Page 34 of 38 Created :29:16 Assistant Professor Microbial

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1 Page 34 of 38 Created :29:16 Assistant Professor Microbial Overarching goals of my research program Precisely estimating, mitigating, and adapting to the many facets of global change is a grand challenge for society in the 21 st century. Soil microbial communities lie at the intersection of the biogeochemical cycles fueling climatological regimes and ecosystem services we rely on. Through training and research, my mission is to advance the understanding of microbial communities to improve predictions of biogeochemical processes and develop creative solutions to sustainability problems. Making up more biomass and diversity than any other group of organisms, microorganisms (bacteria, archaea, fungi) serve as the invisible majority, maintaining the health of their animal hosts, soils, and ecosystems. Recent research, including my own, has shown that contrary to past assumptions, all microbial communities are not created equal; that is, a community is not always optimized to its environment, and in this way, may constrain ecosystem functions. However, it has been difficult to identify when and where additional information about microbial communities can improve our understanding, prediction, and preservation of microbial functions like soil fertility and greenhouse gas sequestration. Revealing this linkage could unlock enormous power for improving sustainability, which makes it a very exciting time to be an early-career microbial ecologist. In my research, I identify microbial traits that link to ecosystem function, laying the groundwork for development of methods that quickly and cheaply assess how microbes are functioning in the soil, and use this information to inform management decisions. The overarching goal of my current research program is to identify how water dynamics influence microbial communities and how, in turn, their function alters ecosystem responses. Below, I show how my current and future research contributes to (1) improving ecosystem modeling in arid ecosystems and (2) rescuing degraded lands and functions, both sustainability goals that integrate with research and training in ESS. I also illustrate how I pursue and create training and outreach activities that closely align and compliment these goals. But much of my work builds on the foundation of linking microbial communities to ecosystem function. Thus, I first describe novel approaches I have developed for studying microbial ecosystem ecology, which can be applied broadly to manage and understand microbiallymediated functions. Innovative approaches that I use to link microbes to ecosystem processes I contend that microbe-ecosystem linkages can be achieved most effectively and efficiently by using targeted assessments, diverse methods, and foundational ecological concepts. I have identified three tenants of my research that aid in linking microbial communities to function, which I utilize to maximize the impact of my research on global challenges: First, my research identifies and targets times and places when microbes are likely to alter ecosystem function. Although microbes mediate many biogeochemical processes, in some circumstances, factors other than the potential of the microbial community constrain process rates. A general hypothesis that drives my research direction is that microbial communities are likely to influence function when ecosystems are in transitional, non-equilibrium states. For example, I have shown that micro-scale interactions between microbes, spatial heterogeneity, and diffusion help explain the unexpectedly large pulse of CO 2 that occurs after a dry soil is rapidly rewet. I have also found microbes can constrain function when dispersal is limited. These non-equilibrium states and changes in dispersal patterns are likely to be more prevalent as climates shift dramatically. My long-term goal is to develop a general framework for when and where microbial information will be most useful for predicting ecosystem function.

2 Page 35 of 38 Created :29:17 Assistant Professor Microbial Second, I focus assessments of microbial communities on microbial physiological traits and life histories in situ. Numerous studies describe taxonomic shifts in microbial community, but the life histories of most taxa identified are unknown. My work has coupled metagenomic sequencing to nucleotide labeling techniques and laboratory mesocosms to describe microbial life histories in situ, and to describe how these physiologies shift under environmental change (Fig. 1). My current work builds off of this, aiming to describe genetic and metabolic signatures of these life histories, which will enable us to easily identify how traits shift in the field. Fig 1. Identifying life history strategies for microbial taxa based on moisture response Third, I utilize quantitative models to understand emergent effects of microbial communities and scale up microbial processes. My work with individual-based models has shown that assembly mechanisms like dispersal can lead to certain microbial communities that are not predictable from environmental variables. I also use ecosystem models, both to direct my research and to scale my findings. Discrepancies between observed and predicted values generated by existing models inform the direction of my empirical work; in addition, I use models to scale microbial functions. For instance, we have recently documented microbes uniquely adapted to mineralize carbon using fog water, and are currently testing the broader significance of this phenomena across space and time with versions of DAYCENT. In my current and future work, I explore possible intermediates to these modeling approaches. With robust proxies of microbial function, I think it will be feasible to incorporate large microbial datasets into models and test whether this additional information (and parameterization) improves ecosystem predictions. I incorporate these approaches, which I see as the most powerful to link microbes and ecosystems, into my graduate training. Students in my lab will leave with strong quantitative skills, many with at least one modeling aspect in their dissertation. I am glad ESS similarly values this skill, which is both marketable, and pushes students to place their findings into a broader context, both scientifically and spatially. Equally valuable, students in my lab learn laboratory and bioinformatics pipelines for analyzing molecular data, but with the expectation that they are testing hypotheses grounded in ecological theory and will couple their genomic assessments with other methods. Finally, I also make efforts to enhance my students training by involving them in collaborative projects and larger-scale networks like the LTER. Ultimately, my research program puts these tenants into action by addressing global challenges in two primary areas: Sustainability goal 1: Improve estimates of biogeochemical cycling in arid ecosystems My work improves our understanding of interactions between microbial communities and decomposition processes unique to drylands. Arid and semi-arid lands cover 40% of global land area and support much of the global population. These regions also account for the majority of inter-annual variation in global net carbon exchange, making accurate predictions of carbon cycling in dry areas of utmost importance. Yet, arid lands are where many ecosystem models report the highest uncertainties. Much of my work in arid lands is based in the Namib Desert, Namibia, an excellent natural laboratory for dryland decomposition research, and a setting that engages diverse students in the study of global change in aridlands. Although it is well-known that microbial activity decreases under low-moisture conditions, my work was the first to show that whole microbial communities vary in their ability to tolerate drought, showing that optimization under one set of rainfall patterns can constrain microbial composition and function when rainfall patterns shift. Developing a full understanding of this relationship will improve

3 Page 36 of 38 Created :29:17 Assistant Professor Microbial predictions of microbially-mediated processes during times when environmental conditions deviate from historical patterns. My current work uses a novel and high-throughput desiccation assay to describe the physiological basis of these drought tolerance strategies. This will not only lead to better predictions of microbial compositional shifts with soil drying, but also will directly link these strategies to function through biogeochemical requirements. Once different strategies have been described, we will identify genetic signatures of these physiologies, which will allow us to detect shifts in strategies in the field. My ongoing work on drought and water dynamics is highly relevant to both local challenges in Colorado, and to many of the well-known research programs at CSU doing complimentary work. An exciting new direction in my research program considers an entirely different source of moisture that fuels microbial activity and biogeochemistry: nonrainfall moisture, or dew, fog, and high humidity. My work in the Namib Desert, Namibia, in collaboration with Kathy and Peter Jacobson (Grinnell College), has documented significant rates of CO 2 flux from grass litter after fog and dew events, and identified distinct microbial taxa that have evolved to take advantage of this type of moisture. Since decomposition that is induced by non-rainfall moisture is wholly unaccounted for in ecosystem models, I assessed the potential contribution of these events to decomposition in a first-order linear, 3- pool decomposition model. Including dew and fog meteorological data from the Namib resulted in 20% faster decomposition rates. I am currently testing the generality of these phenomena by collecting additional data to inform models. We hypothesize that this moisture source could account for a large proportion of decomposition in arid lands, and may explain previously unaccounted for variation in decomposition in other ecosystem as well. I am also exploring how photodegradation or the decomposition of litter by ultraviolet radiation influences dryland decomposition. A graduate student in my laboratory is currently investigating how photodegradation interacts with microbes and moisture using UV manipulations in the Namib, and I would be excited to build collaborations in this work with modelers, microbiologists, and meteorologists at CSU. We integrate our work on this project with education programs at Gobabeb Research and Training Center, a field station where much of our field work takes place, and where I had the position of training and outreach coordinator from (Fig. 2). Gobabeb has administered a summer desertification program (SDP), a 1- month course at Gobabeb for Nambian university students, for over 10 years. I also taught this course in 2005, and am designing an inquiry-based unit on decomposition to integrate with our research in upcoming years. This station is set amidst the spectacular Namib Fig. 2. Leading a field trip on Desert Ecology in the Namib Desert (above) at Gobabeb Research Station in Namibia, Africa (below). ecosystem, and holds great potential for engaging Namibian and US students alike in ecology. In the future I would love to lead a course on desert ecology (or similar) during which students could conduct an independent project in the Namib as Namibian students do the same. This course that has been successfully implemented by my collaborators at Grinnell College, but is feasible at CSU as well.

4 Page 37 of 38 Created :29:17 Assistant Professor Microbial Sustainability goal 2: Improve ecosystem services using microbial assembly and function Soil microbes provide essential services. They control the cycling of nitrogen, which influences nutrient availability for plants, and maintain soil structure and water holding capacity. Since microbial communities vary in their potential to carry out these functions, our ability to optimize and preserve microbially-mediated services demands two things: 1) a fundamental understanding of how community function changes and generates desired, predictable outcomes, and 2) in-depth knowledge of how microbes maintain a specific function of interest, in my case, soil nutrient availability. My research program is currently pushing the boundaries of both areas. There is great potential to preserve certain ecosystem services by managing microbial communities. But utilizing this resource will demand a fundamental understanding of the factors that drive microbial community composition. For instance, the goal of methods such as probiotics or microbial inoculant is to alter the community in a beneficial way, but predicting the circumstances in which the introduction of these invaders achieves a desired function has been challenging. My work aims to improve the potential to manage and manipulate microbes to produce a desired function, and I think the way to achieve this goal is to improve understanding of fundamental community assembly processes like selection and dispersal. Specifically, managing microbes often fails because new immigrants, or invaders, either do not persist in their new environment because selection is so strong, or other processes prevent the community from achieving a certain function. Using an individual-based model, I demonstrated that dispersal rate can be a strong driver of community composition, and that both dispersal limitation, and priority effects under very high dispersal, can significantly alter the predictability of community composition. On the other hand, the distribution of traits in the community was more manageable, suggesting that optimization of traits and not species per se might be a better strategy for managing microbial function. In additional to the theoretical approach described above, my current work tests some of these hypotheses empirically. We recently described microbial communities that disperse through rainfall, and tested whether this dispersal vector is important for soil microbial processes by adding either sterile or ambient rain to intact cores for 7 months. We found that soils that did not receive new colonizers through rain had significantly higher nitrate losses through leaching, largely because they had a decreased capacity to retain water. In addition to sterile and nonsterile rain, we have also manipulated rainfall amount, asking whether colonizing microbes are an important source of new taxa to rescue microbial communities and functions that might otherwise be compromised by drought stress. Most of our current work on microbial communities occurs at a local scale, considering only environmental selection. My work suggests that in order to making microbial ecology and management a more predictive science, we must consider processes other than selection, and expand our view of microbial communities to a regional scale. I am currently lead-pi on a 5-year DOEfunded project to determine how microbes mediate the availability of soil nutrients for perennial grasses in degraded lands. These marginal lands could yield cellulosic bioenergy (e.g. switchgrass), but the feasibility and ecological impacts of this pursuit are unknown. Our project addresses this knowledge gap, and also takes advantage of the opportunity to understand controls on plants-microbe interactions in degraded environments. Degraded lands could be important places where preserving or even manipulating microbial function would substantially increase yields. For instance, Fig. 3. Conceptual framework for DOE-funded grant identifying how plant-microbe interactions influence N availability in degraded lands.

5 Page 38 of 38 Created :29:17 Assistant Professor Microbial preliminary results show that switchgrass (a non-leguminous plant) uses nitrogen that is fixed by freeliving bacteria, but N-fixing capacity decreases when switchgrass is fertilized. This suggests that these lands would benefit from reduced fertilizer use, which would in turn reduce the harmful consequences of fertilizer on watershed biogeochemistry. This project is poised to have a great impact on the field of microbial ecology because it has realworld applications, and uses a multi-disciplinary systems-approach. Our overarching hypothesis is that N transformations (fixation and mineralization) mediated by microbes are strongly controlled by carbon subsidies supplied to them by plant roots (Fig. 3), and we will test each part of this hypothesis with novel techniques. For instance, I proposed to study factors driving plant root exudation using plant transcriptomics and isotopic labeling ( 13 CO 2 ), and will couple this with a comprehensive assessment of the types of microorganisms (e.g. N-fixers) these compounds stimulate using a new high-throughput quantitative PCR system. By utilizing multiple marginal land sites with paired fertilized and nonfertilized cropping systems, my project will be able to assess how these processes affect the nitrogenproviding capacity of the microbial community, and its effect on yields and nitrogen conservation. We will also identify the plant genomic pathways that result in beneficial microbial associations, which could be used to breed plants with naturally healthy microbiomes and catalyze collaborations with crop scientists at CSU. I am also improving the sustainability of ecosystem services by facilitating cross-generational conversations about climate change and agriculture through creativity and art. Through a NAFKI Keck Futures Initiatives and National Academy of Sciences conference on art-science linkages, I have initiated a collaboration with two artists that study movement, engagement, and environmental issues. Their work on outdoor teaching and environmental engagement through physical movement will be applied to education programs at KBS (led by copi Kara Haas), including a 1-week workshop for teachers on outdoor education (planned for August 2016). We will also organize a lunch session that catalyzes conversations between KBS students, researchers, local farmers and stakeholders about shifts in land use and climate in the local area. Undergraduate teaching and integration with CSU ESS curriculum I currently teach Global Change Biology, an upper level undergraduate course brand new to the IBIO curriculum. I have developed the course to cover biological concepts related to global change (e.g. range shifts, evolution, biogeochemistry) in a rigorous way, but also have made room in the course structure for students to place concepts in a larger social context. For example, groups lead class discussion on a scientific paper and the societal issues it relates to, and conduct assignments not only about biological responses but also using ecology to create solutions. A similar course emphasizing organismal and community responses to global change could enhance the ESS curriculum, complimenting more ecosystems-focused courses. In addition, I would be excited to teach more specialized courses in ESS. I am well-qualified to teach Microbial Ecology, but would also be interested in developing a course on Water and Development that integrates ecosystem and watershed science areas. The course would address multiple aspects of water and sustainability such as effects of changing land use on water dynamics, the ecological effects of drought, and biodiversity in aquatic habitats, through a global lens. Guest lecturers from local nonprofit organizations would enhance this aspect of the course, and the course would benefit from the diverse backgrounds of students enrolled in ESS.