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

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质的来源、转化和汇，以及这些成分可能如何因人类活动而变化的能力。由于河口和沿海生态系统是有机碳转化的关键地带，因此了解这些组成部分在河口和沿海系统尤为重要。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的化合物组成，这些化合物的周转速度可能截然不同(几分钟到几千年)。这使得很难确定哪些DOC化合物支持微生物生长，从而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海洋生态系统中驱动微生物代谢的DOC底物。该项目的前提是细菌细胞系统是有机环境的最终化学传感器，当有机底物可获得性、基因活性和新陈代谢之间的关系已知时，可以利用细胞活动基因库(转录本)中记录的信息来深入了解DOC的组成。该项目确定了一个模式海洋细菌的底物-转录物关系，以及底物可用性的生长和代谢结果。当模式生物被直接添加到海岸样品中时，这些见解被用来识别沿海环境中具有生物活性的DOC底物，并用于解释历史和当前环境RNA和DNA数据集。这项工作为推动海洋碳循环的底物以及海洋细菌细胞系统如何受到调控提供了新的见解。开发了可应用于许多不同水环境环境的生物检测方法。该项目培养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细胞培养、生物信息学和微生物新陈代谢的实践研究模块。高中生将通过为水生微生物学实地考察以及随后的样本和数据分析开发的模块来参与。溶解有机碳(DOC)的细菌处理调节着海洋中数十亿吨碳的流动，但将细菌新陈代谢纳入海洋模型的一个重大障碍是无法量化支持细菌新陈代谢及其转化的DOC底物。元转录组学(群落mRNAs测序)有可能成为一种敏感的方法，用于测量浮游细菌对DOC池的反应并深入了解其组成，但目前受到关于转录模式如何与底物可用性相关的知识不足的限制。该项目将通过阐明转录本丰度和碳底物可用性之间的关系，确定支持河口-沿海生态系统微生物新陈代谢及其转化的碳底物。它的目的是通过创建针对特定底物的转录本的定量清单，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，从而弥合模式生物和环境经济学研究之间的差距。该项目的第一部分将在模式海洋细菌中建立全基因组转录-底物关系，以响应个别与环境相关的碳底物。第二个组成部分将确定当细菌暴露在定义和未定义底物的复杂混合物中时，转录和新陈代谢发生变化的程度，揭示转录识别复杂DOC池中单个底物的潜力，以及代谢处理可能如何塑造DOC池的不稳定和难降解成分。最后，这些校准的转录反应将被用来识别驱动河口-海岸系统细菌新陈代谢的DOC底物，方法是通过将模式生物添加到天然海水样本中的DOC下降生物测定，以及通过元翻译对现有DOC池的社区范围浮游细菌的反应。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 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.