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Fusarium presence and pathogen detection in the maize microbiome in South Africa.
Thesis (MSc)--Stellenbosch University, 2022.
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| Format: | Thesis |
| Language: | en_ZA |
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Stellenbosch : Stellenbosch University
2022
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| _version_ | 1867614033391124480 |
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| access_status_str | Open Access |
| author | Schuin, Janine |
| author2 | Jacobs, Karin |
| author_browse | Jacobs, Karin Schuin, Janine |
| author_facet | Jacobs, Karin Schuin, Janine |
| author_sort | Schuin, Janine |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MSc)--Stellenbosch University, 2022. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/125040 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:45:36.533Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/125040 Fusarium presence and pathogen detection in the maize microbiome in South Africa. Schuin, Janine Jacobs, Karin Neriman, Yilmaz Visagie Stellenbosch University. Faculty of Science. Dept. of Microbiology. Fusarium -- Pathogenesis Grain crops -- Diseases and pests -- South Africa Loop-mediated isothermal amplification Fusarium -- Genetic engineering Plant diseases -- Nutritional aspects Soils and nutrition Soils -- Health Microbiomes UCTD Thesis (MSc)--Stellenbosch University, 2022. ENGLISH ABSTRACT: Grain crops are among the most valuable commodities in South African agriculture as they are staple foods that contribute significantly to the local economy. Of these, maize is widely consumed by both livestock and humans and is also employed in a variety of industrial processes. The main challenges affecting grain crop production are available land, drought, pests and plant diseases, all of which contribute considerably to lower crop yield and quality. In South Africa, various pathogenic fungal species have been associated with grain crops. Among these pathogens, Fusarium species are particularly problematic as they produce mycotoxins such as deoxynivalenol and fumonisins which, in large quantities, pose major risks to both the economic well-being of the farmer and the physical well-being of the consumer. They also have essential ecological roles in the breakdown of plant waste, the suppression of plant disease, nutrient cycling (especially C and N), and are important contributors to N20 emissions. As a result, Fusarium constitutes a functionally significant biological component of agricultural soil ecosystems that needs to be better understood. This study, therefore, analysed the diversity and abundance of Fusarium species in different farming systems using next generation sequencing (NGS) as well as determined the efficacy of predicting the presence of pathogenic Fusarium isolates in an ecosystem using loop-mediated isothermal amplification (LAMP) of pathogenic genes. The main findings include the presence of Fusarium as the most common fungal genus in maize samples. A significant difference in Fusarium species diversity and presence was observed between conventional and conservation farms, as well as farms using the same agricultural techniques, where location was more important than the agricultural practice employed. Additionally, a lot of variation was also seen within samples. The in-sample variation was due to different whole microbial community structures and chemical soil profiles, of which soil nitrate concentrations had a significant influence on this variation. Lastly, it was also possible to identify potential pathogenic Fusarium species using loop-mediated isothermal amplification of pathogenic genes. The outcomes of this study show that microbial groups, in this case pathogenic Fusarium, should not be seen in isolation and treated reactively, but considered as part of a community. Future studies should include larger sampling numbers and locations as well as the utilization of methods such as transcriptomics, metabolomics and pathogenicity testing. AFRIKAANSE OPSOMMING: Graangewasse is van die waardevolste kommoditeite in die Suid-Afrikaanse landbou bedryf aangesien dit ‘n stapelvoedsel is wat aansienlik bydra tot die plaaslike ekonomie. Hiervan word mielies wyd verbruik deur beide mens en dier maar ook in 'n verskeidenheid industriële prosesse. Die hoofuitdagings wat mielie produksie raak, is beskikbare grond, droogte, plae en plantsiektes, wat alles aansienlik bydra tot laer oesopbrengs en kwaliteit. In Suid-Afrika is verskeie patogeniese swamspesies met graangewasse geassosieer. Onder hierdie patogene is Fusarium-spesies veral problematies aangesien hulle mikotoksiene soos deoksinivalenol en fumonisiene produseer wat in groot hoeveelhede groot risiko vir beide die ekonomiese welstand van die boer en die gesondheid van die verbruiker inhou. Hulle vertolk verder ook noodsaaklike ekologiese rolle in die afbreek van plant afval, die onderdrukking van plantsiektes, voedingstofsiklusse (veral C en N), en is 'n belangrike bydraer tot N20- vrystellings. Fusarium is dus 'n beduidende funksionele biologiese komponent van landbougrond wat beter verstaan moet word. Hierdie studie het dus die diversiteit en teenwoordigheid van Fusarium spesies in verskillende landboupraktyke ontleed deur gebruik te maak van volgende generasie volgordebepaling (NGS). Die doeltreffendheid van die voorspelling van die teenwoordigheid van patogeniese Fusarium isolate in 'n ekosisteem deur lus-gemedieerde isotermiese amplifikasie (LAMP) van patogeniese gene is ook ge-evalueer. Die hoofbevindinge sluit in dat Fusarium die mees algemene swamgenus in die mieliemonsters is en dat daar 'n beduidende verskil in Fusarium-spesie diversiteit en teenwoordigheid tussen konvensionele en bewarings plase is. ‘n Diversiteits verskil, wat deur ligging verduidelik kon word, is ook gesien op plase wat dieselfde landboutegnieke gebruik. Baie diversiteit is ook binne monsters gesien, die diversiteit was as gevolg van verskillende mikrobiese gemeenskapstrukture en chemiese grondprofiele, waar die nitraat konsentrasie in die grond 'n beduidende invloed op hierdie diversiteit gehad het. Laastens was dit ook moontlik om potensiële patogeniese Fusarium spesies te identifiseer deur lusgemedieerde isotermiese amplifikasie van patogeniese gene. Die uitkomste van hierdie studie toon dat mikrobes, in hierdie geval patogeniese Fusarium, nie in isolasie gesien en reaktief behandel moet word nie. Toekomstige studies moet groter monster getalle en -areas insluit, asook die gebruik van metodes soos transkriptomika, metabolomika en patogenisiteitstoetse. Masters 2022-03-02T11:43:31Z 2022-04-29T12:51:28Z 2022-09-02T03:00:14Z 2022-03 Thesis http://hdl.handle.net/10019.1/125040 en_ZA Stellenbosch University viii, 187 pages application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Fusarium -- Pathogenesis Grain crops -- Diseases and pests -- South Africa Loop-mediated isothermal amplification Fusarium -- Genetic engineering Plant diseases -- Nutritional aspects Soils and nutrition Soils -- Health Microbiomes UCTD Schuin, Janine Fusarium presence and pathogen detection in the maize microbiome in South Africa. |
| title | Fusarium presence and pathogen detection in the maize microbiome in South Africa. |
| title_full | Fusarium presence and pathogen detection in the maize microbiome in South Africa. |
| title_fullStr | Fusarium presence and pathogen detection in the maize microbiome in South Africa. |
| title_full_unstemmed | Fusarium presence and pathogen detection in the maize microbiome in South Africa. |
| title_short | Fusarium presence and pathogen detection in the maize microbiome in South Africa. |
| title_sort | fusarium presence and pathogen detection in the maize microbiome in south africa |
| topic | Fusarium -- Pathogenesis Grain crops -- Diseases and pests -- South Africa Loop-mediated isothermal amplification Fusarium -- Genetic engineering Plant diseases -- Nutritional aspects Soils and nutrition Soils -- Health Microbiomes UCTD |
| url | http://hdl.handle.net/10019.1/125040 |
| work_keys_str_mv | AT schuinjanine fusariumpresenceandpathogendetectioninthemaizemicrobiomeinsouthafrica |