carboxylate platform as a small-scale alternative towards biofuels production.