A multilevel assessment of sediment bioremediation with bioturbating macrofauna Sebastian Vadillo Gonzalez A thesis submitted in fulfillment of the requirement for the degree of Doctor of Philosophy School of Biological, Earth and Environmental Sciences Faculty of Science Supervisors: Prof. Emma Johnston, Dr. Katherine Dafforn and Assoc Prof. Paul E. Gribben JANUARY 17, 2020 Thesis/Dissertation Sheet Surname/Family Name : Vadillo Gonzalez Given Name/s : Sebastian Abbreviation for degree as give in the : PhD University calendar Faculty : Science School : Biological, Earth and Environmental Sciences A multilevel approach on the bioremediation of eutrophic sediments using Thesis Title : benthic macrofauna Abstract 350 words maximum: (PLEASE TYPE) Estuaries and coastal intertidal environments supply important ecosystem services and resources. Within these systems, sediments play a crucial role in processing organic inputs and providing nutrients for local food webs. Benthic macrofauna and sediment microbial communities participate actively in these processes and can interact to influence overall ecosystem function. Through different bioturbation processes, macrofauna can affect biogeochemical cycling in sediments and influence microbial communities. However, anthropogenic derived eutrophication has increased globally in recent years and has been found to negatively impact these systems. Excess inputs of anthropogenic contaminants can disrupt key sediment processes involving macrofauna and microbial communities. Current options for sediment remediation are costly and may result in further impacts on communities. An alternative method for sediment bioremediation involves the application of macrofaunal bioturbators to stimulate microbial processes including contaminant removal. However, to confidently apply such an alternative requires clarity on the effect of macrofauna on contaminants, the contaminant concentrations at which macrofauna will actively affect the sediments, the potential effects of bioturbators on microbial communities, and whether these applications can be applied in situ at large scales. Here I used a systematic review and meta- analysis to analyse current knowledge on the effect of bioturbating macrofauna on contaminants and quantify how this interaction changes depending on relevant biotic and abiotic variables. Secondly, I used an experimental approach with sediment mesocosms to further explore the contaminant thresholds for effective remediation by macrofauna bioturbation and interactions with microbial communities in highly enriched sediments. Finally, a large-scale field experiment was done to explore the influence in situ nitrogen enrichment on microbial communities in the sediment and within macrofauna burrows under variable environmental contexts. The combined results here demonstrate that the effect of macrofauna bioturbation on stimulating bacterial communities in organically enriched sediments is highly taxa driven and additional factors such as macrofauna intraspecific variations in body size, temperature, animal density, magnitude of contamination and site specific organic matter content need to be considered for potential bioremediation and coastal management plans. Declaration relating to disposition of project thesis/dissertation I hereby grant to the University of New South Wales or its agents a non-exclusive licence to archive and to make available (including to members of the public) my thesis or dissertation in whole or in part in the University libraries in all forms of media, now or here after known. I acknowledge that I retain all intellectual property rights which subsist in my thesis or dissertation, such as copyright and patent rights, subject to applicable law. I also retain the right to use all or part of my thesis or dissertation in future works (such as articles or books). 15/01/2020 ……….……………………...…….… Signature Date The University recognises that there may be exceptional circumstances requiring restrictions on copying or conditions on use. Requests for restriction for a period of up to 2 years can be made when submitting the final copies of your thesis to the UNSW Library. Requests for a longer period of restriction may be considered in exceptional circumstances and require the approval of the Dean of Graduate Research. i ORIGINALITY STATEMENT ‘I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged.’ Signed …………………………………………….............. Date ……………………………………………..............15/01/2020 ii Inclusion of publications statement UNSW is supportive of candidates publishing their research results during their candidature as detailed in the UNSW Thesis Examination Procedure. Publications can be used in their thesis in lieu of a Chapter if: • The candidate contributed greater than 50% of the content in the publication and is the “primary author”, ie. the candidate was responsible primarily for the planning, execution and preparation of the work for publication • The candidate has approval to include the publication in their thesis in lieu of a Chapter from their supervisor and Postgraduate Coordinator. • The publication is not subject to any obligations or contractual agreements with a third party that would constrain its inclusion in the thesis Please indicate whether this thesis contains published material or not: This thesis contains no publications, either published or submitted for ☐ publication (if this box is checked, you may delete all the material on page 2) Some of the work described in this thesis has been published and it has been documented in the relevant Chapters with acknowledgement ☒ (if this box is checked, you may delete all the material on page 2) This thesis has publications (either published or submitted for publication) ☐ incorporated into it in lieu of a chapter and the details are presented below CANDIDATE’S DECLARATION I declare that: • I have complied with the UNSW Thesis Examination Procedure • where I have used a publication in lieu of a Chapter, the listed publication(s) below meet(s) the requirements to be included in the thesis. Candidate’s Name Signature Date (dd/mm/yy) Sebastian Vadillo Gonzalez 15/01/2020 iii COPYRIGHT STATEMENT ‘I hereby grant the University of New South Wales or its agents a non- exclusive licence to archive and to make available (including to members of the public) my thesis or dissertation in whole or part in the University libraries in all forms of media, now or here after known. I acknowledge that I retain all intellectual property rights which subsist in my thesis or dissertation, such as copyright and patent rights, subject to applicable law. I also retain the right to use all or part of my thesis or dissertation in future works (such as articles or books).’ ‘For any substantial portions of copyright material used in this thesis, written permission for use has been obtained, or the copyright material is removed from the final public version of the thesis.’ Signed ……………………………………………........................... Date ……10/03/2021……………………………………….............................. AUTHENTICITY STATEMENT ‘I certify that the Library deposit digital copy is a direct equivalent of the final officially approved version of my thesis.’ Signed ……………………………………………........................... Date …10/03/2021………………………………………….............................. iv ACKNOWLEDGMENTS From the moment I came to the UNSW, “contrast” has been the word to describe every day, every feeling and every lesson learned during this path called Ph.D. Everything began as a contrast between what I knew back in Mexico City to what had to be known in a place like Sydney. The food to be had every day, the transport that had to be taken and of course the new skills I had to learn. Everything was different and I had to step up from everything I knew before. In this journey filled with contrasts, I want to thank the people which in my first days in Australia guided me and provided the first taste of a new life. My supervisors of course receive my most sincere acknowledgments: the sweet and always trustworthy Katie Dafforn; the busy and truly amazing Emma Johnston; and the patient and always supportive Paul Gribben. Through their support, I was able to get a scholarship from The Bushell Foundation through the Sydney Institute of Marine Science and have ongoing financial stability through the Australian Research Council Future Fellowship Scheme. Without their help during the beginning, the massive experiment in port Stephens, the fieldwork in New Zealand, the data processing and analysis, and finally the long writing and review process; I wouldn’t have been able to survive or reached this point. I am deeply grateful for everything they did for and with me. In the AMEE lab and the current marine floor in E26, many people that are still here struggling on their journey or were once my examples to