Regulation of nutrient assimilation in streamlined oligotrophic microorganisms

该项目涉及构成微生物多样性的“暗物质”的细胞。这些生物中的许多都适应了地球海洋中的生活，那里的大部分碳通量发生在营养浓度非常低的情况下。一些在这些低营养浓度下生长的微生物--寡养菌--并不调节涉及碳氧化的营养同化的生化途径。相比之下，在更常被研究的营养共生细胞中，营养同化的调节是无处不在的。一个减少调节的细胞例子是海洋中最丰富的生物--Pelagibacter。目前还没有关于低营养生态系统中细胞缺乏营养吸收调控系统的解释。在这项研究中，将结合实验室实验、数学建模和基因组分析来检验关于调节营养同化的成本和收益的假说。研究不同微生物养分同化策略的成本和收益，将有助于预测营养循环的行为，并有助于更好地了解水生生态系统。这项研究还可能帮助科学家理解为什么这么多常见的微生物细胞类型在科学实验室的培养和研究中遇到了挑战。该项目的教育部分将包括培养一名研究生和一名博士后学者。将向教师和高中生介绍一个关于微生物碳循环的工作坊。在这个项目中，研究人员将测试营养吸收系统可能进化为不受调控的假设，原因是(A)在不同频率和幅度的营养脉冲下调节的成本/收益，(B)分子生物学限制，使调节系统在极低的营养水平下有效运行(调节系统中存在过多的随机噪声)，或(C)与趋化作用的协同作用，这通常不是由寡养细胞完成的，因此它们在较低浓度和较短的时间内经历营养斑块，或这些机制的某种组合。将开发一个模型，在基因水平上明确解决同化系统及其调节，考虑蛋白质合成和功能的动态和代谢成本(假设A)。基于代理人(又称基于个体)的建模方法将被用来明确地解决种群异质性(假设B)和通过趋化和扩散的个体运输(假设C)。研究人员还将对一些寡养生物、共养生物和营养物质进行营养上移实验，通过测量转录本丰度和放射性标记营养物质的摄取来表征反应时间和诱导浓度阈值。实验的一个子集还将包括对营养和细胞浓度、蛋白质和代谢物、营养吸收和氧化速度以及生长速度的测量。从这些实验模型中获得的数据将被用来校准和微调模型。调节和摄取之间的协同作用(假设C)也将通过比较寡养和共养的基因组来检验。一名博士后学者和研究生将参与这项研究，并将向高中教师和学生进行推广。该奖项反映了NSF的法定使命，并通过使用基金会的学术价值和更广泛的影响审查标准进行评估，被认为值得支持。

This project concerns cells that compose the "dark matter" of microbial diversity. Many of these organisms are adapted to life in Earth's oceans, where much of carbon flux takes place at very low nutrient concentrations. Some microbes that grow at these low nutrient concentrations' oligotrophs - do not regulate biochemical pathways for nutrient assimilation involving carbon oxidation. In contrast, among the more commonly studied copiotrophs - cells that grow rapidly at high nutrient concentrations - regulation of nutrient assimilation is ubiquitous. An example of a cell that has reduced regulation is Pelagibacter, the most abundant organism in the oceans. At present there exists no explanation for the lack of regulatory systems for nutrient uptake in cells that live in low nutrient ecosystems. In this study, a combination of laboratory experiments, mathematical modeling and genome analysis will be used to examine hypotheses about the costs and benefits of regulating nutrient assimilation. Studying the costs and benefits of different strategies for nutrient assimilation in microbes will aid in the prediction of behavior of nutrient cycles and will lead to a better understanding of aquatic ecosystems. This research may also help scientists understand why so many common microbial cell types have been challenging to grow and study in scientific laboratories. The educational component of this project will involve training a graduate student and a postdoctoral scholar. A workshop on carbon cycling by microorganisms will be presented to teachers and high school students. In this project, the investigators will test the hypotheses that nutrient uptake systems may evolve to be unregulated due to (A) cost/benefit of regulation at different frequencies and magnitudes of nutrient pulses, (B) molecular biological constraints that prevent effective operation of a regulatory system at very low nutrient levels (excessive stochastic noise in the regulatory system), or (C) synergy with chemotaxis, which is typically not done by oligotrophs, so they experience nutrient patches at lower concentrations and for shorter times, or some combination of these mechanisms. A model will be developed to explicitly resolve the assimilation systems and their regulation at the gene level, accounting for the dynamics and metabolic costs of protein synthesis and function (Hypothesis A). An agent-based (aka individual-based) modeling approach will be used to explicitly resolve population heterogeneity (Hypothesis B) and individual transport by chemotaxis and diffusion (Hypothesis C). The investigators will also perform nutrient upshift experiments with a number of oligotrophs, copiotrophs and nutrients, to characterize the response times and induction concentration thresholds by measuring transcript abundance and uptake of radiolabeled nutrients. A subset of experiments will additionally include measurements of nutrient and cell concentrations, proteins and metabolites, nutrient uptake and oxidation rates, and growth rates. The data obtained from these experiments model will be used to calibrate and fine tune the model. The synergy between regulation and uptake (Hypothesis C) will also be tested by comparing genomes of oligotrophs and copiotrophs. A postdoctoral scholar and graduate student will be involved in the research and outreach will be performed to high school teachers and students.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.