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

衰退的根源？

• 批准号: BB/L025892/1
• 负责人: Gary Bending
• 金额: $ 100.76万
• 依托单位: University of Warwick
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FL025892%2F1
• 关键词: Roots; decline; Assembly; Function; Rhizosphere

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.

植物的根与不同的微生物群落密切相关，包括原核生物，如细菌和真核生物，如真菌。这些微生物是有选择性地从土壤中的不同群落中招募的，因为它们靠根系分泌的碳生长。与根相关的微生物以无数种方式与植物相互作用；有些作为共生体促进植物生长，而另一些则是寄生虫，对植物的生长和发育产生有害影响。在过去的几十年里，通过使用对特定病原体具有抗性的作物基因型和通过杀虫剂，可以减少某些病原体在根上的定植，已经实现了对根际微生物的一些控制。然而，有害生物群向作物根际的吸收每年造成全球数千亿英镑的损失。强有力地预测和控制聚集在根区（根际）的群落的策略有可能给社会带来巨大的利益。大多数根际微生物群落的研究都是在不同的地点进行的，使用的技术不允许对存在的分类群进行强有力的鉴定。因此，对于群落是如何从土壤吸收到根际的，特别是在景观尺度上起作用的过程，人们从根本上缺乏了解。此外，我们了解微生物群落如何相互作用以及与植物根系的能力在很大程度上仅限于可以在实验室研究的特定微生物。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方法来获得对形成根际群落组成的过程的基本新认识，并揭示群落内部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，因为由于有害根际生物群的发展而没有处理，OSR产量每年损失6- 25%，称为产量下降。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作物变化相关的微生物变化，确定与产量下降相关的病原体复合物。我们将阐明土壤生物多样性、当地气候、土壤性质、轮作和地理距离在形成根际微生物群落中的相对作用，我们将特别寻求了解控制根际有害生物群富集的因素。我们将解决导致微生物（包括病原体）排斥或招募的特定微生物-微生物相互作用。我们将使用强大的亚转录组学方法来确定植物和微生物在根际表达的特定基因。我们将在三个场点进行轮作试验，调查这些变化，以便了解从健康根际到产量受到有害生物群影响的根际变化的具体变化。最后，我们将确定利用作物基因型和土壤管理操纵土壤生物群向根际吸收的潜力，包括有害生物群。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艺学意义。除了提供对根际生物学的基本新认识外，我们还将获得对OSR产量下降的具体理解。这将包括在短期和中期为工业利益攸关方提供切实机会以提高作物生产力的战略。

项目成果

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes.

对真核生物的分类，命名法和多样性进行修订。

• DOI: 10.1111/jeu.12691
• 发表时间: 2019-01
• 期刊: The Journal of eukaryotic microbiology
• 作者: Adl SM;Bass D;Lane CE;Lukeš J;Schoch CL;Smirnov A;Agatha S;Berney C;Brown MW;Burki F;Cárdenas P;Čepička I;Chistyakova L;Del Campo J;Dunthorn M;Edvardsen B;Eglit Y;Guillou L;Hampl V;Heiss AA;Hoppenrath M;James TY;Karnkowska A;Karpov S;Kim E;Kolisko M;Kudryavtsev A;Lahr DJG;Lara E;Le Gall L;Lynn DH;Mann DG;Massana R;Mitchell EAD;Morrow C;Park JS;Pawlowski JW;Powell MJ;Richter DJ;Rueckert S;Shadwick L;Shimano S;Spiegel FW;Torruella G;Youssef N;Zlatogursky V;Zhang Q
• 通讯作者: Zhang Q

The eukaryome: Diversity and role of microeukaryotic organisms associated with animal hosts

• DOI: 10.1111/1365-2435.13490
• 发表时间: 2019-12-27
• 期刊: FUNCTIONAL ECOLOGY
• 影响因子: 5.2
• 作者: del Campo, Javier;Bass, David;Keeling, Patrick J.
• 通讯作者: Keeling, Patrick J.

Relationships between yield, rotation length, and abundance of Olpidium brassicae and Pyrenochaeta sp. in the rhizosphere of oilseed rape

• DOI: 10.1016/j.apsoil.2019.103433
• 发表时间: 2020-03-01
• 期刊: APPLIED SOIL ECOLOGY
• 影响因子: 4.8
• 作者: Bennett, Amanda J.;Hilton, Sally;Bending, Gary D.
• 通讯作者: Bending, Gary D.

A Novel Signaling Pathway Required for Arabidopsis Endodermal Root Organization Shapes the Rhizosphere Microbiome.

• DOI: 10.1093/pcp/pcaa170
• 发表时间: 2021-05-11
• 期刊: Plant & cell physiology
• 影响因子: 4.9
• 作者: Durr J;Reyt G;Spaepen S;Hilton S;Meehan C;Qi W;Kamiya T;Flis P;Dickinson HG;Feher A;Shivshankar U;Pavagadhi S;Swarup S;Salt D;Bending GD;Gutierrez-Marcos J
• 通讯作者: Gutierrez-Marcos J

Extreme rainfall affects assembly of the root-associated fungal community.

• DOI: 10.1111/nph.14990
• 发表时间: 2018-12
• 期刊: The New phytologist
• 作者: Barnes CJ;van der Gast CJ;McNamara NP;Rowe R;Bending GD
• 通讯作者: Bending GD