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

从土壤到海洋，微生物群落在日常和更广泛的环境中占据主导地位--如果不了解微生物生态系统的功能，就真的无法描述或理解世界是如何运作的。此外，微生物在许多医学背景下都很重要，在这些环境中，它们可以在相互作用丰富的社区中找到。微生物群落在工业中也一直很重要，通常是作为滋扰，但最近也是为了开采。然而，尽管微生物群落无处不在，但在大多数情况下，人们对微生物群落的生态和功能以及它们与周围环境的相互作用知之甚少。推动这一项目的“大”问题如下：通过了解特定环境的物理和化学概况，可以在多大程度上表征该环境的微生物群落的功能？最近分子方法能力的增加和成本的降低已经彻底改变了通过实验识别和表征社区居民和活动的可能性。与此同时，先进的微探头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能够达到微米级。落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什么形式，它都必然需要并纳入当地物理和化学环境的知识--微生物群落是利用当地物理和化学的专家--这个项目开发了这样做所需的数学工具。集结的研究团队致力于强调化学和物理概念在数学生物学家培养中的重要性，并已成功地交叉培养了不同学科的研究生。该项目继续强调这一点，旨在将这一培训扩展到本科生，特别是来自代表性不足群体的学生。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现场的生理、化学和生物现实上。通过该项目，从模型到实验室，再到实地，再到专业实践，正在以综合的方式处理微生物群落对石器文化遗产材料生物退化的影响。这项工作对保护工作具有重要影响，并将为科学管理石材生物退化奠定基础，以便在国际上传播，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，即光合作用驱动的生物膜，特别是碳酸盐岩石上的气下生物膜(气下生物膜通常是非水下微生物群落，在自我分泌的聚合物基质中紧密结合在一起，暴露在空气中)。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遗迹褪色和退化，但同时，通过提供开发和测试微生物生态假说的平台，可以为许多微生物群落提供有用的见解。栖息在室外石材上的生物膜在这方面具有优势。它们包含了在开放、不受控制的环境中生存所必需的生物复杂性，但由于裸露石头的典型条件相对严格，仍然具有易受影响的生态环境，而且众所周知，它们与合作的光合作用和非光合作用的有机体之间存在互惠互利的联系。尤其重要的是，它们的简单性和可获得性使它们非常适合用作开发原型数学方法的主体，这是将基于组学的细胞级代谢模型与基于物理学的社区级功能模型连接起来所需的。在将组学转化为微生物群落的有用理论的广泛计划中，群落数据与群落模型的联系是必不可少的一部分，数学是核心的一部分，而微生物群落理论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在微观尺度上接受组学(如基因组学、转录组学)和物理数据(如温度、光照强度)的多尺度种群模型，并开发数学方法来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。

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.