Collaborative Research: MTM 2: Using successional dynamics, biogeography, and experimental communities to examine mechanisms of plant-microbiome functional interactions

合作研究：MTM 2：利用演替动力学、生物地理学和实验群落来研究植物-微生物组功能相互作用的机制

• 批准号: 2025262
• 负责人: Zachary Freedman
• 金额: $ 28.69万
• 依托单位: University of Wisconsin-Madison
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-01-01 至 2024-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2025262&HistoricalAwards=false
• 关键词: Collaborative; Research; MTM; Using; successional

Microbial communities (microbiomes) play important roles in animals, plants, and even whole ecosystems. However, microbiomes are constantly changing through time and space. These changes can have big impacts on the health of animal or plant hosts and the functioning of entire ecosystems. For this reason, uncovering rules that govern how microbiomes change across time and space is essential for understanding how they affect their hosts and ecosystems. This project builds on previous understanding of different strategies used by microbes to survive and compete for resources and applies it to studying the ecosystem that forms in the ‘pitchers’ of the carnivorous pitcher plant, Sarracenia purpurea. Through a combination of experiments and modeling, the microbiome will be studied to determine how microbial community functions change over time, how the host plant influences microbiome formation, and how the microbiome affects the host plant. The results will be compared with other aquatic, plant- and soil-associated microbiomes, to understand how S. purpurea pitchers can be relevant models for understanding roles of microbiomes in larger ecosystems. The project will train the next generation of scientists in interdisciplinary skills. The researchers will involve undergraduate and graduate students including those who are under-represented in STEM research, train students in coding to develop a Sarracenia microbiome website for public education, develop K-12 educational modules, and present interactive public lectures. This project employs interdisciplinary approaches including molecular genetics, biochemistry, ecological modeling, multivariate statistics, and biogeography to characterize microbiome succession, functions and host interactions. It builds from the Yield-Acquisition-Stress (Y-A-S) predictive framework, which characterizes microbial life history strategies based on functional traits related to cell growth yield (Y), resource acquisition (A) and stress tolerance (S), with the microbiomes changing proportions of these strategies over time. The Y-A-S framework has yet to be applied to microbiome succession or functions important for host and ecosystem health. The project will determine dynamics of functional succession across climatic gradients using field-sampling of natural communities over broad biogeographical scales, test how host factors influence microbiome succession using experimental manipulations of natural pitcher communities, and examine microbiome effects on host fitness using experimental bacterial communities. A cutting-edge approach with Latent Dirichlet Allocation (LDA) and Random Forest models will be used to identify Y-A-S life strategies based on a trait matrix derived from metagenomes, RNA transcripts, and measured biochemical nutrient transformation functions. A meta-analysis will compare succession and function of other plant- and soil-associated microbial communities to explore the generality of rules for microbiomes across ecosystems.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.

微生物群落（微生物组）在动物、植物甚至整个生态系统中发挥着重要作用，然而，微生物组随着时间和空间的变化而不断变化，这些变化会对动植物宿主的健康以及整个生态系统的功能产生重大影响。因此，揭示控制微生物组如何随时间和空间变化的规则对于了解它们如何影响宿主和生态系统至关重要。该项目建立在之前对微生物生存和竞争资源所使用的不同策略的理解之上，并将其应用于研究。生态系统通过实验和建模相结合，我们将研究微生物组，以确定微生物群落功能如何随时间变化、宿主植物如何影响微生物组的形成以及微生物组的形成。微生物组对宿主植物的影响将与其他水生、植物和土壤相关的微生物组进行比较，以了解紫花猪笼草捕虫笼如何成为了解微生物组在更大范围内的作用的相关模型。该项目将培训下一代科学家的跨学科技能，包括那些在 STEM 研究中代表性不足的学生，培训学生编码以开发用于公共教育的瓶子草微生物组网站，开发 K。 -12 个教育模块，并呈现互动公开讲座，该项目采用跨学科方法，包括分子遗传学、生物化学、生态建模、多元统计和生物地理学，以描述微生物组的演替、功能和宿主相互作用。产量-获取-应激 (Y-A-S) 预测框架，该框架根据与细胞生长产量 (Y)、资源获取 (A) 和应激耐受性 (S) 相关的功能特征来描述微生物生命史策略，并且微生物组改变这些策略的比例随着时间的推移，Y-A-S 框架尚未应用于微生物组演替或宿主和生态系统健康的重要功能，该项目将利用自然群落的现场采样来确定跨气候梯度的功能演替动态。将使用潜在狄利克雷分配（LDA）和随机森林模型的尖端方法，利用自然捕虫草群落的实验操作来测试宿主因素如何影响微生物组的演替，并使用实验细菌群落检查微生物组对宿主适应性的影响。基于源自宏基因组、RNA 转录本和测量的生化养分转化功能的性状矩阵来确定 Y-A-S 生命策略。荟萃分析将比较其他植物和土壤相关的演替和功能。该奖项反映了 NSF 的法定使命，并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，被认为值得支持。

项目成果

Exploring Microbiome Functional Dynamics through Space and Time with Trait-Based Theory

利用基于性状的理论探索空间和时间上的微生物组功能动力学

• DOI: 10.1128/msystems.00530-21
• 发表时间: 2021-08
• 期刊: mSystems
• 影响因子: 6.4
• 作者: Bittleston, Leonora S.;Freedman, Zachary B.;Bernardin, Jessica R.;Grothjan, Jacob J.;Young, Erica B.;Record, Sydne;Baiser, Benjamin;Gray, Sarah M.;Malik, Ashish
• 通讯作者: Malik, Ashish