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

合作研究：MTM 2：使用厌氧消化器作为模型系统寻找微生物组动力学的一般规则

• 批准号: 2025235
• 负责人: Alan Hastings
• 金额: $ 69.63万
• 依托单位: University of California-Davis
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-10-01 至 2025-09-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2025235&HistoricalAwards=false
• 关键词: Collaborative; Research; MTM; Searching; General

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.

微生物栖息在地球上几乎每个可想象的环境中，在各种生态系统过程中扮演了不可或缺的角色。微生物组合在特定栖息地中的微生物收集，随着时间的流逝和随着时间的流逝而发生了显着变化。尽管遗传技术的快速进步彻底改变了我们对微生物组的理解，但管理微生物组功能的规则尚待学习。由于其开放性和极高的多样性，了解自然生态系统中这些机制的研究可能很困难。充分捕获这种复杂性会导致在长期尺度上需要非常大的数据集。与开放的天然系统相反，工程化的厌氧消化器（AD）是具有受控环境的封闭系统。广告系统用于废物处理，代表了微生物生物技术的最大工程应用。因此，AD系统提供了理想的模型系统，用于理解有关微生物组功能的规则，因为它们的微生物多样性，环境意义和控制环境的能力。这项研究的目的是确定可用于其他微生物生态系统的广告中微生物组动态的规则。这项研究将为预测工程和自然微生物生态系统中的微生物组行为至关重要。该项目对社会的好处将包括改进工程和自然系统中微生物生态系统的基于科学的管理。其他好处包括培训下一代的微生物组专业人士，这些专业人士具有广泛的跨学科专业知识和技能，以了解和控制微生物组动态。该项目的总体目标是确定有关不同生态系统中微生物组动态的一般生态规则，重点是作为模型微生物生态系统。这将通过研究生态学中存在的物种区域关系是否存在一般规则来实现。选择，分散，多样化和漂移的四个基本生态过程将成为一种通用理论，以解释微生物中微生物群落中的微生物群落如何在时空和时间范围内组装。实现此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组生物多样性，结构和功能在对各种环境变化的响应中的短期（1年）和长期（15年）的稳定性； 2）先进的统计工具将用于阐明AD系统中的基本社区组装机制； 3）将开发新的数学方法来检测响应环境扰动的AD微生物组的瞬态动力学； 4）将开发出新型的元基因组学厌氧消化模型，以提供有效的框架来预测和操纵AD系统的动力学，以实现所需功能。描述AD微生物组动力学的最终规则将在描述各种栖息地的其他微生物中的效用，包括土壤，海洋，湖泊，地下水，地下水，肠道和其他工程系统。将通过研究，培训和讲习班来实现跨学科培训和劳动力发展，以满足微生物组专业人士的未来需求。该奖项反映了NSF的法定任务，并被认为是值得通过基金会的知识分子优点和更广泛影响的评估来评估的值得支持的。

项目成果

Effects of stochasticity on the length and behaviour of ecological transients

• DOI: 10.1098/rsif.2021.0257
• 发表时间: 2021-07-07
• 期刊: JOURNAL OF THE ROYAL SOCIETY INTERFACE
• 影响因子: 3.9
• 作者: Hastings, Alan;Abbott, Karen C.;Zeeman, Mary Lou
• 通讯作者: Zeeman, Mary Lou