Novel insights into the genetic mechanisms underpinning plant-microbiota interactions in the rhizosphere

Student thesis: Master's ThesisMaster of Science


Plants host a complex and diverse microbial community at their root-soil interface, collectively known as the rhizosphere microbiota. Some of these microbes, referred to as plant growth promoting rhizobacteria (PGPRs), are capable of enhancing mineral uptake by the plant, are actively involved in synthesizing and modulating the plant’s synthesis of chemical compounds as well as protecting plants from soil-derived pests and pathogens. Understanding of the molecular interplay between plants and their microbiota provides us with an ecological framework to manipulate the microbiota and its effects for sustainable agriculture. However, the complexity of these interactions, occurring in a very heterogenous environment, often makes it difficult to infer first principles.

In this project I used the model crop Hordeum vulgare (Barley) to investigate the molecular interplay taking place in its rhizosphere using reductionistic approaches.

For my first line of investigation, I used an established protocol for the preparation of synthetic communities (SynCom) in an axenic environment, I created taxonomically distinct SynComs, one consisting of only one phyla of bacteria, Actinobacteria, whilst the other was diverse and mimicked the taxonomic diversity that would be found in a natural barley rhizosphere microbiota. Using a combination of culture-dependent and culture-independent techniques, I investigated what effects these SynComs may be having on their host, as well as the efficacy of their colonisation, and if any of these bacteria could be associated with PGP qualities. I found that the exposure to a living, multi-phyla, community conferred a significant growth benefit to barley seedlings (Tukey post-hoc test p-value = <0.05). Using high throughput 16S rRNA gene amplicon sequencing, I found a distinct microbial configuration of the multi isolate SynCom in comparison to the Actinobacteria SynCom, and heat-killed controls (adonis R2 = 0.8, p-value = 0.0002). Finally, I discovered that the multi-isolate SynCom output was stable across replicated experiments and that there was preferential enrichment of Pedobacter sp., Chryseobacterium sp. and Stenotrophomonas sp. which could be significantly associated to the plant growth promotion phenotype (Wald test, Individual P value <0.01, FDR corrected).

For the second line of investigation, I contributed to an ongoing project, studying genetic differences of wild and domesticated barley genotypes at chromosome 3H in barley. These differences are modulated, at least in part by the recruitment of distinct rhizosphere microbiotas. We investigated if exudate composition was a causative mechanism underpinning microbiota diversification mediated by 3H locus. The exudates collected from these plants and subsequent elemental analysis of nitrogen and carbon content showed that the contents of these elements were stable across time-points, suggesting that total exudation may have reached a steady-state level at the time of microbiota establishment. However, genetic differences (at locus 3H) are not associated to different levels of these elements (Tukey post-hoc test p-value = >0.05); indicating that total carbon and nitrogen per se may not be the driver of microbiota diversification. Downstream GC-MS analysis providing a detailed analysis of the composition of primary metabolites of root exudates (i.e., sugars, amino acids and organic acids) will reveal whether genetic diversity at locus 3H is associated to a different “blend” of chemical compounds capable of shaping microbiota composition.

The findings from these investigations help to form a basis on how we can use a combination of omics technologies, along with SynComs, metagenomic and computational approaches to investigate the genetic mechanisms underpinning plant-microbe interactions in the rhizosphere. In turn, these approaches will expedite the application of the plant microbiota under more relevant agricultural conditions to improve crop nutrition and yield sustainably.
Date of Award2022
Original languageEnglish
SupervisorDavide Bulgarelli (Supervisor)

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