Collaborative Research: Within-host Microbial Communities: Experimentally Scaling Interaction Dynamics Across Sites, Regions, and Continents

生物体内的真菌、细菌和病毒微生物群落极其多样化，它们编码着生物圈中绝大多数的基因。例如，人体内微生物的基因数量是宿主的100倍；几乎所有的自由生物都出现了类似的结果。疾病是宿主-微生物相互作用研究得最好的领域，但宿主体内的微生物也负责一些关键功能，如抗病性、营养吸收和防御食草动物（植物）、消化和减少炎症反应（动物）。然而，尽管微生物对自由生物具有巨大的多样性和重要性，但对控制宿主内微生物群落组成的因素或环境变化影响宿主和微生物群落相互作用和功能的空间尺度尚无预测性认识。即使人类活动导致氮和磷输入增加，物种入侵和灭绝率增加，影响从个体到大陆的尺度上的生物系统，我们对这些变化对宿主内微生物群落的影响知之甚少。该奖项将首次系统地了解植物微生物群落对全球范围内普遍存在的环境变化的反应，并提供有关微生物在植物生产力中的潜在作用的至关重要的信息，以及养活不断增长的人口（到2050年将达到90亿）所必需的知识。该奖项为使用前所未有规模的实验提供资金，以研究控制植物宿主真菌，细菌和病毒微生物的环境因素，范围从单个植物到区域和全球生物气候和土壤梯度。使用定量模型来检验多尺度的经验数据，项目团队的工作将回答三个问题。1)在全球、大陆、区域和地方尺度上，哪些因素对宿主体内的微生物群落控制最强烈？2)宿主内微生物群落如何影响宿主繁殖和对致病微生物的易感性？3)宿主内的共生微生物群落如何影响微生物的生长、竞争能力和成功传播？这项研究将包括在六大洲的30个草原上进行重复实验，代表全球相关的土壤养分变化。在实验营养物和草食处理中，同时收集当地常见牧草寄主以及种植作物寄主（大麦）的数据，将用于辨别共生微生物对植物寄主健康的影响，并将其与其他大规模因素（如气候和每个地点发现的特定微生物）区分开来。高通量测序将用于确定宿主微生物群落在从米到大陆的尺度上的变化。操纵实验和数据建模将阐明微生物群落对宿主繁殖、对微生物疾病的抵抗力以及微生物和疾病的传播的影响。更广泛的影响：草原群落覆盖了地球30%的无冰表面，并且在气候条件变化很大的情况下发生。草原是重要的生态系统，为家养和野生动物提供食物和饲料。在本研究中，草原提供了一个实验系统，以了解驱动微生物群落组成的生态过程及其对植物寄主生长和繁殖的影响。通过阐明微生物群落在宿主健康中的作用，以及环境、空间和时间最影响宿主-微生物相互作用的尺度，这项工作的结果具有改善医学和农业应用的巨大潜力。研究结果可能确定植物对作物病原体抗性的新机制，并将对与LTER和NEON位点和优先级相关的现有微生物序列数据库做出重大贡献。研究小组将通过与Cedar Creek LTER和贝尔自然历史博物馆的合作，将这项工作传达给K-12儿童、本科生和公众。所有微生物数据和活菌种收集都将公开，进一步加强研究基础设施，为进一步发现提供丰富的资源。一如既往，项目pi将优先考虑代表性不足的群体的参与，并在同行评议的期刊上传播结果。

The fungal, bacterial, and viral microbial communities embedded within organisms are extremely diverse and encode the vast majority of genes in the biosphere. For example, microbes in a human account for 100 times more genes than those of their host; similar results are emerging for virtually all free-living organisms. Disease is the best studied host-microbe interaction, but microbes inside hosts also are responsible for critical functions such as disease resistance as well as nutrient uptake and defense against herbivores (plants), and digestion and reduced inflammatory responses (animals). Yet, in spite of the tremendous diversity and importance of microbes to free-living organisms, there is no predictive understanding of the factors controlling within-host microbial community composition or the spatial scales at which environmental changes affect host and microbial community interactions and functions. Even as human activities lead to increased nitrogen and phosphorus inputs and increased rates of species invasions and extinctions, impacting biological systems at scales ranging from individuals to continents, we know little of the effects of these changes on microbial communities within hosts. This award will provide the first systematic understanding of the responses of plant microbial communities to these pervasive environmental changes on a global scale and provide critically important information on the potential role of microbes in plant productivity, knowledge necessary for feeding a growing human population (9 billion by 2050). This award provides funds to use experiments of unprecedented scale to examine the environmental factors controlling a plant host's fungal, bacterial, and viral microbes at scales ranging from individual plants to regional and global bioclimatic and soil gradients. Using quantitative models to examine multi-scale empirical data, the project team's work will answer three questions. 1) What factors most strongly control microbial communities within hosts across global, continental, regional, and local scales? 2) How does the within-host microbial community affect host reproduction and susceptibility to disease-causing microbes? And 3) how do the symbiotic microbial communities within a host affect the growth, competitive ability, and successful transmission of microbes? The research will encompass replicated experiments in 30 grasslands spanning six continents, representing globally-relevant variation in soil nutrients. Concurrent collection of data from locally common grass hosts as well as a planted crop host (barley) within experimental nutrient and herbivory treatments will be used to discern the effects of symbiotic microbes on plant host health and to distinguish these from other large-scale factors such as climate and the specific microbes found in each location. High-throughput sequencing will be used to determine variation in within-host microbial communities at scales ranging from meters to continents. Manipulative experiments and data modeling will clarify the effect of microbial communities on host reproduction, resistance to microbial disease, and the spread of microbes and disease. Broader Impacts: Grassland communities cover 30% of Earth's ice-free surface, and occur across greatly varying climatic conditions. Grasslands are essential ecosystems that provide food and forage for domesticated and wild animal populations. In this research, grasslands provide an experimental system with which to understand the ecological processes driving microbial community composition and its effects on plant host growth and reproduction. Results of this work have great potential for refining medical and agricultural applications by illuminating the role of microbial communities in the health of their hosts, and the scales at which environment, space, and time most affect host-microbe interactions. Results may identify novel mechanisms of plant resistance to crop pathogens and will contribute significantly to existing microbial sequence databases linked to LTER and NEON sites and priorities. The research group will communicate this work to K-12 children, undergraduates, and the general public via collaborations with Cedar Creek LTER and the Bell Museum of Natural History. All microbial data and living culture collections will be made publicly available, further enhancing research infrastructure and providing a rich resource for further discovery. As always, the project PIs will prioritize involvement of underrepresented groups and disseminate results in peer-reviewed journals.