CAREER: PHIRED UP: Phage-Host Interactions integrated into Research on Epiphytic Ecology and Disease using Undergraduate Participation

噬菌体是感染细菌的病毒，是地球上最普遍和最多样化的实体，感染了绝大多数细菌。感染和杀死其细菌宿主细胞的裂解酶可以改变细菌群落概况（谁在那里，以什么密度）以及菌株之间的竞争动力学，具有塑造宿主相关微生物组的明显潜力。噬菌体也可以影响真核生物疾病的结果，直接通过感染和杀死宿主内的细菌病原体，或间接通过改变微生物组，这是已知的在许多植物和动物疾病中发挥作用。该项目使用多年来每月从城市环境（伯克利市）中对梨树进行采样，并进行大规模基因组测序，以确定梨树在火枯病中的作用，火枯病是许多果园物种的农业相关疾病。通过使用同行指导阶梯完全整合本科生研究，这种对叶相关细菌微生物组中噬菌体感染和群落动态的探索将有助于确定哪些细菌是病原体的天然目标，以及这些病原体在病原体密度和微生物群落组成方面的变化。细菌和噬菌体培养方法将与梨树微生物组的多组学分析相结合，以充分阐明微生物如何适应自然界中的细菌，以及这种适应如何影响健康和疾病中的微生物组。长期目标是利用这些关于自然噬菌体介导的选择的数据来确定是否以及如何利用噬菌体来重塑微生物群落和预防疾病。在实验室中已经广泛地研究了细菌和它们的细菌宿主的进化相互作用，但是很少有研究在自然界中研究这些动态。该项目整合了四个模块的本科生研究计划，高通量，细菌和病毒群落的培养独立测序，使用新型梨树疾病系统（Callery 'Bradford'梨树感染农业相关病原体欧文氏菌）来研究细菌群落周转和疾病中的作用。通过教学和研究的紧密结合，依赖于培养的筛选和独立于培养的“组学”方法的结合将允许在短（每月）和长（每年）的时间尺度上跟踪细菌噬菌体动态。总的来说，该项目旨在建立一个无与伦比的噬菌体宿主范围的时间和空间数据集，以研究细菌群落组装，稳定性和病原体入侵中的作用（裂解和温和）。该项目使用经典的经验方法来研究噬菌体适应的强度和规模，并使用新的计算方法来预测噬菌体如何形成微生物网络。产生的数据将提供前所未有的洞察自然界中的细菌噬菌体动态和复杂社区环境中的病毒宿主范围演变。这项研究进一步发展了对植物微生物组和病毒组的基本认识，还将支持开发一种新的疾病生态学模型系统，该系统既适合新兴微生物组领域的本科生培训，又具有深入了解病毒组的独特潜力，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学术价值和更广泛的影响审查标准。

Bacteriophages, the viruses that infect bacteria, are the most ubiquitous and diverse entities on Earth, infecting the vast majority of bacteria. Lytic phages that infect and kill their bacterial host cells can alter bacterial community profiles (who is there and at what density) as well as competitive dynamics among strains, with clear potential to shape host-associated microbiomes. Phages can also impact the outcome of eukaryotic disease, either directly by infecting and killing bacterial pathogens within hosts or indirectly by changing the microbiome, which is known to play a role in many plant and animal diseases. This project uses monthly sampling of pear trees from an urban environment (Berkeley city) across multiple years and large-scale genomic sequencing efforts to determine the role phages play in Fire Blight disease, an agriculturally relevant disease of many orchard species. By fully integrating undergraduate research using a peer mentoring ladder, this exploration of phage infection and community dynamics in leaf-associated bacterial microbiomes will help identify both which bacteria are naturally targeted by phages, and how these phages shape change in pathogen densities and microbiome community composition. Bacterial and phage culturing approaches will be combined with a multi-omics analysis of the pear tree microbiome to fully elucidate how phages adapt to bacteria in nature and how such adaptation impacts the microbiome in health and disease. The long-term aim is to use these data on natural phage-mediated selection to determine if and how phages can be used to reshape microbial communities and prevent disease. The evolutionary interactions of phages and their bacterial hosts has been studied extensively in the lab, but few studies have examined these dynamics in nature. The project integrates a four module undergraduate research program with high-throughput, culture independent sequencing of both bacterial and viral communities to examine the role of phages in bacterial community turnover and disease using a novel Pear Tree disease system (Callery ‘Bradford’ pear trees infected with the agriculturally relevant pathogen Erwinia amylovora). Through the tight integration of teaching and research, the combination of culture-dependent screening and culture-independent ‘omics’ approaches will allow for tracking of bacteria-phage dynamics over both short (monthly) and long (yearly) time scales. Overall, the project aims to build an unparalleled temporal and spatial dataset on phage host range with which to examine the role of phages (both lytic and temperate) in bacterial community assembly, stability, and pathogen invasion. The project uses both classic empirical approaches to study the strength and scale of phage adaptation and new computational approaches to predict how phages shape microbial networks. The data generated will offer unprecedented insight into bacteria-phage dynamics in nature and viral host range evolution in a complex community setting. The research further develops basic understanding of plant microbiomes and viromes, and will also support the development of a new disease ecology model system that is both amenable to undergraduate training in the emerging microbiome field and unique in its potential to gain insight into virome-microbiome interactions in both health and disease.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.