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Tropical Macroalgae As a Natural Alternative for the Mitigation of Methane Emissions in Ruminant Livestock Systems

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ResearchOnline@JCU This file is part of the following reference: Machado, Lorenna (2015) Tropical macroalgae as a natural alternative for the mitigation of methane emissions in ruminant livestock systems. PhD thesis, James Cook University. Access to this file is available from: http://researchonline.jcu.edu.au/46419/ The author has certified to JCU that they have made a reasonable effort to gain permission and acknowledge the owner of any third party copyright material included in this document. If you believe that this is not the case, please contact [email protected] and quote http://researchonline.jcu.edu.au/46419/ Tropical macroalgae as a natural alternative for the mitigation of methane emissions in ruminant livestock systems Thesis submitted by Lorenna Machado BSc, MSc In July 2015 for the degree of Doctor of Philosophy in the Centre for Macroalgal Resources & Biotechnology, and the College of Marine and Environmental Sciences James Cook University Statement of access ______________________________________________________________________ I, the undersigned, the author of this work, understand that James Cook University will make this thesis available for use within the university Library and, via the Australian Digital Theses Network, for use elsewhere. I understand that, as an unpublished work, this thesis has significant protection under the Copyright Act and I do not wish to place any further restrictions upon access to this work. __________________________ _________________________ Signature Date ii Animal ethics ______________________________________________________________________ The research presented and reported in this thesis was conducted according to experimental guidelines approved by CSIRO Animal Ethics Committee (A5/2011) and in accordance with the Australian Code of Practice for the Care and Use of Animals for Scientific Purposes (NHMRC, 2004). iii Electronic copy ______________________________________________________________________ I, the undersigned, the author of this work, declare that the electronic copy of this thesis provided to the James Cook University Library is an accurate copy of the print thesis submitted, within the limits of the technology available. __________________________ _________________________ Signature Date iv Statement of the contribution of others ______________________________________________________________________ This research project was financially supported by the College of Marine and Environmental Sciences and the Graduate Research School of James Cook University, Townsville (JCU), the Advanced Manufacturing Cooperative Research Centre (AMCRC), MBD Energy Limited and the Australian Government through the Australian Renewable Energy Agency (ARENA). The Commonwealth Scientific and Industrial Research Organisation (CSIRO) provided in kind support throughout the thesis under the National Livestock Methane Project. Stipend support was provided by the AMCRC through an International Postgraduate Research Scholarship. My primary supervisor Rocky de Nys (JCU, Townsville, Queensland, Australia) and associate supervisors Nicholas Paul (JCU, Townsville, Queensland, Australia), Marie Magnusson (JCU, Townsville, Queensland, Australia), and Nigel Tomkins (CSIRO, Townsville, Queensland, Australia) provided intellectual guidance, financial support, editorial assistance and advice for research experiments. Nicholas Paul (JCU, Townsville, Queensland, Australia) provided statistical advice (Chapters 2, 3, and 4). Marie Magnusson (JCU, Townsville, Queensland, Australia) provided support in the biochemical analysis of fatty acids (FAME – Chapter 2) and secondary metabolites (Chapter 4). v Nigel Tomkins (CSIRO, Townsville, Queensland, Australia) provided access to laboratories, specialist equipment and the donor steers used throughout this research. Pedro de Paula Silva (JCU, Townsville, Queensland, Australia) assisted with the rumen sampling of animals (Chapters 2, 3 and 4) and provided editorial and statistical advice (Chapters 2, 3, 4, and 5). Robert Kinley (CSIRO, Townsville, Queensland, Australia) assisted with rumen sampling (Chapter 4 and 5) and provided editorial advice (Chapters 3 and 4). Carly Rosewarne (CSIRO, Sydney, New South Wales, Australia) provided access to her laboratories, specialised analytical equipment, and advice and supervision in metagenomics analysis (Chapter 5). She also provided intellectual guidance and editorial advice with microbial experiments. Yi Hu (Advanced Analytical Centre (AAC), JCU, Townsville, Queensland, Australia) conducted all metal analyses of macroalgae biomass (Chapters 2). Shane Askew (AAC, JCU, Townsville, Queensland, Australia) provided analytical advice for the analysis of FAME, gas and volatile fatty acids (VFA) using gas-chromatography mass- spectrometry (Chapters 2, 3, 4 and 5) performed at the ACC (Cairns and Townsville). Peter Isherwood (University of Queensland, Gatton College, Queensland, Australia) performed the VFA and ammonia-N assays (Chapters 2, 3, and 4). Finally, Jeffrey Palpratt was responsible for the handling and maintenance of donor steers at the College of Public Health, Medical and Veterinary Sciences (JCU). vi Acknowledgements ______________________________________________________________________ This PhD has been an amazing experience and a journey of highs and lows, in which I have learnt a great deal through persistence, dedication and an excellent advisory team. My research was made possible due to the help and enthusiastic participation of many people to who I am eternally thankful. I look forward to applying my newly acquired skills to the next challenges of my working life. I would like to thank my primary supervisor Rocky de Nys for believing in me and giving me the incredible opportunity to do this PhD. Rocky, your enthusiasm, support, professionalism, meticulous reviews and invaluable advice on how to improve and how to deal with unexpected situations has certainly guided me to the completion of this thesis. I am forever grateful for having the opportunity to be one of your students. I also want to thank my associate supervisors, Nicholas Paul, Marie Magnusson and Nigel Tomkins whom were always enthusiastic and ready to help, each with strengths that complement the others. Nick, who would guess that a five minutes conversion in the kitchen with you would take me through this unexpected life-changing journey? Your way of seeing things in a clear and straightforward manner has opened my mind many times, when I was too deep into my own thoughts, to see how simple research should be. Marie, your patience to teach me all the methodologies and analytical techniques required for the progress of my PhD and all the time you spent in the lab with me will never be forgotten. Thank you for being available during all meetings and vii in “between meetings”, and for encouraging me to think for myself about the best alternatives to overcome stressful situations. Nigel, you were the last supervisor to guide me but one of the best people I have ever encountered in my life. Your dedication, knowledge and hard work have always inspired me to keep going, even when things did not go as planned and I had to take the painful “executive decision” to change the direction of my research. Even when you were away working on one of your adventures, you gave me the opportunity to always contact you and were always happy to answer my questions. Thank you for all the support, guidance and for introducing me to all your work colleagues and family who I deeply admire. I would also like to thank Carly Rosewarne from CSIRO (Sydney) who warmly welcomed me to her laboratory and patiently helped me throughout all the microbial analysis. I want to thank my dear family for their unconditional support, patience and friendship throughout all my past nine years in Australia. I would like to especially thank my mother Neusa Ruela and my father Pedro Machado for encouraging me to follow my dreams and respecting my choices even when they took me to the other side of the globe. You are my examples that with determination, hard work and a good attitude everything is possible. I am grateful to my sister Lígia Machado for our daily talks and laughs while I was in Australia, you definitely helped me and made me feel loved even when I was so far away from you and your children. I also wish to thank my beloved husband Pedro de Paula Silva for his support and companionship at stressful times. Thank you for looking after me, helping me through all the stages of this thesis, for viii making sure I was well fed and for reminding me that there is more to life than only obligations. Fun times are also important and even better when you are by my side. For their generous assistance in this research and for making this journey much more enjoyable, I would like to acknowledge my colleagues and friends from CSIRO, Jenny Stanford and Robert Kinley, and from MARFU, Alex, Amanda, Ana, Andy, Bec, Ben, Bjoern, Boer, Dave, Giovanni, Jon, Kerri-Lee, Leo, Maria, Matt, Mick, Scotty, Simon, Sophie, Tine, Tom, Vero, Zoe, Zuzu and many others. Last but not least, I would like to thank all my friends from Bergin Massive, Hartini, Lorenzo, Ganesh, Mick, and Kerri-lee for accepting me in their house and making me feel part of their big family during the last year of my PhD. Your friendship, amazing dinners and easy going perception of life will never be forgotten. I also want to thank my closest friends Amanda, Pedro, Rahel, Davina, Jess, Kate and Dicko for all the great
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