Microbial Communities: Theory and Practice

这项提议提出了一项计划，以建立综合的观测和理论工具，用于研究和表征微生物群落，特别是生物膜和垫子的生态。研究的重点是位于黄石国家公园蘑菇泉出水渠道的光合作用驱动的微生物垫生态系统。这个系统是有利的，因为它是孤立的，相对简单，并且可以获得几十年的先前研究。工作将包括：(1)通过现场微传感器测量、水柱样本化学实验室分析、垫子和水中微生物栖息地的基因测序(和伴随分析)确定重要参数，以及(2)垫子生态系统的群落模拟。建模将基于一维生物膜模型，包括光吸收，并结合微生物物种形成模型。将包括主要行会和/或物种以及重要的化学物种，并将根据结合电子转移原理的测量来确定参数。该项目的主要目标是成功地预测垫子内微生物物种的分布，通过将模型预测与实际种群分布测量研究相匹配来测量。在这个项目的过程中，研究生将接受数学和微生物学方法的培训。这项建议提出了一个项目，以促进群落微生物生态理论的发展，以及生活在黄石国家公园蘑菇泉流出物中的一个定义明确和研究充分的光营养微生物群落。据估计，原核生物(细菌和古菌)约占现有生物量的一半。这些微生物中的大多数生活在复杂的生物膜群落中，利用可用的化学自由能源。因此，它们是几乎所有地球化学循环的关键组成部分，它们承担着全球光合作用预算的很大比例，它们总是对所有多细胞生物体构成威胁(在微生物看来，它们是吸引人的自由能量和底物的来源)，同时，它们帮助所有动物的消化(我们为它们带来自由能量，它们帮助提取能量)，等等。无论以什么标准衡量，这些微生物的生态以及它们所居住的群落都是一个引起人们极大兴趣的话题。微生物群落能够对环境变化做出相对较快的反应，特别是那些相对缓慢的、目前广泛关注的那种长期变化。因此，它们可能为气候变化对环境的影响提供了一个有用的统计数据。然而，在提取这些信息之前，更好地了解这些生态系统的运作将是至关重要的。微生物群落对许多工程系统也越来越感兴趣(包括与这一提议特别相关的光合作用驱动的微生物生物燃料生产)。与几乎所有的工程微生物系统一样，这些努力中最重要的挑战之一是生态稳定性：微生物群落将相当迅速地进化，以适应它们自己的目的，而这些目的可能与高效、商业规模的燃料生产的工程目标不一致。在所有这些观点的推动下，本提案旨在通过数学建模与现场和实验室研究的协调研究来推动微生物群落种群理论的发展。

This proposal presents a plan to construct integrated observational and theoretical tools for studying and characterizing the ecology of microbial communities, biofilms and mats in particular. The focus of study is a photosynthetically-driven microbial mat ecosystem located in the effluent channels of Mushroom Spring, Yellowstone National Park. This system is advantageous because of its isolation, relative simplicity, and the availability of decades of prior study. Work will consist of (1) characterization of important parameters through on-site microsensor measurements, laboratory analyses of chemistry of water column samples, and gene sequencing (and accompanying analysis) of microbial inhabitants both in the mats as well as in the water, as well as (2) community modeling of the mat ecosystem. The modeling will be based on 1D biofilm models, including light absorption, combined with a microbial speciation model. Key guilds and/or species, along with important chemcial species, will be included and parameters will be determined based on measurements combined with electron transfer principles. The principle goal of the project is to successfully predict distribution of microbial species within the mat, measured by matching model predictions to actual population distribution measurement studies. In the course of this project, a graduate student will be trained in both mathematical as well as microbiology methods.This proposal presents a program to advance theory of community microbial ecology in conjunction with a well-defined and well-studied phototrophic microbial community living in the effluent of Mushroom Spring, Yellowstone National Park. Prokaryotes (bacteria and archaea) are estimated to make up approximately half of extant biomass. Most of these microbes live in complex biofilm communities that exploit available sources of chemical free energy. As such, they are key components of almost all geochemical cycles, they are responsible for a large percentage of the global photosynthesis budget, they are everpresent threats to all multicellular organisms (which are, in the eyes of a microbe, appealing sources of free energy and substrates), while, at the same time, they assist in digestion in all animals (we bring free energy to them, and they help extract it), and so on. By any measure, ecology of these microbes, and the communities in which they reside, is a topic of keen interest. Microbial communities are able to react comparatively quickly to environmental variations, particularly those relatively slow, secular changes of the sort that are of wide current interest. Thus they potentially present a useful statistic for effects of climate change on the environment. However, a better understanding of the workings of these ecosystems will be essential before such information can be extracted. Microbial communities are also of increasing interest in many engineered systems (including, of particular relevance to this proposal, photosynthetically-driven microbial biofuel production). One of the most important challenges in these efforts, as in almost all engineered microbial systems, is ecological stability: microbial communities will evolve fairly rapidly to suit their own purposes, purposes which may not be consistent with the engineering goals of efficient, commercial-scale fuel production. With all of these points as motivation, this proposal aims to advance the state of microbial community population theory through a coordinated study of mathematical modeling with field and laboratory study.