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

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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.