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

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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.