BE/GEN-EN: Analysis of Factors Determining the Ecological Function and Resilience of Microbial Communities

摘要环境化学在很大程度上受微生物活动和地球化学相互作用的控制。 自然系统中大多数群落的复杂性质使得很难解开这种相互作用的具体机制。一个复杂的因素是，大多数微生物尚未被分离，因此它们的生物化学和地球化学循环中的实际作用在很大程度上是未知的。 该项目将在代谢网络层面研究一个社区，以开发和测试社区恢复力和功能的生态模型。 大约五个成员的社区是来自地下极端酸性矿山排水（AMD）网站内的矿体。环境地球化学是简单的，因为矿石存款是~95%的黄铁矿（FeS 2），并收到最小的固定碳和氮的输入。 自养生物只有两种能量来源：需氧铁和硫氧化。这些和其他特征使得该系统易于进行生物反应器实验和建模，从而可以记录生态系统的结构和功能。两组假设的基础上建立的生态原则将进行测试。 首先，负责固氮和氧化元素硫的微生物被假设为关键物种，因为它们对群落的影响与它们的丰度不成比例。 扰动研究将用于检验这一假设。 其次，铁氧化生物被假设为适应较高的pH值条件。 微生物定殖黄铁矿表面，并通过一系列的物种演替事件，导致在最佳的低pH值（促进演替）的顶极群落。生物反应器社区中早期到晚期殖民者的身份和代谢特征将在一系列的8个洗脱扰动处理中确定，以检验这一假设。这项研究的核心产品将是一个基因组使能阐明的代谢途径，调节和决定个别物种和社区的生存。 将分析基因组数据和基因表达，以识别和监测负责亚铁（主要硫化物氧化剂）和硫（关键产酸反应）氧化以及CO2和固氮的基因的活性。 将开发形而上学营养模型来描述系统和测试假设。 这种建模技术特别擅长处理复杂系统中的非线性。 成果将包括演替和物种相互作用的生态理论与遗传水平的分辨率的第一次测试，和学生在生态学的新方法的发展培训。

AbstractEnvironmental chemistry is largely controlled by the interplay between microbial activity and geochemistry. The complex nature of most communities in natural systems makes it difficult to unravel the specific mechanisms of this interaction. A compounding factor is that most microorganisms have not been isolated, and thus their biochemistry and actual roles in geochemical cycling are largely unknown. This project will study a community at the level of its metabolic network in order to develop and test ecological models for community resilience and function. The approximately five member community is derived from a subsurface extreme acid mine drainage (AMD) site within an ore body. The environmental geochemistry is simple because the ore deposit is ~95% pyrite (FeS2), and receives minimal inputs of fixed carbon and nitrogen. Energy is supplied to autotrophs from only two sources: aerobic iron and sulfur oxidation. These and other characteristics make the system tractable to bioreactor experiments and modeling that can document ecosystem structure and function. Two groups of hypotheses based on established ecological principles will be tested. First, microorganisms responsible for nitrogen fixation and oxidation of elemental sulfur are hypothesized to be keystone species because their impact on the community is disproportionate to their abundance. Perturbation studies will be used to test this hypothesis. Second, iron-oxidizing organisms are hypothesized to be adapted to higher pH conditions. Microbes colonize pyrite surfaces, and through a series of species succession events, lead to a climax community at an optimal low pH (facilitative succession). The identity and metabolic characteristics of early to late colonizers in bioreactor communities will be determined in a series of eight washout-perturbation treatments in order to test this hypothesis. The central product of this study will be a genome-enabled elucidation of the metabolic pathways that regulate and determine survival of individual species and the community. Genome data and gene expression will be analyzed to identify and monitor activity of genes responsible for oxidation of ferrous iron (the primary sulfide oxidant) and sulfur (the key acid generating reaction), and CO2 and nitrogen fixation. Metaphysiological trophic models will be developed to describe the system and test hypotheses. This modeling technique is particularly adept at handling non-linearities in complex systems. Outcomes will include the first tests of ecological theories of succession and species interactions with genetic-level resolution, and students trained in the development of new approaches to ecology.