Microbial Ecology and Diversity: Genomics and Metagenomics in a Yellowstone Hotspring

国际物理学会认为，在数学、微观和宏观物理以及微生物生物学等重大问题相结合的“物理微生物生态”领域，存在着尚未开发和具有变革性的机遇。拟议工作的目的是让PI和一名研究生沉浸在最先进的微生物生态学实验室--Ward微生物学实验室(蒙大拿州立大学土地资源和环境科学系)的方法和材料中。这项拟议的工作旨在让PI和指定的研究生熟悉基于分子的微生物生态学的方法和结果，包括其优点和缺点。长期成果包括解决以下问题：微生物生态、微生物多样性和微生物群落中固有的物理过程是如何相互联系的？第二个预期成果将是开发与微生物生物学家有效沟通和合作的能力，并开发培训数学学生进行同样操作的能力。沃德实验室研究了30年来黄石国家公园碱性硅质温泉出水渠道中存在的微生物垫群落，作为微生物群落组成、结构和功能的模型。PI将与研究生一起加入Ward实验室一年，以参与三个项目：向他们介绍分析微生物群落组成和结构的当代分子方法，同时将结果整合到建模工作中(从而也向合作的生物学家介绍数学可能性)。(I)群落多样性和群落地形并置将通过采样和构建psaA克隆文库，结合微传感器测量，然后进行生态类型分析来研究。其目的是确定流体流动和伴随效应(例如，剪切力、温度梯度、扩散边界层的变化等)的影响。关于社区多样性。(2)将使用荧光素激活的细胞分类器测量聚球藻的温度适应能力，并将其与其他物理量，特别是光参数产生的适应能力进行比较，目的是开发足够的数据，以便与基于温度的物种形成模型进行比较。(Iii)将对Ward实验室一名本科生目前的一项研究进行分析和建模，该研究的重点是由于环境扰动(例如光线强度或质量的变化)而造成的人口迁移(通过PSAA数据量化)。

The PI believes that there are unexploited and transformative opportunities for developing a field of "physical microbial ecology" where non-trivial problems of mathematics, micro- and macro-scale physics, and microbial biology are combined. The aim of the proposed work is to immerse the PI and a graduate student in the methods and materials of a state of the art microbial ecology laboratory, the Ward microbiology lab (Department of Land Resources and Environmental Sciences, Montana State University). The proposed work is meant to familiarize the PI and the designated graduate student in the methods and results of molecular-based microbial ecology, including both its strengths and weaknesses. The long term outcomes include addressing the following question: how do microbial ecology, microbial diversity, and the physical processes inherent in microbial communities interrelate? A second expected outcome will be developing a capability for effectively communicating and collaborating with microbial biologists, and developing a capability for training mathematics students to do the same.The Ward Lab has investigated microbial mat communities that exist in the effluent channels of alkaline siliceous hot spring in Yellowstone National Park for 30 years as models of microbial community composition, structure and function. The PI, together with the graduate student will join the Ward lab for one year in order to engage in three projects: introducing them to contemporary molecular methods of analyzing microbial community composition and structure while simultaneously integrating results into modeling efforts (thereby also introducing the cooperating biologists to mathematical possibilities).(i) Community diversity and community topography juxtaposition will be studied using sampling and construction of psaA clone libraries, in conjunction with microsensor measurements, followed by ecotype analysis. The purpose is to identify influence of fluid flow and attendant effects (e.g., shear force, temperature gradients, variations in diffusive boundary layers, etc.) on community diversity. (ii) Synechococcus temperature adaptations will be measured, using a fluorescene activated cell sorter, and compared with adaptations resulting from other physical quantities, particularly light parameters, with the purpose developing sufficient data for comparison with models of temperature-based speciation. (iii) A current study, by an undergraduate student in the Ward lab, focused on population shift (quantified through psaA data) due to environmental perturbation, e.g. changes in light intensity or quality, will be analyzed and modeled.