In southern Africa, the connections between climate and the water–energy–food nexus are strong. Physical and socioeconomic exposure to climate is high in many areas and in crucial economic sectors. Spatial interdependence is also high, driven, for example, by the regional extent of many climate anomalies and river basins and aquifers that span national boundaries. There is now strong evidence of the effects of individual climate anomalies, but associations between national rainfall and gross domestic product and crop production remain relatively weak. The majority of climate models project decreases in annual precipitation for southern Africa, typically by as much as 20% by the 2080s. Impact models suggest these changes would propagate into reduced water availability and crop yields. Recognition of spatial and sectoral interdependencies should inform policies, institutions and investments for enhancing water, energy and food security. Three key political and economic instruments could be strengthened for this purpose: the Southern African Development Community, the Southern African Power Pool and trade of agricultural products amounting to significant transfers of embedded water. | This work was supported by the following Belmont Forum members: US National Science Foundation (grant number 1342742), UK Natural Environment Research Council (grant number NE/L008785/1) and the South Africa National Research Foundation (grant number 86975), according to each agency’s policies. T.K. and K.L. are funded, through IRI THESys, by the German Excellence Initiative. IFPRI’s contribution is under the CGIAR Research Program on Water, Land and Ecosystems. | http://www.nature.com/nclimate | hb2016 | Geography, Geoinformatics and Meteorology

Notwithstanding the dispersed nature of the water, energy and food (WEF) nexus scholarship in the African continent, its strategic importance to the African agenda has gained widespread attention in research and planning circles. In this regard, the bibliometric science mapping and content analysis of the WEF nexus scientific publication trends, the conceptual, intellectual and social structures, as well as the inherent paradigmatic shifts in the WEF nexus body of knowledge in the African continent have been undertaken, using the nexus body of literature accessed from the Web of Science and Scopus core collection databases. The review results confirmed that, whilst the WEF nexus scholarship has expanded since 2013, there is also evidence of growth in the conceptual, intellectual and social structures of the WEF nexus in the African continent. These shifts have resulted in the emergence of hot topics (subfields) including modelling and optimization, climate variability and change, environmental ecosystem services sustainability, and sustainable development and livelihoods. The review further determined that these structures have evolved along two main perspectives of WEF nexus research development, i.e., the interdisciplinary and transdisciplinary domains. In support of the interpretation of the visual analytics of the intellectual structure and changing patterns of the WEF nexus research, the shifts in positivist, interpretivist and pragmatic paradigmatic perspectives (these are underpinned by the ontology, epistemology, and methodology and methods) are considered when explaining WEF nexus research shifts: (a) From the unconnected silo paradigms that focus on water, energy and food (security concerns) to interconnected (and sometimes interdependent or nested) linkages or systems incorporating environmental, social-economic and political drivers (also viewed as subfields) in a bid to holistically support the Sustainable Development Goals (SDGs) across the African continent; and (b) in the evaluation of the WEF nexus scholarship based on novel analytical approaches. We contend that whilst the theories of science change underpin this apparent expansion, the macro-economic theory will find use in explaining how the WEF nexus research agenda is negotiated and the Integrative Environmental Governance (IEG) is the duly suited governance theory to bridge the inherent disconnect between WEF nexus output and governance processes uncovered in the literature. Overall, operational challenges and opportunities of the WEF nexus abound, transitioning the WEF nexus research to practice in Africa, motivating the need to take advantage of the scholar–practitioner research underpinnings, as contemplated in the transdisciplinary research approach, which is characterised by the dual quest for new knowledge and considerations of use. Yet, there is need for more coordinated and collaborative research to achieve impact and transition from WEF nexus thinking to WEF nexus practice. | The Water Research Commission of South Africa. The APC was funded by the University of KwaZulu-Natal’s Centre for Transformative Agricultural and Food Systems. | https://www.mdpi.com/journal/sustainability | dm2022 | Geography, Geoinformatics and Meteorology | School of Health Systems and Public Health (SHSPH)

Promoting household food security and reducing malnutrition rates of a growing population with the same amount of water is a challenge facing South African nutritionists and agriculturalists alike. Apart from non-food related effects of agriculture in general, the crop and livestock production practices of the South African smallholder farmer may have nutritional implications, primarily when practised on residential land and resulting in home consumption. Yet, few studies have systematically investigated the impact thereof. It appears that crop diversification, gender issues and nutrition education are among the important factors that strengthen the link between agriculture and nutrition. Since food production is the most water-intensive activity in society, nutritional water productivity (i.e. nutrition per volume water) of foods and the nutritional water footprint of diets should be investigated in order to achieve a sustainable solution. This implies that both the demand for a diet consisting predominantly of water-productive plant products, as well as the supply thereof, be addressed.

Dissertation (MSc (Microbiology))--University of Pretoria, 2007. | A total of 94 Salmonella isolates were collected from three catchments areas in Eritrea. These isolates were recovered from clinical and environmental sources. Biochemical tests using gelatin hydrolysis and tartrate utilization test were employed to differentiate between Salmonellasubspecies. All Salmonellaisolates were identified as Salmonellasubspecies I and were then subjected to molecular characterization. Polymerase chain reaction (PCR) and amplified fragment length polymorphism (AFLP) were employed to identify and establish possible relationships between the clinical isolates and environmental sources. Two sets of oligonucleotide primers specific for genes from S. Typhimurium and S. Enteritidis were used for the PCR reaction. Of the 94 Salmonellaisolates characterized only 6 were S. Typhimurium strains. To type the Salmonellaisolates AFLP was used. Clustering the AFLP patterns using the un-weighed pair-group method using arithmetic means (UPGMA) revealed 15 clusters. Of the 94 Salmonellaisolates collected, 48 (51%) strains were serologically identified. These serotypes include, 21 SalmonellaEmek (43.7%), 19 SalmonellaHeidelberg (39.5%), 7 of the 13, 22, 23; z undetermined serotype (14.5%), and 2 SalmonellaTyphimurium strains (4.1%). The AFLP data in the present study indicated a possible relationship between the clinical isolates and those obtained from environmental sources. | Microbiology and Plant Pathology | unrestricted

Masters Degree. University of KwaZulu-Natal, Pietermaritzburg. | Urban farming, in its small scale comprises of various production systems and practices that can lead to poor soil conditions, water pollution and the extension of climate change impacts. Moreover, smallholder farmers are in turn challenged by climate change impacts including heavy rainfall, high temperatures, hailstorms and pests exacerbated by the lack of knowledge, institutional support, governance framework, limited financial resources and technology. As a result, farmers are vulnerable to urban farming and environmental risks that affect the farmers’ food and nutrition security. On the other hand, if done well, urban farming (UF) can benefit the urban environment through flood water mitigation, water infiltration and greening of the environment, while improving food security. The study was conducted in the communities of Sobantu, Sweetwaters and Mpophomeni, in KwaZulu-Natal. This study employed a mixedmethods research approach, which combines quantitative and qualitative analysis. The quantitative approach used a survey questionnaire to elicit responses from 78 urban and periurban smallholder farmers who were purposefully selected to participate in the study. Focus group discussions and field observations were used to collect in-depth qualitative data about the challenges urban farmers faced in urban farming. Additionally, the logit regression model was used to identify factors that influence the farmers adoption of urban farming management practices. The study revealed that the majority of the farmers were faced with environmental problems including poor soil conditions, water quality and access problems and climate change impacts, of which had an impact on crop yield and farm profit. Furthermore, results showed that 69.2% of farmers were aware of the environmental implications of urban farming. However, it was found that due to the farmers limited financial resources, farmers identified urban farming mainly as a source of income and a strategy to obtain extra food and less for the benefit of the environment. The study found that market availability (p=0.003), training on soil management (p=0.0011) and access to credit (p=0.097) were significant factors in the adoption of urban farming practices. The study further revealed that the farmers adoption of urban farming and water quality management practices were challenged by socio-economic and institutional factors such as the lack of knowledge, farmer training, access to markets, access to credit and poor extension support. An environmental management framework was provided to address the challenges that hinder the smallholder farmers adoption of urban farming and water quality management practices. | Authour's Keywords: urban farming, environmental management, food security, climate change impacts.

Thesis (MScFoodSc)--Stellenbosch University, 2024. | ENGLISH ABSTRACT: To investigate Ultraviolet (UV) irradiation as an effective disinfection method for irrigation water irrespective of microbiological recovery, several studies were conducted. These studies monitored the recovery of bacteria following various UV doses, two UV sources and diverse water matrixes. From these studies it was found that river water in the Western Cape used for irrigation have higher Escherichia coli (E. coli) counts than recommended in the South African irrigation water guidelines. This could lead to fresh produce contamination if not addressed at farm level before use. Although UV has been identified as a potential disinfection method to be applied to irrigation water before use, its constant efficacy is still being questioned in practice. The aim of this study was to investigate the survival potential of food pathogens in river water with varying physico-chemical characteristics after UV-C irradiation treatment to improve the safety of fresh produce. The first research chapter (chapter 3), concentrated on optimising the recovery experimental design and determining the influence of water matrix on the survival of L. monocytogenes, Salmonella spp. and E. coli strains. This was done by measuring the low-pressure UV dose response and recovery under light and dark conditions by way of colony count comparisons. Findings indicate that the physico-chemical characteristics (Ultraviolet transmission percentage (UVT%), total suspended solids (TSS), total dissolved solids (TDS) and turbidity) that influence light penetration negatively, influence UV disinfection efficacy and recovery potential of bacteria negatively. S. enterica indicated a higher recovery potential than E. coli and therefore E. coli should not be used as the only indicator of UV disinfection efficacy. Applying a higher UV dose (60 mJ.cmˉ²) did however prove the ability to overcome the challenges posed by bacterium types with higher UV resistance and changing physico-chemical characteristics of the water matrix to an extent when utilising a low-pressure UV collimated beam device. The second research chapter (chapter 4) employed a deoxyribonucleic acid (DNA) dye molecular investigation to distinguish whether the increase in colony counts ensuing the recovery period was due to active cells multiplying, viable but non-culturable (VBNC) cells resuscitating and reproducing, or DNA damage being repaired and consequent cell replication taking place. DNA recovery could not be confirmed via Hoechst dye staining and fluorescence intensity measurements by means of spectrofluorometry. The colony counts observed for these same bacterial strains succeeding the recovery period, could possibly be assigned to VBNC cells that resuscitate once placed in the ideal growth environment as is the case with plate count methods. The third research chapter (chapter 5) focussed on practically implementing UV irradiation on larger volumes (1 000L) of river water used for irrigation purposes by treatment in a medium-pressure UV disinfection pilot plant. The results pointed toward medium pressure UV being more effective at reducing bacteria in raw river water, but allows more recovery to take place, than low pressure UV. By increasing the UV dose administered by the medium pressure UV source, the recovery of bacteria was decreased substantially. Surviving bacteria were identified to be opportunistic pathogens which could still pose a health risk. Overall, it was recognized from this study that a higher UV dose (60 mJ.cmˉ²) can overcome the challenges posed by low water quality. Salmonella spp. indicated a higher potential for UV resistance and opportunistic pathogens found in bacterial communities are more likely to survive UV-C treatment. Medium pressure UV decreased the bacterial populations significantly and therefore could still be utilised as part of a hurdle strategy to improve the safety of irrigation water from contaminated river sources. | AFRIKAANSE OPSOMMING: Ten einde UV-bestraling as 'n effektiewe ontsmettingsmetode vir besproeiingswater te ondersoek, ongeag mikrobiologiese herstel, is verskeie studies uitgevoer. Hierdie studies het die herstel van bakterieë gemonitor na verskeie UV-doserings, twee UV-bronne en diverse watermatrikse. Uit hierdie studies is gevind dat rivierwater in die Wes-Kaap wat vir besproeiing gebruik word, hoër Escherichia coli (E. coli) tellings het as wat in die Suid-Afrikaanse besproeiingswaterriglyne aanbeveel word. Dit kan lei tot besmetting van vars produkte indien dit nie voor gebruik op die plaas aangespreek word nie. Alhoewel UV geïdentifiseer is as 'n potensiële ontsmettingsmetode om voor gebruik op besproeiingswater toegepas te word, word die konstante doeltreffendheid daarvan steeds in die praktyk bevraagteken. Die doel van hierdie studie was om die oorlewingspotensiaal van voedselpatogene in rivierwater met wisselende fisies-chemiese eienskappe na UV- C bestralingsbehandeling te ondersoek om die veiligheid van vars produkte te verbeter. Die eerste navorsingshoofstuk (hoofstuk 3), het gekonsentreer op die optimalisering van die herstel eksperimentele ontwerp en die bepaling van die invloed van watermatriks op die oorlewing van Listeria monocytogenes, Salmonella spp. en E. coli-spesies deur die lae-druk UV dosis reaksie en herstel onder lig en donker toestande te meet by wyse van kolonietelling vergelykings. Dit het bevind dat die fisies-chemiese eienskappe (UVT%, TSS, TDS en troebelheid) wat ligpenetrasie negatief beïnvloed, UV- ontsmettingseffektiwiteit en herstelpotensiaal van bakterieë negatief beïnvloed. Salmonella enterica het die hoogste herstelpotensiaal aangedui en is nie akkuraat voorgestel deur die E. coli resultate nie. Die toediening van 'n hoër UV-dosis het egter die vermoë bewys om die uitdaging van bakterieëtipe en watermatriks tot 'n mate te oorkom wanneer 'n laedruk UV-gekollimeerde straaltoestel gebruik word. Die tweede navorsingshoofstuk het 'n molekulêre ondersoek gebruik om te onderskei of die toename in kolonietellings wat die herstelperiode gevolg het, te wyte was aan aktiewe selle wat vermenigvuldig het, VBNC-selle wat resussiteer en reproduseer, of DNA-skade wat herstel is en gevolglike selverplisering wat plaasvind. DNS-herwinning kon nie deur middel van Hoechst-kleurstofkleuring en fluoressensie- intensiteitmetings deur middel van spektrofluorometrie bevestig word nie. Die kolonietellings wat waargeneem is vir dieselfde bakteriese stamme wat die herstelperiode opvolg, kan moontlik toegeken word aan VBNC-selle wat resussiteer sodra dit in die ideale groeiomgewing geplaas is, soos die geval is met plaattellingmetodes. Die derde navorsingshoofstuk het gefokus op die praktiese implementering van UV-bestraling op groter volumes (1 000L) rivierwater wat vir besproeiingsdoeleindes gebruik word deur behandeling in 'n mediumdruk UV-ontsmettingsproefaanleg. Die resultate het daarop gewys dat mediumdruk UV meer effektief is om bakterieë in rou rivierwater te verminder, maar laat meer herstel plaasvind as laedruk UV. Deur die UV-dosis toegedien deur die mediumdruk UV-bron te verhoog, is die herstel van bakterieë aansienlik verminder. Oorlewende bakterieë is geïdentifiseer as opportunistiese patogene wat steeds 'n gesondheidsrisiko kan inhou. Oor die algemeen is uit hierdie studie erken dat 'n hoër UV-dosis (60 mJ.cmˉ²) die uitdagings wat deur lae waterkwaliteit gestel word, kan oorkom. Salmonella spp. het 'n hoër potensiaal vir UV-weerstand aangedui en opportunistiese patogene wat in bakteriese gemeenskappe gevind word, is meer geneig om UV- C-behandeling te oorleef. Mediumdruk UV het die vermoë om die bakteriese populasies aansienlik te verminder en kan dus steeds gebruik word as deel van 'n hekkiestrategie om die veiligheid van besproeiingswater uit besmette rivierbronne te verbeter. | Masters

Sixty–six (66) food and ten (10) water samples from Nsukka metropolis were screened for the presence of coliforms using the Most probable number (MPN) technique and direct plate count on MacConkey agar/broth and Eosin Methylene Blue (EMB) agar for isolating those from both faecal and human origin. The isolates were characterized biochemically analysed using standard conventional methods. The geometric mean counts (GMC) using MPN ranged from 1-180 faecal coliforms per 100 ml for both food and water samples. However, food samples (66.7%) served in plates and water sources (83.3%) showed apparent signs of contamination probably from the human and water sources, handling and storage unlike foods from the pots that had no trace of contamination. Faecal coliforms were E. coli (42.4%) and Klebsiella pneumonia (37.4%) and others(20.20%)of non-human origin. The E. coli count ranged between 22.2% (“abacha”) and 83.3% (beans ,rice, yam) as well as water(50.0% ).Thus, there was no significant difference (p>0.05) between the indicator organisms (E. coli) in the food, storage vats and water sources. The faecal and human coliforms in foods and water were indications of foodborne diseasesKeywords: Food, Water, Coliforms, Vending, Contamination

Thesis (PhD)--University of Pretoria, 2018. | Diarrheagenic Escherichia coli (DEC) has been implicated in foodborne outbreaks worldwide and additionally associated with childhood stunting in the absence of diarrhoea. DEC are pathogenic E. coli that cause human gut gastrointestinal infections. They are categorized based on how they elicit disease into groups called pathotypes. Infection is extraordinarily common, but the routes of transmission have not been determined. This work categorized into three phases 1, 2 and 3 aimed at characterizing pathogenic E. coli previously isolated from food sources and irrigation water in South Africa. In phase 1, the study characterized 205 E. coli strains previously isolated from producer distributor bulk milk (PDBM)(n=118), irrigation water (n=48), irrigated lettuce (n=29) and street vendor coleslaw (n=10) in South Africa. Enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enteroaggregative E. coli (EAEC) and diffusely adherent E. coli (DAEC) were sought. The study used PCR and partial gene sequencing for all 205 strains while 46 out of 205 that showed poor resolution were subsequently characterized using cell adherence (HeLa cells). PCR and partial gene sequencing of aatA and/or aaiC genes confirmed EAEC (2%, 5 out of 205) as the only pathotype. Strains from Genbank showing ?80% nucleotide sequence similarity with those used in this study based on possession of the aaiC gene included 10 clinical and 5 food strains. On the other hand, all strains from GenBank (n=22) showing high nucleotide sequence similarity (?80%) to those from this study based on possession of the aatA gene were clinical. Cluster analysis of sequenced EAEC strains with E. coli strains in GenBank showing ?80% nucleotide sequence similarity based on possession of aaiC and aatA generated distinct clusters of strains separated predominantly based on their source of isolation (food source or human stool). This suggested a potential role of virulence genes in source tracking. EAEC 24%, 11 out of 46 strains (PDBM=15%, irrigation water=7%, irrigated lettuce=2%) was similarly the predominant pathotype followed by strains showing invasiveness to HeLa cells, 4%, 2 out of 46 (PDBM=2%, irrigated lettuce=2%), using cell adherence. All strains that were not characterized based on possession of virulence genes and cell adherence assays were designated as non-DEC. These non-DEC strains were subsequently used as the basis for characterization in phase 2. In phase 2, the study assayed non-DEC strains from environmental sources in South Africa for phenotypes that may be associated with intestinal dysfunction (ID). DEC strains were also used. The strains had previously been isolated from PDBM, irrigated lettuce, street vendor coleslaw and irrigation water. In-vitro assays included; biofilm formation (n=38), extracellular polymeric substance (EPS) formation (n=38), cytotoxic activity (n=10), disruption of tight junctions and induction of Interleukin 8 (IL-8) on polarized T-84 cells (n=20). The number of strains tested for each assay differed, depending on prior molecular and phenotypic characterization that signalled potential pathogenicity. Subsequently, all strains having data points for all analyses were used to compute Principal Component Analysis (PCA) plot curves to infer associations amongst test strains. Biofilm formation varied based on pathotype (DEC and non-DEC) and source of isolation suggesting these two factors influence persistence within a defined environmental niche. Additionally, DEC isolated from irrigated lettuce had significantly higher (p?0.05) biofilm formation in both media compared to all strains including DEC standard controls suggesting irrigated lettuce as a potential source of persistent pathogenic strains. All strains were able to form EPS suggesting ability to form mature biofilms. Of the (60%, 6 out of 10) strains showing cytotoxic activity, most (83%, 5 out of 6 strains) were non-DEC isolated from food sources. Mean percentage reduction in initial TER (a measure of intestinal disruption) in all test strains, was comparable (53.5 to 73.8%) to that observed in the standard DEC. Additionally, IL-8 induction from strains isolated from PDBM (139pg/mL), irrigation water (231.93pg/mL) and irrigated lettuce (152.98pg/mL) was significantly higher (p?0.05) than in the commensal strain aafa. PCA categorized strains based on sources of isolation and showed potential for use in source tracking. This study shows that non-DEC strains along the food chain possess characteristics that may lead to ID. However further investigations with a larger collection of strains may provide a clearer link to these observations. | Food Science | PhD

Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2008. | In this study, geophysical measurements (Electrical Resistivity Tomography-ERT) and remote sensing techniques were applied in the Thukela river basin at various scales to complement the classical hydrometeorological networks. Detailed process hydrological studies were carried out at the Potshini catchment in the Thukela river basin to provide an in-depth understanding of the influence of different land use management practices, notably the impact of conservation tiJlage practices, on runoff generation and soil moisture retention characteristics at field scale. The general trend that was observed in the field studies is that conservation tillage systems influenced the partitioning of rainfall, by significantly reducing surface runoff over agricultural lands under conservation tillage practices, with a reduction ranging from 46 to 67%. The field soil-water balance studies also indicated that more soil moisture was retained in plots under conservation tillage practices compared to plots under conventional tillage and hence the wider adoption of such a practice could influence the partitioning of rainfall across scales. The field based study was integrated into catchment process studies where a classical hydrometrical network was complemented with geophysical measurements (ERT) along catchment transects to determine the interaction of the surface and sub-surface water and the relative contribution of the subsurface water to catchment response. The study revealed that the shallow ground water contributes significantly, close to 75%, of the stream flows in the Potshini catchment, especially during the dry seasons, with the response of the shallow ground water being a function of both the rainfall intensity and daily total amount. The potential of integrating the catchment process studies with the larger river basin scale was explored through the evaporative term of the water balance by applying the Surface Energy Balance Algorithm for Land (SEBAL), a remote sensing methodology, to estimate total evaporation (ET) from the Moderate Imaging Spectroradiometer (MODIS) satellite images. This was validated with ground measurements from a Large Aperture Scintilometer (LAS) installed in the Potshini catchment. Good comparison was established between the remotely sensed estimates and LAS measurements with a deviation range of between -14 to 26% on discrete days, where the deviation was defined as the departure of the remotely sensed estimates of ET from the respective LAS measurements. The results from this study compare well with results from similar studies in other countries with different climatic conditions. Subsequently, the evaporative water use of various land uses in the upper Thukela river basin was assessed using MODIS images. Commercial forestry was identified to be the land use with a consistent and relatively high evaporative water use In the study area. High evaporation rates over water bodies were observed during the wet summer season when both the natural and man made water bodies were at full capacity. Nevertheless, it is recognized that the inherent low resolution ofthe MODIS images could have impacted on the SEBAL results. Finally, a conceptual framework, drawing the strengths of classical hydrometeorological networks, geophysical measurements, isotope tracers and remote sensing is suggested with the potential of enhancing our understanding and conceptualization of hydrological determinants across scales. The relevance of the framework to water resources management is highlighted through its application to the Potshini catchment and the Thukela river basin using results and findings from this study.