Monitoring Forest Damage with Mass Spectrometry-Based Metabolomics Methods

Carla António, PhD, leads the Plant Metabolomics Lab at the University of Lisbon, Portugal. She has published extensively on the mass-spectrometry based metabolomics of plant abiotic and biotic stress responses.

List of Contributors xiii

Preface xix

1 Forest Tree Metabolomics Under a Changing Climate 1
AnaMargarida Rodrigues and Carla António

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, Thaís 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 Cañizares, Juan Manuel Acién,Miguel González-Guzmán, 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 Adrián Lopez de Andrade, Vinícius 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, María Brígida Fernández de Simón, and Jesús Rodríguez-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 Adrián 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
Jesús Rodríguez-Calcerrada, AnaMargarida Rodrigues, Carla António, Rosana López, Jorge Domínguez, Juan Sobrino-Plata, Luis Gil, and Juan Antonio Martín

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 António

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