DISSERTATION RESEARCH: A trait-based approach for understanding the relationship between microbial community assembly and metabolic function

细菌构成了地球生物多样性的大部分，几乎栖息在我们星球的每个角落。 细菌是驱动地球生物化学循环的引擎，有助于维持生命。 每天都有科学论文发表，讨论在每一个可以想象的生态系统中生活着什么类型的细菌。科学家们已经发现了与环境（例如温度，pH值等）相关的细菌群落组成模式。或宿主（例如病史、癌症状态等）这些特征，但所观察到的模式的根本原因仍然不清楚。将这些模式与微生物如何相互作用及其环境的一般概念框架联系起来，将有助于科学家更好地管理直接影响人类的系统中的微生物，如人类病原体和废水处理厂。 这项研究将是解决这一知识差距的一个步骤，通过调整基于功能特性（性状）的植物系统中开发的框架，以微生物生态学，允许使用机械方法检查湖泊细菌多样性和生态系统过程之间的联系。 该项目分析的计算工作流程将公开提供，并用于创建开放获取的在线教育工具，以帮助教学计算分析，科学再现性和编程素养。最后，这个工作流程将放在一起，在美国生态学会会议上教授半天的研讨会。 本研究探讨了细菌多样性和次级生产力之间的关系是如何受到决定群落组装的性状的限制。通过比较基因组分析公布的和新重建的细菌基因组的环境基因组数据，该项目将确定DNA推断的（a）响应性状，控制细菌群落组成的差异和（B）的影响性状，确定是否存在多样性生产力的关系。 确定的基因和推断的特征将有助于扩大目前对细菌群落组装和过程如何影响生态系统功能的了解。 这种理解将改善微生物群落和生态系统生态学原理之间的联系。

Bacteria compose the majority of the planetary biodiversity and inhabit almost every corner of our planet. Bacteria are the engines that drive Earth's biogeochemical cycles and help to sustain life. Scientific papers are published daily on what types of bacteria live in every imaginable ecosystem. Scientists have found patterns of bacteria community composition in relation to environmental (e.g. temperature, pH, etc.) or host (e.g. disease history, cancer state, etc.) characteristics, but the underlying reasons for the observed patterns remain unclear. Connecting these patterns to a general conceptual framework of how microbes interact with each other and their environment will help scientists to better manage microbes in systems that directly affect people such as human pathogens and wastewater treatment plants. This research will be a step towards addressing this gap in knowledge by adapting frameworks developed in plant systems based on functional characteristics (traits) to microbial ecology, allowing examination of connections between lake bacterial diversity and ecosystems processes using a mechanistic approach. A computational workflow of this project's analysis will be publicly available and used to create open access online educational tools to aid in teaching computational analyses, scientific reproducibility, and programming literacy. Finally, this workflow will be put together to teach a half day workshop at the Ecological Society of America conference. This research examines how the relationship between bacterial diversity and secondary productivity is constrained by the traits that determine community assembly. Through a comparative genomic analysis of published and newly reconstructed bacterial genomes from environmental genomic data, this project will identify DNA-inferred (a) response traits that control the differences in bacterial community composition and (b) effect traits that determine the presence or absence of a diversity-productivity relationship. The identified genes and inferred traits will help expand current understanding of how bacterial community assembly and processes affect ecosystem function. This understanding will improve linkages between microbial community and ecosystem ecology principles.