Biocomplexity: The Roles of Resources, Competition, and Predation in Microbial Degradation of Organic Matter

细菌在元素循环和生物圈功能中起着至关重要的作用。我们对细菌的代谢多样性以及它们所进行的反应途径了解甚多。然而，在简单的实验室系统之外，我们无法确切地预测细菌生长、代谢和有机物矿化的速度。这个项目是关于理解，在机械和定量的水平上，是什么影响了自然界中细菌的活动。虽然最初这个问题似乎很简单，但研究人员认为，它的解决方案一直难以捉摸，因为涉及到复杂的过程。这种复杂性存在于生物组织（个体、群体、群落）的多个层面，也存在于细菌所处环境的微观空间异质性中。这项研究的最终目标是开发和测试一个模型，该模型将预测自然系统中有机物循环的速率。这样的模型必须包括控制资源（反应物）对细菌的可用性的物理和化学因素，不同细菌种群之间的相互作用（潜在竞争），以及细菌和它们的捕食者之间的相互作用。该项目的短期目标和明确目标是在天然有机质背景下关注一种环境-河口沉积物-和一类有机质-多环芳烃（PAHs）。该方法的中心是建模和经验主义之间的紧密耦合，因为我们相信，只有在稳定的相互作用下，模型和实验才能产生新的、有用的知识。我们将开发的模型考虑了自下而上（例如，资源可用性）和自上而下（例如，捕食）对细菌活性的控制。河口沉积物将被用作建模和实验测试的环境基质，因为这些沉积物由于其广泛变化的化学和物理性质，组成它们的有机和无机成分的混合物以及同时发生的化学，物理和生物过程而具有内在的复杂性和异质性。双环和多环芳烃（PAHs）将被选择作为一种反应物，仅供系统中某些类型的细菌使用。因此，多环芳烃的时间变化率将被用作社区某些成员活动的晴雨表。这将提供一个敏感和具体的模型预测和实验数据的比较。模型的结构将考虑到生物和非生物成分特性的可变性。这些模型的框架将包括沉积物特性的空间异质性、种群动态（包括竞争和捕食）、营养物质和多环芳烃传质以及分子动力学模拟。复杂性将逐渐增加，正如模型预测与实验结果紧密耦合所表明的那样。该小组的专业知识包括生态学、工程学、环境地球化学和微生物学。本研究将提供不同层次的教育和培训机会。具体而言，该项目将包括加强环境技术和工程教育的本科和研究生课程的机制；扩大学生的研究训练，探索环境系统内部和之间的动态相互作用，并将由多学科的教师调查小组指导；并通过合作学习计划为5-8年级科学课程的在职教师提供丰富的机会。

ABSTRACTOCE-0120610Bacteria play crucial roles in cycling of elements and thus the functioning of the biosphere. We know a great deal about the metabolic diversity of bacteria, and the pathways of the reactions they perform. Outside of simple laboratory systems, however, we cannot predict with any certainty the rates at which bacteria grow, metabolize, and mineralize organic matter. This project is about understanding, at a mechanistic and thus quantitative level, what affects the activity of bacteria in nature. While initially the problem seems straightforward, the investigators believe that its solution has been elusive because there are complex processes involved. This complexity exists over several levels of biological organization (individual, population, community), and in the microscale spatial heterogeneity of the environments in which bacteria function. The ultimate goal of this study is to develop, and test, a model that will predict the rates of organic matter cycling in natural systems. Such a model must include the physical and chemical factors controlling the availability of resources (reactants) to bacteria, interactions (potentially competitive) among different bacterial populations, and interactions among bacteria and their predators. The shorter-term goal, and the explicit goal of this project, is to focus on one type of environment - estuarine sediments - and one category of organic matter - polycyclic aromatic hydrocarbons (PAHs) in a background of natural organic matter. The approach centers on a tight coupling between modeling and empiricism, since it is our belief that models and experiments lead to new, useful knowledge only when there is a steady interaction. The model we will develop considers both bottom-up (e.g., resource availability) and to-down (e.g., predation) controls on bacterial activity. Estuarine sediment will be used as the environmental matrix for modeling and experimental testing inasmuch as these sediments are inherently complex and heterogeneous due to their widely varied chemical and physical properties, the mixtures of organic and inorganic constituents of which they are composed, and the simultaneous occurrence of chemical, physical, and biological processes. Bicyclic and polycyclic aromatic hydrocarbons (PAHs) will be chosen as a type of reactant that is used by only certain types of bacteria in the system. Thus, the time rate of change in PAHs will be used as a barometer of the activity of some members of the community. This will provide a sensitive and specific comparison of model predictions and experimental data. Models will be structured to account for variability in properties of the biological and abiotic components. The framework of the models will include spatial heterogeneity in sediment properties, population dynamics including competition and predation, nutrient and PAH mass transfer, and molecular dynamic simulations. Complexity will be added incrementally, as indicated by closely coupling model predictions with experimental results. The expertise of the group assembled to conduct the proposed research encompasses ecology, engineering, environmental geochemistry, and microbiology. Educational and training opportunities, on a variety of levels, will be built into this research. Specifically, the project will include mechanisms to enhance coursework in both undergraduate and graduate programs in environmental technology and engineering education; to broaden student research training that will explore dynamic interactions within and among environmental systems and will be directed by a multidisciplinary team of faculty investigators; and to provide enrichment opportunities for in-service teachers of science courses in grades 5-8 through a partners-in-learning program.