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Thesis Is Presented for the Degree of Doctor of Philosophy of the University of Western

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Thesis Is Presented for the Degree of Doctor of Philosophy of the University of Western Exploring molecular and hydroecology of lithifying and non-lithifying microbial mats from hypersaline lakes at Rottnest Island, Western Australia by Juliana Mendes Monteiro MSc, BSc This thesis is presented for the degree of Doctor of Philosophy of The University of Western Australia School of Agriculture and Environment Environmental Sciences 2020 THESIS DECLARATION I, Juliana Mendes Monteiro, certify that: This thesis has been substantially accomplished during enrolment in this degree. This thesis does not contain material which has been submitted for the award of any other degree or diploma in my name, in any university or other tertiary institution. In the future, no part of this thesis will be used in a submission in my name, for any other degree or diploma in any university or other tertiary institution without the prior approval of The University of Western Australia and where applicable, any partner institution responsible for the joint-award of this degree. This thesis does not contain any material previously published or written by another person, except where due reference has been made in the text and, where relevant, in the Authorship Declaration that follows. This thesis does not violate or infringe any copyright, trademark, patent, or other rights whatsoever of any person. The following approvals were obtained prior to commencing the relevant work described in this thesis: - 2015/244021 – Rottnest Island Research Permit, issued by The Rottnest Island Authority (RIA); - SF010314 – License to Take Fauna for Scientific Purposes, issued by The Department of Biodiversity, Conservation and Attractions, formerly The Department of Parks and Wildlife. This thesis contains published work and/or work prepared for publication, some of which has been co-authored. Signature: Date: 07 August 2020 ii AUTHORSHIP DECLARATION: CO-AUTHORED PUBLICATIONS This thesis contains work that has been published and/or prepared for publication, some of which has been co-authored. Details of the work: Mendes Monteiro, J., Bischoff, K., Gleeson, D. B., Vogwill, R., 2020 (in prep.). Hydroecological interactions between microbial mats from hypersaline lakes at Rottnest Island and their surrounding aquatic environment. Prepared to be submitted to Hydrology and Earth System Sciences. Location in thesis: Chapter 2 Student contribution to work: Conducted the literature review, undertook the experimental work, analyzed the majority of the data, and wrote paper with the contribution of editing and reviewing from the co-authors. Co-author signatures and dates: Details of the work: Mendes Monteiro, J., Vogwill, R., Bischoff, K., Gleeson, D. B., 2019. Comparative metagenomics of microbial mats from hypersaline lakes at Rottnest Island (WA, Australia), advancing our understanding of the effect of mat community and functional genes on microbialite accretion. Limnology and Oceanography, 00:1–17. doi:10.1002/lno.11323 Location in thesis: Chapter 3 Student contribution to work: Conducted the literature review, undertook the experimental work, analyzed the majority of data, and wrote paper with the contribution of editing and reviewing from the co-authors. Co-author signatures and dates: iii AUTHORSHIP DECLARATION: CO-AUTHORED PUBLICATIONS Details of the work: Mendes Monteiro, J., Vogwill, R., Bischoff, K., Gleeson, D. B., 2020 (in prep.). Seasonal variability in taxonomic and functional capacity of lithifying and non-lithifying microbial mats from hypersaline lakes at Rottnest Island (Western Australia). Prepared to be submitted to Frontiers in Microbiology. Location in thesis: Chapter 4 Student contribution to work: Conducted the literature review, undertook the experimental work, analyzed the majority of data, and wrote paper with the contribution of editing and reviewing from the co-authors. Co-author signatures and dates: Details of the work: Bischoff, K., Wilson, M. E. J., Mendes Monteiro, J., Vogwill, R., George, A. D., 2020 (under second review). Sedimentology of coastal carbonate lakes. Sedimentology, Manuscript ID SED-2019-OM-036.R1. Location in thesis: Appendices Student contribution to work: Contributed to fieldwork and sampling, as well as editing and reviewing the paper (10% contribution). Co-author signatures and dates Student signature: Date: 07/08/2020 I, Deirdre Gleeson, certify that the student’s statements regarding their contribution to each of the works listed above are correct. As all co-authors’ signatures could not be obtained, I hereby authorize inclusion of the co- authored work in the thesis. Coordinating supervisor signature: Date: 07/08/2020 iv ACKNOWLEDGMENTS This PhD research was supported by an Australian Government Research Training Program (RTP) Scholarship. It was also supported by the C. F. H and E. A. Jenkins Postgraduate Research Scholarship (stipend scholarship). This PhD research was funded by The Rottnest Island Authority and logistically supported by The Rottnest Island Authority staff, Shane Kearney, Cassyanna Thomas, Luke Wheat, and Shirley Wills. I would like to acknowledge the Convocation of UWA Graduates for granting me the Convocation Postgraduate Research Travel Award, which has supported this PhD research. I would also like to acknowledge the Graduate Research School for supporting this PhD research with the GRS Travel Award. I would like to acknowledge all technical assistance that was kindly provided by the technician team from The University of Western Australia School of Agriculture and Environment, Hazel Gaza, Michael Smirk, Chris Brouwer and Louise Heyworth for the support with DNA extraction, inductively coupled plasma-atomic emission spectrometry (ICP-AES) and high pressure ion chromatography (HPIC) that are described in Material and Methods of Chapter 2, 3 and 4 of this thesis. I would like to thank my research comrade and friend Belinda Martin for kindly supporting me with part of the statistical analysis described in Chapter 3 and 4 of this thesis. Thank you so much for your patience and friendship. I would like to thank Karl Bischoff not only for being a research collaborator and co-author in some publications that have arisen from this research but also for his genuine friendship and kind support during challenging times. I would like to thank my supervisor Dr Ryan Vogwill for the academic support and constant encouragement. Thank you for believing on my potential. v ACKNOWLEDGEMENTS I would like to demonstrate my deepest appreciation and gratitude to my Principal and Coordinating supervisor Dr Deirdre Gleeson, for the amazing support throughout these challenging last four years. Words cannot express how deeply grateful I am for having a supervisor like you. Lastly, I would like to thank those who have always supported me behind the scenes. I could have not accomplished this milestone without your love and care. Thank you very much my Soka Gakkai friends, my dearest family (Brazilian and Australian), and my beautiful and beloved husband. “None of us can exist in isolation. Our lives and existence are supported by others in seen and unseen ways, be it by parents, mentors or society at large. To be aware of these connections, to feel appreciation for them, and to strive to give something back to society in a spirit of gratitude is the proper way for human beings to live.” Daisaku Ikeda. vi TABLE OF CONTENTS THESIS DECLARATION......................................................................................................... ii AUTHORSHIP DECLARATION: CO-AUTHORED PUBLICATIONS .............................. iii ACKNOWLEDGEMENTS ....................................................................................................... v ABBREVIATIONS ................................................................................................................. iix FIGURES .................................................................................................................................. xi ABSTRACT ............................................................................................................................ xvi Chapter 1 ................................................................................................................................... 1 General Introduction and Literature Review ............................................................................. 1 1.1 General Introduction ....................................................................................................... 1 1.2 Microbial mats ................................................................................................................ 1 1.3 Microbialites ................................................................................................................... 4 1.4 Microbial mats from hypersaline environments ............................................................. 5 1.5 Microbial mats in Rottnest Island ................................................................................... 8 1.6 Thesis aim and research objectives ............................................................................... 10 Chapter 2 ................................................................................................................................. 11 2.1 Introduction ................................................................................................................... 12 2.2 Material and Methods ................................................................................................... 15 2.2.1 Study area and sampling sites ...............................................................................
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