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

合作研究：MIM：定义控制微生物组相互作用的规则，这对于使用固氮微生物群落模型提供关键生态系统功能至关重要

• 批准号: 2125063
• 负责人: Elizabeth Kujawinski
• 金额: $ 109.95万
• 依托单位: Woods Hole Oceanographic Institution
• 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: 2021-10-01 至 2025-09-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2125063&HistoricalAwards=false
• 关键词: Collaborative; Research; MIM; Defining; rules

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.

单细胞微生物是在地球上驱动大多数生态系统的看不见的引擎。虽然越来越多的意识到非随机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，功能和维护的理解受到限制。为了解决这一知识差距，项目团队的建议提出了使用环境重要的，菌落形成的蓝细菌trichodesmium及其相关的微生物组作为模型系统，以定义允许这种微生物关联在整个全球海洋中始终如一地存在的规则。研究团队将通过整合来自多个学科的最新技术来量化管理微生物组的交互。这项工作将开发一条管道，以识别可用于微生物组稳定性和功能至关重要的微生物相互作用和交换，该稳定性和功能可以应用于生物学和地质科学中的其他系统。由于Trichodesmium是海洋氮的基石来源，因此该项目的数据对于预测海洋初级生产和提供了实验室测试的框架至关重要，该框架用于调查更广泛地控制微生物组相互作用的规则。除了这些学科级别的广泛影响外，这项工作还将培训多个博士学位。以及这两个机构的本科生，并开发了一门新课程，旨在增加代表性不足的小组参与微生物组研究。新的本科课程，元基因组全球环境微生物学（Meta-GEM），将整合项目的数据，包括微生物学培训，生物信息学研讨会，所有项目教师的心理，以及一个以学生为中心的，为期三天的周末周末训练室，在Catalina Island的箭牌海洋科学中心。参与的学生将获得第一手研究经验，并将与发展中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毛trichodesmium和特定的细菌分类数据转换为这个全球重要的社区中定义的辅助微生物相互作用。由于有证据表明，毛tricho虫通过出色的特定代谢产物选择其微生物组，因此定义关系的目的是可进行的，及时的和变革性的，可以一般地理解自然社区的微生物相互作用。最近在跨大西洋毛状菌群菌落上的宏基因组学研究表明，毛状体微生物组由非随机的，独特的大多数字母型杆菌和细菌菌组成，并具有前者一贯共核的生物新颖的进化枝。本文中，研究团队将对自然微生物组以及在轴原和混合实验室实验中的USC Trichodesmium培养物收集菌株中应用整体“ OMIC方法”，机器学习算法，高通量培养技术和数值模型，以测试三个假设。特别是，该团队假设生物相互作用会通过以下方式影响毛tho虫，而通过以下方式通过非随机的，部分可解散的表征群落来提高健身性，从而可以“劳动分裂”； （ii）增强社区内的氮和碳回收利用，从而改变了更广泛的生态系统的氮和碳通量； （iii）稳定社区，以使其“检查”以“检查” - 但是，这种稳定效果可能会在环境变化时破坏。该奖项反映了NSF的坚定使命，并被认为是通过基金会的知识分子优点和更广泛的审查标准来评估来通过评估来获得的支持。