ADVANCE Fellows Award: Functional and Structural Patterning of Microbial Communities in a Natural Soil Ecosystem

由于微生物种群在远离典型人类感知的时空尺度上运行，过去很难研究它们在复杂生态系统行为中的作用。然而，随着分子方法结合计算工具的广泛使用，这些限制正在迅速减少。微生物硝化作用、氨氧化作用和反硝化作用都在全球氮循环中起着关键作用。对农业使用/滥用过量氮肥的担忧是基于环境失衡，这种失衡可能导致土壤微生物多样性减少和水生生态系统富营养化，以及地下水中硝酸盐积累增加，这可能直接影响人类健康。缺少的是一幅功能微生物群落的完整“图景”，因为它适用于特定系统中的氮循环。在本项目期间，将生成原状土壤的多季节时空数据。此外，还将评估系统的操控以及人为干扰对微生物群落动态的影响，并将其与生态系统的“驱动因素”联系起来。目前已有研究生态系统结构多样性的分子技术。扩增片段长度异质性(ALH)和末端限制性片段长度多态(TRFLP)是查询微生物群落结构的常用方法。然而，有必要继续完善和扩大微生物群落图谱，使之适用于功能基因。这些分子数据将与土壤物理、生物地球化学和化学数据相关联。由于这一综合社区分析将产生丰富的数据，还将继续开发能够更好地询问这些数据的生物和生态信息学工具。分子生物学、土壤科学和计算科学的结合对于在原地揭开复杂微生物群落的复杂性是必不可少的。该项目的长期目标是确定需要在多大范围内跟踪这些关键组成部分，以便制定社区范围的生态系统图景。一旦确定了规模，就会对微生物群落有很多了解，因为它们在氮循环过程中相互作用，并对自然或引入的环境“驱动因素”做出反应。

Because microbial populations operate at spatio-temporal scales far removed from typical human perception, it has been difficult in the past to investigate their role in complex ecosystem behavior. However, with the expanded use of molecular methods combined with computational tools, these limitations are rapidly decreasing. Microbial nitrification, ammonia oxidation, and denitrification all play critical roles in the global nitrogen cycle. Concerns over the agricultural use/misuse of excessive nitrogenous fertilizers are based on the environmental imbalance that can produce decreased microbial diversity in soils and eutrophication of aquatic ecosystems, as well as increased nitrate accumulation in groundwater, which can directly impact human health. What is lacking is a complete 'picture' of the functional microbial community as it applies to nitrogen cycling in a specific system. Multi-seasonal spatio-temporal data for undisturbed soil will be generated during this project. In addition, manipulation of the system and the impact that anthropogenic disturbances may have on microbial community dynamics in situ will be assessed and linked to the ecosystem's 'drivers'. Molecular techniques for studying the structural diversity in ecosystems are now available. Both amplicon length heterogeneity (ALH) and terminal restriction fragment length polymorphisms (TRFLP) are often used to query microbial community structure. However, there is a need to continue to refine and expand microbial community profiling to functional genes. These molecular data will then be correlated with the physical, biogeochemical, and chemical soil data. Because of the wealth of data that will be produced in this comprehensive community analysis, bio- and eco-informatics tools that can better interrogate those data will also continue to be developed. The integration of molecular biology, soil science, and computational science is essential to unraveling the intricacies of complex microbial communities in situ. The long-term goal of this project is to determine at what scale these critical components need to be tracked in order to develop a community-wide ecosystem picture. Once the scale is determined, much will be learned about microbial communities as they interact during nitrogen cycling and respond to natural or introduced environmental 'drivers'.