Excellence in Research: From genomics to ecophysiology: the adaptive metabolic strategy of heterotrophic marine Cyclobacterium species

海洋中的大多数微生物生物多样性位于稀有生物圈的范围内。这些稀有微生物对生态系统动态至关重要，并在碳循环中发挥核心作用，从吸收、储存、转化、输出到地球上最大的有机碳库的再矿化。类杆菌是降解高相对分子质量溶解有机碳(DOM)的关键分子。在这个研究项目中，海洋环状杆菌大西洋-IS是类杆菌的一员，也是稀有生物圈的一部分，将被研究以确定海洋环状杆菌大西洋-IS如何根据海洋环境中存在的不同DOM调整其生长。该项目将研究大西洋海洋梭子藻如何根据海洋环境中存在的不同DOM调整其生长，从而加强对复杂碳水化合物的微生物降解以及使用不同有机碳所涉及的分子过程的了解。这项研究对于理解海洋生态系统中稀有细菌类群的功能生态学意义具有重要意义。本研究对色彩专业本科生进行了积极参与。学生将获得涵盖分子生物学方法、微生物生理学和定量数据分析的知识和技能。这一培训将有助于留住STEM学生，增加多样性，并促进劳动力发展。该项目将加强首席研究员的研究能力，并在历史悠久的黑人学院和大学(HBCU)建立研究能力。HBCU和伍兹霍尔海洋研究所将建立伙伴关系。从大西洋底栖水中采集的海洋梭子藻大西洋-IS的注释草案基因组含有比预期数量更多的多糖利用基因、水解酶和运输相关蛋白质，这些蛋白质使细菌能够在饥荒条件下生存，并在DOM丰富时开花。此外，它还包含大量的调节基因，这些基因可能对于产生对环境中DOM变化的快速和适应性代谢反应至关重要。这位首席研究员将检验这一假设，即海洋梭子蟹具有大量的多糖利用基因、转运蛋白和调节基因，能够适应贫瘠海洋中不断变化的碳源。这一假说将通过结合转录学、蛋白质组学和生理学方法来验证，以了解各种转运蛋白和调控网络的表达，这些转运蛋白和调控网络触发了海洋中丰富的精选多糖和多聚糖的使用。特别是，将确定各种运输系统对不同碳源的反应以及对变化的碳源的反应速度。最终，这项研究将加强对海洋中异养细菌及其生态生理学的了解。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。

The majority of microbial biodiversity in the ocean lies within the realm of the rare biosphere. These rare microbes are essential for ecosystem dynamics and play a central role in the carbon cycle from assimilation, storage, transformation, export, and remineralization of the largest pool of organic carbon on the planet. The members of bacteroidetes, are emerging as key players in the degradation of high molecular weight dissolved organic carbon (DOM). In this research project, Cyclobacterium marinum Atlantic-IS, a member of bacteroidetes and part of the rare biosphere, will be studied to determine how C. marinum Atlantic-IS adjusts its growth in response to different DOM present in the marine environment. This project will examine how C. marinum Atlantic-IS adjust its growth in response to different DOM present in the marine environment and thus will enhance the understanding of microbial degradation of complex carbohydrates and the molecular processes involved in the usage of different organic carbons. This research has implications for understanding functional ecological significance of rare bacterial taxa in ocean ecosystems. This study actively engages undergraduate students of color. Students will gain knowledge and skillsets spanning molecular biology methods, microbial physiology, and quantitative data analysis. This training will contribute to student retention in STEM, increase diversity, and workforce development. This project will strengthen research capabilities of the principal investigator and build research capacity at a historically Black College and University (HBCU). A partnership between the HBCU and Woods Hole Oceanographic Institution will be established. The annotated draft genome of C. marinum Atlantic-IS, which was collected from benthic water of the Atlantic Ocean, contains higher than expected number of polysaccharide utilization genes, hydrolases, and transport-related proteins that would allow the bacterium to survive under famine conditions and bloom when DOM is abundant. In addition, it contains a large number of regulatory genes, which could be pivotal for the generation of swift and adaptable metabolic responses to changing DOM in the environment. The principal investigator will test the hypothesis that C. marinum with its large number of polysaccharide utilization genes, transporters, and regulatory genes is able to adapt to changing carbon sources in oligotrophic oceans. This hypothesis will be tested by combining transcriptomics, proteomics, and physiological approaches to understand the expression of various transporters and regulatory networks that trigger the use of select polysaccharides and polymeric glycans thought to be abundant in the ocean. In particular, the expression of numerous transporter systems in response to different carbon sources and the speed of response to changing carbon sources will be determined. Ultimately, this research will enhance the understanding of heterotrophic bacteria in the ocean and their ecophysiology.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.