Deciphering the contribution of root hairs in barley to the structure and function of the rhizosphere bacterial microbiota

Abstract

The thin layer of soil surrounding and influenced by plant roots, termed the rhizosphere, defines a distinct and selective microhabitat compared to that of the surrounding soil: the bulk soil. The microbial populations that reside in the rhizosphere, commonly referred to as the rhizosphere microbiota, participate in a variety of interactions with their host plant ranging from parasitic to mutualistic relationships. Due to the contribution of the microbiota to pathogen protection and nutrient uptake the rhizosphere microbiota has emerged as a determinant of crop yield. Consequently, a better understanding of plant-microbiota interactions in the rhizosphere can pave the way for novel applications enhancing sustainable crop yield and global food security. Experimental evidence indicates that the host plant is the driver of, at least in part, the rhizosphere microbiota, but genetic relationships underpinning these interactions are not fully understood. Filling this knowledge gap will allow plant breeders to select novel crops which better interact with the soil biota and, at the same time, biotechnologists can profit from microbial genetic information to develop a new generation of inoculants for agriculture.

In this PhD project barley (Hordeum vulgare L.), the world’s 4th and UK’s 2nd most cultivated cereal, was used as an experimental model to dissect plant-bacteria interactions in the rhizosphere. The hypothesis that root hairs: the tubular outgrowths of the root epidermis, modulate the physical and chemical environment in the rhizosphere to facilitate the colonisation of members of the microbiota implicated in mineral uptake was tested. To test this hypothesis, three interconnected experimental approaches were developed:

By using 16S rRNA gene amplicon sequencing, it was demonstrated that the presence and development of root hairs are a determinant of nearly one fifth of the barley rhizosphere microbiota, with a bias for members of the order Actinomycetales, Burkholderiales, Rhizobiales, Sphingomonadales, and Xanthomonadales.

In order to gain further insights into the molecular basis of this differential recruitment, the project went on to investigate both the physical and chemical environment conditioned by root hairs. A pilot investigation of the rhizodeposition profiles using GC-MS of wild type and root hair mutants revealed that plant-genotype dependent patterns among the 69 amino and organic acids were detected and a further 23 sugars and sugar alcohols detected, pointing at root secretion as an additional selective layer in the barley rhizosphere. Additionally, an amplicon sequencing survey of soil cores with different density, mimicking presence/absence of plant root hairs, revealed that this physical parameter is capable of triggering the differential enrichment of bacteria associated with the orders Bacillales, Burkholderiales and Xanthomonadales but not Actinomycetales. Thus, the physical perturbation of the soil environment alone cannot be the sole recruitment cue for the barley microbiota. However, it does indicate that soil density contributes, in part, to microbial recruitment.

Finally, to discern the full genetic potential of plant-associated bacteria, an indexed bacterial collection of the barley microbiota was constructed by isolating, on synthetic media, individual rhizosphere bacteria. A total of 85 isolates were further selected for full genome sequencing including members of the orders Actinomycetales, Flavobacteriales and Xanthomonadales. A comparative genomic approach was deployed to identify plant-growth promoting traits among 53 of these isolates.

This experimental work was complemented with a critical appraisal of efforts to communicate to and increase the awareness of the general public on the importance of the plant microbiota for global food security.

In the long term, the scientific outputs of this project can be deployed to devise novel strategies aimed at enhancing sustainable crop production in the UK and to globally and increase the awareness of the general public to global food security, particularly with the potential of the bacterial isolate library to be used in collaboration with multiple research groups investigating a range of microbial approaches to improve crop sustainability.

Date of Award	2020
Original language	English
Sponsors	Biotechnology and Biological Sciences Research Council & James Hutton Ltd.
Supervisor	Davide Bulgarelli (Supervisor)