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A Process(Oriented Biogeochemical Model for Marine Ecosystems

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A Process(Oriented Biogeochemical Model for Marine Ecosystems A process-oriented biogeochemical model for marine ecosystems: Development, numerical study, and application Marcos Duarte Mateus January 2006 ii Contents Abstract vii Resumo ix Acknowledgments xi Overview xv 1 Introduction 1 1.1 A glance at the state-of-the-art . 3 1.2 A changing paradigm . 6 1.2.1 Variable internal composition . 6 1.2.2 Structured based models . 7 1.2.3 Chlorophyll to Carbon ratio . 7 1.2.4 Multi-element models . 7 1.3 Model complexity . 9 1.4 The MOHID modelling system . 11 1.5 Becoming operational . 14 1.6 Rationale . 14 2 Model mohid.Life.1.0 structure 17 2.1 Introduction . 17 2.1.1 Major guidelines . 18 2.1.2 Basic equations . 21 2.1.3 Generic units system . 23 2.1.4 Baseline philosophy . 25 2.1.5 Dependence on other MOHID modules . 26 2.1.6 Light climate . 26 2.2 Producers module . 27 2.2.1 Background review . 27 2.2.2 Basic module outline . 35 2.2.3 Carbon dynamics . 38 2.2.4 Nitrogen and phosphorus dynamics . 43 2.2.5 Myxotrophy . 47 iii iv CONTENTS 2.2.6 Mass balance equations . 48 2.3 Consumers module . 48 2.3.1 Background review . 48 2.3.2 Basic module outline . 50 2.3.3 Carbon dynamics . 51 2.3.4 Nutrient dynamics . 53 2.3.5 Mass balance equations . 54 2.4 Decomposers module . 56 2.4.1 Background review . 56 2.4.2 Basic module outline . 59 2.4.3 Carbon dynamics . 60 2.4.4 Nutrient dynamics . 62 2.4.5 Bacterial mediated organic matter hydrolysis . 63 2.4.6 Mass balance equations . 65 2.5 Biochemistry module . 65 2.5.1 Background review . 65 2.5.2 Basic module outline . 69 2.5.3 Organic matter . 69 2.5.4 Nitrogen . 70 2.5.5 Silica . 71 2.5.6 Oxygen . 71 2.5.7 Mass balance equations . 72 3 Assessing model performance 75 3.1 Introduction . 75 3.2 Function plots . 75 3.2.1 Producers . 76 3.2.2 Consumers . 84 3.2.3 Decomposers . 89 3.3 Long time run . 90 3.3.1 Basic settings . 90 3.3.2 Trophic relations . 91 3.3.3 Simulation . 96 3.3.4 Model Forcing . 96 3.3.5 Results . 98 3.3.6 Dynamic elemental composition . 107 3.4 Testing temporal resolution . 114 3.5 Sensitivity analysis . 117 3.5.1 Methodology . 119 3.5.2 Result matrix and discussion . 123 CONTENTS v 4 Real case application: the Tagus estuary 141 4.1 Introduction . 141 4.1.1 Basic concepts in estuarine ecology . 142 4.1.2 Tagus estuary characterization . 143 4.2 Methods . 144 4.2.1 Model implementation . 144 4.2.2 Monitored sites and model calibration . 152 4.3 Results . 153 4.3.1 Model calibration . 153 4.3.2 Data from sampling sites . 153 4.3.3 Temperature and salinity . 154 4.3.4 Cohesive sediments . 156 4.3.5 Nutrients . 156 4.3.6 Dissolved oxygen concentrations . 166 4.3.7 Phytoplankton . 166 4.3.8 Decomposers . 168 4.3.9 Consumers . 173 4.3.10 Organic matter and biogenic silica . 175 4.4 Discussion . 175 4.4.1 Hydrodynamic processes . 181 4.4.2 Abiotic conditions . 182 4.4.3 Limitation to production . 184 4.4.4 Residence time . 184 4.4.5 Underwater light climate control . 186 4.4.6 Temperature and predation . 187 4.4.7 Nutrient control . 188 4.4.8 Producers chlorophyll biomass . 191 4.4.9 Producer groups . 194 4.4.10 Heterotrophic bacterial patterns . 194 4.4.11 Nutrient cycles . 198 4.4.12 Relevance of sediment processes . 203 4.4.13 Improving the operational tool . 204 4.5 Preliminary conclusions . 205 5 General discussion 207 5.1 Bulk quantity models vs. structured based models . 207 5.2 Photoadaptation and dynamic C:Chla ratios . 208 5.3 Production control . 210 5.4 The microbial loop and organic matter components . 212 5.5 Sensitivity analysis . 213 6 Concluding remarks 215 vi CONTENTS A Model comparison 229 A.1 Introduction . 229 A.2 Methodology . 230 A.2.1 Model runs . 230 A.2.2 Compared variables . 231 A.2.3 Result analysis . 231 A.3 Results and discussion . 232 A.3.1 Nutrients . 232 A.4 Oxygen . 232 A.5 Biological groups . 232 A.6 Organic matter . 238 A.7 Conclusions . 243 Abstract Over the last two decades, biogeochemical modelling in marine environments underwent considerable advances. The MOHID system has followed this trend, re‡ecting now the state-of-the-art in circulation models. As such, the driving force beyond the present work was to equip the MOHID system with a model that also re‡ects the state-of-the-art in biogeochemical modelling. To achieve this purpose, mohid.Life.1.0 was developed, a model for marine systems that is able to describe biogeochemical processes with greater detail than the NPZ approach already implemented in MOHID. This work not only contains the description of the model with its process-oriented baseline philosophy, but it also addresses its behaviour when subject to standard tests. The model is also tested in a real case scenario with an application to the Tagus Estuary, Portugal. The model performance shows that the model has the ability to respond to di¤erent conditions in a realistic way. Results also show that the model reproduces the basic functioning of water- column food webs and nutrient dynamics in marine systems. In the Tagus application, the model helped to address uncertainties in knowledge of the functioning of this particular system, and also to reinforce some assumptions made in other experimental and numerical studies. Keywords: Ecological models; process-oriented; biogeochemical cycles; water-quality; MOHID system; Tagus estuary. vii viii ABSTRACT Resumo Durante as últimas décadas, a modelação biogeoquímica dos ambientes mar- inhos tem experimentado avanços signi…cativos. O sistema MOHID tem seguido esta tendência e re‡ecte actualmente o estado da arte na mode- lação da circulação oceânica. A principal força motriz deste trabalho foi equipar o sistema MOHID com um modelo que re‡ectisse o estado da arte da modelação biogeoquímica. Para alcançar este objectivo foi desenvolvido o modelo mohid.Life.1.0, mais detalhado do que a aproximação Nutrientes –Fitoplâncton –Zooplâncton anteriormente implementada no sistema MO- HID. Para além de uma descrição do algoritmo do modelo e da sua …loso…a de base, este trabalho contém uma análise do comportamento do modelo quando sujeito a diferentes testes. O modelo foi também testado numa apli- cação a um cenário real, nomeadamente ao Estuário do Tejo, Portugal. O comportamento do modelo mostrou a sua capacidade para responder de uma forma realista a diferentes condições. Os resultados mostraram também que o modelo reproduz o funcionamento básico das teias alimentares na coluna de água e da dinâmica de nutrientes dos sistemas marinhos. Na aplicação ao Estuário do Tejo, o modelo permitiu abordar algumas incertezas em relação ao funcionamento do sistema e reproduziu correctamente os mecan- ismos geralmente assumidos, tanto em estudos numéricos como em estudos experimentais, como controlo do sistema. Palavras-chave: Modelos ecológicos; orientado por processos; ciclos biogeoquímicos; qualidade da água; sistema MOHID; Estuário do Tejo. ix x RESUMO Acknowledgments First of all, I must express my gratitude to Prof. Ramiro Neves. Among many things, I am grateful for his invitation to join the MARETEC “gang” and to pursue my PhD Thesis under his supervision, for putting up with me for so long, for keeping my mind in a constant struggle, and for widening my vision on so many things. I am also thankful to Prof. Helena Galvão for agreeing to co-supervise my work and for the assistance that kept me on the right tracks in the early days of my work. Then there is a myriad of friends and colleagues that somehow, and in so many di¤erent ways, have given a decisive contribution to improve the qual- ity of this work and to keep me focused: Prof. Henrique Coelho, a colleague and a friend, responsible for what can be called my “academic career”; Ana Barbosa for the contagious enthusiasm and some really valuable lessons on “phytoplankton ecology”; Job Baretta for the priceless lessons, for the thor- ough corrections of early versions of this manuscript and spirited comments, and above all for taking me serious; Luis Fernandes for the assistance in the …rst steps of this project and especially for naming the model "Life"; Rui Caldeira and Hernani Theias for or all the comments and suggestions, es- pecially for helping me overcome the initial shock of using LATEXas the text editor for this work; Pedro Galvão for all the fruitful philosophical discus- sion on the role of models in science and anywhere else (especially those at 8 a.m.); Rosa for helping me out with the "units" problems; Guillaume Ri‡et for making his work my own with no strings attached; So…a Saraiva for the valuable data and help; José Chambel and Francisco Campuzano for the support in the right moment; João Robert for the “smash!”attitude; Paulo Chambel for proof reading this work and for walking with me the extra (and …nal) mile; Ricardo Lemos for the absolute commitment to reading as much of this work as was humanly possible in such a short time and for the valuable corrections; all the friends in the BMP Class of 93 (Universidade do Algarve) for the inspiration and support. Finally, I’mespecially indebted to my family, particularly to my parents and grandparents, for believing that I am making a man of myself.
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