Investigating Riverine Impact upon the Coral Reefs of Los Cayos Cochinos, Honduras by Jonathan Peter Shrives Linacre College Thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy University of Oxford Department of Zoology Michealmas Term 2009 OSS Student No: 12873 To my family (both biological and academic!) and my friends without your help I would never have made it this far 'And when you gaze long into an abyss, the abyss gazes also into you.' – Nietzsche 'Some days you’re the pigeon… Other days, you’re the statue.' – Anon CONTENTS i ii Acknowledgements I would like to take this opportunity to thank all those who made this thesis possible, and without whose kind support, this project could never have taken place. Firstly and foremost, I would like to express my heartfelt thanks to my supervisors Dr. Martin Speight and Dr. Greg Cowie. In every way possible, none of this could have ever happened without their support, kindness and tutelage. Thank you also to the members of the Tropical Ecology Research Group, past and present, who made me feel part of ‘the family’ and made it such a great place to work and study. I would also like to thank the members of my supervisory committee; Prof. James Crabbe for his continued advice and support on conferences and all things ‘meta’ and international. Dr. Peter Henderson and all of the staff at Pisces Conservation, who have been invaluable in kindly providing me with much of the statistical software used in this thesis. This project would not have been possible without the funding and Support of Operation Wallacea and the States of Jersey Department for Education, Sport and Culture, or the Universities of Oxford and Edinburgh. I would like to thank Andy Gibbs and his team at Jersey Careers and also the Jersey Scholarship fund and the CWCS Bequest. I would especially like to thank Dr. Tim Coles and all of the staff at Operation Wallacea, who gave me the opportunity and kind support to conduct this research. I would also like to thank Kathy Wilden, Dr. Matthias Hammer and all off the staff at Biosphere Expeditions, in conjunction with Dr. Gregor Hodgson and all at Reef Check. Working for Operation Wallacea and Biosphere Expeditions over the last few years has quite literally changed my life, and provided me with experience, opportunities and friends that I shall never forget. It has been my privilege to work with and supervise many undergraduate dissertation students during my time in Honduras. However several students deserve special mention for their hard work and inspiration and good humour, which have lightened even the darkest times over the years; James Lea, Catherine Talbott, Ian Hendy, Amelia Wenger, Jess Stephenson, Jen Riley, Pip Thompson, Lou Mallam, Emily Long, Roisin McCallum and Catherine Hall. iii In both Honduras and the UK I have had the pleasure of working with the kind support of several colleagues. At the University of Oxford I would like to especially thank Clive Hambler, Joe Nunez-Mino, Dr. Robi Bagchi, Dr. Sammy De Grave and their respective research groups and all the students and staff at Linacre College, for the banter, support and advice over the years. I would like to also thank Prof. David Rogers and Dr. David Benz for their advice and support in Remote Sensing. Also all the staff and students of the Orielton field trips for the unforgettable experiences! The Ecology Journal Club and its members also provided important support (and cake!) over the years, as did the Linacre Boat Club and the OUYC. A big thank you also to the all the Doctors, Nurses and Physio’s in the UK and Honduras, that helped me after my accident in 2006 and Malaria in 2009. In Honduras I received the kind support of too many to mention, but I would like to make special thanks to the following: Adoni Cubas, Tony Ives, Alicia Medina and Elias Aguilar for their friendship and support. Italo Bonila needs special mention (or attention?!) for leading me astray, many a time over the years, but also for his high quality teaching of Spanish, which certainly ‘helped’ breakdown the language barrier over the years! Thanks also to all of the staff of the Honduran Coral Reef Fund for their logistical support and use of the labs and accommodation in Los Cayos Cochinos. I would also like to thank to the kind people and government of Honduras for their permission and support to conduct this study. I would also like to thank my colleagues at the States of Jersey Environment Department and the Fisheries and Marine Resources section for their kind encouragement and backing during the last few months of writing up. Last, but by no means least, a huge thank you to my amazing friends and family. Over the years (and in no particular order!); Tom Mullier, Patrick Denning, John and Marianne Thomson, John and Katie Carlin, Steve Green, Mike Logan, Tara Mclaughlin, Dan Thoms, Scott Boback and all the ‘Boeroes’, Natalie Bown, James Saunders, Meghan Treleaven, Tom Shaw, Kerstin Zechner, Erica Boschin, Naseer Qayum, ‘McPhilin’, Pablo, Emma Kennedy, Emma Low, Fiona MacLachlan, Klaire Lander, Alicia Glassco, Jessica Carilli-Young, Antares Ramos-Alvarez and Jess Jaxion-Harm, to name but a few, have all helped me make it through this far! iv Declaration I hereby declare that the work described in this thesis was conducted by myself, under the supervision of Dr. M. R. Speight, with the exception of those instances where the contribution of others has been specifically acknowledged. Throughout this thesis all sources of information have been specifically acknowledged using a citation to referenced work. Some data used in this thesis have been published previously as follows: Some of the data and results used in the geochemical assessment chapter and the Scleractinian disease and mortality chapter have been published as conference proceedings of the 11th International Coral Reef Symposium, Ft. Lauderdale, Florida. Session 10. ‘How Does Black Band Disease Affect the Benthic Ecology of Reefs in Los Cayos Cochinos, Honduras?’ In conjunction with the following authors: James S. E. Lea and Martin R. Speight. I hereby confirm that this thesis has not been submitted for a degree at another university. Jonathan Peter Shrives Trinity Term 2009 OSS No. 12873 v Abstract This investigation used a combination of oceanographic and marine ecological techniques to determine the role of rivers in influencing the benthic community structure of the coral reefs in Los Cayos Cochinos, Honduras. Principal objectives were; the detection of inter and intra-site variation in benthic community structure; the comparison of local rivers and sediment sources; comparison of riverine impact with other sources of Scleractinian mortality; discussion of the suitability of the methodologies used, towards further integration of oceanographic and marine ecological techniques in studying coral reefs and riverine impact. Reefs in Los Cayos Cochinos were found to have lower Scleractinian cover (13.31% S.D. ± 19.24) than the regional mean average (~24%). Almost a third of these corals were Agaricia tenufolia, a putatively sediment tolerant, foliose coral. Macroalgae were found to be the dominant cover with a mean of 55% (S.D. ± 29.50). Not all sites had the reef crest as the region of highest Scleractinian cover or diversity. Sites did form clear biotopes with 67% dissimilarity in cluster analysis. Location of the sample sites had an effect, with community structure varying according to exposure, or suspended particulate matter levels. Remote sensing data showed that the Rio Aguán was not the principal cause of high primary productivity or sedimentation, showing coastal rivers had a greater year-round influence. Fresh water run-off from the local islands was a stronger signal than the rivers during the dry season. Variations in δ13C, δ15N and reef patch dynamics showed that areas near private island developments were of a possible concern than the community of Chachahuate or rivers. Patch dynamic analysis showed some high diversity sites were increasingly under threat from sedimentation, more so than competition, coral disease or bleaching. The use of Scleractinian cover alone to judge ‘reef health’, was found to be deficient here, without the use of diversity indices. Dissolved nutrient analysis was also found unsuitable for this study. Isotopic analysis successfully determined both anthropogenic inputs and elucidated upon adaptation and niche differentiation of the dominant macroalgae genera in Los Cayos Cochinos. Remote sensing was found to be the most cost effective and powerful tool for determining riverine influence. The use of a novel intra-site GIS methodology, allowed comparison of community structure, however it would benefit further from integration with more advanced statistics such as nearest-neighbour analysis. vi List of Tables Table 3.1. Summary of Skewness and Kurtosis for Percentage cover data Table 3.2. Analysis of Similarity (ANOSIM) results for the grouping of sites. Table 4.1. Summary comparison of SPM and Flux rates from other studies, taken from a review by Rogers (1990) Table 4.2. Concentrations of dissolved nutrients and chlorophyll-a in sea water samples measured by colourimetry. Concentrations are in micromoles (μM), except for chlorophyll-a, which is presented in milligrams per Litre (mg/L). BDL = Below Detection Limits. - = no sample. C1- C4 = Coastal Transect. T1-T4 = Trujillo Transect. Table 4.3. Results of SPM sampled from river streams inland from the coast Table 4.4. Comparison of δ13C, δ15N and C:N values for sediment from Suspended Particulate Matter (SPM) samples from sites in 2008 and 2007. Table 4.5. Comparison of δ13C, δ15N and C:N values for sediment from Suspended Particulate Matter (SPM) samples from rivers and transects sampled in 2008 and 2007.