Transitions: Modeling microbial community metabolic interactions under extreme conditions

转变：模拟极端条件下微生物群落代谢相互作用

• 批准号: 2118274
• 负责人: Amy Schmid
• 金额: $ 75万
• 依托单位: Duke University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2118274&HistoricalAwards=false
• 关键词: Transitions; Modeling; microbial; community; metabolic

This goal of this research is to determine how microbes living in extreme conditions communicate metabolically. Microbial extremophiles are remarkable examples of life’s resilience, thriving in hot springs at boiling temperatures, in brine lakes saturated with salt, and in deserts once thought to be sterile. This project uses extremophiles that live in high salt as a test system to map and model how nutrients flow through microbial communities, enabling resilience during times of food scarcity. The metabolism of salt-adapted microbes is poorly understood but produces chemicals and enzymes of interest to biotechnology. The proposed research is therefore expected to reveal general principles of biological resilience and present novel approaches for future industrial applications of extremophile metabolic products. These activities will enable a transition in the PI's research direction from molecular experiments in pure laboratory cultures to field ecology and metabolic modeling. The goal of the education plan is to foster inclusive learning experiences that span disciplinary lines. Together with students and postdocs from her group, the PI will form “co-learning teams" in which the team leader learns, alongside students in the field, how to sample and collect data. In these vertically integrated teams, the perspective that everyone is learning together is expected to lessen power dynamics and promote a positive research culture where all team members feel welcome and valued. The proposed research tests the hypothesis that hypersaline microbial communities interact to maintain stability despite changes in salinity and nutrient availability. Hypersaline-adapted archaea, or halophiles, provide a unique model for investigating the metabolic interactions in microbial communities. Member species share a common hypersaline habitat but exhibit extensive diversity in how they generate energy. Nutrients are intermittently available in hypersaline lakes during seasonal variation, resulting in severe energy stress. In response, halophiles have evolved a wide array of possible metabolic solutions to survive on the same pool of scarce resources. Hypersaline microbial communities have great potential to reveal general principles of community resilience to environmental perturbation. However, knowledge regarding the mechanisms of community interactions remain largely uncharacterized. In the proposed work, the PI and collaborators address these questions by pursuing the following objectives: (a) constructing constraint-based models for hypersaline communities to explain and predict metabolic interactions; (b) sampling the Great Salt Lake microbial communities over temporal and spatial gradients to test model predictions; (c) testing model predictions in synthetic communities grown in the lab under ecologically relevant conditions. To accomplish these aims, a comprehensive Professional Development Plan is proposed, including intensive study in metabolic modeling and training in field ecology during trips to the Great Salt Lake. The proposed models are expected to enable highly accurate predictions of flux distributions in microbial communities. This research enables the PI to launch a new and exciting research direction, building on prior work that discovered mechanisms of transcriptional regulation of metabolic networks in archaeal extremophiles.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.

这项研究的这一目标是确定生活在极端条件下的微生物如何进行代谢沟通。微生物极端友善是生命韧性的显着例子，在沸腾温度下在温泉中繁荣起来，在盐水饱满的盐湖中，曾经被认为是无菌的沙漠中。该项目使用居住在高盐中的极端友友作为测试系统来绘制和建模营养素如何流过微生物群落，从而在食物稀缺时期有能力韧性。适应盐的微生物的代谢知之甚少，但生物技术产生了感兴趣的化学物质和酶。因此，拟议的研究预计将揭示生物弹性的一般原则，并为极端代谢产品的未来工业应用提供新的方法。这些活动将使PI的研究方向从纯实验室培养物中的分子实验到现场生态学和代谢建模。教育计划的目的是培养涵盖纪律线条的包容性学习经验。 PI与她小组的学生和博士后一起组成“共同学习团队”，在该团队中，团队负责人与该领域的学生一起学习如何采样和收集数据。在这些垂直整合的团队中，人们期望每个人一起学习的观点都可以减少动力动力，并促进积极的研究文化，在该文化中，所有团队成员都感到受欢迎和受到重视。提出的研究检验了高盐微生物群落相互作用以维持盐度和养分可用性的稳定目的地变化的假设。高盐适应的古细菌或卤素为研究微生物群落中的代谢相互作用提供了独特的模型。成员物种具有共同的超盐栖息地，但在产生能量方面暴露了广泛的多样性。在季节性变化期间，在催眠湖中，营养物质可间歇地获得，导致严重的能量应力。作为回应，卤素已经发展了各种可能的代谢溶液，以在同一稀缺资源池中生存。高盐微生物群落具有巨大的潜力，可以揭示社区对环境扰动的韧性一般原则。但是，关于社区互动机制的知识在很大程度上仍然没有表现。在拟议的工作中，PI和合作者通过追求以下对象来解决这些问题：（a）为超盐盐群落构建基于约束的模型，以解释和预测代谢相互作用； （b）将大盐湖微生物群落对临时和空间梯度进行取样以测试模型预测； （c）在生态相关条件下在实验室中生长的合成群落中的测试模型预测。为了实现这些目标，提出了一项全面的专业发展计划，包括在前往大盐湖的旅行期间对代谢建模和训练的深入研究。预计所提出的模型将对微生物群落中通量分布进行高度准确的预测。这项研究使PI能够在先前的工作基础上启动一个新的令人兴奋的研究方向，该研究发现了古老极端友善的代谢网络对代谢网络的转录机制。该奖项反映了NSF的法定任务，并通过使用基金会的知识分子优点和更广泛的影响审查标准来通过评估来诚实地支持。