ResearchOnline@JCU This file is part of the following reference: Howells, Emily (2011) Coral symbionts in warming seas: population dynamics, adaptation and acclimatisation of Symbiodinium. PhD thesis, James Cook University. Access to this file is available from: http://researchonline.jcu.edu.au/34422/ 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/34422/ Coral symbionts in warming seas: Population dynamics, adaptation and acclimatisation of Symbiodinium Thesis submitted by Emily Howells BSc. Hons December 2011 for the degree of Doctor of Philosophy in the School of Marine and Tropical Biology James Cook University Statement on the contribution of others The research in this thesis was primarily designed, undertaken, analysed and written-up by Emily Howells. Contributions from collaborators are outlined at the beginning of each Chapter. Intellectual and editorial support was provided the supervisory team of Prof. Bette Willis (James Cook University), Dr. Madeleine van Oppen (the Australian Institute of Marine Science) and Dr. Line Bay (James Cook University and the Australian Institute of Marine Science). Funding for the research undertaken in this thesis was obtained from AIMS@JCU, the Marine and Tropical Sciences Research Facility, the Australian Research Council, and James Cook University. Stipend was provided by an Australian Postgraduate Award, a Queensland Smart State Scholarship, and the James Cook University Graduate Research School. Conference and workshop travel was supported by AIMS@JCU, the James Cook University Graduate Research School, the Australian Coral Reef Society, and the Australian Research Centre of Excellence for Coral Reef Studies. This thesis is dedicated to the inspirational women in my family Victoria, Barbara, Dorothy and Peggy Acknowledgements Thank you to my family for their continual love and support, especially David Abrego, Victoria Howells, Stephen Howells, Barbara Johns, Ross Aitken and Dorothy Johns. Many wonderful people in Townsville I have been fortunate to become friends with during my PhD journey. Thank you to my lab and office mates at JCU. I am especially grateful for those of you that provided support through laughter, coffees, dinners and drinks – thank you Vivian Cumbo, Kim Lema, Eneour Puill-Stephan, Michelle Condy, Kate Nairn, Adrian Lutz, Carolyn Luder, David Crossman, Kerryn Johns, Allison Paley, Joe Pollock, Petra Lundgren, Ally Beeden, James Moore, Bryan Murphy, Heidi Luter, Neesha Copley, Jean-Baptiste Raina, Manue Botte, Patricia Warner, Francois Seneca, Evan Goulden and Hugo Harrison. For their guidance and feedback during my PhD, I thank my supervisory team, Bette Willis, Madeleine van Oppen and Line Bay. During field sample collection and coral spawning, a number of people provided valuable assistance including, David Abrego, Andrew Baird, Ray Berkelmans, Stuart Beveridge, Miin Chua, Michelle Condy, Vivian Cumbo, Scott Gardiner, Erin Graham, Joleah Lamb, Nicholas Larsen, Raechel Littman, Petra Lundgren, Adrian Lutz, James Moore, Aurelie Moya, Bryan Murphy, Andrew Negri, Joe Pollock, Eneour Puill-Stephan, Tom Stevens, James Tan, Gergely (Greg) Torda, Joost van Dam, Patricia Warner, James White, Peter Williams (Keppel Dive Centre), James Woodford, Yujie Zheng, the AIMS Mariculture staff, the AIMS Water Quality Monitoring team and the crew of the RV Cape Ferguson. During my lab and experimental work at AIMS, Jason Doyle, Lesa Peplow and Andy Muirhead patiently taught me molecular and chemistry techniques and assisted with trouble-shooting. Beth Ballment provided continued laboratory support. David Abrego, Ray Berkelmans, Vivian Cumbo, Florita Flores, Paolo Momigliano, Andrew Negri and Sven Uthicke provided useful technical advice or assited with crucial equipment. Samples and data shared by others enabled me to test molecular markers in the lab, select useful sampling sites and enhance the scope of my research outcomes. For their generosity I thank, David Abrego, Victor Beltran, Ray Berklemans, David Crossman, Kevin Gunn, Alison Jones, Nathan Kirk, Mike Mahoney, Britta Schaffelke, Scott Santos, Craig Steinberg, Daniel Thornhill and Linda Tonk. I also thank the AIMS IT support staff for helping me overcome computing and password failures, Dave Stockham, Mick Adams and Wendy Hiles-Stewart in stores, and Mike Hall for ordering coffee supplies. At JCU, I thank Sue Reilly for preparing histological slides and Ainsley Calladine for processing my samples at the Genetic Analysis Facility. Project logistics were assisted by Phil Osmond, Karen Wood, Vince Puella, Gordon Bailey, Savita Francis, as well as the biological stores, finance and facilities management vehicles teams. Candidature matters were assisted by Debbie Ford, Dianne Bailey, the staff of the Graduate Research School and the staff of the AIMS@JCU office. Publications arising from the research in this thesis Chapter 2. Howells EJ, Willis BL, Bay LK, van Oppen MJH. Spatial isolation and disturbance shape the genetic structure of Symbiodinium populations. Molecular Ecology, in review Chapter 3. Howells EJ, Jones AM, Bay LK, van Oppen MJH, Willis BL. A change in Symbiodinium C2 microsatellite population composition harboured by a reef building coral following bleaching. Marine Ecology Progress Series, in review Chapter 4. Howells EJ, Beltran VH, Larsen NW, Bay LK, Willis BL, van Oppen MJH (2012). Coral thermal tolerance is shaped by local adaptation of photosymbionts. Nature Climate Change 2: 116-120 Chapter 5. Howells EJ, Berkelmans R, van Oppen MJH, Willis BL, Bay LK (2011). Historical thermal regimes define limits to coral acclimatisation. Ecology, http://dx.doi.org/10.1890/12-1257.1 Appendix I. Bay LK, Howells EJ, van Oppen MJH (2009). Isolation, characterisation and cross amplification of thirteen microsatellite loci for coral endosymbiotic dinoflagellates (Symbiodinium clade C). Conservation Genetics Resources 1: 199-203 Appendix II. van Oppen MJH, Souter P, Howells EJ, Heyward A, Berkelmans R (2011). Novel genetic diversity through somatic mutations: Fuel for adaptation of reef corals? Diversity 3: 405-423 i Abstract Endosymbiotic photosymbionts, belonging to the dinoflagellate genus Symbiodinium, enable corals to succeed as dominant reef builders under ambient conditions, yet are also sensitive to anomalous changes in their thermal environment. Stressful temperatures cause photosynthetic damage to Symbiodinium, which can initiate lethal or sub-lethal coral bleaching. The capacity of Symbiodinium to resist and respond to stress (i.e. resilience) is crucial for the future persistence of corals. The aim of research presented in this thesis was to evaluate the influence of Symbiodinium population traits on the resilience of corals to warming seas. For within-type populations of Symbiodinium, spatial and temporal patterns of genetic diversity were investigated along with the potential for genetic adaptation and physiological acclimatisation to different thermal environments. Populations of the generalist Symbiodinium types C1, C2 and D (ITS1 rDNA) were used as a model system in the bleaching sensitive coral, Acropora millepora, on inshore reefs of the Great Barrier Reef (GBR). Genetic diversity and connectivity were estimated for Symbiodinium C2 populations using eight polymorphic microsatellite DNA markers. At the central GBR, Symbiodinium C2 assemblages were genotyped in more than 400 colonies of A. millepora sampled at 7 sites (0.4 to 13 km apart) across a 12 year period. Within-host and within-reef assemblages were genetically diverse (up to 7 alleles per microsatellite locus per coral colony), with significant structure observed at all spatial and temporal scales investigated. Differentiation among sites accounted for 19-27% of the total genetic variation and was consistent with restricted hydrodynamic dispersal of Symbiodinium and the nature of local disturbance regimes. Differentiation among sampling years accounted for a lesser 7% of the total genetic variation and was associated with significant coral mortality during bleaching and cyclone events. Bleached corals hosted less diverse Symbiodinium C2 assemblages than healthy corals, indicating that genotypes may be lost during bleaching-induced reductions in Symbiodinium densities. Such population bottlenecks were investigated in more detail by following changes in Symbiodinium C2 assemblages before and after a severe bleaching episode at sites in the southern GBR. A 10 % decline in reef-wide genetic ii diversity of Symbiodinium C2, including the loss of 16 alleles, was observed after the bleaching episode. The appearance of a few novel alleles after bleaching, combined with the high density of Symbiodinium on coral reefs, suggests that recovery of genetic diversity lost through bleaching is possible. However, if bleaching events become more frequent and severe, the genetic diversity of Symbiodinium populations could become eroded, especially as lost diversity is unlikely to be readily replenished by re-seeding from adjacent reefs. Conversely, limited genetic connectivity between reefs may have positive implications for populations by promoting adaptation to local environmental conditions. Adaptation of Symbiodinium populations was examined by comparing the thermal tolerance of Symbiodinium type C1