Fungal composition and mycotoxin contamination of commercial wheat in South Africa in association with climate and agronomic practices

Thesis (MScAgric)--Stellenbosch University, 2021.

ENGLISH ABSTRACT: Mycotoxigenic fungi play an important role in wheat production. They produce toxic secondary metabolites that are detrimental to human and animal health and some of these fungi are also phytopathogens. Fusarium spp. are also responsible for Fusarium head blight which is one of the most destructive diseases of wheat, globally while Fusarium mycotoxins deoxynivalenol (DON), nivalenol and zearalenone (ZEA) are most frequently detected in wheat grain. Alternaria spp. are ubiquitously associated with wheat in most regions and can cause black point, leaf blight and leaf spot on wheat. Mycotoxins produced by this genus, such as alternariol, alternariol monomethyl ether and tenuazonic acid, frequently contaminate wheat grain. Other mycotoxigenic fungi present in wheat grain include Penicillium spp. that can produce ochratoxins, Aspergillus spp. that can produce ochratoxin and aflatoxin and Claviceps spp. that produces ergot alkaloids. Disease and mycotoxin contamination caused by mycotoxigenic fungi can be managed with the integrated use of tillage practices, crop rotation, fungicides, host resistance and disease forecasting systems. To determine the fungal composition and mycotoxin contamination in commercial wheat grain in South Africa, wheat was sampled over two seasons at 49 locations across all major wheat production regions. A total of 4 223 fungal isolates were obtained with Alternaria as the predominant genus (87%) followed by Fusarium and Epicoccum (4%), respectively. Fusarium graminearum (25%) and F. poae (15%) were the Fusarium spp. with the highest abundance and incidence in samples. The biggest difference in fungal composition was found between the production regions of the Western Cape and those isolated from the rest of South Africa. Samples from the Western Cape had a higher abundance of Alternaria spp., but the fungal diversity in these samples were lower than samples from other provinces. DON was detected in 12 samples and 3-acetyldeoxynivalenol in three samples, while 15-acetyldeoxinivalenol, ZEA and sterigmatocystin were only detected in one sample each. To determine the influence of agronomic practices and climate on fungal composition and mycotoxin contamination, information on agronomic practices was obtained from growers and weather data (humidity and temperature) was measured with data loggers at each location. Associations were found between the incidence of DON and rotations with F. graminearum host crops (maize, wheat, barley and soybeans) and also between irrigation and the incidence of Cladosporium, Epicoccum, Penicillium, Nigrospora, F. brachygibbosum, the Fusarium incarnatum-equiseti species complex, F. poae and F. oxysporum. A positive correlation was found between F. graminearum and DON contamination. Correlations were also found between weather conditions before anthesis and the abundance of Alternaria, Epicoccum, Nigrospora and F. brachygibbosum. This study reports on the fungal composition and natural mycotoxin contamination of commercial wheat in South Africa in association with weather and agronomic practices. It revealed the distribution of fungal genera in the different wheat production areas and showed that mycotoxin contamination is relatively low in South African wheat grain. It further highlights certain relationships between climate, agronomic practices, fungal composition and mycotoxin contamination in commercial wheat. Future studies should use polymerase chain reaction- based methods to determine fungal biomass in wheat grain to allow for the accurate determination of correlations between weather variables and fungi in grain.

AFRIKAANSE OPSOMMING: Mikotoksigeniese swamme speel ’n belangrike rol in koring produksie. Hulle produseer giftige sekondêre metaboliete wat skadelik is vir mense en diere en sommige van hierdie swamme is ook patogenies. Fusarium spp. is ook verantwoordelik vir Fusarium aarskroei wat wêreldwyd een van die skadelikste siektes op koring is terwyl Fusarium mikotoksiene deoksinivalenol (DON), nivalenol and zearalenone (ZEA) word die meeste in koringgraan gevind. Alternaria spp. is oorheersend op koring in meeste streke en kan ook Swart punt, Blaarskroei en Blaarvlek op koring veroorsaak. Mikotoksiene wat deur hierdie genus geproduseer word, soos alternariol, alternariol-monometiel-eter en tenuasoniesesuur, kontamineer gereeld koringgraan. Ander mikotoksigeniese swamme wat op koringgraan voorkom sluit in Penicillium spp. wat okratoksiene produseer, Aspergillus spp. wat okratoksiene en aflatoksiene produseer en Claviceps spp. wat ergotalkaloïede produseer. Siekte en mikotoksien-kontaminasie wat deur mikotoksigeniese swamme veroorsaak word kan beheer word deur die geïntegreerde gebruik van grondbewerking, wisselbou, swamdoders, gasheerweerstand en siekte-voorspellingsisteme Om die swam-samestelling en mikotoksien kontaminasie op kommersiële koringgraan in Suid-Afrika te bepaal, is graanmonsters oor twee seisoene op 49 lokaliteite oor alle hoof koring produksie streke versamel. ’n Totaal van 4 223 swam isolate is verkry uit die graanmonsters. Alternaria was die oorheersende genus (87%) gevolg deur Fusarium en Epicoccum (4% elk). Fusarium graminearum (25%) en F. poae (15%) was die Fusarium spp. met die hoogste voorkoms en getalle. Die grootste verskil in swam-samestelling tussen monsters was verkry tussen die streke in die Wes-Kaap en dié in die res van Suid-Afrika. Monsters uit die Wes- Kaap het hoër Alternaria getalle gehad, maar die swam diversiteit in hierdie mosters was laer as dié van ander provinsies. DON was in 12 monsters gevind en 3-asetieldeoksinivalenol in drie monsters. Mikotoksiene, 15-asetieldeoksinivalenol, ZEA en sterigmatosistien was net in een monster elk gevind. Om die invloed van verbouingspraktyke en klimaat op swam-samestelling en mikotoksien-kontaminasie te bepaal, is inligting oor die verbouingspraktyke by produsente verkry en weer data (humiditeit en temperatuur) is met dataloggers gemeet by elke lokaliteit. Assosiasies is gevind tussen die voorkoms van DON en wisselbou met F. graminearum gasheer gewasse (mielies, koring, gars en sojabone) en ook tussen besproeiing en die voorkoms van Cladosporium, Epicoccum, Penicillium, Nigrospora, F. Brachygibbosum, die Fusarium incarnatum-equiseti spesies kompleks, F. poae en F. oxysporum. ’n Positiewe korrelasie is gevind tussen F. graminearum and DON-kontaminasie. Korrelasies is ook gevind tussen die weerstoestande voor blomtyd en die en die hoeveelheid Alternaria, Epicoccum, Nigrospora and F. brachygibbosum isolasies in monsters. Hierdie studie doen verslag oor swam-samestelling en natuurlike mikotoksien kontaminasie in kommersiële koring in Suid-Afrika. Dit onthul die verspreiding van swam genera in die verskeie produksie streke en wys ook dat mikotoksien kontaminasie in Suid- Afrikaanse koringgraan relatief laag is. Verder lig dit seker verhoudings tussen klimaat, verbouingspraktyke, swam-samestelling en mikotoksien-kontaminasie in koringgraan uit. Toekomstige studies moet gebruik maak van polimerasekettingreaksie gebaseerde tegnieke om swam biomassa in koringgraan te bepaal sodat korrelasies tussen weer-veranderlikes en swamme akkuraat bepaal kan word.

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