Measuring and Modelling the Primary Production of a Sea Lough in Northern Ireland Elisa Capuzzo A thesis submitted in partial fulfilment of the requirements of Edinburgh Napier University, for the award of Doctor of Philosophy April 2011 Misura ciò che è misurabile, e rendi misurabile ciò che non lo è. Galileo Galilei [Measure what is measurable and make measurable what is not] 2 Acknowledgements According to the Cambridge dictionary, a „scientist‟ is an expert who studies or works in one of the sciences. I feel extremely lucky because in the last 5 years I have been given the chance to be supervised, directed, taught and supported by 3 scientists who I admire. I am extremely grateful to Dr. Richard Gowen, Prof. Paul Tett and Dr. Linda Gilpin for the trust they put in me and my work, and for the effort and time they spent providing feedback, comments and constructive criticisms to this work. Their inspiring examples have given me the basis to become an enthusiastic and proficient scientist. I am thankful to the Northern Ireland Lough Agency for funding this PhD and to the Agri-Food and Bioscience Institute (AFBI) for providing all the facilities and equipment needed. I am particularly grateful to Dr. Adam Mellor, William Clarke, Ann Marie Crooks, Andrew McDougall and all the staff of the Aquatic Branch of AFBI for helping during sampling events and for assisting me with broken instruments. I am grateful to Brian Stewart, Raymond Gilmore and Claire Smyth for carrying out the analysis of chlorophyll and dissolved nutrients concentrations, and for the assistance in the laboratory. I am also grateful to Dr. Bob Foy and Harry Nicholson (AFBI) for providing the hourly solar irradiance data measured by the AFBI weather station in Hillsborough. A special thank to Dr. Heather Moore for her friendship and being trusting enough to sit in a car with me when I was still not sure on which side of the road to drive. The sampling events will not have been possible without the help of the crew of the FPV Mytilus, and the fishing vessels of Brian Cunninghan and Oliver Finnegan. I am thankful to Ciaran McGonigle for providing estimates of SPM concentration for the sampling activity in 2006. I would like also to thank Dr. Grahame Savidge of Queen‟s University Belfast for providing part of the equipment for the experiments. A special acknowledgment to my current employer CEFAS for giving me the opportunity to take time off from work for finishing this research project. I am also thankful to my colleagues and friends in Lowestoft for giving me motivation in concluding this study. 3 During the last 5 years I have been on a journey that has led my knowledge and understanding of the marine ecosystem to get stronger year after year. It was also a „physical‟ journey that took me from Italy to Northern Ireland, Scotland and England, where I meet lots of friends. Some of them crossed my path temporarily; others are still walking along side with me. Nevertheless I am very grateful to all of them. I would like to thank in particular all the occupiers of the postgraduate room G30 in AFBI, and the occupiers of the room D8 in Edinburgh Napier University, for sharing with me hard work as well as a good laugh over a nice cup of coffee. I am particularly grateful to Dr. Enrique Portilla for transposing a script from Matlab into R syntax, which formed an integral part of the PhD research. A special thank to the guys of 25 University Avenue in Belfast, for their friendship and support during my first 2 years away from home; my spoken English would not be so good without them! I am very grateful to Dolan and his lovely family for sharing some of my happiest memories in Northern Ireland and for made me feel like a member of the family. I am thankful to all the speakers and lecturers I listened to during conferences, workshops, symposia and university lectures for fuelling my interest and love for the marine environment. This journey would have not been possible without the support and precious friendship of my dear friends „little Cordula‟, Daniela and Chiara; the distance made our friendship even stronger. A special thank to my „tango partner‟ for leading me through some up and downs of my life. All my gratitude goes to my family for being there in every moment; they kept me going with their love, long international phone calls and emergency parcels of Italian goodies. My last acknowledgement is for David, who „effortlessly‟ makes my life so beautiful. 4 Table of content Abstract ....................................................................................................................... 9 Outline of the thesis .................................................................................................. 11 Acronym list .............................................................................................................. 13 CHAPTER 1 ............................................................................................................. 15 1.1 Introduction .......................................................................................................... 16 1.2 Aim and testable hypotheses ................................................................................ 18 1.3 Sampling site: Carlingford Lough ........................................................................ 19 1.4 Definition of primary production and its importance .......................................... 22 1.5 History of primary production measurements...................................................... 22 1.6 Physiology and biochemistry of photosynthesis .................................................. 24 1.7 Respiration ........................................................................................................... 25 CHAPTER 2 ............................................................................................................. 27 2.1 Introduction to Carlingford Lough ....................................................................... 28 2.2 Methods ................................................................................................................ 35 2.2.1 Sampling ................................................................................................... 35 2.2.2 CTD calibrations ....................................................................................... 36 2.2.3 Phytoplankton ........................................................................................... 37 2.2.4 Nutrients .................................................................................................... 39 2.2.5 Chlorophyll and calculation of chlorophyll standing stock ...................... 40 2.2.6 Suspended Particulate Matter (SPM) ........................................................ 41 2.2.7 Data analysis ............................................................................................. 42 2.3 Results .................................................................................................................. 44 2.3.1 Physical variables ...................................................................................... 44 2.3.2 Nutrients .................................................................................................... 48 2.3.3 Chlorophyll and Suspended Particulate Matters ....................................... 54 2.3.4 Phytoplankton population ......................................................................... 57 2.4 Discussion ............................................................................................................ 72 2.4.1 Physical and chemical variables ............................................................... 72 2.4.2 Biological variables ................................................................................... 76 5 2.5 Conclusions .......................................................................................................... 81 CHAPTER 3 ............................................................................................................. 82 3.1 Introduction .......................................................................................................... 83 3.1.1 The electromagnetic spectrum .................................................................. 83 3.1.2 Inherent optical properties ........................................................................ 84 3.1.3 Vertical attenuation coefficient (apparent optical properties) ................... 86 3.1.4 Measurements of the underwater light field.............................................. 91 3.1.5 How to derive Kd ....................................................................................... 93 3.2 Methods ................................................................................................................ 97 3.2.1 In situ measurements of the underwater light field ................................... 97 3.2.2 Estimates of Kd .......................................................................................... 98 3.2.3 Calculation of surface incident PAR and daily surface mixed layer irradiance .......................................................................................................... 102 3.2.4 Data analysis ........................................................................................... 102 3.3 Results ................................................................................................................ 104 3.3.1 Seasonal trends of surface irradiance, Secchi depth,