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Differences in Eubacterial and Archaeal Soil Communities Along a Precipitation Transect in the Mojave Desert

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Differences in Eubacterial and Archaeal Soil Communities Along a Precipitation Transect in the Mojave Desert San Jose State University SJSU ScholarWorks Master's Theses Master's Theses and Graduate Research Spring 2011 Differences in Eubacterial and Archaeal Soil Communities Along a Precipitation Transect in the Mojave Desert Elaine Pressly Bryant San Jose State University Follow this and additional works at: https://scholarworks.sjsu.edu/etd_theses Recommended Citation Bryant, Elaine Pressly, "Differences in Eubacterial and Archaeal Soil Communities Along a Precipitation Transect in the Mojave Desert" (2011). Master's Theses. 3913. DOI: https://doi.org/10.31979/etd.w3cc-vjrr https://scholarworks.sjsu.edu/etd_theses/3913 This Thesis is brought to you for free and open access by the Master's Theses and Graduate Research at SJSU ScholarWorks. It has been accepted for inclusion in Master's Theses by an authorized administrator of SJSU ScholarWorks. For more information, please contact [email protected]. DIFFERENCES IN EUBACTERIAL AND ARCHAEAL SOIL COMMUNITIES ALONG A PRECIPITATION TRANSECT IN THE MOJAVE DESERT A Thesis Presented to The Faculty of the Department of Biological Sciences San José State University In Partial Fulfillment Of the Requirements for the Degree Master of Science by Elaine Pressly Bryant May 2011 © 2011 Elaine Pressly Bryant ALL RIGHTS RESERVED The Designated Thesis Committee Approves the Thesis Titled DIFFERENCES IN EUBACTERIAL AND ARCHAEAL SOIL COMMUNITIES ALONG A PRECIPITATION TRANSECT IN THE MOJAVE DESERT by Elaine Pressly Bryant APPROVED FOR THE DEPARTMENT OF BIOLOGICAL SCIENCES SAN JOSÉ STATE UNIVERSITY May 2011 Dr. Sabine Rech Department of Biological Sciences Dr. Leslee Parr Department of Biological Sciences Dr. Christopher P. McKay NASA Ames Research Center ABSTRACT DIFFERENCES IN EUBACTERIAL AND ARCHAEAL SOIL COMMUNITIES ALONG A PRECIPITATION TRANSECT IN THE MOJAVE DESERT by Elaine Pressly Bryant Deserts occupy one third of the total land mass of Earth, yet little is known about microbial soil communities under conditions of low precipitation and humidity. The Mojave Desert of the Southwestern United States provides an opportunity to observe microbial communities along a precipitation transect. The diversity of these communities can elucidate which specific groups of Eubacteria and Archaea are best adapted to limited liquid water. Two methods were utilized to determine patterns and trends of the microbial soil communities under varying precipitation levels. Viable plate counts allowed comparison of culturable microorganisms over a four-year period. Molecular techniques distinguished unculturable Eubacteria from Archaea. The results indicated three trends. First, the number of culturable microbes decreased from 107 to 106 CFUs/g dry soil as the annual precipitation decreased. Also, the diversity of the eubacterial communities increased as the annual precipitation decreased, indicated by Shannon-Wiener indices increasing from 3.51 to 3.76. Finally, the diversity increases for archaeal communities were small, producing Shannon-Wiener indices from 1.21 to 1.36. Possible indicator bacteria for desertification processes were suggested by the increasing numbers and diversity of cyanobacteria at the drier sample sites. ACKNOWLEDGEMENTS This work was supported by the NASA Graduate Student Research Program #NNX07AV93H for 2006-7, 2007-8, and 2008-9, and the SJSU Department of Biological Sciences Departmental Fellowship, 2006. This research would not have been possible without the assistance of several outstanding individuals: Sabine Rech – Thank you for accepting me as your graduate student. I don‟t believe I could have found a better advisor. You have provided insight during confusing periods, encouragement in the face of contamination, and a calm rationale when frustrations occurred. I am in your debt, and look forward to continuing to work with you in your lab. Chris McKay– Thank you for suggesting the Mojave precipitation transect and supporting me through the NASA GSRP. I am also appreciative for inclusion in the Spaceward Bound Expeditions in the Mojave and Australia. I have enjoyed working with you and becoming acquainted with the cohort of scientists involved in SB. It has been an incredible learning experience and I hope to continue to be involved in desert research. Leslee Parr – Thank you for your encouragement, support, and suggestions on my research. I value your opinions and appreciate your participation on my committee. Monika Kress – Thank you for offering me the initial opportunity to work in Astrobiology. You were responsible for introducing me to Chris and starting this research effort in the Mojave. I‟ll forever be in your debt for that, and hope we can combine our research again someday. Doris Spanggord – Thank you for introducing me to microbiology and allowing me to tutor so I could “really learn it!” Paula Matheus-Carnevali – It was tremendous fun working with you in the early days of our research. I learned quite a lot from you and have missed you since you moved on to your PhD program. I have looked at your thesis numerous times for clarification and am always touched by your acknowledgements. Thanks for your friendship, kindness, and sharing your insight all those hours in the lab. Milena Lilles & June Shinseki – You two have saved my sanity more times than I can count. I appreciate your laughter, your concern, your insight, and your friendship more than you will ever know. Thank you for being there. v There are groups of people to whom I owe many thanks for their time, efforts, results, and friendship: The Environmental Microbiology Laboratory assistants: Antranig, April, Behnaz, Bianca, Carlo, Dionne, Eric, Giovanni, Katya, Kim, Mahsa, Maria, Mihn Tri, Rawni, Steven, Trang, Vahig, and Victor You dedicated scores of hours cloning gene sequences, performing plasmid preps, running agarose gels for restriction digests, and analyzing sequence data. I am forever in your debt. The participants of the NASA Spaceward Bound Mojave Expeditions 2007, 2008, 2009 and 2010. To the teachers who gladly participated in sample collections, culture inoculations, and DNA extractions – your enthusiasm for my work was intoxicating, and I am thrilled many of you have adapted my techniques to enhance learning in your science classrooms. To the scientists: Henry Sun, Jim Nienow, Penny Boston, Rosalba Bonaccorsi, Heather Smith, Mike Spilde, Rakesh Mogul, Jamie Molaro, Jim Thompson, Bill Leibman , Andrew Duncan, Liza Coe, Linda Conrad , Christy Thompson Benjamin Hulsey – thanks for all your suggestions, discussions, friendship, and occasional help in the lab! To the support staff: Robert Fulton, Jason Wallace, – thanks for your help with the on-site lab and the rainfall data. You made working at DSC a pleasure. The participants of the NASA Spaceward Bound Australia Expedition 2009 To the teachers: Jo, Nicci, Jane, Mark, Naomi, Liz, Keith, Steven, and Luther – Thanks for introducing us to Down Under, helping with sample collection and processing, and teaching us how to drive on the wrong side of the road – you were fabulous and I am so proud to call you friends To the scientists: Reut Abromovich, Adrian Brown, Vic Gostin, Jen Heldmann, Eriita Jones, Shannon Rupert, and Johnathan Clark – it was wonderful meeting you and I look forward to running into you again someday. To the support staff: David and Maureen Cooper, Guy Murphy, Nina Stanfield, and David Wilson – you made the expedition a very pleasant experience. Thanks for your efforts and company. vi The SJSU Biological Sciences Support staff: Art Valencia, Veronica Zavala, Matt Voisinet, and Tim Andriese Thanks for all your assistance when problems with media, equipment, and procedures appeared. You are wonderful people with which to work. Finally, I must thank my family for their patience, love, support and encouragement: My parents, David and Velma Pressly – you always supported my love of science, encouraged me to think for myself, and never insisted that I “act like a girl.” Thanks for the telescope, the late nights stargazing, and for trusting me. I hope I‟ve made you proud. My children, Michael and Camille - I appreciate you putting up with my class schedules, my long hours studying, and my frequently mentioned love of microbiology. Thanks for helping with lab stuff when I needed you. I am very proud of you both and look forward to a bit more time with you. My husband, David – You will never know how appreciative I am that you have supported me these many years in my extended education. I now feel I am doing what I love – the teaching, the lab work, and the expeditions. I am also thrilled that you wanted to become involved as my field and lab assistant. We‟ve had so much fun and gotten to know many wonderful people. I love you very much and hope we‟re still driving out to the desert in another 31 years!!!!!! vii TABLE OF CONTENTS List of Tables .......................................................................................................xi List of Figures..............................................................................................…....xiii Preface …………………………………………………………………………………xv Chapter 1: Literature Review………………………………………………………….1 Introduction………………………………………………………………………1 Diversity of Microorganisms……………………………………………...........2 Diversity Measurements…………………………………………….………...14 Physical Characteristics of Deserts………………………………………….16 Soil Microbial Diversity...……………………………………………………...21 Microbial Diversity in Arid Desert ......……………………………………….23 Microbial Diversity in Semi-arid Deserts………………………….………....28 Microbial
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