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Rhizosphere microbiome assembly and function in the Brassicaceae
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Monaghan, Ellis Beltrami (2021) Rhizosphere microbiome assembly and function in the Brassicaceae. PhD thesis, University of Warwick.
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Official URL: http://webcat.warwick.ac.uk/record=b3763698
Abstract
The rhizosphere microbiome is of great importance to plant health and function being described as the plants ‘second genome’ and an essential component in the host plants biology, ecology, and evolution. Subsequently, understanding the assembly and function of rhizosphere microbiomes can be seen as essential to the development of modern agriculture with the aim of developing microbial based agricultural tools. However, a systematic understanding of how the microbiota assembles and functions as a whole in relation to the plant host is not fully developed. Therefore, this thesis investigated the assembly and functionality of rhizosphere microbiomes in two important Brassicaceae plant species, Brassica napus and Arabidopsis thaliana to develop understanding of rhizosphere microbiome assembly and functionality. Analysis of rhizosphere microbiome assembly in response to plant genetic diversity was assessed in the key crop species B. napus. The rhizosphere soil and root microbiomes of four B. napus genotypes (or cultivars) with distinct root architecture and exudate profiles were assessed in a large-scale field trial. This investigation indicated that these genotypes did not alter microbiome composition at the community level. However, indicator species analysis and inter-taxon community network analysis identified significant indicator taxa for each genotype and genotype specific network architectures. In addition, the diversity of root and rhizosphere soil communities were found to be significant explanatory variables of biomass and yield in certain genotypes. Together these results indicate that genotypic influences on the rhizosphere microbiome are complex and can be nuanced. Functionality of the fungal rhizosphere microbiome of B. napus was also investigated in this thesis. A collection of fungal isolates from root and rhizosphere soil samples of B. napus were successfully isolated and utilised in plant – microbe co-incubation studies. This collection included isolates representative of many taxa present in the UK B. napus rhizosphere mycobiome and included, taxa correlated positively and negatively with B. napus yield and, several potentially pathogenic and endophytic taxa. Six taxa with deleterious impacts on B. napus seedling biomass were identified. Taxa correlated with yield were also successfully screened, however, no significant impacts on biomass were identified. This indicated that their potential influence on yield may occur through other means. Finally, analysis of rhizosphere mycobiome assembly in response to A. thaliana genotypes with immune phytohormone production and sensitivity mutations was carried out. Wild-type Col0 and three immune phytohormone mutant A. thaliana genotypes with either, hypersensitivity to Abscisic acid, deficiency in Abscisic acid production and deficiency in Salicylic acid production were analysed. This thesis presents the first research regarding fungal microbiome assembly in a Salicylic acid deficient plant mutant and the first research on any microbiome assembly in Abscisic Acid mutant plants. Immune phytohormone genetic diversity was not found to alter community diversity indices. However, significant enrichments of Basidiomycota were identified in Abscisic acid mutants. In addition, immune phytohormone deficient genotypes were not found to form ‘deleterious’ root mycobiomes. In addition, microbiome transfer using mutant conditioned soils were not found to alter community composition, diversity, and plant biomass in subsequent Wild-type A. thaliana. Together the results presented in this thesis develop our understanding of plant – microbiome assembly and functionality in the Brassicaceae and plants in general.
Item Type: | Thesis (PhD) | ||||
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Subjects: | Q Science > QK Botany Q Science > QR Microbiology |
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Library of Congress Subject Headings (LCSH): | Plant-microbe relationships, Plant-microbe relationships -- Genetic aspects, Rhizosphere, Cruciferae, Abscisic acid | ||||
Official Date: | March 2021 | ||||
Dates: |
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Institution: | University of Warwick | ||||
Theses Department: | School of Life Sciences | ||||
Thesis Type: | PhD | ||||
Publication Status: | Unpublished | ||||
Supervisor(s)/Advisor: | Bending, G. D. (Gary D.) ; Grant, Murray | ||||
Sponsors: | Midlands Integrative Biosciences Training Partnership ; Biotechnology and Biological Sciences Research Council (Great Britain) ; University of Warwick ; Vegetable Research Trust ; Rank Prize | ||||
Format of File: | |||||
Extent: | xxii, 201 leaves : illustrations | ||||
Language: | eng |
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