Collaborative Research: Dimensions: Integrating phylogenetics, ecophysiology, and transcriptomics to understand the diversity of hornwort-cyanobacterium symbiosis

合作研究：维度：整合系统发育学、生态生理学和转录组学，了解金鱼藻-蓝藻共生的多样性

• 批准号: 1831428
• 负责人: Fay-Wei Li
• 金额: $ 112.32万
• 依托单位: Boyce Thompson Institute Plant Research
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-01-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1831428&HistoricalAwards=false
• 关键词: Collaborative; Research; Dimensions; Integrating; phylogenetics

Only a few remarkable plants can form beneficial partnerships with nitrogen-fixing bacteria. These include a few species of bryophytes, ferns, cycads, and a small group of flowering plants. Because of their importance to crops, a lot of research has focused on the relationship between legumes and the bacteria that fix nitrogen for them - rhizobia. Much less is known about an even more widespread partnership between plants and cyanobacteria. Because cyanobacteria are generally less dependent on the plant host than rhizobia, they could be an excellent partner for engineering helpful nitrogen fixation into crop plants. However, our current understanding of plant-cyanobacterium partnerships is poor. The species and genetic diversity of helpful cyanobacteria is virtually unexplored. Similarly, the plant genes involved in these partnerships remain unknown. Hornworts, one of the three bryophyte lineages, are an outstanding system to study plant-cyanobacterial relationships. This study will investigate phylogenetic, functional, and genetic aspects of the hornwort-cyanobacterium partnership. In doing so, the research will explore an array of questions that will provide new insights into how these unique plants interact with their bacterial partners to fix nitrogen. One postdoctoral fellow, three graduate, ten undergraduate, and five high school students will be trained. In partnership with the Science Teachers Association of New York State, an educational video will be made. This video will showcase the various forms of plant-cyanobacterium relationships. The goals of this research are first to uncover the phylogenetic diversity of hornworts and cyanobionts. Then to elucidate the functional diversity of symbiotic nitrogen-fixation. Finally, the research will reveal the genetic components of the association between hornworts and their cyanobionts. The researchers will reconstruct the hornwort tree-of-life using a phylogenomic approach. Then, for each hornwort sample, the genetic diversity of the cyanobiont community will be characterized. Comparing the hornwort and cyanobiont diversity will shed light on host-symbiont specificity. The research will also study patterns of co-evolution, and the roles of cyanobacterial symbiosis in hornwort evolution. Next, population and microcosm studies will be used to test the interaction among hornwort microbiome diversity, environmental variables, and nitrogen-fixation rates. Finally, multiple pure hornwort and cyanobiont cultures will be isolated. Once isolated, their symbioses will be reconstituted under controlled environmental conditions in the laboratory. Time-course RNA-seq data will be generated to identify putative genes that are core for symbiosis establishment and linked to variation in symbiotic behaviors. The results of this research will enable comparisons across all three major forms of plant-microbe mutualistic interaction to fully characterize the evolutionary and genetic underpinnings of symbioses.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.

只有少数杰出的植物可以与固氮细菌形成有益的伙伴关系。这些植物包括几种蕨类植物、苏铁和一小群开花植物。由于它们对农作物的重要性，许多研究都集中在豆科植物和为它们固氮的细菌-根瘤菌之间的关系上。关于植物和蓝藻之间更广泛的伙伴关系，我们知道的要少得多。由于蓝细菌通常比根瘤菌对植物宿主的依赖性更小，因此它们可能是将有益的固氮工程化到作物中的极好伙伴。然而，我们目前对植物-蓝细菌伙伴关系的理解很差。有益的蓝藻的物种和遗传多样性几乎是未开发的。同样，参与这些伙伴关系的植物基因仍然未知。角苔是苔藓植物三大谱系之一，是研究植物与蓝细菌关系的杰出系统。本研究将探讨金鱼藻-蓝细菌合作关系的系统发育，功能和遗传方面。在这样做的过程中，该研究将探索一系列问题，这些问题将为这些独特的植物如何与它们的细菌伙伴相互作用以固氮提供新的见解。将培养一名博士后，三名研究生，十名本科生和五名高中生。将与纽约州科学教师协会合作制作一部教育录像。本视频将展示植物与蓝藻关系的各种形式。本研究的目的是首次揭示金鱼藻和蓝藻的系统发育多样性。阐明共生固氮功能的多样性。最后，这项研究将揭示金鱼藻和它们的蓝藻之间的关联的遗传成分。研究人员将使用基因组学方法重建金鱼藻的生命树。然后，对于每个金鱼藻样本，氰生菌群落的遗传多样性将被表征。比较金鱼藻和蓝藻的多样性将揭示宿主共生体的特异性。这项研究还将研究共同进化的模式，以及蓝细菌共生在金鱼藻进化中的作用。接下来，人口和微观研究将用于测试金鱼藻微生物组多样性，环境变量和固氮率之间的相互作用。最后，将分离多种纯金鱼藻和蓝藻培养物。一旦分离，它们的共生体将在实验室的受控环境条件下重建。将生成时程RNA-seq数据，以确定推定的基因，这些基因是共生建立的核心，并与共生行为的变化有关。这项研究的结果将使所有三种主要形式的植物-微生物互惠互动的比较，以充分表征共生的进化和遗传基础。这个奖项反映了NSF的法定使命，并已被认为是值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估的支持。

项目成果

Extremely low genetic diversity in the European clade of the model bryophyte Anthoceros agrestis

• DOI: 10.1007/s00606-020-01676-6
• 发表时间: 2020-04-04
• 期刊: PLANT SYSTEMATICS AND EVOLUTION
• 影响因子: 1.9
• 作者: Dawes, Thomas N.;Villarreal, Juan Carlos A.;Forrest, Laura L.
• 通讯作者: Forrest, Laura L.

Decolonizing botanical genomics

植物基因组学去殖民化

• DOI: 10.1038/s41477-021-01041-6
• 发表时间: 2021
• 期刊: Nature Plants
• 影响因子: 18
• 作者: Li, Fay-Wei

Dynamic plastid and mitochondrial genomes in Chaetopeltidales (Chlorophyceae) and characterization of a new chlorophyte taxon

• DOI: 10.1002/ajb2.16015
• 发表时间: 2022-06-09
• 期刊: AMERICAN JOURNAL OF BOTANY
• 影响因子: 3
• 作者: Robison，Tanner;Nelson，Jessica M.;Li，Fay-Wei
• 通讯作者: Li，Fay-Wei

Complete Genomes of Symbiotic Cyanobacteria Clarify the Evolution of Vanadium-Nitrogenase

• DOI: 10.1093/gbe/evz137
• 发表时间: 2019-07-01
• 期刊: GENOME BIOLOGY AND EVOLUTION
• 影响因子: 3.3
• 作者: Nelson, Jessica M.;Hauser, Duncan A.;Li, Fay-Wei
• 通讯作者: Li, Fay-Wei

A novel thylakoid-less isolate fills a billion-year gap in the evolution of Cyanobacteria

• DOI: 10.1016/j.cub.2021.04.042
• 发表时间: 2021-07-12
• 期刊: CURRENT BIOLOGY
• 影响因子: 9.2
• 作者: Rahmatpour, Nasim;Hauser, Duncan A.;Li, Fay-Wei
• 通讯作者: Li, Fay-Wei