Collaborative Research: Connecting Omics to Physical and Chemical Environment in Community Microbial Ecology

合作研究：将组学与群落微生物生态学中的物理和化学环境联系起来

• 批准号: 1516951
• 负责人: Tianyu Zhang
• 金额: $ 10万
• 依托单位: Montana State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-09-01 至 2018-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1516951&HistoricalAwards=false
• 关键词: Collaborative; Research; Connecting; Omics; Physical

From soils to oceans, microbial communities are dominant in the quotidian and wider environments -- one really cannot describe or understand how the world works without understanding the functions of its microbial ecosystems. Further, microbes are important in many medical contexts, where they are found in richly interacting communities. Microbial communities have, as well, always been important in industry, generally as nuisances, but more recently also for exploitation. Yet, despite their ubiquity, ecology and function of microbial communities and their interaction with their surroundings is poorly understood in most circumstances. The "big" question that motivates this project is the following: To what extent can the function of a microbial community of a given environment be characterized from knowing the physical and chemical profile of that environment? Recent increase in power and coincident decrease in cost of molecular methods has revolutionized the potential to experimentally identify and characterize community inhabitants and activity. At the same time, development of sophisticated microprobe and imaging technology has enabled resolution, down to the microscale, of the chemical environment in which microbial communities function. What lags is the capability to extract community function from that data. Whatever the form this capability ultimately takes, it will by necessity require and incorporate knowledge of the local physical and chemical environment -- microbial communities are specialists in exploiting their local physics and chemistry -- and this project develops the mathematical tools needed to do so. The assembled research team is committed to emphasizing the importance of chemical and physical concepts in the training of math biologists, and has already successfully cross-trained graduate students from different disciplines. This project continues this emphasis and aims to extend this training to undergraduate students, particularly from underrepresented groups. The team aims (i) to bridge the training gap between mathematical biology and microbial ecology, and (ii) to focus attention of mathematical biologists on in situ physio-chemical and biological realities. Through this project the impact of microbial communities on biodeterioration of stone cultural heritage materials is being addressed in an integrated way, from model to lab to the field to professional practice. This work has an important impact on conservation efforts and will establish a beginning basis for the scientific management of stone biodeterioration that can be disseminated internationally and facilitate collaboration among heritage managers. The investigators study an important microbial community type, namely biofilms driven by photosynthesis, particularly as subaerial biofilms (subaerial biofilms are generally non-submerged microbial communities, living together in close proximity in self-secreted polymeric matrices and exposed to air) on carbonate stones. The context of the project is cultural environments, specifically microorganisms that attach to stone and grow as biofilms. These communities can discolor and degrade cultural monuments, but, at the same time, can offer useful insights into many microbial communities by providing platforms for developing and testing hypotheses of microbial ecology. Biofilms inhabiting outdoor stonework have advantages in this respect. They contain the essential biocomplexity for survival in open, uncontrolled environments, but, because of the relatively stringent conditions typical of exposed stone, still have amenable ecologies, and also are known to demonstrate mutually beneficial associations with cooperating photosynthetic and nonphotosynthetic organisms. Particularly important, their simplicity and accessibility make them well suited for use as subjects for development of prototype mathematical methodology needed for connecting omics-based cell-level metabolic models to physics-based community-level function models. The linkage of community data to community model is an essential piece, and one for which mathematics is central, in the broad program of transforming omics into useable theory of microbial communities which, in turn, is central to the program of modern microbiology. This project aims to construct multiscale population models capable of accepting omics (e.g., genomics, transcriptomics) and physical (e.g., temperature, light intensity) data at the microscale, and to develop mathematical methods for bridging the gap between community level omics and community level population models. The core target are the modes of regulation among microbial community members and how they are effected by the physical environment.

从土壤到海洋，微生物群落在南极洲和更广泛的环境中占主导地位----如果不了解微生物生态系统的功能，就无法描述或理解世界是如何运作的。此外，微生物在许多医学环境中很重要，它们存在于丰富的相互作用的社区中。微生物群落在工业中也一直很重要，通常是作为公害，但最近也用于开发。然而，尽管它们无处不在，但在大多数情况下，对微生物群落的生态和功能及其与周围环境的相互作用知之甚少。激发这个项目的“大”问题如下：在多大程度上可以通过了解特定环境的物理和化学概况来表征该环境的微生物群落的功能？ 最近增加的功率和一致的降低成本的分子方法已经彻底改变了潜在的实验识别和表征社区居民和活动。与此同时，先进的微探针和成像技术的发展使微生物群落发挥作用的化学环境的分辨率达到了微观尺度。滞后的是从这些数据中提取社区功能的能力。无论这种能力最终采取何种形式，它都必然需要并融入当地物理和化学环境的知识-微生物群落是利用其当地物理和化学的专家-该项目开发了这样做所需的数学工具。该研究团队致力于强调化学和物理概念在数学生物学家培训中的重要性，并已成功地交叉培训了来自不同学科的研究生。该项目继续强调这一点，旨在将这种培训扩大到本科生，特别是代表性不足的群体。该团队的目标是（i）弥合数学生物学和微生物生态学之间的培训差距，（ii）将数学生物学家的注意力集中在原位生理化学和生物现实上。通过这个项目，微生物群落对石头文化遗产材料生物退化的影响正在以综合的方式得到解决，从模型到实验室到现场再到专业实践。这项工作对保护工作产生了重要影响，并将为科学管理石头生物退化奠定基础，可在国际上传播，并促进遗产管理人员之间的合作。研究人员研究了一种重要的微生物群落类型，即由光合作用驱动的生物膜，特别是作为碳酸盐岩上的陆上生物膜（陆上生物膜通常是非淹没的微生物群落，在自我分泌的聚合物基质中紧密靠近并暴露于空气中）。该项目的背景是文化环境，特别是附着在石头上并作为生物膜生长的微生物。这些群落可以使文化古迹变色和退化，但同时，通过为开发和测试微生物生态学假设提供平台，可以为许多微生物群落提供有用的见解。生物膜栖息在室外的石雕在这方面具有优势。它们含有在开放的、不受控制的环境中生存所必需的生物复杂性，但是，由于暴露的石头典型的相对严格的条件，它们仍然具有顺从的生态学，并且还被认为与合作的光合和非光合生物表现出互利的关联。特别重要的是，它们的简单性和可访问性使它们非常适合用作开发原型数学方法所需的连接基于组学的细胞水平的代谢模型，以物理为基础的社区水平的功能模型的主题。群落数据与群落模型的联系是将组学转化为可用的微生物群落理论的广泛计划中的一个重要部分，数学是其中的核心，而这反过来又是现代微生物学计划的核心。该项目旨在构建能够接受组学的多尺度人口模型（例如，基因组学，转录组学）和物理（例如，温度、光照强度）数据，并开发数学方法，以弥合社区水平组学和社区水平种群模型之间的差距。核心目标是微生物群落成员之间的调节模式以及它们如何受到物理环境的影响。