Growth, Vibriosis, and Streptococcosis Management in Shrimp-Tilapia Polyculture Systems, and the Role of Quorum Sensing Gene cqsS in Vibrio harveyi Virulence Item Type text; Electronic Dissertation Authors Naim, Sidrotun Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 02/10/2021 13:06:33 Link to Item http://hdl.handle.net/10150/268595 GROWTH, VIBRIOSIS, AND STREPTOCOCCOSIS MANAGEMENT IN SHRIMP-TILAPIA POLYCULTURE SYSTEMS, AND THE ROLE OF QUORUM SENSING GENE cqsS IN Vibrio harveyi VIRULENCE By Sidrotun Naim ________________________ A Dissertation Submitted to the Faculty of the DEPARTMENT OF SOIL, WATER, AND ENVIRONMENTAL SCIENCE In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY In the Graduate College THE UNIVERSITY OF ARIZONA 2012 2 THE UNIVERSITY OF ARIZONA GRADUATE COLLEGE As members of the Dissertation Committee, we certify that we have read the dissertation prepared by Sidrotun Naim entitled “Growth, Vibriosis, and Streptococcosis Management in Shrimp-Tilapia Polyculture Systems, and the Role of Quorum Sensing Gene CqsS in Vibrio harveyi Virulence” and recommend that it be accepted as fulfilling the dissertation requirement for the Degree of Doctor of Philosophy. ______________________________ _______________________ Kevin M. Fitzsimmons, PhD Date November 20, 2012 ______________________________ _______________________ Donald V. Lightner, PhD Date November 20, 2012 ______________________________ _______________________ Charles P. Gerba, PhD Date November 20, 2012 ______________________________ _______________________ Carlos R. Pantoja-Morales, PhD Date November 20, 2012 Final approval and acceptance of this dissertation is contingent upon the candidate’s submission of the final copy of the dissertation to the Graduate College. I hereby certify that I have read this dissertation prepared under my direction and recommend that it be accepted as fulfilling the dissertation requirement. ____________________________________________ ____________________ Dissertation Co-Director: Kevin M. Fitzsimmons, PhD Date December 03, 2012 ____________________________________________ ____________________ Dissertation Co-Director: Donald V. Lightner, PhD Date December 03, 2012 3 STATEMENT BY AUTHOR This dissertation has been submitted in partial fulfillment of requirements of an advanced degree at the University of Arizona and is deposited in the University Library to be made available to borrowers under rules of the Library. Brief quotations from this dissertation are allowable without special permission, provided that accurate acknowledgment of source is made. Requests for permission for extended quotation from or reproduction of this manuscript in whole or in part may be granted by the head of the major department or the Dean of the Graduate College when in his or her judgment the proposed use of the material is in the interest of scholarship. In all other instances, however, permission must be obtained from the author. Signed: Sidrotun Naim 4 DEDICATION In the loving memories of: Father Abidullah, it was his dream to see his children achieve the highest education. Maternal grandmother (Eyang Putri Kusniyah) and grandfather (Eyang Kakung M. Komar), who looked after me during high school, and taught me to be the best person in serving others, the same mystical teaching I received from my paternal grandparents. A sister and confidante, Khairunnisa Ajie. This loss is a void I can’t seem to seal. My highest gratitude to my mother, Siti Muslichah, the linchpin of the family; and my parents Djuariah and Wahyu for their patience. My sisters and brothers: Faras, Salman, Iir, Inul, Anna, Jannah, Mia, Ibnu, Diyah, Imma, for their love and continuous support. Dedi Priadi, the father of my son, for always being there for me during all the good time (I don’t remember any bad moment with you). My mentors since undergraduate years who have changed me at some points: Dr. Erly Marwani, Dr. Rizkita Rachmi, Dr. Intan Ahmad, Dr. Wijayono Sarosa, Dr. Ram Mohan, Dr. Brian Paterson, Cut Desyana, Nana Firman, Miftah Rakhmat, Dr. Siti K. Chaerun. Elhurr, my son, be the best person who serves others and searches for knowledge. Latifa, Amira, Muntazhar, Syifa, Syauqi, Ayden, Akhtar, Abel, Faishal, Ara, Jules, Delshady, Delazady, Majda, Dava, Dirham, and their generations: Your mothers are the best friends and sisters one can ask. Shrimp and tilapia farmers around the world, who hope that their farmings would improve their quality of lives. (Tucson, December 3, 2012, the virtual 46th anniversary of my parents) 5 ACKNOWLEDGMENTS My graduate career at the University of Arizona was one of the extraordinary experiences in my life. In 3 years and 3 months, I finished 3 graduate programs: one PhD and two MS degrees. I had the privilege of not only advancing my research skills and enhancing my academic standings, but also trying to understand the Americans and other people’s ways of life and perspectives. As I was just about to finish my PhD study, for the reasons I didn’t quite understand, Dr. Max L. Nibert from Harvard Medical School, and Dr. Bonnie L. Bassler from Princeton University Molecular Biology Department, agreed to train me as a postdoc fellow in their labs. I will continue working on dsRNA viruses and Vibrios, which were part of my trainings in Arizona with a few great mentors such as Dr. Kevin Fitzsimmons, Dr. Donald V. Lightner, and Dr. Judith K. Brown. I thank the Schlumberger Foundation Faculty for the Future Program, the US Department of State Fulbright Presidential Program, the UNESCO-L’Oréal For Women in Science Program, and the University of Arizona Graduate Tuition Award Program, for providing different fellowships and research funding. The following persons had unique contributions to my study: Dr. Kevin Fitzsimmons, my major advisor, the world authority on tilapia and aquaponics. Under his direction, I had learned different aspects of aquaculture, a far better experience than what I expected. Apart from academic life, he gives a good example of helping and sharing his time with others. More than a mentor, I consider him as my second father. Dr. Donald V. Lightner, the world authority on shrimp diseases. Becoming a shrimp pathologist was the original purpose when I began my studies. I had learned three greatest advices from him: (1) everything needs to be confirmed, (2) to be careful, never assume anything without enough evidence, and (3) to say “I don’t know”. Committee members: Dr. Charles Gerba for his insight on the microbiology aspect, Dr. Carlos Pantoja for histopathology training, Dr. Edward Glenn for research design, and Linda Nunan for molecular biology training. Dr. Bonnie L. Bassler from Princeton University, the Beacon of Quorum Sensing (QS) study. She refined the QS chapter of this dissertation, on the weekend after Hurricane Sandy hit Princeton, and days before she had to deliver a big talk. A stroke of luck, our paths crossed in Paris, and will continue for a lifetime more collaboration. She is an epitome of goodness and happiness, role model, friend, and second mom in my life. 6 The Indonesian team: Ating Yuniarti and her students from Brawijaya University, and Ninik Setyorini from East Java Fisheries Agency in Bangil, for running the Indonesian experiments (chapters 3 and 4). Mohammad Bahrelfi Belafiff, for bioinformatics training on Bayesian analysis. Mary Riina for the dissertation proof-reading, Jennifer Wood and Alicia Velasquez for their help on administrative issues. Members of the University of Arizona Aquaculture Pathology Lab: Rita Redman- Lightner, Leone Mohney, Kathy Tang-Nelson, Solangel Navarro, Brenda Noble, and Paul Schofield. Apart from academic life, friendship is a rare find. We don’t know how it happens or how it starts, but we know the special life it always brings. I would like to thank the following persons: Fellow Wildcats (graduate students) in SWES and Vet Science since the beginning of my study: Jason, Rafael, Kyle, Cesar, Fernando, Loc, Tekie, Eric, Brunno. Pamila, thanks for being a friend and confidante in a field dominated by boys. Indonesian community in Tucson and Phoenix. Indonesian student association (Permias) Tucson. Islamic community in Tucson. Nahdhatul-Ulama USA-Canada, Australia, and Germany, for hosting me in Europe Indonesian Student Association and School of Life Sciences and Technology (SITH-ITB) alumni in Gent, Belgium for hosting me. Faculty for the Future (FFTF) sisterhood, particularly the fellows in the US and the Indonesian fellows: Stef, Esther, Nat, Ruth, Taryn, Sharanya, Aretha, Witri, Zoila, Ova, Betty, Wiratni, Puri, Gayatri, Fatma, Sobia, Lena, Anicia, and others. Time flies, the sisterhood gets stronger. Indonesian students and Fulbright brothers/sisters: Wanto, Dani, Beivy, Budi, Yumar, Andri, Witri, Wilis, Shanty, Lusia, Endah, Rita, Suzie, Dike, Ika, Atik, Astri, Kristian, Pam, and others. Eve Millon, ‘si tu aimes il faut partir’, till our paths cross again! (Tucson, 12-12-2012) 7 TABLE OF CONTENTS PAGE LIST OF FIGURES ................................................................................................... 11 LIST OF TABLES ....................................................................................................