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Defining functional microbiomes of wheat (Triticum aestivum) and maize (Zea mays), under regenerative management practices, in South Africa
Thesis (PhD)--Stellenbosch University, 2026.
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| Format: | Thesis |
| Language: | English |
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Stellenbosch : Stellenbosch University
2026
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| _version_ | 1867613765522948096 |
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| access_status_str | Open Access |
| author | Page, Lucan Dylan |
| author2 | Jacobs, Karin |
| author_browse | Jacobs, Karin Page, Lucan Dylan |
| author_facet | Jacobs, Karin Page, Lucan Dylan |
| author_sort | Page, Lucan Dylan |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (PhD)--Stellenbosch University, 2026. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/135966 |
| institution | Stellenbosch University (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:41:20.497Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2026 |
| publishDateRange | 2026 |
| publishDateSort | 2026 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/135966 Defining functional microbiomes of wheat (Triticum aestivum) and maize (Zea mays), under regenerative management practices, in South Africa Page, Lucan Dylan Jacobs, Karin Stellenbosch University. Faculty of Science. Dept. of Microbiology. Thesis (PhD)--Stellenbosch University, 2026. Page, L. D. 2026. Defining functional microbiomes of wheat (Triticum aestivum) and maize (Zea mays), under regenerative management practices, in South Africa. Unpublished doctoral dissertation. Stellenbosch: Stellenbosch University [online]. Available: https://scholar.sun.ac.za/items/16dbc9d6-deef-4c17-b932-2a59db14f654 Soil microbiomes are complex, interconnected assemblages of microorganisms that underpin fundamental ecosystem processes, including nutrient cycling, pathogen and drought resistance, and soil structural development. Despite their central role in ecosystem functioning, the dynamics of soil microbiomes under regenerative agricultural systems remain poorly understood, particularly within semi-arid South African environments. Understanding how agricultural management practices shape these communities is critical to designing resilient and sustainable food production systems. This dissertation investigated how regenerative agricultural practices influence the rhizosphere microbiome of cereal crops, focusing on two complementary systems: wheat grown under controlled regenerative conditions in the Western Cape, and maize cultivated by commercial farmers in the Free State and KwaZulu-Natal. Together, these studies aimed to elucidate how management intensity, crop-rotation, and environmental conditions interact to shape microbial community structure, diversity, and functional potential. Microbial communities were characterized using 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing, supported by quantitative PCR (qPCR)-, targeting nitrogen-cycling genes, and soil geochemical analyses. This integrative approach provided a multidimensional perspective of rhizosphere dynamics across contrasting agricultural environments. In the wheat study, crop rotation exerted limited influence on overall microbial community composition. The Medicago-wheat and wheat–wheat rotations exhibited the greatest overlap, whereas canola-wheat rotations were the most distinct. Host selection and drought conditions emerged as the primary determinants of microbiome differentiation. These findings suggest that short-term rotational changes may exert weaker selective pressures on microbial communities than host-driven or environmental factors. During the vegetative growth stage, rhizosphere communities converged, indicating strong host-mediated selection. Following senescence, microbial communities shifted toward taxa associated with saprophytic and yeast functional groups. Microorganisms associated with arid and saline environments, were enriched, likely reflecting the legacy of the severe drought between 2015 and 2019, highlighting the adaptive capacity and resilience of soil microbiomes under prolonged climatic stress. In the maize study, agricultural management practices and host selection were the principal drivers of rhizosphere microbiome composition. Bacterial communities in regenerative farms showed the greatest overlap during vegetative stages, while fungal communities were primarily structured by regional location. Regenerative systems exhibited significantly higher abundances of functional groups associated with nitrification and aerobic ammonia oxidation compared with conventional management, suggesting enhanced nitrogen turnover and potential reductions in fertilizer dependency. These findings were corroborated by qPCR analyses, which revealed elevated copy numbers of nitrogen-cycling genes in regenerative farms during vegetative growth. In contrast to the wheat systems, drought-associated taxa were less evident, likely due to the use of irrigation systems that mitigated water stress. Collectively, this dissertation provides novel insights into how regenerative agricultural management shapes rhizosphere microbiomes across diverse agroecosystems. The results demonstrate that while specific practices such as crop-rotation may have limited direct effects, holistic regenerative management fosters microbial communities with enhanced functional potential, particularly in nitrogen cycling. This research identifies host selection, drought, and crop developmental stage as key determinants of microbial community assembly and offers a framework for designing agricultural systems that harness microbiome functionality to improve soil health, nutrient use efficiency, and resilience under future climatic uncertainty. Doctoral 2026-04-16T10:06:31Z 2026-04-16T10:06:31Z 2026-03 Thesis https://scholar.sun.ac.za/handle/10019.1/135966 en Stellenbosch University 245 pages application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Page, Lucan Dylan Defining functional microbiomes of wheat (Triticum aestivum) and maize (Zea mays), under regenerative management practices, in South Africa |
| title | Defining functional microbiomes of wheat (Triticum aestivum) and maize (Zea mays), under regenerative management practices, in South Africa |
| title_full | Defining functional microbiomes of wheat (Triticum aestivum) and maize (Zea mays), under regenerative management practices, in South Africa |
| title_fullStr | Defining functional microbiomes of wheat (Triticum aestivum) and maize (Zea mays), under regenerative management practices, in South Africa |
| title_full_unstemmed | Defining functional microbiomes of wheat (Triticum aestivum) and maize (Zea mays), under regenerative management practices, in South Africa |
| title_short | Defining functional microbiomes of wheat (Triticum aestivum) and maize (Zea mays), under regenerative management practices, in South Africa |
| title_sort | defining functional microbiomes of wheat triticum aestivum and maize zea mays under regenerative management practices in south africa |
| url | https://scholar.sun.ac.za/handle/10019.1/135966 |
| work_keys_str_mv | AT pagelucandylan definingfunctionalmicrobiomesofwheattriticumaestivumandmaizezeamaysunderregenerativemanagementpracticesinsouthafrica |