Regulation of nutrient assimilation in streamlined oligotrophic microorganisms

这个项目关注的是构成微生物多样性“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都发生在非常低的营养浓度下。在这些低营养浓度环境下生长的一些微生物——寡养菌——不调节包括碳氧化在内的营养同化的生化途径。相反，在更常被研究的共养细胞（在高营养浓度下快速生长的细胞）中，营养同化的调节是普遍存在的。海洋中最丰富的生物Pelagibacter就是调节能力降低的细胞的一个例子。目前，对于生活在低营养生态系统中的细胞缺乏营养摄取的调节系统，还没有任何解释。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设。研究微生物中不同营养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。这项研究也可以帮助科学家理解为什么这么多常见的微生物细胞类型很难在科学实验室中生长和研究。这个项目的教育部分将包括培养一名研究生和一名博士后。教师和高中生将参加微生物碳循环的研讨会。在这个项目中，研究人员将测试以下假设：营养摄取系统可能会进化为不受管制的，原因是：(A)不同频率和强度的营养脉冲调节的成本/收益，(B)在非常低的营养水平下阻碍调节系统有效运行的分子生物学限制（调节系统中过度的随机噪声），或(C)与趋化性的协同作用，这通常不是由寡养生物完成的。所以它们在较低浓度和较短时间内经历营养斑块，或者这些机制的某种组合。将开发一个模型来明确解决同化系统及其在基因水平上的调控，考虑蛋白质合成和功能的动力学和代谢成本（假设A）。基于主体（又名基于个体）的建模方法将用于明确解决群体异质性（假设B）和个体通过趋化性和扩散的迁移（假设C）。研究人员还将对一些寡养、共养和营养物质进行营养上升实验，通过测量转录物丰度和放射性标记营养物质的吸收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营养和细胞浓度、蛋白质和代谢物、营养摄取和氧化速率以及生长速率的测量。从这些实验模型中获得的数据将用于校准和微调模型。调节和摄取之间的协同作用（假设C）也将通过比较寡养生物和共养生物的基因组来检验。一名博士后学者和研究生将参与研究，并将向高中教师和学生进行推广。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识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.