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

植物根与各种微生物群落密切相关，包括细菌等原核生物和真菌等真核生物。这些微生物选择性地从栖息在土壤中的不同群落中招募，这是由于它们在根部渗出的碳上生长。根相关微生物以多种方式与植物相互作用;一些作为促进植物生长的共生体，而另一些是可能对生长和发育产生有害影响的寄生虫。在过去的几十年中，通过使用对特定病原体具有抗性的作物基因型以及通过杀虫剂，已经实现了对根际微生物的一些控制，这可以减少某些病原体在根部的定殖。然而，有害生物群向农作物根际的补充每年造成全球数千亿英镑的损失。对根际微生物群落的预测和调控具有潜在的社会效益，大部分根际微生物群落的研究都是在不同的地点进行的，所使用的技术不允许对存在的类群进行强有力的鉴定。因此，人们根本不了解群落是如何从土壤进入根际的，特别是在景观尺度上运作的过程。此外，我们了解微生物群落如何相互作用以及与植物根系相互作用的能力在很大程度上限于适合在实验室中研究的特定微生物。下一代测序（NGS）技术的进步为我们解决根际微生物群落结构和功能的能力提供了范式转变的机会。我们将使用最新的NGS方法对塑造根际群落组成的过程进行根本性的新理解，并解开群落内决定其对植物影响的相互作用和功能。我们将使用油菜（OSR）作为模型系统，因为OSR产量每年损失6- 25%，称为产量下降，这是由于有害根际生物群的发展，对此没有处理。至关重要的是，我们早期的工作已经开始揭示与从健康到患病OSR作物的变化相关的微生物变化，确定了与产量下降相关的病原体复合体。我们将阐明土壤生物多样性，当地气候，土壤特性，旋转和地理距离在形成根际微生物群落的相对作用，我们将特别寻求了解控制根际有害生物群富集的因素。我们将解决特定的微生物-微生物相互作用，导致排斥或招募微生物，包括病原体。我们将使用强大的元转录组学方法来确定植物和根际微生物表达的特定基因。我们将在三个现场的旋转实验中研究这些变化，以便我们能够了解与从健康根际到产量受到有害生物群发展影响的根际变化相关的具体变化。最后，我们将确定潜在的操纵招募土壤生物群进入根际，包括有害生物，利用作物基因型和土壤管理。重要的是，我们的工作将在田间进行，使用OSR的商业作物，因此我们的工作结果将具有直接的农学相关性。除了提供根际生物学的基本新的理解，我们将获得在OSR产量下降的具体理解。这将包括为工业利益攸关方提供切实机会的战略，以在短期和中期内提高作物生产力。

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.