EAGER: Soil Microhabitats and the Generation, Maintenance, and Significance of Microbial Diversity

地球的土壤拥有非凡的生物多样性，细菌和真菌等土壤微生物控制着许多重要的过程，包括养分循环，分解死去的植物和动物，以及产生或消耗二氧化碳和甲烷等大气气体。土壤通常是混合不良的环境，在时间和空间上都可能发生极大的变化，pH值或养分有效性等基本特性在不到1毫米的范围内发生变化，水和氧含量在短短几分钟内就会发生巨大变化。这种空间和时间的变化可能是土壤孕育如此多种多样微生物的核心原因——土壤中同时存在大量不同的“微栖息地”，支持了广泛的生态策略。土壤混合不良这一简单的事实可能也是土壤微生物如此多样化的一个核心原因：在混合良好的环境中被其他微生物淘汰的特定生物体或微生物群，当它们被隔离在土壤团聚体或孔隙中时，可能会茁壮成长，仅仅是因为它们与其他类似的微栖息地断开连接。本研究的目的是描述在土壤中发现的产生和维持特殊微生物多样性的不同过程的相对重要性。拟议的研究将解决一个关键问题——土壤环境的哪些具体过程和特征驱动了这种巨大的生物多样性？试图在微观尺度上识别这些现象存在固有的风险。该项目将为一名研究生提供研究培训。这项研究的结果可以通过更好地管理和理解土壤微生物及其控制的过程而产生高回报，并且还可以增强或改变我们对从海洋到人体等许多其他环境中构建微生物群落的生态过程的理解。与提出的实验相结合，研究人员将开发一个可探索的虚拟现实（VR）土壤环境。这种虚拟现实体验将产生一种尺度感：观众将从人类尺度开始，从那里他们将放大到集合体，在那里他们将能够使用虚拟现实耳机进入并探索微生物尺度的土壤孔隙网络。在这个EAGER项目中，PI建议使用创造性和高风险的方法来测试微观尺度上微生物多样性变化如何导致生态系统功能变化的机制方面。解决这个具有挑战性的问题的概念和研究设计必须解决碳利用效率、多样性和生态系统功能之间的联系。本研究的关键问题是：选择、扩散和漂移在确定(A)未混合与频繁混合土壤中土壤细菌群落组成的相对贡献是什么？(B)环境与低氧条件？(C)非饱和条件与饱和条件？相应的假设是：(A)混合土壤将导致群落越来越相似，主要是通过增加分散；(B)低氧条件将对适应这些条件的群落施加选择压力，但不会显著影响扩散；(C)随着水分增加而减少的氧的选择性作用将大于水分促进的扩散作用。该方法将在一系列巢式实验中使用50毫克“微生境”中的天然土壤群落，其中调整微生境的水分和氧气条件，同时改变土壤混合的频率。研究人员将利用高通量扩增子测序来表征细菌群落组成，并利用统计模型来量化选择、扩散和漂移在确定土壤细菌群落组成中的相对重要性。作为这些研究的一部分，研究生将接受微生物生态学方法的培训。利用x射线扫描和建模创建的土壤集合体3D模型，PI和她的团队将开发一种虚拟现实体验，让观众“游览”微生物的世界。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。

Earth’s soils host extraordinary biological diversity, and soil microbes such as bacteria and fungi govern many important processes, including cycling nutrients, decomposing dead plants and animals, and producing or consuming atmospheric gases such as CO2 and methane. Soils are generally poorly mixed environments and can be extremely variable in both time and space, with fundamental properties such as pH or nutrient availability changing over less than 1 millimeter, and water and oxygen content varying dramatically over the course of just minutes. This spatial and temporal variation is likely a core part of the reason why soils harbor such a vast diversity of microbes - the simultaneous existence of a multitude of different “microhabitats” within the soil supports a wide range of ecological strategies. The simple fact that soils are poorly mixed is likely also a core reason soils are so microbially diverse: specific organisms or groups of microbes that would be out-competed by other microbes in a well-mixed environment may thrive when they are isolated within soil aggregates or pores, simply because they are disconnected from other similar microhabitats. The goal of this research is to characterize the relative importance of the different processes that generate and maintain the exceptional microbial diversity found in soils. The proposed research will address a critical question - which specific processes and characteristics of the soil environment drive this great biodiversity? There is inherent risk in attempting to identify these phenomena at the micro-scale. The project will provide research training for a graduate student. The results from this study could have a high payoff through better management and understanding of soil microbes and the processes that they govern, and could also enhance or transform our understanding of the ecological processes structuring the microbial communities of numerous other environments, ranging from the ocean to the human body. In conjunction with the proposed experiments, researchers will develop an explorable virtual reality (VR) soil environment. This VR experience will engender a sense of scale: the viewer will start at human-scale, from which they will zoom in to the aggregate, where they will be able to enter and explore the soil pore network at the scale of a microbe using a VR headset.In this EAGER project, the PI proposes to use creative and high risk approaches to test mechanistic aspects of how changes in microbial diversity at the microscale might result in changes in ecosystem function. The conceptual and research designs to address this challenging question will have to tackle making linkages between carbon use efficiency, diversity and ecosystem function. The key questions of this research are: What are the relative contributions of selection, dispersal, and drift in determining soil bacterial community composition in (A) unmixed vs. frequently mixed soil? (B) ambient vs. low-oxygen conditions? (C) unsaturated vs. saturated conditions? The corresponding hypotheses are: (A) Mixing soil will result in increasingly similar communities, largely through increased dispersal; (B) Low-oxygen conditions will impose selective pressure for communities adapted to those conditions, but will not significantly affect dispersal; (C) The selective effects of the reduced oxygen that accompanies increased moisture will be greater than the increased dispersal facilitated by moisture. The approach will use natural soil communities in “microhabitats” of 50 mg in a nested series of experiments where the microhabitat moisture and oxygen conditions are adjusted, while also varying frequencies at which soils are mixed. The researchers will draw on high-throughput amplicon sequencing to characterize bacterial community composition and statistical modelling to quantify the relative importance of selection, dispersal, and drift in determining soil bacterial community composition. A graduate student will be trained in microbial ecology methods as part of these studies. Using a 3D model of a soil aggregate created using X-ray scanning and modelling, the the PI and her team will develop a VR experience that will allow viewers to “take a tour” of the world of a microbe.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.