MTM2: Drivers of functional redundancy across microbiomes

微生物是所有生态系统的重要组成部分。人类活动已经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——可以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，当一种微生物灭绝时，会有另一种微生物等待取代它的位置。如果人类活动导致功能冗余的大量损失，那么微生物生态系统将变得越来越脆弱，越来越容易崩溃。该项目通过实验研究、理论建模和新颖的计算方法来描述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性各异。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，并培养跨学科研究的研究生和博士后科学家。该项目还通过社交媒体、视频和为大学一年级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。栖息地复杂性的降低与微生物组分类和功能多样性的降低有关。相比之下，对功能冗余的影响-即跨分类群功能的双重程度-知之甚少。然而，功能冗余是生态系统稳定性和恢复力的关键预测指标。因此，了解功能冗余丢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宿主相关（人类、小鼠、植物）和环境（大块土壤、河口和海洋）微生物组中栖息地复杂性和功能冗余相关的生态规则。具体来说，这个项目是：1.；确定基本功能冗余（基因编码）和实现功能冗余（主动表达）随生境复杂性的变化。2. 开发深度学习算法来识别和连接宏基因组和亚转录组中的功能冗余，然后将这些算法与更传统的技术进行比较。3. 描述基因组内部（核心vs辅助）和分类群之间（如基于基因组大小、休眠、生长速率）的冗余划分，确定这种划分如何促进冗余的维持，并预测不同划分方案对栖息地复杂性的影响。4. 通过对分类多样性的影响以及环境过滤和生态位划分等机制，建立功能冗余与栖息地复杂性联系的理论模型。该项目由理解生命规则：微生物组理论和机制项目资助，该项目是由生物科学理事会新兴前沿部门管理的美国国家科学基金会十大理念的一部分。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。

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.