Collaborative Research: MIM: Defining the rules governing microbiome interactions critical for providing key ecosystem functions using a model diazotroph community

单细胞微生物是驱动地球上大多数生态系统的看不见的引擎。虽然越来越多的人认识到非随机微生物协会可以为单个细胞提供集体优势，但我们对这些相互作用的起源，功能和维持的理解是有限的。为了解决这一知识差距，项目团队建议使用对环境具有重要意义的菌落形成蓝细菌Trichodesmium及其相关微生物组作为模型系统，以定义允许这种微生物协会在全球海洋中持续存在并蓬勃发展的规则。研究小组将通过整合来自多个学科的最先进技术来量化管理微生物组的相互作用。这项工作将开发一个管道，用于识别微生物的相互作用和交换，这对微生物组的稳定性和功能至关重要，可应用于生物和地质科学中的其他系统。由于束毛藻是海洋氮的关键来源，因此该项目的数据对于预测海洋初级生产力至关重要，并为研究更普遍的微生物组相互作用规则提供了实验室测试框架。除了这些学科层面的更广泛的影响，这项工作将培养多个博士学位。和本科生在这两个机构，并开发一个新的课程，旨在增加代表性不足的群体参与微生物组研究。新的本科课程，METAgenomic全球环境微生物学（META-GEM），将整合来自该项目的数据，包括微生物学培训，生物信息学研讨会，所有项目教师的指导和以学生为中心的为期三天的周末研讨会在卡塔利纳岛的箭牌海洋科学中心。参与的学生将获得第一手的研究经验，并将与发展和经验丰富的科学家建立持久的联系。该项目旨在将海洋广泛的束毛藻和特定的细菌类群共存数据转化为定义的兼性微生物相互作用在这个全球重要的社区。由于有证据表明束毛藻通过分泌特定的代谢物来选择其微生物组，因此定义关系的目标对于自然群落中微生物相互作用的一般理解是易于处理的，及时的和变革性的。最近对跨大西洋束毛藻菌落的宏基因组研究表明，束毛藻微生物组由一个非随机的、不同的类群组成，主要是α-变形菌和拟杆菌，前者的生物学新分支一直共存。在此，研究团队将在纯和混合实验室实验中将整体组学方法，机器学习算法，高通量培养技术和数值模型应用于天然微生物组和USC Trichodesmium Culture Collection菌株，以测试三种假设。具体来说，研究小组假设生物相互作用通过以下方式影响束毛藻：（i）通过非随机的、部分可分离的、允许“劳动分工”的表生群落的共同进化来增加适应性;（ii）增强群落内的氮和碳循环，从而改变氮和碳向更广泛的生态系统的通量;以及（iii）稳定社区，使得利基重叠的机会被“控制”-然而，这种稳定作用可能会因环境变化而被破坏。该奖项反映了NSF的法定使命，并被认为值得支持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。

Single-celled microbes are the unseen engines that drive most ecosystems on planet Earth. While there is growing appreciation that non-random microbial associations can provide a collective advantage to individual cells, our understanding of the origins, function and maintenance of these interactions is limited. To address this knowledge gap, the project team proposes to use the environmentally important, colony-forming cyanobacterium Trichodesmium and its associated microbiome as a model system to define the rules that allow this microbial association to exist consistently and thrive throughout the global oceans. The research team will quantify the interactions governing the microbiome by integrating state-of-the-art techniques from multiple disciplines. This work will develop a pipeline for identifying microbial interactions and exchanges that are critical for microbiome stability and function that can be applied to other systems in the biological and geological sciences. As Trichodesmium is a keystone source of nitrogen to the ocean, data from this project will be essential for predicting oceanic primary production and providing a lab-tested framework for investigating the rules that govern microbiome interactions more generally. In addition to these discipline-level broader impacts, this work will train multiple Ph.D. and undergraduate students at both institutions and develop a new course designed to increase underrepresented group involvement in microbiome research. The new undergraduate course, METAgenomic Global Environmental Microbiology (META-GEM), will integrate data from the project and include microbiology training, bioinformatics workshops, mentoring from all project faculty and a student-centric, three-day weekend symposium at the Wrigley Marine Sciences Center on Catalina Island. Involved students will gain firsthand research experience and will make lasting connections with developing and seasoned scientists.This project aims to translate ocean wide Trichodesmium and specific bacterial taxa co-occurrence data into defined facultative microbial interactions in this globally important community. Because there is evidence that Trichodesmium selects its microbiome by excreting specific metabolites, the goal of defining relationships is tractable, timely, and transformative for general understanding of microbial interactions in natural communities. Recent metagenomic work on trans-Atlantic Trichodesmium colonies has shown that the Trichodesmium microbiome consists of a non-random, distinct group of mostly Alphaproteobacteria and Bacteroidia with a biologically novel clade of the former consistently co-occurring. Herein the research team will apply holistic ‘omic approaches, machine learning algorithms, high-throughput culturing techniques, and numerical models to natural microbiomes and to USC Trichodesmium Culture Collection strains in axenic and mixed laboratory experiments to test three hypotheses. Specifically, the team hypothesizes that biotic interactions influence Trichodesmium by: (i) increasing fitness through the coevolution of a non-random, partially dissociable epibiotic community that allows ‘division of labor’; (ii) enhancing nitrogen and carbon recycling within the community and thus altering nitrogen and carbon fluxes to the broader ecosystem; and (iii) stabilizing the community such that niche-overlapping opportunists are kept ‘in check’ - however, this stabilizing effect can be disrupted upon environmental change.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.