Bilateral BBSRC - Embrapa. Exploitation of the rhizosphere microbiome for sustainable wheat production

Current models predict that the world's population will reach 9 billion by 2050 and that crop yields will need to increase by 70-100% to sustain the population growth. Wheat is the UK's most highly grown cereal, with high average yields in comparison with the world average. However, there are concerns that rates of wheat yield increases have now stalled. In contrast, Brazil is currently a net wheat importer, but recent initiatives, including the cultivation of wheat in tropical savannah areas (the Cerrado), aim to increase production and productivity so that Brazil will initially become self-sufficient in wheat production and eventually an exporter of this globally important crop. Developing improved and advanced sustainable wheat production methods, therefore, is a priority research area for both countries, as evidenced by the joint wheat research programme between Embrapa and BBSRC.

Current intensive agricultural practices that depend on unsustainable levels of inorganic fertilisers, pesticides and other chemical inputs are environmentally damaging and unsustainable - it is clear that expansion of these agricultural practices to meet future needs is not economically or environmentally feasible and so we urgently need to explore other options to meet the global food security challenge.
Plants are colonized by an astounding number of microorganisms that can reach cell densities much greater than the number of plant cells. Recent research has found that soil microbes benefit crop plants in a number of ways, including improved plant nutritional status and disease suppression. However, the exact nature of these communities and the microbial partners required are poorly understood, let alone the mechanisms by which they benefit host plants. As such, it is important that we determine how the soil microbial community influences wheat plant health to achieve sustainable intensification of production.
Determining the optimum composition of soil microbiomes associated with plants, especially the root systems (the rhizosphere), to inform sustainable soil management strategies represents a novel and unique strategy to boost plant growth and health that has not previously been attempted. The rhizosphere microbiome can provide a range of functions to sustain plant development such as: nitrogen fixation, nutrient solubilisation or defence against pathogens. However, elucidation of the mechanisms underlying beneficial interactions between microbes and plants are not well understood. Understanding these mechanisms will be key to developing the rhizosphere microbiome for sustainable wheat production, and is central to the work planned in this proposal.

In this project, we will elucidate the relative importance of the host plant (both modern and ancestral wheat) in terms of genotype and root chemistry, as well as farming practices such as crop rotation and fertilisation regime, in shaping the wheat rhizosphere microbiome. The microbiome will be assessed using meta-genomic and meta-transcriptomic techniques; whereas the plant host genotype will be determined using diversity arrays technology and plant root chemistry through metabolomics. We will also identify keystone members of the rhizosphere microbiome through 'proof of principle' experiments to assess how manipulation of the microbiome structure influences plant performance. As such, we will obtain a holistic understanding of the factors influencing the microbiome structure, as well as how the microbiome influences both crop health and yield - both of which are required to optimise microbiome function for enhanced plant production in a sustainable manner.

The project aims to determine the optimum rhizosphere microbiome for crop-soil management to sustainably increase wheat yields. The project will be delivered through four work packages (WP). WP 1 and 2 aim to determine the main drivers of microbiome community structure and function. There are superb field resources at Rothamsted that we will utilise to assess the role of land-use change (Highfield field) and fertiliser regime (Broadbalk field) in shaping the microbiome. In addition, the Rothamsted heritage wheat field trials, which houses 40 long and short straw varieties, will be assessed. We will perform pot experiments using a further 15 ancestral wheat species with various combinations of the A, B and D genomes with diploid, tetraploid and hexaploid representation. We will compare microbiome phylogeny and functional diversity with modern cultivars.
We will perform next-generation amplicon sequencing to ascertain the prokaryotic and eukaryotic community composition. Next, we will perform shotgun metagenomics and meta-transcriptomics on a selection of these samples with contrasting microbiome structure and plant growth characteristics to gain unprecedented insights into the drivers of microbial community composition and function in the rhizosphere and link these to plant performance. We will isolate bacterial libraries from this selection of plant cultivars and these will be grouped phylogenetically and screened for plant growth-promoting functions.
In WP3, we will investigate root chemistry and its role in shaping the plant microbiome, and the key organisms in synthetic community experiments will be identified in WP4. Additionally in WP4, we will perform microbiome-swapping experiments in order to ascertain whether particular wheat cultivars are better able to recruit and utilise a more beneficial microbiome. Finally, we will perform small-scale field trials with microbial inoculants and communities that show plant boosting potential from the pot trials in WP4

Plant-microbe interactions in the rhizosphere can have significant impacts on crop yields. In this project, we will implement next-generation sequencing technologies to understand the dynamics of wheat rhizosphere microbial assembly and function. We will link this to plant genotype and root chemistry to obtain insights to promote the development of microbially enhanced sustainable agriculture. The research outcomes of this project will impact positively on a wide range of beneficiaries, as outlined below.

1) The project will be of value to a range of agricultural stakeholders and end-users in both the UK and Brazil. It will identify how the wheat rhizosphere microbiome is influenced by the host plant cultivar and fertilisation practice, as well as how the microbiome influences plant growth and yield. These are important considerations as current agricultural practices are not tenable and we require novel solutions to feed a growing global population in a sustainable manner. The results produced in this study could contribute to developing novel crop-land management practices, directly benefitting farmers in the long term. The research outcomes should also be relevant and transferrable to other important crops.
2) The academic community with interests in soil biology, as well as host-microbe interactions (both agricultural and medical) will directly benefit from the research outcomes of this project over the short, medium and long term. We will disseminate results to the research community through publications in broad scope, high impact peer-reviewed journals, presenting talks at international (e.g. ISME and Rhizosphere 5) and local conferences (SGM and SFAM meetings) and making data from the project publically available. The international research community will also benefit from the development and strengthening of relationships between researchers in the UK and Brazil.
3) The agricultural industry, in particular those with an interest in promoting sustainable agriculture, will directly and immediately benefit from this work, including crop breeders and farmers. The agro-tech industry will benefit from enhanced understanding of the importance of the microbiome and its function for plant yield. The creation of synthetic communities, as outlined in WP4, could also provide this sector with knowledge as how to optimise plant yields and this project is likely to identify microbial strains with potential to be used as inoculant strains. There will, therefore, also be an indirect economic benefit to the UK and Brazil in the long term as this information gained in this project will lead to improvements in the agricultural industry.
4) The outputs from this project will indirectly benefit government (e.g. DEFRA) and industrial organisations (e.g. AHDB, NFU) by guiding future policies regarding food security. By determining the optimum rhizosphere microbiome composition for maximum wheat yield return, the project will help to develop sustainable soil management practices with reduced inputs of resources, such as fertilisers, whilst increasing yield return and food security in the UK and Brazil.
5) Society will benefit through better cultivation of crops as well as through dissemination of knowledge to apply cutting edge next generation sequencing techniques and data interpretation in this project to other disciplines. The research outcomes of this project will directly improve food security over the short and long term for societies worldwide by informing the development of crop-soil strategies to increase the sustainability of wheat yields.
6) This project will have direct and immediate beneficial impacts on the environment. Understanding how the rhizosphere microbiome composition as part of soil management optimally affects wheat yield would reduce the inputs of fertilisers to crops, thereby reducing the damaging effects of fertilisers to soil and water ecologies.