CAREER: Discovering hidden drivers of rhizosphere symbiosis and parasitism

公共摘要-提案IOS-2047684标题：职业：根际寄生和共生的隐藏驱动因素该项目重点关注植物寄生线虫，以植物为食的微小蠕虫，估计造成全球25%的作物产量损失，每年耗资1000亿美元。已经发现自然发生的细菌生活在这些蠕虫中，这些蠕虫可能会驱动它们的生存并直接对植物造成破坏性影响。这些细菌存在于一些最具破坏性的线虫中，与目前用于控制蚊媒疾病的细菌有关，这表明它们可能有望用于农业控制策略，减少使用有毒化学品来控制线虫。该项目使用全球采样，DNA和RNA测序，计算机软件开发和新颖的实验来揭示这些广泛分布的细菌的功能，并弥合传统上分离的植物病理学，线虫学和微生物学领域，以克服理解根际生态的重大障碍。该项目还研究了气候变化和土地利用等压力因素如何影响这些细菌，线虫和植物之间的相互作用。该项目将通过整合由主办西班牙裔服务机构的生物信息学跨学科科学计划进行的研究活动，与以公民科学和根际生物建模为中心的国家研究外展计划，以及针对传统上代表性不足的群体的高中生基因组学当地同行指导计划，产生社会和教育影响。植物寄生线虫（PPN）在土壤中无处不在，对农作物造成重大损失，并对整个陆地生态系统的植物造成影响。最近的工作表明，这些线虫宿主细菌内共生体，包括Wolbachia和Cardinium，这是众所周知的昆虫在驱动其宿主的生物学作为生殖寄生虫或互利共生发挥关键作用。然而，这些内共生体在PPN中的作用尚不清楚。这个CAREER项目旨在揭示驱动这些内共生体，PPN和植物之间三方相互作用的动力学。研究活动将（1）通过鸟枪宏基因组学、种群基因组学、数据库挖掘和生物信息学确定全球范围内自然种群中PPN内共生体的生态和进化力量;（2）通过在根培养物、植物和透明土壤上进行共生体清除实验，使用宿主-共生体基因表达分析，直接测试内共生体对宿主线虫适合度、表型和植物寄生性的影响;（3）利用计算模型和温度胁迫下的移植植物群落研究PPN内共生体和胁迫因子（如气候和土地利用变化）的双重效应。这些实验将验证PPN内共生体通过控制宿主繁殖或提供铁/血红素或脂质来驱动三方动力学的假设，并探索生物防治的分子靶点。该项目通过开发和整合基于公民科学的采样，本科生生物信息学挑战计划和夏季高中基因组学学者计划来整合研究，教育和推广目标，以参与和培训本研究中代表性不足的群体。预计成果将形成对这些根际相互作用的新的基本理解，生成生物信息学软件，并改善多组学培训。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的知识价值和更广泛的影响审查标准进行评估来支持。

Public Abstract – Proposal IOS-2047684Title: CAREER: Hidden drivers of parasitism and symbiosis in the rhizosphereThis project focuses on plant-parasitic nematodes, tiny worms that feed on plants, causing an estimated 25% of crop yield loss globally and costing $100 billion annually. Naturally occurring bacteria have been discovered living within these worms that may drive their survival and direct their devastating impacts on plants. These bacteria, present in some of the most damaging nematodes, are related to bacteria currently used to control mosquito-borne diseases, suggesting they may hold promise for agricultural control strategies that reduce the use of toxic chemicals to control nematodes. This project uses global sampling, DNA and RNA sequencing, computer software development, and novel experiments to uncover the function of these widespread bacteria and bridge traditionally separated fields of plant pathology, nematology, and microbiology to overcome significant roadblocks to understanding rhizosphere ecology. This project also examines how stressors such as climate change and land use affect the interactions between these bacteria, nematodes, and plants. This project will have societal and educational impacts through integrating research activities performed by an interdisciplinary science program in bioinformatics at the hosting Hispanic Serving Institution with national research-outreach programs centered on citizen science and rhizosphere biomodelling, and a local peer-mentoring program in genomics for high school students targeting traditionally underrepresented groups.Plant-parasitic nematodes (PPNs) are ubiquitous in soils, causing significant losses to agricultural crops and impacts on plants across terrestrial ecosystems. Recent work shows these nematodes host bacterial endosymbionts, including Wolbachia and Cardinium, which are well-known in insects to play a critical role in driving their host’s biology as either reproductive parasites or mutualists. Yet, the role of these endosymbionts in PPNs is unknown. This CAREER project seeks to uncover the dynamics driving the tripartite interactions between these endosymbionts, PPNs, and plants. Research activities will (1) determine the ecological and evolutionary forces acting on PPN endosymbionts globally across natural populations through shotgun metagenomics, population genomics, database mining, and bioinformatics; (2) directly test endosymbiont impacts on host nematode fitness, phenotype, and plant parasitism through symbiont-clearing experiments on root-cultures, plants, and transparent soils, using host-symbiont gene expression analysis; and (3) investigate the dual effects of PPN endosymbionts and stressors such as climate and land use change using computational models and transplanted plant communities under temperature stress. These experiments will test the hypothesis that PPN endosymbionts drive the tripartite dynamics through controlling host reproduction or providing iron/heme or lipids and explore molecular targets for biocontrol. The project integrates research, education, and outreach objectives by developing and incorporating Citizen Science-based sampling, an undergraduate Bioinformatics Challenge program, and a summer high school Genomics Scholar program to engage and train underrepresented groups in this research. Outcomes are expected to form a new foundational understanding of these rhizosphere interactions, generate bioinformatics software, and improve training in multi-omics.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.