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

微生物群落(微生物群)在动物、植物乃至整个生态系统中扮演着重要的角色。然而，微生物群在时间和空间上不断变化。这些变化可能会对动物或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，揭示微生物群如何在时间和空间上变化的规则对于了解它们如何影响宿主和生态系统是至关重要的。这个项目建立在以前对微生物为生存和争夺资源所使用的不同策略的理解基础上，并将其应用于研究肉食性猪笼草(Sarracenia Purpurea)‘瓶子’中形成的生态系统。通过实验和建模相结合的方式，将对微生物群进行研究，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群的形成，以及微生物群如何影响宿主植物。这些结果将与其他与水生、植物和土壤相关的微生物群进行比较，以了解紫毛委陵菜如何成为理解微生物群在更大生态系统中的作用的相关模型。该项目将培训下一代科学家的跨学科技能。研究人员将包括本科生和研究生，包括那些在STEM研究中代表性不足的学生，培训学生在编码方面开发用于公共教育的Sarracenia微生物组网站，开发K-12教育模块，并提供互动公共讲座。该项目采用跨学科的方法，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，以表征微生物组的演替、功能和宿主相互作用。它建立在产量-获取-压力(Y-A-S)预测框架的基础上，该框架基于与细胞生长产量(Y)、资源获取(A)和逆境耐受性(S)相关的功能特征来表征微生物生活史策略，这些策略的微生物群比例随着时间的推移而变化。Y-A-S框架尚未应用于微生物群落的演替或对宿主和生态系统健康具有重要作用的功能。该项目将通过在广泛的生物地理尺度上对自然群落进行实地采样来确定跨气候梯度的功能演替的动态，通过对天然猪笼草群落的实验操作来测试宿主因素如何影响微生物群演替，并使用实验细菌群落来检查微生物群对宿主适合性的影响。潜在狄利克雷分配和随机森林模型的前沿方法将被用来识别Y-A-S的生命策略，该方法基于从元基因组、核糖核酸转录本和测量的生化营养转化功能获得的特征矩阵。荟萃分析将比较其他与植物和土壤相关的微生物群落的演替和功能，以探索生态系统微生物群落规则的普遍性。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.