Bacteria as biosensors of marine carbon and energy flow: Quantitative links between substrates, transcriptomics, and metabolism

细菌作为海洋碳和能量流的生物传感器：底物、转录组学和代谢之间的定量联系

• 批准号: 1850692
• 负责人: Scott Gifford
• 金额: $ 48.75万
• 依托单位: University of North Carolina at Chapel Hill
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-01 至 2025-01-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1850692&HistoricalAwards=false
• 关键词: Bacteria; biosensors; marine; carbon; energy

The formation and flux of organic material is the foundation of ocean ecosystems, which in turn, substantially influences the global carbon cycle. As such, a fundamental goal in the ocean sciences is increasing our ability to identify marine organic matter's sources, transformations, and sinks, as well as how these components may change due to anthropogenic activities. Understanding these components is especially important in estuarine and coastal systems given these ecosystems are critical zones of organic carbon transformations. However, the dissolved organic carbon (DOC) pool in these systems consists of numerous different compounds from a multitude of sources that can turn over at vastly different rates (minutes to millennia). This makes it difficult to identify which DOC compounds support microbial growth, limiting the incorporation of microbial metabolism into predictive ecosystem models. Novel approaches are therefore needed to identify the DOC substrates driving microbial metabolism in ocean ecosystems. This project is premised on the idea that the bacterial cellular system is the ultimate chemical sensor of the organic environment and that the information recorded in the cell's active gene pool (transcripts) can be leveraged to make insights into DOC composition when the relationships between organic substrate availability, gene activity, and metabolism are known. This project identifies substrate-transcript relationships for a model marine bacterium, as well as the growth and metabolic outcomes of substrate availability. These insights are used to identify the biologically active DOC substrates in coastal environments when the model organism is added directly to coastal samples, and to interpret both historical and current environmental RNA and DNA data sets. This work provides novel insights into the substrates driving the ocean's carbon cycle and how marine bacterial cellular systems are regulated. Bioassays are developed that can be applied in many different aquatic environment settings. The project trains graduate and undergraduate students directly involved in the research and minority undergraduates will be recruited to use research modules for hands-on study of cell cultivation, bioinformatics, and microbial metabolism. High school students will be engaged through a module developed for an aquatic microbiology field trip and subsequent sample and data analysis.Bacterial processing of dissolved organic carbon (DOC) mediates the flux of gigatons of carbon in the ocean, yet a significant hurdle to incorporating bacterial metabolism into ocean models is the inability to quantify the DOC substrates supporting bacterial metabolism and their transformation. Metatranscriptomics (sequencing of community mRNAs) has the potential to be a sensitive method for surveying bacterioplankton responses to the DOC pool and making insights into its composition but is currently limited by insufficient knowledge as to how transcriptional patterns relate to substrate availability. This project will identify carbon substrates supporting microbial metabolism and their transformation in estuarine-coastal ecosystems by elucidating the relationships between transcript abundances and carbon substrate availability. It aims to bridge the gap between model organism and environmental -omic studies by creating quantitative inventories of transcripts in response to defined substrates, and then using these calibrated transcriptional signals to interpret environmental DOC bioassays and metatranscriptomes. The first component of the project will establish genome-wide transcript-substrate relationships in a model marine bacterium in response to individual, environmentally-relevant carbon substrates. The second component will determine the extent to which transcription and metabolism are altered when the bacterium is exposed to complex mixtures of defined and undefined substrates, revealing the potential for transcription to identify individual substrates within a complex DOC pool and how metabolic processing may shape the DOC pools labile and refractory components. Finally, these calibrated transcriptional responses will be used to identify the DOC substrates driving bacterial metabolism in an estuarine-coastal system via DOC drawdown bioassays in which the model organism is added to natural seawater samples, as well as community wide bacterioplankton responses to the extant DOC pool via metatranscriptomics.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.

有机物质的形成和流动是海洋生态系统的基础，而海洋生态系统又对全球碳循环产生重大影响。因此，海洋科学的一个基本目标是提高我们识别海洋有机物的来源、转化和汇的能力，以及这些成分如何因人类活动而发生变化。了解这些组成部分是特别重要的河口和沿海系统，因为这些生态系统是有机碳转化的关键区域。然而，这些系统中的溶解有机碳（DOC）池由来自多种来源的许多不同化合物组成，这些化合物可以以截然不同的速率（几分钟到几千年）转换。 这使得难以确定哪些DOC化合物支持微生物生长，限制了将微生物代谢纳入预测生态系统模型。因此，需要新的方法来确定驱动海洋生态系统中微生物代谢的DOC底物。该项目的理念是细菌细胞系统是有机环境的最终化学传感器，并且当有机底物可用性，基因活性和代谢之间的关系已知时，可以利用细胞活性基因库（转录本）中记录的信息来深入了解DOC组成。 该项目确定了模式海洋细菌的底物-转录本关系，以及底物可用性的生长和代谢结果。当将模式生物直接添加到沿海样本中时，这些见解可用于识别沿海环境中的生物活性DOC底物，并解释历史和当前环境RNA和DNA数据集。 这项工作为驱动海洋碳循环的底物以及海洋细菌细胞系统如何受到调节提供了新的见解。 开发了可应用于许多不同水生环境设置的生物测定。 该项目培训直接参与研究的研究生和本科生，少数民族本科生将被招募使用研究模块进行细胞培养，生物信息学和微生物代谢的实践研究。高中生将通过一个模块开发的水生微生物学实地考察和随后的样品和数据analysis.Bacterial处理溶解有机碳（DOC）介导的海洋中的十亿吨碳通量，但一个显着的障碍，将细菌代谢到海洋模型是无法量化的DOC基板支持细菌代谢及其转化。 元转录组学（测序的社区mRNA）有可能是一个敏感的方法，调查浮游细菌的DOC池的反应，并深入了解其组成，但目前有限的知识，如何转录模式与基板的可用性。本项目将通过阐明转录本丰度和碳基质可用性之间的关系，确定支持河口海岸生态系统中微生物代谢及其转化的碳基质。它旨在通过创建响应于限定底物的转录物的定量清单，然后使用这些校准的转录信号来解释环境DOC生物测定和元转录组，来弥合模式生物和环境组学研究之间的差距。该项目的第一个组成部分将在一个模式海洋细菌中建立全基因组转录-底物关系，以响应个体的、与环境相关的碳底物。第二部分将确定当细菌暴露于已定义和未定义底物的复杂混合物时，转录和代谢改变的程度，揭示转录识别复杂DOC池内的单个底物的潜力，以及代谢处理如何塑造DOC池不稳定和难治组分。最后，这些校准的转录响应将用于通过DOC下降生物测定来识别河口-沿海系统中驱动细菌代谢的DOC底物，其中将模式生物添加到天然海水样品中，以及通过元转录组学对现存DOC池的社区范围内的浮游细菌反应。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的学术价值和更广泛的影响审查标准。