The genetic control of root attachment and colonisation in Rhizobium leguminosarum
<p>The legume-<em>Rhizobium</em> symbiosis is a key source of environmentally clean nitrogen in agriculture. Of up to 70 million tonnes of nitrogen that are fixed into agricultural systems by biological nitrogen fixation each year, 40 million are fixed by rhizobia in symbiosis with...
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| Other Authors: | |
| Format: | Thesis |
| Language: | English |
| Published: |
2023
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| _version_ | 1811141170473992192 |
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| author | Cocker, C |
| author2 | Poole, P |
| author_facet | Poole, P Cocker, C |
| author_sort | Cocker, C |
| collection | OXFORD |
| description | <p>The legume-<em>Rhizobium</em> symbiosis is a key source of environmentally clean nitrogen in agriculture. Of up to 70 million tonnes of nitrogen that are fixed into agricultural systems by biological nitrogen fixation each year, 40 million are fixed by rhizobia in symbiosis with legumes. Attachment to and colonisation of host plant roots are essential precursors to formation of a successful nitrogen-fixing symbiosis between <em>Rhizobium</em> strains and their host legumes but are less well-characterized than other stages of symbiosis formation. This work investigates the genetic basis for root surface attachment and colonisation in <em>Rhizobium leguminosarum</em> on both a whole genome scale and an individual pathway scale.</p>
<p>Development of a differential spin method of separating attached and colonising bacteria from plant root material allows investigation of gene expression that is unique to bacteria that are interacting with the root surface, where previous studies have combined bacterial samples in bulk soil with those attached to the root surface. This method is used to investigate transcriptomic changes in <em>Rhizobium leguminosarum</em> bv viciae 3841 during colonisation of the barley rhizoplane, and attachment to and colonisation of the pea rhizoplane. Comparison of transcriptomic changes during colonisation of the pea and barley rhizoplanes reveals that Rlv3841 is substantially better adapted to growth on the pea rhizoplane. Downregulation of central carbon metabolism, synthesis of metabolic intermediates, cell division, DNA repair and cell wall synthesis during colonisation of barley roots suggest that Rlv3841 grows much more slowly on the barley rhizoplane than in laboratory culture, or on the pea rhizoplane, possibly due to a lack of adaptation to the carbon sources found in barley root exudates.</p>
<p>The comparison of the Rlv3841 transcriptome during attachment to and colonisation of the pea rhizoplane carried out in this work represents, to my knowledge, the first such study on a rhizobial diazotroph and its host legume. A substantial amount of overlap was shown between the significantly differentially regulated genes during attachment and colonisation transcriptomes in Rlv3841. Functions upregulated during both processes included ABC transport, DNA repair and genes involved in determining cell surface characteristics. Expression of genes involved in motility and chemotaxis was significantly reduced during both attachment and colonisation. However, around 40% of differentially regulated genes differed between the two processes, showing that distinct sets of genes are involved in each stage of interaction with the rhizoplane. In particular, genes involved in breakdown of malonate, GABA and fatty acids were significantly upregulated in attachment, while inositol catabolism was significantly upregulated during colonisation, suggesting that different carbon sources may be important for each process to take place.</p>
<p>Finally, this work characterises the <em>ecfE</em> operon, which is upregulated during attachment to and colonisation of the pea rhizoplane, as well as during colonisation of the barley rhizoplane. The promoter (P<em>lppE</em>) is only active in cells adhering to the root elongation zone, where rapid cell elongation happens, allowing <em>R. leguminosarum</em> to detect a region of the root with new surface area that is free of pre-existing microbial communities. This specific spatial activation happens in response to a root-associated glycoprotein, likely a germin-like protein, that is expressed to optimal levels in the root elongation zone. EcfE is revealed to play a role in mediating expression of an iron-related attachment pathway that facilitates the lifestyle switch between free-living and colonising bacteria.</p> |
| first_indexed | 2024-09-25T04:33:37Z |
| format | Thesis |
| id | oxford-uuid:81ef0403-af03-4c62-a84d-c857a9e032ce |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-09-25T04:33:37Z |
| publishDate | 2023 |
| record_format | dspace |
| spelling | oxford-uuid:81ef0403-af03-4c62-a84d-c857a9e032ce2024-09-09T15:37:37ZThe genetic control of root attachment and colonisation in Rhizobium leguminosarumThesishttp://purl.org/coar/resource_type/c_db06uuid:81ef0403-af03-4c62-a84d-c857a9e032ceEnglishHyrax Deposit2023Cocker, CPoole, PKelly, SVan der hoorn, R<p>The legume-<em>Rhizobium</em> symbiosis is a key source of environmentally clean nitrogen in agriculture. Of up to 70 million tonnes of nitrogen that are fixed into agricultural systems by biological nitrogen fixation each year, 40 million are fixed by rhizobia in symbiosis with legumes. Attachment to and colonisation of host plant roots are essential precursors to formation of a successful nitrogen-fixing symbiosis between <em>Rhizobium</em> strains and their host legumes but are less well-characterized than other stages of symbiosis formation. This work investigates the genetic basis for root surface attachment and colonisation in <em>Rhizobium leguminosarum</em> on both a whole genome scale and an individual pathway scale.</p> <p>Development of a differential spin method of separating attached and colonising bacteria from plant root material allows investigation of gene expression that is unique to bacteria that are interacting with the root surface, where previous studies have combined bacterial samples in bulk soil with those attached to the root surface. This method is used to investigate transcriptomic changes in <em>Rhizobium leguminosarum</em> bv viciae 3841 during colonisation of the barley rhizoplane, and attachment to and colonisation of the pea rhizoplane. Comparison of transcriptomic changes during colonisation of the pea and barley rhizoplanes reveals that Rlv3841 is substantially better adapted to growth on the pea rhizoplane. Downregulation of central carbon metabolism, synthesis of metabolic intermediates, cell division, DNA repair and cell wall synthesis during colonisation of barley roots suggest that Rlv3841 grows much more slowly on the barley rhizoplane than in laboratory culture, or on the pea rhizoplane, possibly due to a lack of adaptation to the carbon sources found in barley root exudates.</p> <p>The comparison of the Rlv3841 transcriptome during attachment to and colonisation of the pea rhizoplane carried out in this work represents, to my knowledge, the first such study on a rhizobial diazotroph and its host legume. A substantial amount of overlap was shown between the significantly differentially regulated genes during attachment and colonisation transcriptomes in Rlv3841. Functions upregulated during both processes included ABC transport, DNA repair and genes involved in determining cell surface characteristics. Expression of genes involved in motility and chemotaxis was significantly reduced during both attachment and colonisation. However, around 40% of differentially regulated genes differed between the two processes, showing that distinct sets of genes are involved in each stage of interaction with the rhizoplane. In particular, genes involved in breakdown of malonate, GABA and fatty acids were significantly upregulated in attachment, while inositol catabolism was significantly upregulated during colonisation, suggesting that different carbon sources may be important for each process to take place.</p> <p>Finally, this work characterises the <em>ecfE</em> operon, which is upregulated during attachment to and colonisation of the pea rhizoplane, as well as during colonisation of the barley rhizoplane. The promoter (P<em>lppE</em>) is only active in cells adhering to the root elongation zone, where rapid cell elongation happens, allowing <em>R. leguminosarum</em> to detect a region of the root with new surface area that is free of pre-existing microbial communities. This specific spatial activation happens in response to a root-associated glycoprotein, likely a germin-like protein, that is expressed to optimal levels in the root elongation zone. EcfE is revealed to play a role in mediating expression of an iron-related attachment pathway that facilitates the lifestyle switch between free-living and colonising bacteria.</p> |
| spellingShingle | Cocker, C The genetic control of root attachment and colonisation in Rhizobium leguminosarum |
| title | The genetic control of root attachment and colonisation in Rhizobium leguminosarum |
| title_full | The genetic control of root attachment and colonisation in Rhizobium leguminosarum |
| title_fullStr | The genetic control of root attachment and colonisation in Rhizobium leguminosarum |
| title_full_unstemmed | The genetic control of root attachment and colonisation in Rhizobium leguminosarum |
| title_short | The genetic control of root attachment and colonisation in Rhizobium leguminosarum |
| title_sort | genetic control of root attachment and colonisation in rhizobium leguminosarum |
| work_keys_str_mv | AT cockerc thegeneticcontrolofrootattachmentandcolonisationinrhizobiumleguminosarum AT cockerc geneticcontrolofrootattachmentandcolonisationinrhizobiumleguminosarum |