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

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阐明这种相互作用的具体机制。一个复杂的因素是，大多数微生物还没有被分离出来，因此它们的生物化学和在地球化学循环中的实际作用在很大程度上是未知的。该项目将在其代谢网络水平上研究一个社区，以开发和测试社区恢复力和功能的生态模型。这个大约有5个成员的群落来自于一个矿体内的地下极酸矿井排水（AMD）站点。矿床中硫铁矿（FeS2）含量约为95%，固定碳、氮输入量极少，环境地球化学特征简单。提供给自养生物的能量只有两个来源：好氧铁和硫氧化。这些特征和其他特征使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。两组基于既定生态原则的假设将被测试。首先，负责固氮和单质硫氧化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。微扰研究将用于检验这一假设。其次，铁氧化生物被假设为适应更高的pH条件。微生物在黄铁矿表面定植，并通过一系列物种演替事件，形成一个最佳低pH的顶极群落（促进演替）。为了验证这一假设，生物反应器群落中早期到晚期殖民者的身份和代谢特征将在一系列8个冲洗-扰动处理中确定。本研究的核心成果将是对调节和决定个体物种和群落生存的代谢途径的基因组化阐明。将分析基因组数据和基因表达，以确定和监测负责亚铁（主要硫化物氧化剂）和硫（关键的产酸反应）氧化以及二氧化碳和固氮的基因的活性。将发展形而上学的营养模型来描述系统和检验假设。这种建模技术特别擅长处理复杂系统中的非线性问题。结果将包括对演替和物种相互作用的遗传水平分辨率的生态理论的第一次测试，以及对学生进行生态学新方法发展的培训。

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.