Exploiting the root microbiome to improve plant fitness

描述（由申请人提供）：生产性粮食作物的种植是一个重大的公共卫生问题，因为良好的营养是促进人类健康的基础。然而，依赖化肥是不可持续的，使用化肥造成的环境污染威胁着人类健康。产生肥沃作物的替代策略是利用植物促生长细菌（PGPB），其存在于邻近植物根（根际）的土壤中和根内生隔室（EC）内的不同微生物群落中。作为对植物来源碳源的回报，PGPB通过有益的免疫刺激和增加植物的生物可利用养分来增加植物生物量。具体而言，PGPB是氮的宝贵来源，是大多数天然土壤中的限制性营养素和化学肥料的主要成分。不幸的是，目前用PGPB种植农田作物的努力经常失败， 这可能是由于与原生土壤微生物群落的竞争和有限的EC定殖效率。因此，有必要研究EC定植PGPB的背景下，根微生物群落和不断变化的氮条件。赞助商实验室先前的工作使用16 S核糖分型来定义在自然土壤中生长的模式植物拟南芥的根微生物组。根EC的微生物组成是两个分类上不同的，比散装土壤的多样性较低，这表明有植物和/或细菌来源的因素支配根EC社区组合。在低氮胁迫下，植物调节氮同化代谢途径的活性，并改变释放到根际的根系分泌物的组成。结合根构型的全球变化，这些氮素状况的反应可能会影响根际群落结构。该项目的目标是确定根微生物组的结构如何响应氮胁迫而变化，以及这些社区水平的变化如何影响社区内单个PGPB的有益活动。通过结合细菌遗传学，生化测定和比较基因组学，该项目还将有助于确定核心EC殖民和PGP性状所需的改善植物生长在低氮条件下。这些努力的结果将有助于我们了解直接影响大田作物健康的自然根际群落的动态。重要的是，该项目的结果还将有助于开发基于PGPB的新型策略，这些策略可以在自然微生物土壤群落中竞争，以环境友好的方式提高作物表现，通过减少有害肥料的使用和改善营养直接改善人类健康。

DESCRIPTION (provided by applicant): The cultivation of productive food crops is a major public health issue, as good nutrition is the foundation for promoting human fitness. Yet, reliance on chemical fertilizers is not sustainable and subsequent environmental contamination from their use threatens human health. An alternative strategy for generating fertile crops is to exploit plant growth-promoting bacteria (PGPB) that exist within diverse microbial communities in soil adjacent to plant roots (rhizosphere) and inside the root endophytic compartment (EC). In return for plant-derived carbon sources, PGPB increase plant biomass through beneficial immune stimulation and increasing bioavailable nutrients to the plant. Specifically, PGPB are a valuable source of nitrogen, the limiting nutrient in most natural soils and the main component of chemical fertilizers. Unfortunately, current efforts to inoculate field crops with PGPB often fail, likely due to competition with native soil microbial communities and limited EC colonization efficiency. Thus, there is a demand to study EC colonization by PGPB both in the context of the root microbiome community and changing nitrogen conditions. Previous work in the sponsor's lab used 16S ribotyping to define the root microbiome of the model plant Arabidopsis thaliana grown in natural soils. The microbial composition of the root EC was both taxonomically distinct from and less diverse than that of bulk soil, suggesting there are plant- and/or bacterial-derived factors governing root EC community assemblage. Under low nitrogen stress, plants modulate activity of metabolic pathways involved in nitrogen assimilation and change the composition of root exudates released into the rhizosphere. Combined with global changes in root architecture, these nitrogen status responses likely influence rhizosphere community structure. The goal of this project is to determine how the structure of the root microbiome changes in response to nitrogen stress, and how these community-level changes influence beneficial activities of individual PGPB within the community. By combining bacterial genetics, biochemical assays, and comparative genomics, this project will also help define core EC colonization and PGP traits required for improving plant growth in low nitrogen conditions. Results from these efforts will contribute to our understanding of the dynamics of natural rhizosphere communities that directly impact the health of field crops. Importantly, results from this project will also aid in the development of novel PGPB-based strategies that can compete in natural microbial soil communities to increase crop performance in an environmental friendly matter, directly improving human health through reduced usage of harmful fertilizers and improved nutrition.