List of Contributors xiii
Preface xix
1 Forest Tree Metabolomics Under a Changing Climate 1
AnaMargarida Rodrigues and Carla Antonio
1.1 Introduction 1
1.2 Forest Damage 2
1.3 Forest Tree Metabolomics 5
1.4 Conclusion and Future Perspectives 7
2 ExperimentalMethodology for Clonal Forest Research 15
Isabel Carrasquinho and Elsa Gonçalves
2.1 Introduction 15
2.2 Defining the Objectives of an Experiment 16
2.3 Sampling Strategies to Represent the Species 17
2.4 Planning and Establishing the Experimental Design 17
2.5 Examples of the Implementation of Field Trials to Quantify Genetic Variability within a Species 19
2.6 Statistical Analysis and Quantification of Genetic Variability within a Species 25
2.7 Conclusions 27
3 Sample Preparation for Forest TreeMetabolomics 35
Pia Guadalupe Dominguez, Thais Regiani Cataldi, Ilka Nacif Abreu, Thomas Moritz, and Ilara Gabriela Frasson Budzinski
3.1 Experimental Design for Metabolomics 35
3.2 Sampling and Quenching of Tree Tissue Material 37
3.3 Labeling of Tree Tissues 46
3.4 Metabolite Extraction and Mass Spectrometry-Based Metabolite Analysis 50
3.5 Conclusions 55
4 Systems Biology as a Tool to Uncover Interdisciplinary Links within the Complex Forest Tree System 71
Pia Guadalupe Dominguez, Ilka Nacif Abreu, ThomasMoritz, and Ilara Gabriela Frasson Budzinski
4.1 Systems Biology 71
4.2 Strategies for Data Integration and Network Analysis 72
4.3 Integration of Genomics and Metabolomics Data 82
4.4 Systems Biology to Provide Clues for Metabolite Annotation in Different Tree Species in Recent Years 91
4.5 Challenges in IntegratingMetabolomics and Other Omics 93
4.6 Conclusion and Future Perspectives 94
5 AWorkflow for Metabolomics of Forest Tree Biotic Stress Response and Applications for Management 109
Anna O. Conrad, Caterina Villari, and Pierluigi Bonello
5.1 Introduction 109
5.2 Methods 111
5.3 Application 116
5.4 Case Studies 117
5.5 Conclusions and Future Perspectives 119
6 Analysis of Volatile Organic Compounds 127
Andrea Ghirardo and Federico Brilli
6.1 Plant Volatile Organic Compounds 127
6.2 Methodologies for Detecting Plant VOCs 136
6.3 Analytical Systems for Measuring Plant VOCs 140
6.4 Concluding Remarks and Future Perspectives 167
7 Assessing Specialized Metabolites in Tree Bark Using Wide-Targeted LC-MS Analysis 187
Maria Kenosis Emmanuelle Galingay Lachica,MutsumiWatanabe, and Takayuki Tohge
7.1 Introduction 187
7.2 Materials and Methods 189
7.3 Data Analysis 192
7.4 Data Interpretation 198
7.5 Conclusions and Future Perspectives 199
8 Plant Hormone Analysis in Forest Tree Species 205
Eva Canizares, Juan Manuel Acien,Miguel Gonzalez-Guzman, and Vicent Arbona
8.1 Importance of Forest Tree Species 205
8.2 Plant Hormones andTheir Roles in Plant Physiology, Biochemistry, and Development 208
8.3 Forest Tree Sampling 213
8.4 AnalyticalMethods for Plant Hormone Analysis and Profiling 217
8.5 Applications of Plant Hormone Profiling to Understand Forest Tree Physiology 222
8.6 Future Prospects in Plant Hormone Analysis 225
9 Metabolomics of Nutrient-Deprived Forest Trees 235
Sara Adrian Lopez de Andrade, Vinicius Henrique de Oliveira, and PauloMazzafera
9.1 Introduction 235
9.2 Macronutrient Deficiency andWood Production 237
9.3 General Use of Mass Spectrometry-Based Metabolomics to Study Wood 244
9.4 Tree Nutrition and Metabolome 248
9.5 Final Remarks 253
10 The Impact of Drought on PlantMetabolism in Quercus Species - From Initial Response to Recovery 267
Juan Sobrino-Plata, Francisco Javier Cano, Ismael Aranda, Maria Brigida Fernandez de Simon, and Jesus Rodriguez-Calcerrada
10.1 Introduction 267
10.2 PrimaryMetabolic Pathways and Metabolite Levels 276
10.3 Secondary Metabolic Pathways and Metabolite Levels 282
10.4 The Transport of Metabolites within the Plant - Transport Rates and Sap Composition 285
10.5 The Release of Metabolites Outside the Plant 288
10.6 Conclusions 293
11 Metabolomics of Forest Tree Responses to Fluctuations of Temperature and Elevated Atmospheric CO2 315
Fernanda Rezende Castro-Moretti, Daniela Feltrim, Sara Adrian Lopez de Andrade, and PauloMazzafera
11.1 Introduction 315
11.2 Metabolic Response of Trees to Temperature Changes 318
11.3 Temperature Effect on Primary Metabolism 319
11.4 Temperature Effect on SecondaryMetabolism 321
11.5 Effects of Elevated CO2 on Tree Metabolism 323
11.6 CO2 Effects on Isoprene Emissions 327
11.7 CO2 and Plant Productivity 327
11.8 Acclimation After a Long Period of CO2 Exposure 328
11.9 The Interactive Effect of Elevated CO2 and High Temperature in Trees 328
11.10 Conclusions and Future Perspectives 331
12 Integration of Primary Metabolism with Physiological and Anatomical Data to Assess Dutch Elm Disease Susceptibility in Three Elm Species - A Case Study 343
Jesus Rodriguez-Calcerrada, AnaMargarida Rodrigues, Carla Antonio, Rosana Lopez, Jorge Dominguez, Juan Sobrino-Plata, Luis Gil, and Juan Antonio Martin
12.1 Impacts of Dutch Elm Disease on Plant Metabolism and Its Modulation by Climate 343
12.2 Material and Methods 348
12.3 Results 356
12.4 Discussion 373
12.5 Conclusions 377
13 Metabolomics of Pinus spp. in Response to Pinewood Nematode Infection 389
AnaMargarida Rodrigues, Marta Nunes da Silva, Marta Vasconcelos, and Carla Antonio
13.1 Introduction 389
13.2 Mass Spectrometry-Based Metabolite Responses to Pinewood Nematode Infection 391
13.3 Disease Management 398
13.4 Conclusions and Future Perspectives 407
References 408
Index 421
