Collaborative Research: MTM 2: Searching for General Rules Governing Microbiome Dynamics Using Anaerobic Digesters as Model Systems

微生物几乎栖息在地球上每一个可以想象到的环境中，在各种生态系统过程中发挥着不可或缺的作用。微生物组，特定栖息地的微生物集合，随着时间和地点的不同而发生显著变化。尽管基因技术的快速发展已经彻底改变了我们对微生物组的理解，但控制微生物组功能的规则仍有待了解。由于自然生态系统的开放性和极高的多样性，研究了解这些机制可能很困难。要充分捕捉这种复杂性，就需要在长时间尺度上使用非常大的数据集。与开放的自然系统相比，工程厌氧消化池（ADs）是封闭的系统，具有受控的环境。AD系统在全球范围内用于废物处理，代表了微生物生物技术的最大工程应用。因此，AD系统由于其微生物多样性、环境重要性和控制环境的能力，为理解微生物组功能的规则提供了理想的模型系统。本研究的目的是确定控制ad中微生物组动力学的规则，这些规则可用于其他微生物生态系统。这项研究将为预测工程和天然微生物生态系统中微生物组的行为提供关键的基础知识。这个项目给社会带来的好处将包括在工程和自然系统中改进基于科学的微生物生态系统管理。其他好处包括培养下一代微生物组专业人员，他们具有广泛的跨学科专业知识和技能，可以理解和控制微生物组动力学。该项目的总体目标是确定控制不同生态系统中微生物组动态的一般生态规则，重点关注ADs作为模型微生物生态系统。这将通过研究生态学中已知存在的物种-区域关系是否存在一般规则来实现。选择、扩散、多样化和漂移这四个基本的生态过程将作为解释微生物群落中微生物群落如何跨越空间和时间组装的一般理论。实现这一目标的具体研究目标包括以下任务：1)实验室AD系统将用于确定微生物群落多样性、结构和功能在各种环境变化下的短期（1年）和长期（15年）稳定性；2)先进的统计工具将用于阐明AD系统中潜在的社区组装机制；3)将开发新的数学方法来检测AD微生物组对环境扰动的瞬态动态响应；4)将开发新的元基因组学厌氧消化模型，为预测和操纵AD系统的动力学功能提供有效框架。所得到的描述AD微生物组动力学的规则将被测试用于描述来自各种栖息地的其他微生物组，包括土壤、海洋、湖泊、地下水、肠道和其他工程系统。跨学科培训和劳动力发展将通过研究、培训和研讨会来实现，以满足未来对微生物组专业人员的需求。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Microorganisms inhabit almost every imaginable environment on Earth, playing integral roles in various ecosystem processes. Microbiomes, collections of microbes in specific habitats, change significantly from place to place and over time. Although rapid advances in genetic technologies have revolutionized our understanding of microbiomes, the rules governing microbiome function are yet to be learned. Research to understand these mechanisms in natural ecosystems can be difficult due to their open nature and extremely high diversity. Adequately capturing this complexity results in a need for extremely large datasets over long time scales. By contrast to open natural systems, engineered anaerobic digesters (ADs) are enclosed systems with controlled environments. AD systems are used globally for waste treatment and represent the largest engineering application of microbial biotechnology. As such, AD systems provide an ideal model system for understanding the rules governing microbiome function because of their microbial diversity, environmental significance, and the ability to control the environment. The goal of this research is to identify the rules controlling microbiome dynamics in ADs that can be used for other microbial ecosystems. This study will provide fundamental knowledge critical to predicting microbiome behavior in engineered and natural microbial ecosystems. Benefits to society resulting from this project will include improved science-based management of microbial ecosystems in both engineered and natural systems. Additional benefits include the training of the next generation of microbiome professionals with broad interdisciplinary expertise and skills to understand and control microbiome dynamics. The overall goal of this project is to identify general ecological rules governing microbiome dynamics in different ecosystems with a focus on ADs as model microbial ecosystems. This will be achieved by examining whether general rules exist for species-area relationships as are known to exist in ecology. The four fundamental ecological processes of selection, dispersal, diversification, and drift will serve as a general theory to explain how microbial communities in microbiomes are assembled across space and time. Specific research objectives to achieve this goal include the following tasks: 1) Laboratory AD systems will be used to determine the short- ( 1 year) and long-term (15 years) stability of microbiome biodiversity, structure, and function in responses to various environmental changes; 2) Advanced statistical tools will be used to elucidate underlying community assembly mechanisms in AD systems; 3) Novel mathematical approaches will be developed to detect the transient dynamics of AD microbiomes in response to environmental perturbations; and 4) Novel metagenomics-enabled anaerobic digestion models will be developed to provide effective frameworks for predicting and manipulating the dynamics of AD systems for desired functions. Resulting rules describing AD microbiome dynamics will be tested for their utility in describing other microbiomes from a variety of habitats including soils, marine, lacustrine, groundwater, gut, and other engineered systems. Cross-disciplinary training and workforce development will be achieved through research, training, and workshops to meet future needs for microbiome professionals.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.