RUI: Diurnal and circadian regulation of the plant microbiome

植物与各种土壤微生物在整个生命周期中的特定相互作用对植物在自然界中的生长和生存起着重要的作用。植物作为固着生物，直接受到环境条件持续但可预见的变化的影响。这包括24小时的光/暗周期，植物根据这个周期来调整它们的各种生理过程。为了确保成功的相互作用，植物影响某些土壤微生物组的概况，甚至可能是生物学，使它们与植物生理过程中的每日变化保持同步。更好地理解这一动态调控将为理解一些土壤微生物成功地与植物根系相互作用的机制和过程提供有价值的信息。由于植物与土壤微生物的每日相互作用的总和是它们对植物长期益处的基础，因此在分子水平上理解这些日常相互作用是重要的。通过植物育种控制这些日常相互作用，可能会通过与某些天然微生物的有效相互作用来提高植物生产力，减少农业作业对昂贵的合成肥料的依赖。该项目还提供了宝贵的机会，让本科生和高中生参与科学研究，并向他们介绍自然和可持续的食品生产方法。微生物群对宿主的健康和营养状况有深远的影响。在动物中，光和宿主的生物钟，一个细胞自主的内部生物计时器，在许多代谢和生理过程中产生大约24小时的节律，调节宿主-微生物组的相互作用。这项研究的第一个目的是利用元基因组学方法研究拟南芥生物钟在其与内圈(根部内部)细菌微生物群相互作用中的作用。植物的生物钟将在环境和遗传上受到破坏。将通过在DNA和RNA水平上对细菌16S-核糖体(R)基因进行测序来确定内层和土壤细菌谱的24小时波动，以更好地了解生物钟调节的作用。第二个目标是使用后转录切除法确定这种动态相互作用背后的根和细菌途径。根和细菌的转录本都将去除核糖体RNA，并进行测序，以确定一些内层细菌与拟南芥根相互作用的可能机制和过程。第三个目标是使用生理学方法研究每日细菌波动对植物表现的影响。通过在正常的光/暗周期或长时间持续光照两代中种植拟南芥、番茄和大豆植株，土壤将得到调节。通过每周测量总叶径和叶柄长度、株高、叶绿素含量和气孔导度来评估拟南芥、番茄和大豆植株在这些改良土壤上的表现。这项研究的结果将是对昼夜节律对植物寄主和植物内生微生物之间关系的影响的综合分析。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

The specific interactions of plants with various soil microorganisms throughout their life cycle play important roles in plant growth and survival in nature. Being sessile organisms, plants are directly affected by the continuous but predictable changes in environmental conditions. This includes the 24-hour light/dark cycle according to which plants adjust their various physiological processes. To ensure successful interaction, plants influence the profile and possibly the biology of certain groups of soil microorganisms such that they stay in synchrony with the daily changes in the plant physiological processes. A better understanding of this dynamic regulation would provide valuable information towards understanding the mechanisms and processes through which some soil microbes successfully interact with plant roots. Since the summation of the daily plant interactions with the soil microbes is the basis for their long-term benefits on the plants, understanding these daily interactions at the molecular level is important. The manipulation of these daily interactions through plant breeding may allow for improved plant productivity through efficient interaction with certain natural microbes, reducing the dependency of agricultural operations on expensive synthetic fertilizers. This project also provides valuable opportunities to engage undergraduate and high-school students in scientific research and introduce them to the natural and sustainable approaches of food production. The microbiome has profound effect on a host's health and nutritional status. In animals, light and the host's circadian clock, a cell-autonomous internal biological timekeeper that generates roughly 24-hour rhythms in many metabolic and physiological processes, regulate host-microbiome interactions. The first aim of this research is to study the roles of the Arabidopsis thaliana's circadian clock on its interaction with the bacterial microbiome in the endosphere (inhabiting the root interior) using a metagenomic approach. The plant circadian clock will be disrupted environmentally and genetically. The 24-hour fluctuations in the endospheric and soil bacterial profiles will be determined by sequencing bacterial 16S-ribosomal (r) genes at both the DNA and RNA level to better understand the role of the circadian clock regulation. The second aim is to identify the root and bacterial pathways underlying this dynamic interaction using a metatranscriptomic approach. Both root and bacterial transcriptomes will be depleted of ribosomal RNAs and sequenced to identify possible mechanisms and processes through which some endospheric bacteria interact with Arabidopsis roots. The third aim is to investigate the role of daily bacterial fluctuations on plant performance using a physiological approach. Soils will be conditioned by growing Arabidopsis, tomato, and soybean plants in normal light/dark cycles or prolonged constant light for two generations. The performance of Arabidopsis, tomato, and soybean plants on these conditioned soils will be assessed by weekly measurements of total leaf diameter and petiole length, plant height, chlorophyll content, and stomatal conductance. The outcome from this research will be an integrated analysis of circadian impacts on the relationship between plant hosts and their endophytic microbiomes.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.