A systems biology framework to uncover rules governing robustness of a microbial community

该项目正在揭示微生物群落如何适应其环境的变化，以实现强大的生物技术解决方案，例如以可持续的方式生产高价值商品化学品。对于微生物群落来说，适应资源可获得性的波动是一个耗费巨大的过程，需要数百到数千个基因的调节。该项目正在描述推动这种适应过程的微生物群落的分子和细胞网络。该项目的活动是使用系统生物学方法将微生物群落作为一个整体进行研究。具体地说，利用现代测序技术，该项目正在调查受控的环境波动如何导致两种生物的合成微生物群落的所有基因的表达发生变化，这两种微生物在包括湖泊沉积物、土壤和人类肠道在内的不同环境中发挥着核心作用，有助于每年10亿吨碳的循环这一生物地球化学重要过程。通过开发创新的计算建模技术，这些数据正在被分析，以揭示调控网络如何驱动社区范围内动态的基因表达变化，通过代谢途径协调流量变化，并最终表现为社区整体适合度的提高。通过这样做，该项目正在对微生物群落的适应过程产生一种预测性和机械性的理解。基于对适应过程的预测性和机械性理解的假设正在通过对社区的细胞和分子网络进行有针对性的遗传和环境操纵来检验。该项目产生的研究能力、预测模型和知识广泛适用于公共和私营部门的研究和生物技术计划，包括美国国家科学基金会MCB和iOS部门的项目。为了确定广泛的覆盖面，该项目正在利用国家科学基金会资助的长期努力，让妇女、少数族裔和弱势学生和教师参与进来，将该项目产生的当前科学概念和实践带入高中课堂。该项目开发的课程正在美国所有50个州和全球100个国家进行传播。该奖项反映了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。

This project is uncovering how a microbial community adapts to changes in its environment to enable powerful biotechnology solutions, such as the production of high value commodity chemicals in a sustainable manner. Adapting to fluctuations in resource availability is an energetically expensive process for a microbial community, requiring the modulation of hundreds to thousands of genes. This project is characterizing the molecular and cellular networks of a microbial community that drive this adaptive process. Activities in this project are using a systems biology approach to study a microbial community as a whole. Specifically, using modern sequencing technologies this project is investigating how controlled environmental fluctuations induce changes in the expression of all genes of a synthetic microbial community of two organisms that play a central role across diverse environments, including lake sediment, soil, and the human gut, contributing to a biogeochemically important process of cycling 1 gigaton of carbon annually. By developing innovative computational modeling technologies these data are being analyzed to uncover how regulatory networks drive the dynamic community-wide gene expression changes, to coordinate flux changes through metabolic pathways, and ultimately manifest in overall improved fitness of the community. In so doing, this project is generating a predictive and mechanistic understanding of the adaptive processes of a microbial community. Hypotheses based on the predictive and mechanistic understanding of the adaptive process are being tested using targeted genetic and environmental manipulation of the cellular and molecular networks of the community. The research capabilities, predictive models, and knowledge being generated in this project are widely applicable to research and biotechnology programs in the public and private sectors, including projects across the MCB and IOS Divisions of NSF. To ascertain wide outreach, this project is leveraging a long-term NSF-funded effort to engage women, minorities, and disadvantaged students and teachers, to bring current science concepts and practices generated by this project into high school classrooms. Curricula developed in this project are being disseminated across all 50 states in the US and across 100 countries worldwide.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.