The presence of faecal pollution, and potential plant pathogens associated with onion production, in the Lower Vaal River

Thesis (MSc)--Stellenbosch University, 2015.ENGLISH ABSTRACT: Industrial and sewage pollution of the Vaal River pose a threat to sustainable agriculture along the Lower Vaal River in the Northern Cape of South Africa. In this region, the Vaal River is used to irrigate onion fields via centre-pivot irrigation systems. However, irrigation water originating from rivers may, in addition to human pathogens, contain waterborne plant pathogens that are washed into river systems by agricultural surface runoff, posing a threat to crop production. Thus, the goals of this study were firstly to screen for both faecal contamination in the Lower Vaal River, as well as the onion pathogen Fusarium oxysporum f. sp. cepae (Focep). Subsequently, the efficacy of a calcium hypochlorite containing disinfectant, i.e. „HTH® Super Shock It‟, was determined to remove coliform bacteria and Fusarium spores from the river water within 16 s. This is the contact time allowed for a disinfectant when water is treated at the hub of a centre-pivot irrigation system, before it is dispersed via the first sprinklers in a typical centre-pivot irrigation system. Surface water samples, as well as water from various pump stations used for irrigation, were collected over a period of three years at sampling sites along a 159 km stretch of the Vaal River. Sample analyses revealed that faecal coliforms were always present (7.19 x 105 CFU/100 ml). Also, 59 Fusarium isolates were obtained from the water, as well as eight Fusarium isolates from onion bulbs that were cultivated in fields irrigated by water from the river. Molecular identification revealed that the isolates belonged to four Fusarium species, i.e. Fusarium brachygibbosum, Fusarium incarnatum-equiseti, Fusarium solani and Fusarium oxysporum, the latter being the dominant species represented by 52 isolates. The pathogenicity of the Fusarium isolates was determined against onion bulbs (Lombardi cultivar), and it was found that none of the water isolates caused basal rot and were therefore not representatives of Focep. However, four F. oxysporum isolates obtained from the onion bulbs were found to be Focep belonging to the vegetative compatibility group (VCG) 0425, previously known to be prevalent in the Western Cape Province. Despite the fact that no pathogenicity toward onion could be confirmed among the waterborne Fusarium isolates, subsequent screening for virulence factors, i.e. SIX (secreted in xylem) genes, revealed the presence of the SIX7 gene in some isolates. These isolates may therefore be potentially pathogenic to crops other than onion cultivated in the Lower Vaal region. A concentration of 1.50 mg/L „HTH® Super Shock It‟ was discovered to effectively remove 100% of faecal coliforms within 16 s from the water, while Fusarium spores were removed at 7.50 mg/L after 3600 s. Thus, while the disinfectant may be ineffective at removing fungal plant pathogens from a centre-pivot irrigation system within the required time, the results indicate that it will remove coliform bacteria from the water before it is dispersed onto crops.AFRIKAANSE OPSOMMING: Industriële en rioolbesoedeling van die Vaalrivier stel volhoubare landbou langs die Laer Vaalrivier in die Noord-Kaap in gevaar. In hierdie streek word die Vaalrivier gebruik om uielande deur middel van spilpuntbesproeiing nat te lei. Besproeiingswater uit riviere mag, saam met menslike patogene, ook watergedraagde plantpatogene bevat wat in die riviersisteme beland deur oppervlakte-afloop van boerderye, en dus „n gevaar inhou vir oes-produksie. Die oorhoofse doelwitte van hierdie studie was dus eerstens om die vlak van fekale kontaminasie van die Laer Vaalrivier te bepaal, en ook om vas te stel of die uie-patogeen Fusarium oxysporum f. sp. cepae (Focep) in die rivier voorkom. Die doeltreffendheid van „n kalsium-hipochlorietbevattende ontsmettingsmiddel, naamlik „HTH® Super Shock It‟, om kolivorme bakterieë en Fusarium spore binne 16 s uit die rivierwater te verwyder, is gevolglik bepaal. Dit is die kontaktyd wat vir „n ontsmettingsmiddel toegelaat word wanneer water by die spil van „n spilpuntbesproeiingstelsel behandel word, voor dit deur die eerste sproeiers van „n tipiese spilpuntbesproeiingstelsel versprei word. Oppervlakwatermonsters, asook water uit verskeie pompstasies wat vir besproeiing gebruik word, is oor 'n tydperk van drie jaar by monsternemingsterreine binne 'n 159 km gedeelte van die Vaalrivier versamel. Monsteranalises het getoon dat fekale kolivorme altyd teenwoordig was (7.19 x 105 CFU/100 ml). Daar is ook 59 Fusarium isolate uit die water gekry, asook agt Fusarium isolate van uiebolle wat verbou is in lande wat met water uit die rivier besproei is. Molekulêre indentifikasie het getoon dat die isolate tot vier Fusarium spesies, naamlik Fusarium brachygibbosum, Fusarium incarnatum-equiseti, Fusarium solani en Fusarium oxysporum behoort, waarvan laasgenoemde die dominante spesies is en deur 52 van die isolate verteenwoordig word. Die patogenisiteit van die Fusarium isolate teenoor uiebolle (Lombardi kultivar) is bepaal, en daar is gevind dat nie een van die waterisolate wortelvrot veroorsaak het nie, en dus nie verteenwoordigers van Focep is nie. Vier F. oxysporum isolate wat van uiebolle in die lande verkry is, is egter gevind om Focep te wees wat tot die vegetatiewe verenigbare groep (VCG) 0425 behoort, wat voorheen bekend was om in die Wes-Kaap voor te kom. Ten spyte van die feit dat geen patogenisiteit (teenoor uie) onder die watergedraagde Fusarium isolate bevestig kon word nie, het daaropvolgende siftings vir virulensiefaktore, naamlik SIX (“secreted in xylem”) gene, die teenwoordigheid van die SIX7-geen in sommige isolate getoon. Hierdie isolate mag dus potensieel patogenies wees vir gewasse anders as uie wat in die Laer Vaal-gebied verbou word. n Konsentrasie van 1.50 mg/L „HTH® Super Shock It‟ is benodig om 100% fekale kolivorme effektief binne 16 s uit die water te verwyder, terwyl Fusarium spore verwyder is teen 7.50 mg/L na 3600 s. Terwyl die ontsmettingsmiddel dus oneffektief is om fungus plantpatogene binne die verlangde tydperk uit die spilpuntbesproeiingstels te verwyder, toon resultate dat dit wel kolivorme bakterieë uit die water sal verwyder voor dit oor die gewasse versprei kan word.Master