MTM2: Drivers of functional redundancy across microbiomes

微生物是所有生态系统的重要组成部分。人类活动影响了广泛的自然生态系统中的微生物，包括海洋、土壤和人类肠道。在大多数情况下，人类简化了这些环境，导致存在的不同微生物种类的数量减少，这些微生物可以执行的不同功能的数量也相应减少。这两种损失都与生态系统健康的下降有关。目前尚不清楚的是，人类介导的生态系统简化是否会导致微生物“功能冗余”的损失--即能够执行任何给定功能的不同微生物物种的数量。功能冗余很重要，因为它提供了生态系统保障--在一个冗余的系统中，当一个微生物物种灭绝时，会有另一个微生物物种等待取而代之。如果人类活动导致功能冗余的巨大损失，那么微生物生态系统将变得越来越脆弱，越来越容易崩溃。该项目正在利用实验研究、理论建模和新的计算方法来表征各种生态系统中微生物的功能冗余，这些生态系统的栖息地复杂程度各不相同。该项目的最终目标是确定控制微生物生态系统复杂性、功能冗余和健康之间关系的规则，并在跨学科研究方面培训研究生和博士后科学家。该项目还通过社交媒体渠道、视频和为一年级大学生开发跨学科课程，帮助本科生和公众了解科学的重要性。栖息地复杂性的减少与微生物组、分类学和功能多样性的减少有关。相比之下，对功能冗余的影响--即功能在不同分类群之间重复的程度--鲜为人知。然而，功能冗余是生态系统稳定性和复原力的关键预测指标。因此，了解功能冗余正在丧失的程度对于预测微生物生态系统将如何应对未来的变化至关重要。该项目的总体目标是确定与寄主相关的(人、鼠、植物)和环境(散装土壤、河口和海洋)微生物群的栖息地复杂性与功能冗余有关的生态规则。具体来说，这个项目是：1.确定基本功能冗余(基因编码)和已实现功能冗余(主动表达)如何随栖息地复杂性而变化。2.开发深度学习算法来识别和链接元基因组和元翻译中的功能冗余，并将这些算法与更传统的技术进行比较。3.确定基因组内(核心与附属)和分类群之间(例如基于基因组大小、休眠、生长速率)的冗余划分的特征，确定这种划分如何促进冗余的维持，并预测不同划分方案下生境复杂性的影响如何不同。4.开发理论模型，通过对分类多样性和环境过滤和生态位划分等机制的影响，将功能冗余与栖息地复杂性联系起来。该项目由了解生命规则：微生物组理论和机制计划资助，该计划通过生物科学局新兴前沿分部作为NSF十大想法的一部分进行管理。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Microbes are essential components of all ecosystems. Human activity has impacted microbes across a wide range of natural ecosystems, including oceans, soils, and human guts. In most cases, humans simplify these environments, resulting in a decrease in the number of different microbial species present and a corresponding decrease in the number of different functions that these microbes can perform. Both losses have been linked to decreases in ecosystem health. What is not well understood is whether human-mediated ecosystem simplification causes losses in microbial ‘functional redundancy’ – the number of different microbial species that can perform any given function. Functional redundancy is important, because it provides ecosystem insurance – in a redundant system, when one microbial species goes extinct, there is another waiting to take its place. If human activity is driving large losses in functional redundancy, then microbial ecosystems will become more and more fragile, and more and more prone to collapse. This project is characterizing the functional redundancy of microbes in a variety of ecosystems that range in habitat complexity by using experimental research, theoretical modelling, and novel computational methods. The end goals of this project are to identify rules that govern the relationship between complexity, functional redundancy and health of microbial ecosystems as well as train graduate students and postdoctoral scientists in interdisciplinary research. This project is also helping to educate undergraduate students and the public about the importance of science through social media outlets, videos, and the development of interdisciplinary curricula for first year college students. A decrease in habitat complexity has been linked to decreases in microbiome taxonomic and functional diversity. By contrast, effects on functional redundancy – that is, the extent of duplicity of function across taxa – are poorly known. Functional redundancy, however, is a key predictor of ecosystem stability and resilience. Thus, understanding the extent to which functional redundancy is being lost is critical for predicting how microbial ecosystems will respond to future change. The overall goal of this project is to identify the ecological rules relating habitat complexity to functional redundancy in both host-associated (human, mouse, plants), and environmental (bulk soils, estuarine and marine) microbiomes. Specifically, this project is: 1. Determining how fundamental functional redundancy (gene encoded) and realized functional redundancy (actively expressed) vary with habitat complexity. 2. Developing deep learning algorithms to identify and link functional redundancy in metagenomes and metatranscriptomes, and then comparing these algorithms to more traditional techniques. 3. Characterizing the partitioning of redundancy within genomes (core vs. accessory) and among taxa (e.g. based on genome size, dormancy, growth rate), determining how this partitioning facilitates maintenance of redundancy, and predicting how the impacts of habitat complexity differ with distinct partitioning schemes. 4. Developing theoretical models linking functional redundancy to habitat complexity via effects on taxonomic diversity and mechanisms like environmental filtering and niche partitioning.This project is funded by the Understanding the Rules of Life: Microbiome Theory and Mechanisms Program, administered as part of NSF's Ten Big Ideas through the Division of Emerging Frontiers in the Directorate for Biological Sciences.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.