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Understanding Rumen Microbial Community Structure and Function Towards Decreasing Methane Emissions

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Understanding Rumen Microbial Community Structure and Function Towards Decreasing Methane Emissions University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Theses and Dissertations in Animal Science Animal Science Department Spring 5-2021 UNDERSTANDING RUMEN MICROBIAL COMMUNITY STRUCTURE AND FUNCTION TOWARDS DECREASING METHANE EMISSIONS Allison L. Knoell University of Nebraska-Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/animalscidiss Part of the Agriculture Commons, and the Animal Sciences Commons Knoell, Allison L., "UNDERSTANDING RUMEN MICROBIAL COMMUNITY STRUCTURE AND FUNCTION TOWARDS DECREASING METHANE EMISSIONS" (2021). Theses and Dissertations in Animal Science. 212. https://digitalcommons.unl.edu/animalscidiss/212 This Article is brought to you for free and open access by the Animal Science Department at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Theses and Dissertations in Animal Science by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. UNDERSTANDING RUMEN MICROBIAL COMMUNITY STRUCTURE AND FUNCTION TOWARDS DECREASING METHANE EMISSIONS by Allison L. Knoell A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Doctor of Philosophy Major: Animal Science (Ruminant Nutrition) Under the Supervision of Professors Samodha C. Fernando and Paul J. Kononoff Lincoln, Nebraska May, 2021 UNDERSTANDING RUMEN MICROBIAL COMMUNITY STRUCTURE AND FUNCTION TOWARDS DECREASING METHANE EMISSIONS Allison Leigh Knoell, Ph.D. University of Nebraska, 2021 Advisors: Samodha C. Fernando and Paul J. Kononoff Ruminants are vital to feeding an emerging population. Resource use is continually being limited due to this growth, therefore, production of high-quality animal protein sources, such as meat and milk, are challenged. Meeting the demands for these consumables, while utilizing fewer resources, is a task the livestock industry is currently facing. The rumen microbiome is extensive and serves to provide several metabolic requirements for the animal for growth. Recently, a significant amount of research is being driven towards understanding the rumen microbiome due to its large effect on metabolic requirements. A study was conducted to replace alfalfa with nonforage fiber sources in dairy cows. It was determined milk yield and intake are maintained when nonforage fibers replace forage sources, while decreasing methane levels. Water consumption decreased when cows were fed a straw and dried distillers grains and solubles mixture in replacement of alfalfa. The microbial community observed no differences in alpha diversity measures, despite the abundance of some taxa being correlated with methane production. These dietary treatments do not alter microbial community composition to determine performance differences. Examination into substrate production by these microbes may provide insight into how energy is diverted in dairy cows fed nonforage fiber sources. A metagenomic analysis was conducted characterizing the genomic capacity within the microbial community in beef cattle fed diets based on forage quality to evaluate methane mechanisms within the microbial community. In high-quality forage diets, the propionate pathway becomes enhanced, acting as a hydrogen sink for methanogenesis. Betaproteobacteria genes were identified to be present in the propionate pathway, which becomes enhanced in high-quality forage-based diets, indicating a syntrophic relationship may be occurring to reduce methane emissions in beef cattle. Keywords: beef cattle, dairy cow, nonforage fiber, metagenomic, methane, rumen microbiome iv Dedication I dedicate this work to my family and to the graduate students who helped in these experiments. v Acknowledgements I am extremely grateful for having the opportunity of pursuing my doctorate with Dr. Fernando and Dr. Kononoff in Ruminant Nutrition focusing on microbial ecology at the University of Nebraska. This was a unique experience and I am forever grateful for this opportunity. The guidance, direction, challenge, and support will forever make me a better scientist. My deepest gratitude goes to Dr. Samodha Fernando and Dr. Paul Kononoff, who offered to co-advise me during this time to explore both the microbial and applied aspect of ruminant nutrition. The mentorship, kindness, patience, encouragement, and understanding in some of the hardest times of my life have been instrumental to my success here. I am beyond thankful to have you as advisors. I want to thank the members of my committee, Dr. Galen Erickson, Dr. Matt Spangler, Dr. Kathy Hanford, and Dr. Rick Stowell. Thank you for taking the time to be on my committee. Your accomplishments and knowledge make me strive to only be better in this continuously merging interdisciplinary field. The graduate students, so many have come and gone during my time here and I am blessed for the friendships I have made. My lab, the Fernando lab (Chris, Nirosh, Wes, Waseem, Alison, Ema, and Esther) whom I knew I could always rely on, everyone one of you are amazing and gentle people. The friendships I made here are lifetime, and I could not have done this without you. You all have talked me off the edge, and for that your support and assistance is immeasurable. The knowledge I have gained from each of you is unparalleled and I cannot begin to thank you enough. vi The dairy lab, again students have come and gone, but I cherish the friendships I have made in this group. I learned so much, got covered in so much, and wouldn’t trade the laughs and work for anything. Erin and Darren, you two were instrumental in teaching me in the dairy. You both were always fun to talk to and I could count on a laugh or sports talk anytime I was down there. The teaching and kindness you showed me, when I knew nothing of dairy life, holds a special place with me. Thank you. Paulina and Napo, I cannot begin to describe how blessed I am to have met you. You are such amazing people and helped me along the way in more ways I can count. Thank you for friendship, I cherish it completely. The beef group, many have also come and gone, I am blessed to get to know so many wonderful people who were always willing to help with samplings. Jana, Hannah, Melissa, and Ashley, you amazing strong women, are simply the best. I enjoyed our talks about science and about the most random subjects. These friendships are lifetime, and I am so thankful to have met you. The fact that I can call each of you a close friend is such a blessing to me. Your support while finishing especially, has been encouraging and helped to get me through. To my family. The love, support, and encouragement through this is overwhelming. Thanks for putting up with me during this time. My mom has always cheered me on and kept me going in challenging times. Seeing my niece and nephew born and grow during this time has brought such a positive light to my life. I love you all. Dad, you left us way too soon. It made finishing this degree even harder. I miss you like crazy every day. You always told me to “just do it and get it done” and always asked vii “when will you be done?”, well Dad, I am finally done. I wish you were here to see it and celebrate. I know you are with me in spirit. viii Table of Contents DISSERTATION INTRODUCTION ............................................................................ 19 CHAPTER 1 ................................................................................................................. 21 REVIEW OF LITERATURE ........................................................................................ 21 Introduction ....................................................................................................... 21 Members of the Rumen Microbial Community .................................................. 22 Bacteria ............................................................................................................. 22 Archaea ............................................................................................................. 24 Protozoa............................................................................................................. 25 Fungi ................................................................................................................. 27 Bacteriophages................................................................................................... 27 Investigating the Rumen Microbial Community ................................................. 28 Pathways of Enteric CH4 Production in the Rumen ............................................ 29 Biochemical pathways of methanogenesis in ruminants ..................................... 30 Nutritional Strategies for CH4 Mitigation ........................................................... 34 Effect of forage-based diets and quality on CH4 production ............................... 35 Effect of concentrate-based diets and quality on CH4 production........................ 37 Alternative hydrogen sinks ................................................................................. 39 - 2- NO3 and SO4 supplementation ........................................................................ 40 Ionophores ......................................................................................................... 44 Lipid supplementation........................................................................................ 46 Alfalfa replacement in lactating dairy cattle
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