Roots of decline? Assembly and Function of the Rhizosphere Microbiome in Relation to Yield Decline

Plant roots live in close association with diverse communities of microbes, including prokaryotes such as bacteria, and eukaryotes such as fungi. These microbes are selectively recruited from the diverse communities which inhabit soil as a result of their growth on carbon exuded from roots. Root associated microbes interact with the plant in a myriad of ways; some act as symbionts which promote plant growth, while others are parasites which can have deleterious impacts on growth and development. Some control of rhizosphere microbes has been achieved in the last few decades through the use of crop genotypes resistant to specific pathogens, and via pesticides, which can reduce colonization of roots by some pathogens. However, the recruitment of detrimental biota to the rhizosphere of crop plants is responsible for global losses of many hundreds of billions of pounds annually. Strategies to robustly predict and manipulate the communities which assemble in the root zone, termed the rhizosphere, has potential to deliver great benefits to society.

Most studies of rhizosphere microbial communities have been conducted at disparate sites using techniques which do not allow robust identification of taxa present. As a result, there is a fundamental lack of understanding about how communities become recruited from the soil into the rhizosphere, particularly processes which operate on the landscape scale. Furthermore, our ability to understand how microbial communities interact with each other and with plant roots is largely limited to specific microbes which are amenable to study in the laboratory. Advances in the power of next generation sequencing (NGS) technologies provide opportunities for a paradigm shift in our ability to resolve the structure and function of rhizosphere microbial communities.

We will use the latest NGS methods to derive fundamental new understanding of the processes which shape the composition of rhizosphere communities, and unravel the interactions and functions within the community which determine their effects on plants. We will use oilseed rape (OSR) as a model system, because OSR yields suffer 6-25 % annual losses, termed yield decline, because of the development of detrimental rhizosphere biota, for which there is no treatment. Crucially, our earlier work has begun to unravel microbial shifts associated with a change from healthy to diseased OSR crops, identifying a complex of pathogens associated with yield decline.

We will elucidate the relative roles of soil biodiversity, local climate, soil properties, rotation and geographical distance in shaping the rhizosphere microbial community, and we will particularly seek to understand factors which control the enrichment of detrimental biota within the rhizosphere. We will resolve specific microbe-microbe interactions which lead to exclusion or recruitment of microbes, including pathogens.

We will use powerful metatranscriptomic methods to determine the specific genes which are expressed by plants and microbes in the rhizosphere. We will investigate these changes in rotational experiments at three field sites, so that we can understand the specific changes associated with a change from a healthy rhizosphere to one in which yield is impacted by development of an detrimental biota. Lastly we will identify the potential to manipulate recruitment of soil biota into the rhizosphere, including detrimental biota, using crop genotype and soil management.

Importantly, our work will be conducted in the field, using commercial crops of OSR, so that the results of our work will have immediate agronomic relevance. In addition to providing fundamental new understanding of rhizosphere biology, we will derive specific understanding of yield decline in OSR. This will include strategies to deliver tangible opportunities for industrial stakeholders to increase crop productivity in the short and medium term.

Using established field sites across the UK, rhizosphere samples will be collected from 32 OSR cropping locations. Prokaryotic and eukaryotic microbe community composition will be determined using amplicon sequencing. Communities will be differentiated into core species which are widely distributed and locally abundant, and satellite species which are infrequent and rare. We will elucidate the role of management, environmental variables and distance as drivers of community assembly. Co-occurrence and co-exclusion relationships of rhizosphere taxa will also be determined. We will also focus on understanding those factors which determine distribution and assembly of specific taxa which our earlier work has suggested contribute to OSR yield decline. We will also determine relationships between microbiome composition and yield. Field experiments will be used to investigate changes in microbial community organisation and functioning during the transition from a healthy to a diseased state associated with yield decline. We will use 3 separate locations in order to investigate the extent to which changes in function are conserved across the landscape. Rhizosphere soil metatranscriptomes and root transcriptomes will be sequenced, and in particular, networks associated with microbial pathogenesis, and host defence and nutrition will be characterised. We will investigate the potential to manipulate the assembly of the rhizosphere microbiome through crop genotype and soil management. Four OSR genotypes which we have shown have contrasting root metabolomes will be grown in rotational field experiments and targeted amplicon sequencing used to study community assembly, including pathogens associated with yield decline. We will use a unique field resource at Rothamsted to determine scope for using soil management to influence recruitment of taxa into the root microbiome, including pathogens associated with yield decline.

Plant -microbe interactions in the rhizosphere can have major impacts on crop yields, with pathogens generating global losses of billions of pound annually. In this project we provide fundamental new understanding about the factors which control the assembly of rhizosphere communities, and will use cutting edge next generation sequencing (NGS) methods to unravel the mechanisms by which plants affect, and are affected by, microbial communities. Importantly, we will use oilseed rape (OSR) as the model system for our research since it suffers from 'yield decline' arising from the development of a detrimental microbiome, which causes UK losses of £43-86 million/year. Our research will impact the following groups:

(1) The academic community, particularly those with interests in agricultural systems biology, plant-soil interactions, plant pathology and environmental microbiology. Researchers will particularly benefit from our use of NGS approaches to unravel plant-microbe-soil interactions, and from engineering the rhizosphere biota for beneficial functions. We will engage with researchers through journal papers and at key scientific conferences. The sequencing experiments are a valuable experimental resource for workers in related fields. We will open this data to other researchers for complimentary work, providing added value to the experiments.

(2) The agricultural industry, particularly stakeholders with an interest in promoting productivity and sustainability, including crop breeders, land managers and farmers. Industry will benefit from new scientific knowledge which will provide novel approaches to manage the rhizosphere: (a) we will identify microbial contributors to yield at the landscape scale, including, potentially, new pathogens, and soil and environmental characteristics which relate to pathogen distribution. This will underpin development of new crop protection strategies (eg via pesticides) (b) we will identify co-exclusion and co-occurrence relationships within the microbiome which could facilitate development of novel biocontrol approaches (c) we will identify changes in microbial function, and associated plant responses as it changes from a healthy to unhealthy state. This could lead to targeted gene and physiology based crop improvement strategies (d) we will provide soil management options to mitigate development of yield decline; this will provide tangible outputs to farmers within the project timeframe (e) we will elucidate the potential for rhizosphere microbiome engineering through crop genotype which could lead to rotational strategies, and breeding approaches, to manipulate the rhizosphere.

While providing outputs to the OSR industry (see letters of support from United Oilseeds and Elsoms) the principles of the work, and the tools we will develop, will be relevant to stakeholders across the industry (see letters of support from Agrii and Origin Fertilisers).

(3) Government (eg Defra) and industry organisations (eg NFU, HGCA) with a role in supporting and promoting the competitiveness of UK agriculture; in particular the research addresses the priorities of HGCA (see letter of support).

We will form a project steering group with industrial and government stakeholders which will advise on technology transfer. We will engage with these stakeholders through workshops at Warwick in months 24 and 42, project newsletters and the project website, which will provide a summary of project progress.

We also intend to engage strongly with the public. In addition to press releases, production of a video iCast and a project website, we plan a series of events at the Natural History Museum, London, where science derived from the project will be communicated directly to the public, including schoolchildren.

Society will benefit from trained researchers adept at multidisciplinary working, with skills in ecology, agricultural science and microbiology, and cutting edge NGS methods.