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。虽然人们越来越认识到非随机微生物组合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、功能和维持的了解有限。为了解决这一知识差距，项目组建议使用对环境重要的形成菌落的蓝藻Trichodesum及其相关微生物组作为模型系统，以确定允许这种微生物组合在全球海洋中持续存在和蓬勃发展的规则。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。这项工作将开发一条确定微生物相互作用和交换的管道，这些微生物相互作用和交换对微生物组的稳定性和功能至关重要，可以应用于生物和地质科学的其他系统。由于毛霉是海洋氮素的重要来源，该项目的数据将对预测海洋初级生产力和提供实验室测试的框架，以研究更广泛地管理微生物群相互作用的规则至关重要。除了这些学科层面的更广泛影响外，这项工作还将在这两个机构培训多名博士和本科生，并开发一门新课程，旨在增加未被充分代表的群体对微生物组研究的参与。新的本科课程，元基因组学全球环境微生物学(META-GEM)，将整合该项目的数据，包括微生物学培训、生物信息学研讨会、所有项目教职员工的指导，以及在卡塔利纳岛箭牌海洋科学中心举行的为期三天的以学生为中心的周末研讨会。参与的学生将获得第一手的研究经验，并将与不断发展和经验丰富的科学家建立持久的联系。本项目旨在将海洋中毛霉菌和特定细菌分类群的共生数据转化为这个全球重要社区中明确的兼性微生物相互作用。由于有证据表明，毛霉菌通过排泄特定的代谢物来选择其微生物群，因此定义关系的目标是易于处理、及时和具有变革性的，以便于对自然群落中微生物相互作用的一般理解。最近关于跨大西洋木霉菌落的元基因组学研究表明，毛霉菌微生物群由一组非随机的、不同的主要由变形杆菌和杆状杆菌组成，前者在生物学上一直是新的分支。在这里，研究小组将在无菌和混合实验室实验中，将整体经济学方法、机器学习算法、高通量培养技术和数值模型应用于自然微生物群和南加州大学木霉培养收集菌株，以验证三个假设。具体地说，该团队假设生物相互作用通过以下方式影响毛霉菌：(I)通过非随机、部分可分离的共生群落的共同进化来提高适合度，从而允许“分工”；(Ii)增强群落内的氮和碳循环，从而改变对更广泛生态系统的氮和碳通量；以及(Iii)稳定群落，使生态位重叠的机会主义者受到‘控制’--然而，这种稳定效应可能会在环境变化时被破坏。这一裁决反映了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。

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.