THE EFFECTS OF A COMBINATION OF SODIUM BENZOATE, POTASSIUM SORBATE, AND SODIUM NITRITE ON THE COMPOSITION OF THE MICROBIAL COMMUNITY, FERMENTATION, AND AEROBIC STABILITY OF WHOLE-PLANT CORN SILAGE AND HIGH MOISTURE CORN by Érica Benjamim da Silva A dissertation submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Animal and Food Sciences Summer 2018 © 2018 Érica Benjamim da Silva All Rights Reserved THE EFFECTS OF A COMBINATION OF SODIUM BENZOATE, POTASSIUM SORBATE, AND SODIUM NITRITE ON THE COMPOSITION OF THE MICROBIAL COMMUNITY, FERMENTATION, AND AEROBIC STABILITY OF WHOLE- PLANT CORN SILAGE AND HIGH MOISTURE CORN by Érica Benjamim da Silva Approved: __________________________________________________________ Limin Kung, Jr., Ph.D. Chair of the Department of Animal and Food Sciences Approved: __________________________________________________________ Mark W. Rieger, Ph.D. Dean of the College of Agriculture and Natural Resources Approved: __________________________________________________________ Douglas J. Doren, Ph.D. Interim Vice Provost for Graduate and Professional Education I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Limin Kung, Jr., Ph.D. Professor in charge of dissertation I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Tanya F. Gressley, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Amy S. Biddle, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Richard E. Muck, Ph.D. Member of dissertation committee ACKNOWLEDGMENTS The journey that led to this dissertation started when I left my homeland Brazil and moved to the United States. I knew I would face many challenges and adversities when pursuing a Ph.D. degree in another country. What I did not know was that I would meet so many extraordinary people and have so many great experiences that would forever change who I used to be. As I move to the next chapter of my life, I will always remember my Ph.D. journey with a deep sense of gratitude. Therefore, I would like to thank everyone who helped me directly or indirectly with this dissertation. I would like to express the most profound appreciation to my advisor Dr. Limin Kung Jr., who received me in his group with open arms. His passion and dedication to the field inspire me to be a better professional. Without his guidance and help, this dissertation would not have been possible. My highest appreciation to my committee members, Dr. Amy Biddle, Dr. Tanya Gressley, and Dr. Richard Muck, for all the time and effort dedicated to my dissertation and for pushing the animal sciences field forward. I would like to acknowledge all the faculty, staff, and farm staff of the Department of Animal and Food Sciences, which were always ready to help. Also, I would like to thank my labmates Becca Savage, Megan Smith, Steph Polukis, Katie iv Pacer, Rachel Mester, Anette Gray, and Mike Palillo who had an essential role in the outcome of this dissertation and who made work fun. I am grateful to all my Brazilian friends from Delaware that made this place feel like home, and to all friends from Brazil that supported me before and during this process. A special thank you to my boyfriend Richard and to the best dog ever Ria for supporting me during the worst moments and for always making me laugh. I would like to acknowledge Salinity (Goteborg, Sweden) for providing partial funding for these studies and the Coordination for the Improvement of Higher Education Personnel for the scholarship (99999.013556/2013-04). I dedicate this dissertation to my parents Ana and Osmar and to my brother Caio, who are always by my side even when they are thousands of miles away. Without their continued support and dedication to make me feel loved and capable none of this would have been possible. v TABLE OF CONTENT LIST OF TABLES .............................................................................................................. x LIST OF FIGURES ......................................................................................................... xiii ABSTRACT ..................................................................................................................... xix INTRODUCTION .............................................................................................................. 1 Chapter 1 LITERATURE REVIEW ........................................................................................... 4 Whole-Plant Corn Silage and High Moisture Corn ......................................................4 Silage Microorganisms .................................................................................................6 Lactic Acid Bacteria (LAB) ..................................................................................... 6 Yeasts ....................................................................................................................... 7 Molds ....................................................................................................................... 8 Clostridia .................................................................................................................. 9 Enterobacteria .......................................................................................................... 9 Acetic Acid Bacteria .............................................................................................. 10 Bacilli and Listeria ................................................................................................. 11 The Ensiling Process and Microbial Succession ........................................................11 The Use of Chemical Additives in Silage Production ................................................15 Effects of Sodium Benzoate, Potassium Sorbate, and Sodium Nitrite on the Fermentation and Aerobic Stability of Corn Silage and HMC ..................................20 Objectives .................................................................................................................. 27 REFERENCES ...........................................................................................................28 2 EFFECTS OF A CHEMICAL ADDITIVE ON THE COMPOSITION OF THE FUNGAL COMMUNITY, FERMENTATION, AND AEROBIC STABILITY OF CORN SILAGE ................................................................................................... 40 Abstract.......................................................................................................................40 Introduction ................................................................................................................42 vi Objectives ...................................................................................................................43 Materials and Methods ...............................................................................................44 Crops and Silos ...................................................................................................... 44 Aerobic Stability Measurements ............................................................................ 44 Chemical Analysis ................................................................................................. 45 Microbial Analysis ................................................................................................. 47 Fungal Microbiome Analysis ................................................................................. 48 Statistical Analysis ................................................................................................. 49 Results and Discussion ...............................................................................................50 Chemical and Microbial Characteristics of Fresh Forage ..................................... 50 Chemical Properties, Microbial Populations, and Aerobic Stability of Silage and TMR ....................................................................................................................... 50 The Composition of the Fungal Community ......................................................... 53 Conclusions ................................................................................................................56 TABLES .....................................................................................................................57 FIGURES ...................................................................................................................63 REFERENCES ...........................................................................................................69