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，非随机的微生物关联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，集落形成的蓝藻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关联在全球海洋中持续存在并茁壮成长的规则。研究小组将通过整合来自多个学科的最先进技术来量化控制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，可以应用于生物和地质科学的其他系统。由于Trichodesmium是海洋氮的重要来源，该项目的数据对于预测海洋初级生产至关重要，并为研究更普遍地控制微生物群相互作用的规则提供了一个实验室测试的框架。除了这些学科层面的广泛影响外，这项工作还将培养两所机构的多名博士和本科生，并开发一门新课程，旨在增加未被充分代表的群体参与微生物组研究。新的本科课程metagenomics Global Environmental Microbiology （META-GEM）将整合项目数据，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以及在卡塔利娜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。该项目旨在将海洋范围内的毛霉菌和特定细菌分类群的共生数据转化为这一全球重要群落中确定的兼性微生物相互作用。因为有证据表明，木霉菌通过排泄特定的代谢物来选择其微生物组，因此，定义关系的目标是易于处理的，及时的，并且对自然群落中微生物相互作用的一般理解具有变革性。最近对跨大西洋trichodesium菌落的宏基因组研究表明，trichodesium微生物组由一个非随机的、独特的主要由α变形菌和拟杆菌组成的群体组成，前者的一个生物学上的新分支一直共同发生。在这里，研究团队将应用整体组学方法、机器学习算法、高通量培养技术和数值模型，对天然微生物组和USC trichodesium Culture Collection菌株进行无菌和混合实验室实验，以测试三个假设。具体来说，研究小组假设生物相互作用通过以下方式影响毛霉：(i)通过非随机的、部分可分离的表观生物群落的共同进化来增加适应性，从而允许“劳动分工”；㈡加强群落内氮和碳的再循环，从而改变向更广泛生态系统的氮和碳通量；（iii）稳定社区，使生态位重叠的机会主义者受到“控制”——然而，这种稳定效果可能会因环境变化而中断。该奖项反映了美国国家科学基金会的法定使命，并通过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，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.