Microbial Communities: Theory and Practice

本文提出了构建综合观测和理论工具的计划，以研究和表征微生物群落，特别是生物膜和垫的生态学。研究的重点是位于黄石国家公园蘑菇泉流出通道的光合作用驱动的微生物席生态系统。该系统的优势在于它的隔离性、相对简单性以及几十年的前期研究成果。工作将包括：(1)通过现场微传感器测量对重要参数进行表征，对水柱样品的化学成分进行实验室分析，对草席和水中的微生物居民进行基因测序（及相关分析），以及(2)草席生态系统的群落建模。建模将基于一维生物膜模型，包括光吸收，结合微生物物种形成模型。关键行业和/或物种，以及重要的化学物种，将包括在内，参数将根据测量结合电子转移原理确定。该项目的主要目标是通过将模型预测与实际种群分布测量研究相匹配来成功预测垫内微生物物种的分布。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训练。该提案提出了一个计划，以推进群落微生物生态学理论，并结合生活在黄石国家公园蘑菇泉流出物中的一个定义良好且研究充分的光养微生物群落。据估计，原核生物（细菌和古细菌）约占现存生物量的一半。这些微生物大多生活在复杂的生物膜群落中，利用可利用的化学自由能来源。因此，它们是几乎所有地球化学循环的关键组成部分，它们负责全球光合作用预算的很大一部分，它们对所有多细胞生物都是永远存在的威胁（在微生物的眼中，它们是吸引人的自由能量和基质的来源），同时，它们帮助所有动物消化（我们给它们带来自由能量，它们帮助提取它），等等。无论以何种标准衡量，这些微生物的生态学，以及它们居住的群落，都是一个令人感兴趣的话题。微生物群落能够相对较快地对环境变化作出反应，特别是那些目前广泛关注的相对缓慢的长期变化。因此，它们可能为气候变化对环境的影响提供有用的统计数据。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。微生物群落在许多工程系统中也越来越受关注（包括与本提案特别相关的光合作用驱动的微生物生物燃料生产）。在这些努力中，最重要的挑战之一，就像在几乎所有的工程微生物系统中一样，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，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。以这些观点为动机，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进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.