Investigating the connectivity of microbial food webs using thermodynamic models, stable isotope probing and genomics

地球的宜居性在一定程度上是通过微生物的行动来维持的，这些微生物不断分解死亡的有机物质，并回收所有活着的有机体所需的化学元素。地球的微生物群，也被称为微生物群，由细菌和古生菌以及捕食它们的原生生物和病毒组成。相互作用的微生物复杂而动态的环境可能很难分离和理解，因为在一升水或一克土壤中可以发现多达10亿个细菌和古生菌，以及100亿个病毒。分子生物学的最新进展开始让科学家能够确定环境样本中存在哪些微生物，以及种群数量如何随着时间的推移而变化，以及这些生物正在做什么，比如从大气中消耗二氧化碳。为了了解和预测微生物群落如何对环境变化做出反应，或者如何将它们用于生物技术、能源生产或污染修复，科学家们构建了数学模型。在一个数学模型中恰当地表示极其不同的微观世界中的所有微生物相互作用是一个巨大的挑战。该项目的研究人员开发了一种新的建模方法，该方法利用了一种理论，该理论认为，复杂的系统--可以以许多不同的方式组装的系统--很可能会自我安排和组织，以最大限度地消耗可用能量，比如食物或阳光中的能量。这一被称为最大熵产生(MEP)的理论还预测了微观群落应该如何构建；也就是说，谁吃谁。为了验证这一理论，研究人员将使用实验室微观世界结合分子生物学技术来确定自然微生物群落的结构，并将它们与模型做出的预测进行比较。该项目还将支持一名博士后研究人员，并每年为2-5名本科生提供研究培训。基于MEP理论的初步建模结果表明，由强大的捕食者-被捕食者链构成的微生物食物网在利用资源和耗散自由能量方面是有效的，而高度连接的通才食物网阻碍了资源的有效利用，无法找到MEP解决方案。微生物群落组织起来形成强耦合的捕食者-被捕食者链的假设将用接种了自然微生物群落的实验室恒化器来检验。食物网络结构将用稳定的同位素探测技术进行评估，并通过对标记的群落进行测序来识别活跃的消费者和他们的捕食者。这些实验的结果不仅将促进基于达尔文的MEP模型的发展，而且还将有助于我们从理论上理解微生物群落是如何组织起来的，以促进可用自由能的消散，并推动作为所有生态系统基础的微生物系统的消费-资源理论。

The habitability of Earth is maintained in part by the actions of microscopic organisms that continuously breakdown dead organic material and recycle the chemical elements needed by all living organisms. The Earth's microbiome, as it is also known as, consists of bacteria and archaea as well as protists and viruses that prey upon them. The complex and dynamic milieu of interacting microscopic organisms can be difficult to disentangle and understand because as many as a billion bacteria and archaea, and 10 billion viruses, can be found in a liter of water or a gram of soil. Recent advances in molecular biology are beginning to allow scientists to determine which microscopic organisms are present in an environmental sample, as well as how population numbers change over time and what the organisms are doing, such as consuming carbon dioxide from the atmosphere. To understand and predict how microbial communities respond to environmental changes, or how they can be used in biotechnology, energy production or remediation of pollution, scientists construct mathematical models. Properly representing all the microbial interactions in extremely diverse microscopic worlds in a mathematical model is a great challenge. Researchers for this project have developed a novel modeling approach, which exploits a theory that argues complex systems - ones that can be assembled in many different ways - will likely arrange and organize themselves to maximize their consumption of usable energy, such as found in food or sunlight. The theory, known as maximum entropy production (MEP), also predicts how microscopic communities should be structured; that is, who eats whom. To test the theory, researchers will use laboratory microcosms combined with molecular biological techniques to determine the structure of natural microbial communities and compare them to predictions made by the model. The project also will support one postdoctoral researcher, and provide research training for 2 to 5 undergraduate students each year.Preliminary modeling results based on the MEP theory show that microbial food webs constructed of strong predator-prey chains are effective at utilizing resources and dissipating free energy, while highly connected generalist food webs prevent effective use of resources and do not locate MEP solutions. The hypothesis that microbial communities organize to form strongly coupled predator-prey chains that are weakly interconnected will be tested with laboratory chemostats inoculated with natural microbial communities. Food web structure will be assessed with stable isotope probing techniques and the active consumers and their predators identified by sequencing of the labeled community. The results from the experiments will not only facilitate development of Darwin-based MEP models, but will also contribute significantly to our theoretical understanding of how microbial communities organize to facilitate the dissipation of available free energy as well as to advance consumer-resource theory for microbial systems that are the foundation of all ecosystems.