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，包括循环养分，分解死亡的植物和动物，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，并且在时间和空间上都是非常可变的，基本特性如pH值或养分可用性在不到1毫米的范围内发生变化，水和氧含量在短短几分钟内变化巨大。这种空间和时间的变化可能是土壤中微生物如此多样的核心原因-土壤中同时存在多种不同的“微生境”支持广泛的生态策略。土壤混合不良的简单事实可能也是土壤微生物如此多样化的核心原因：在混合良好的环境中，特定的生物或微生物群体可能会被其他微生物竞争，当它们被隔离在土壤团聚体或孔隙中时，它们可能会茁壮成长，仅仅是因为它们与其他类似的微生境断开。本研究的目的是描述不同过程的相对重要性，这些过程产生和维持土壤中发现的异常微生物多样性。拟议的研究将解决一个关键问题-土壤环境的哪些特定过程和特征驱动了这种巨大的生物多样性？试图在微观尺度上确定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管理的过程来获得高回报，并且还可以增强或改变我们对构建许多其他环境（从海洋到人体）微生物群落的生态过程的理解。结合拟议的实验，研究人员将开发可探索的虚拟现实（VR）土壤环境。这种VR体验将产生规模感：观众将从人类尺度开始，从那里他们将放大到聚合物，在那里他们将能够使用VR耳机进入和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生物多样性在微观尺度上的变化如何导致的机制方面，生态系统功能的变化。解决这一挑战性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：在（A）未混合与经常混合的土壤中，选择、扩散和漂移在确定土壤细菌群落组成方面的相对贡献是什么？(B)环境与低氧条件？(C)不饱和与饱和条件下的对比？相应的假设是：（A）混合土壤将导致越来越相似的群落，主要是通过增加扩散;（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）随着湿度增加而减少的氧气的选择效应将大于湿度促进的扩散。该方法将在一系列嵌套实验中使用50毫克“微生境”中的自然土壤群落，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和统计建模，以量化选择，分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，一名研究生将接受微生物生态学方法的培训。通过X射线扫描和建模创建的土壤聚合物3D模型，PI和她的团队将开发一种VR体验，让观众可以“参观”微生物的世界。该奖项反映了NSF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.