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Investigating Structure and Function of Rhizosphere Associated Microbial Communities in Natural and Managed Plant Systems

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Investigating Structure and Function of Rhizosphere Associated Microbial Communities in Natural and Managed Plant Systems Investigating Structure and Function of Rhizosphere Associated Microbial Communities in Natural and Managed Plant Systems Richard Rosario Rodrigues Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Genetics, Bioinformatics, and Computational Biology Mark A. Williams Bingyu Zhao Roderick V. Jensen David R. Bevan March 16, 2016 Blacksburg, Virginia Keywords: Metagenomics, Biological nitrogen fixation, Associative nitrogen fixers, Rhizosphere, Switchgrass, Invasive plants Copyright 2016, Richard R. Rodrigues Investigating Structure and Function of Rhizosphere Associated Microbial Communities in Natural and Managed Plant Systems ! Richard Rosario Rodrigues! ! ABSTRACT! ! Many plants, especially grasses, have Nitrogen (N) as their growth-limiting nutrient. Large amounts of N fertilizer (>100 kg N ha-1) are used in managed systems to maximize crop productivity. However, the plant captures less than 50% of the (~12 million tons per year, U.S.) applied N-fertilizer. The remaining mobile N lost through leaching and denitrification accumulates in waterways and the atmosphere, respectively. Losses of fertilizers create environmental and economic concerns globally and create conditions that support the invasion of exotic plants in the natural landscapes. There is thus a need to come up with biological solutions to better manage nitrogen for plant growth and ecosystem sustainability. Microbial communities in the rhizosphere are known to potentially have beneficial effects on plant growth. Diazotrophs, for example, are bacteria that can convert the atmospheric nitrogen to ammonia, a process called “nitrogen fixation.” Utilizing the natural process of associative nitrogen fixation to support most of the plant’s N needs would substantially reduce fertilizer use and thus reduce production and environmental costs. The goal of this dissertation was to determine the structure and function of root-zone microbial communities for increasing productivity of native plants. Towards this end, we study the root-zone bacterial and fungal communities of native and exotic invasive plants. This study identifies that shifts in rhizosphere microbial communities are associated with invasion and highlights the importance of rhizosphere associated structure and function of microbes. A study of root-zone associated microbes in switchgrass (Panicum virgatum L.) - a U.S. native, warm-season, perennial, bioenergy crop indicates that high biomass yield ! and taller growth are associated with increased plant N-demand and supportive of bacteria with greater rates of N2-fixation in the rhizosphere. Another crucial outcome of the thesis is a better description of the core and cultivar-specific taxa that comprise the switchgrass root-zone associated microbiome. The work in this dissertation has brought us closer to designing N supply strategies by utilizing the natural microbial communities to balance the N-cycle in agroecosystems and support a sustainable environment. ! Investigating Structure and Function of Rhizosphere Associated Microbial Communities in Natural and Managed Plant Systems ! Richard Rosario Rodrigues! ! General Audience Abstract The capability to grow crops while also taking care of the environment is a major scientific challenge for global sustainability. Plants, especially grasses, cannot directly utilize the nitrogen gas, which is abundant in our atmosphere. The resulting nitrogen limitation serves as a bottleneck in plant production. Extreme amounts of chemical nitrogen-based fertilizers added to increase plant yield pollute land, air, and water. These in turn, affect human and marine health and come with massive economic costs of more than 500 billion U.S. dollars, annually. One major advance to achieve sustainable plant production would be to harness and further develop plant-microbial technologies. This dissertation was aimed towards identifying bacteria that grow in the plant’s root- zone and promote plant growth. Towards this end, we have characterized the microbes in the root-zones of natural and managed plant systems that may help to meet the plant’s changing nitrogen requirements. Indeed, such “diazotrophic” bacteria, for example, can serve as alternatives to chemical fertilizers, help to produce high-quality, nutritious food and are ultimately responsible for the large majority of protein found on planet Earth. The research is thus an important step forward in the production of healthy plants, soils, and clean water for a sustainable global environment. By better describing the complex, highly diverse, plant associated bacterial communities the scientific community is closer to managing the activities of these crop- associated bacteria. Using such plant-microbial associations will allow for growth on low- fertility land, restore soil health, and provide other ecosystem benefits, such as the production of high-quality forage for livestock and feedstock for making biofuels. Yield of other grasses (e.g. rice, maize, wheat), like switchgrass, are limited by nitrogen; hence it is possible to transfer our research insights to food crops as well. Increasing crop production using sustainable methods can help to satisfy the world food and fuel demands, while simultaneously enhancing the quality of life and health of the environment. ! v! Dedicated to my loving family! Nathubai (Aajimai), Bavatis (Shepai), Philomena (Nana) & Francis (Pappa) Maria (Mummy) & Rosario (Daddy) Charles (Brother) & Neelam (Fiancée) I had this opportunity only because of their determination, efforts, love, and support. vi! ! Acknowledgements I want to sincerely express my gratitude to my advisor, Dr. Mark A. Williams, whose support has been pivotal to my Ph.D. I want to thank him particularly for going above and beyond to help me in my personal and professional life. I am fortunate to have learned from an intellect, Dr. Williams, who is an equally humble person and genuinely cares for others. I honestly enjoyed working with him. I would like to express my deep appreciation to Dr. David Bevan and Dr. Roger Harris for the support and mentoring. I want to thank my committee members, Dr. Bingyu Zhao and Dr. Roderick Jensen, for their guidance and thought-provoking suggestions. I want to thank my lab members, especially Rosana Pineda, for providing suggestions when I was choosing an advisor and showing me the ropes when I was new to the lab. I want to thank all the undergraduates in our lab for their help. I also want to thank Kerri Mills and Dennie Munson for their technical assistance. I am grateful to Virginia Tech’s Department of Horticulture, Graduate Student Assembly, and Genetics, Bioinformatics, & Computational Biology Program for providing a nurturing environment and helping me grow as a person. Last but not least, I want to thank my family for their support in my pursuit of a Ph.D. vii! ! Attribution Several collaborators have helped in the research in the different chapters presented as part of this dissertation. Their contributions are described below. Chapter 2: Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity, 2015, PLoS ONE 10(10): e0141424. Authors and affiliations: Richard R. Rodrigues1, Rosana P. Pineda2, Jacob N. Barney3, Erik T. Nilsen4, John E. Barrett4, Mark A. Williams1,2 1Interdisciplinary Ph.D. Program in Genetics, Bioinformatics, and Computational Biology; 2Department of Horticulture; 3Department of Plant Pathology, Physiology, and Weed Science; 4Department of Biological Sciences; Virginia Tech, Blacksburg, VA. Conceived and designed the experiments: RRR RPP JNB ETN JEB MAW. Performed the experiments: RRR RPP. Analyzed the data: RRR RPP MAW ETN. Contributed reagents/materials/analysis tools: RRR RPP JNB ETN JEB MAW. Wrote the paper: RRR MAW JNB RPP ETN. Chapter 3: Microbial Communities and Diazotrophic Activity Differ in the Root-Zone of Alamo and Dacotah Cultivars of Switchgrass. Authors and affiliations: Richard R. Rodrigues1, Jinyoung Moon2, Bingyu Zhao2, Mark A. Williams1,2 1Interdisciplinary Ph.D. Program in Genetics, Bioinformatics, and Computational Biology; 2Department of Horticulture; Virginia Tech, Blacksburg, VA. Conceived and designed the experiments: RRR JM BZ MAW. Performed the experiments: RRR JM. Analyzed the data: RRR JM MAW. Contributed reagents/materials/analysis tools: RRR BZ MAW. Wrote the paper: RRR JM BZ MAW. Chapter 4: The Search for the Core Microbiome in Switchgrass Rhizosphere. Authors and affiliations: Richard R. Rodrigues1, Mark A. Williams1,2 1Interdisciplinary Ph.D. Program in Genetics, Bioinformatics, and Computational Biology; 2Department of Horticulture; Virginia Tech, Blacksburg, VA. Conceived and designed the experiments: RRR MAW. Performed the experiments: RRR. Analyzed the data: RRR. Wrote the paper: RRR MAW. viii! ! Table of Contents CHAPTER 1. Introduction ..................................................................................................... 1 Importance of nitrogen in agriculture ..................................................................................... 1 Negative effects of reactive N on environment and ecosystem’s vegetative structure ....... 1 Biological nitrogen fixation as an alternative to N fertilizers ............................................... 3 Symbiotic versus associative nitrogen fixers ............................................................................. 4 Switchgrass as a system to
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