University of New Mexico UNM Digital Repository Biology ETDs Electronic Theses and Dissertations 12-1-2015 The impact of temperature, pH and environmental heterogeneity on prokaryotic diversity in Yellowstone National Park thermal springs Xiaoben Jiang Follow this and additional works at: https://digitalrepository.unm.edu/biol_etds Recommended Citation Jiang, Xiaoben. "The impact of temperature, pH and environmental heterogeneity on prokaryotic diversity in Yellowstone National Park thermal springs." (2015). https://digitalrepository.unm.edu/biol_etds/57 This Dissertation is brought to you for free and open access by the Electronic Theses and Dissertations at UNM Digital Repository. It has been accepted for inclusion in Biology ETDs by an authorized administrator of UNM Digital Repository. For more information, please contact [email protected]. Xiaoben Jiang Candidate Biology Department This dissertation is approved, and it is acceptable in quality and form for publication: Approved by the Dissertation Committee: Cristina Takacs-Vesbach, Chairperson Robert Sinsabaugh Diana Northup Laura Crossey i THE IMPACT OF TEMPERATURE, PH AND ENVIRONMENTAL HETEROGENEITY ON PROKARYOTIC DIVERSITY IN YELLOWSTONE NATIONAL PARK THERMAL SPRINGS by XIAOBEN JIANG B.S., Biotechnology, Shanghai Fisheries University, 2000 M.S., Biology, Brigham Young University, 2010 DISSERTATION Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Biology The University of New Mexico Albuquerque, New Mexico December 2015 ii DEDICATION To my parents iii ACKNOWLEDGMENTS With sincere gratitude, I thank my advisor, Dr. Cristina Takacs-Vesbach, for her guidance and support throughout the process of my dissertation work. Her broad knowledge, deep insight and great enthusiasm promoted the development and accomplishment of my dissertation projects. Not only has she enhanced my research experience, but my future career in science as well. The four years working with Dr. Takacs-Vesbach will benefit me all through my life. I am indebted to my committee members, Dr. Robert Sinsabaugh, Dr. Diana Northup and Dr. Laura Crossey for their advice and support. I mostly owe thanks to Daniel Colman, who has provided his time, advice, enlightenment and encouragement and has been my best friend since we met. I would like to specially thank: David Van Horn, Jordan Okie, George Rosenberg and Heather Buelow. I also want to extend thanks to my mother and father for their unending love, support and encouragement, throughout the pursuit of my PhD. iv The Impact of Temperature, pH and Environmental Heterogeneity on Prokaryotic Diversity in Yellowstone National Park Thermal Springs by Xiaoben Jiang ABSTRACT Yellowstone National Park (YNP) is one of the largest and most diverse hydrothermal areas on Earth. Extensive culture-independent studies in YNP thermal springs have shown dramatic taxonomic and metabolic diversity in microbial communities. We conducted a survey of bacterial communities along temperature gradients in three alkaline springs with similar geochemistries at the local scale. With these data, we investigated the influence of environmental variables on bacterial community diversity and assemblages along a broad temperature range using high throughput 454 pyrosequencing. Previous studies have suggested that pH is the driver of microbial diversity in thermal springs among geographical regions or at the global scale, whereas the temperature is an important factor controlling microbial diversity in springs within a similar pH range or within an individual geographical region. Our results revealed that temperature was the most important environmental variable to shape the structure of bacterial communities at the local scale. Similar community structure was observed in the sites with similar temperatures, irrespective of the origin of the thermal spring. The results of this study expand our current knowledge of the role of temperature in controlling community structure in YNP alkaline thermal springs. v In addition to temperature, pH is also a crucial factor in determining microbial assemblages in thermal springs. Although thermal springs in YNP are characterized by a broad range of pH (1-10), the pH distribution is bimodal. Most of springs are either vapor-dominated acidic springs or water-dominated neutral to slightly alkaline springs. Yet the intermediate pH (e.g., pH 4-5) habitats have been overlooked. The dearth of information on microbial communities in the intermediate pH sites has still hindered an understanding of the whole picture of microbial diversity in YNP thermal springs. We conducted the first metagenomic investigation of microbial phylogenetic and functional diversity in a pH 4 and low temperature site. We uncovered a high proportion of Chloroflexi, Bacteroidetes, Proteobacteria and Firmicutes in this site. Functional comparison indicated that the community was enriched in the COG functions related to energy production and conversion, transcription and carbohydrate transport, possibly to result from high microbial dynamics. This is the first study to examine a pH 4 and low temperature habitat, which is a key step towards an understanding of the whole picture of microbial diversity in YNP thermal springs. Local environmental heterogeneity may also be responsible for the assemblages and distribution of some microbial groups. We examined microbial diversity and community composition in ten filamentous thermal springs with similar physiochemical properties in the Shoshone area by using the barcoded amplicon pyrosequencing approach. Despite all these samples from the same type of springs, statistical analyses suggest that the relatively small variation of environmental variables such as temperature, pH and conductivity among the springs can shape microbial composition. Additionally, we conducted a metagenomic analysis on a previously uninvestigated high temperature vi and pH filamentous habitat. The results indicated that the site was exclusively dominated by the family Aquificaceae, and functions related to aerobic respiration and amino acid synthesis were enriched. The research presented here is an in-depth investigation of thermal springs, enhanced by high-throughput community sequencing and a combination of environmental data. The work will fill the knowledge gap for microbial communities in uninvestigated habitats and offer a basis for understanding microbial ecology in global thermal springs. vii Table of Contents Chapter 1 ............................................................................................................................. 1 Microbes and Microbial Ecology in Thermal Springs of Yellowstone National Park ....... 1 Background ......................................................................................................................... 1 References ........................................................................................................................... 6 Chapter 2 ........................................................................................................................... 17 Influence of Temperature on Bacterial Community Structure in Three Alkaline Thermal Springs of Yellowstone National Park .............................................................................. 17 Abstract ............................................................................................................................. 18 Materials and Methods ...................................................................................................... 21 Results ............................................................................................................................... 25 Discussion ......................................................................................................................... 28 Conclusions ....................................................................................................................... 36 References ......................................................................................................................... 38 Tables and Figures ............................................................................................................ 55 Chapter 3 ........................................................................................................................... 70 Taxonomic and Functional Insights of a Low Temperature pH 4 Thermal Spring Microbial Community in Yellowstone National Park ...................................................... 70 Abstract ............................................................................................................................. 71 Introduction ....................................................................................................................... 72 Materials and Methods ...................................................................................................... 74 Results ............................................................................................................................... 79 Discussion ......................................................................................................................... 83 Conclusions ....................................................................................................................... 91 References ......................................................................................................................... 93 Tables and Figures .........................................................................................................