Monitoring Forest Damage with Mass Spectrometry-Based Metabolomics Methods

Name: Monitoring Forest Damage with Mass Spectrometry-Based Metabolomics Methods
Brand: Wiley-ISTE
Price: 142.99 EUR
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Carla Antonio(Herausgeber*in)

Wiley-ISTE (Verlag)

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Erschienen am 27. Oktober 2023

464 Seiten

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978-1-119-86873-6 (ISBN)

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Inhalt

Cover
Title Page
Copyright
Contents
List of Contributors
Preface
Chapter 1 Forest Tree Metabolomics Under a Changing Climate
1.1 Introduction
1.2 Forest Damage
1.2.1 Abiotic Forest Damage
1.2.2 Biotic Forest Damage
1.3 Forest Tree Metabolomics
1.4 Conclusion and Future Perspectives
References
Chapter 2 Experimental Methodology for Clonal Forest Research
2.1 Introduction
2.2 Defining the Objectives of an Experiment
2.3 Sampling Strategies to Represent the Species
2.4 Planning and Establishing the Experimental Design
2.5 Examples of the Implementation of Field Trials to Quantify Genetic Variability within a Species
2.5.1 Pinus pinea L. in Portugal
2.5.2 Pinus pinaster Aiton in Portugal
2.6 Statistical Analysis and Quantification of Genetic Variability within a Species
2.6.1 Statistical Analysis
2.6.2 Genetic Parameters
2.6.2.1 Quantification of Genetic Variability within a Species
2.6.2.2 Broad-Sense Heritability
2.6.2.3 Selection and Genetic Gain
2.7 Conclusions
Acknowledgments
References
Chapter 3 Sample Preparation for Forest Tree Metabolomics
3.1 Experimental Design for Metabolomics
3.2 Sampling and Quenching of Tree Tissue Material
3.2.1 Leaf Sampling
3.2.2 Wood Tissue Sampling
3.2.3 Phloem Sap Sampling
3.2.4 Xylem Sap Sampling
3.2.5 Root Sampling
3.2.6 Techniques for Separating Cell Types in Complex Tissues
3.2.6.1 Laser-assisted Microdissection
3.2.6.2 Fluorescence-activated Cell Sorting
3.2.7 Measuring Metabolites Without Cell or Tissue Separation
3.3 Labeling of Tree Tissues
3.3.1 C-labeling
3.3.1.1 Labeling of Whole Trees
3.3.1.2 Labeling of Tree Tissues
3.3.2 N-labeling
3.3.2.1 Labeling Through the Canopy of Whole Trees
3.3.2.2 Labeling Through Roots of Whole Trees
3.3.2.3 Stem Injection
3.3.3 Dual Labeling of C and N
3.4 Metabolite Extraction and Mass Spectrometry-Based Metabolite Analysis
3.4.1 Untargeted and Targeted Metabolomics
3.4.2 Chemical Derivatization Methods
3.5 Conclusions
References
Chapter 4 Systems Biology as a Tool to Uncover Interdisciplinary Links within the Complex Forest Tree System
4.1 Systems Biology
4.2 Strategies for Data Integration and Network Analysis
4.2.1 Element-Based Integration
4.2.2 Pathway-Based Integration
4.2.3 Mathematical Integration
4.2.4 Integration of Transcriptomics and Metabolomics Data
4.2.5 Integration of Proteomics and Metabolomics Data
4.2.6 Integration of Multi-omics Data
4.3 Integration of Genomics and Metabolomics Data
4.3.1 Linkage Analysis
4.3.2 Genome-wide Association Studies
4.3.3 Genomic Selection
4.4 Systems Biology to Provide Clues for Metabolite Annotation in Different Tree Species in Recent Years
4.5 Challenges in Integrating Metabolomics and Other Omics
4.6 Conclusion and Future Perspectives
References
Chapter 5 A Workflow for Metabolomics of Forest Tree Biotic Stress Response and Applications for Management
5.1 Introduction
5.2 Methods
5.2.1 Research Question
5.2.2 Sample Selection and Processing
5.2.3 Analytical Methods
5.2.4 Chemometrics
5.2.5 Pre-processing
5.2.6 Classification
5.2.7 Regression
5.2.8 Variable Selection
5.2.9 Validation
5.2.10 Available Tools for Analyzing Metabolomics Data
5.3 Application
5.3.1 Detection of Diseased and Pest-Infected Trees
5.3.2 Identifying Resistant Trees
5.3.3 Landscape-Level Applications
5.4 Case Studies
5.4.1 Ash
5.4.2 Oak
5.4.3 Pine
5.5 Conclusions and Future Perspectives
Acknowledgments
References
Chapter 6 Analysis of Volatile Organic Compounds
6.1 Plant Volatile Organic Compounds
6.1.1 Ecological and Physiological Functions of Plant VOCs
6.1.1.1 VOCs and Biotic Stresses
6.1.1.2 VOCs and Abiotic Stresses
6.1.2 Controls of Plant VOC Emissions
6.1.2.1 Constitutive VOC Emissions
6.1.2.2 Stress-Induced VOC Emissions
6.2 Methodologies for Detecting Plant VOCs
6.2.1 Static Headspace Analysis
6.2.2 Dynamic Headspace Analysis
6.2.3 Eddy Covariance
6.3 Analytical Systems for Measuring Plant VOCs
6.3.1 Thermal Desorption Gas Chromatography Mass Spectrometry
6.3.1.1 Sample Collection
6.3.1.2 TD-GC-MS Measurements
6.3.1.3 Qualitative Analysis
6.3.1.4 Blank Measurements
6.3.1.5 Internal Standard
6.3.1.6 Quantitative Analysis
6.3.1.7 Deconvolution
6.3.1.8 Applications of TD-GC-MS in Plant VOC Analysis
6.3.2 Proton Transfer Reaction Mass Spectrometry
6.3.2.1 General Principles and Analytical Instrument Development
6.3.2.2 Quantification of VOC Concentrations: Direct Calibration and Theoretical Calculation
6.3.2.3 Application of PTR-MS in Plant VOCs Analysis
6.3.2.4 Computational Approaches to Analyze PTR-MS Data
6.4 Concluding Remarks and Future Perspectives
References
Chapter 7 Assessing Specialized Metabolites in Tree Bark Using Wide-Targeted LC-MS Analysis
7.1 Introduction
7.2 Materials and Methods
7.2.1 Plant Cultivation and Sampling
7.2.2 Sample Aliquoting
7.2.3 Extraction of Specialized Metabolites from Tree Bark Tissue
7.2.4 LC-MS Analysis of Polar Fractions
7.3 Data Analysis
7.3.1 Peak Evaluation
7.3.2 Peak Annotation
7.3.2.1 Tandem Mass Spectrometry (MS/MS, MSn)
7.3.2.2 Reference Plant Compounds and Extracts with Literature Data
7.3.2.3 Database Search
7.3.2.4 Mutant Analysis
7.3.2.5 Peak Annotation by the Prediction of Pathway
7.4 Data Interpretation
7.5 Conclusions and Future Perspectives
References
Chapter 8 Plant Hormone Analysis in Forest Tree Species
8.1 Importance of Forest Tree Species
8.2 Plant Hormones and Their Roles in Plant Physiology, Biochemistry, and Development
8.2.1 Main Plant Hormones Involved in the Interaction of Plants with Their Environment
8.3 Forest Tree Sampling
8.3.1 Issues Related to Forest Tree Population Structure and Distribution
8.3.2 Practical Aspects Related to Forest Tree Tissue Harvesting and Preservation
8.3.3 Important Considerations Regarding the Extraction of Plant Hormones
8.4 Analytical Methods for Plant Hormone Analysis and Profiling
8.5 Applications of Plant Hormone Profiling to Understand Forest Tree Physiology
8.6 Future Prospects in Plant Hormone Analysis
Acknowledgments
References
Chapter 9 Metabolomics of Nutrient-Deprived Forest Trees
9.1 Introduction
9.2 Macronutrient Deficiency and Wood Production
9.2.1 Nitrogen
9.2.2 Phosphorus
9.2.3 Potassium
9.2.4 Calcium
9.2.5 Sulphur
9.2.6 Magnesium
9.2.7 Micronutrients
9.3 General Use of Mass Spectrometry-Based Metabolomics to Study Wood
9.4 Tree Nutrition and Metabolome
9.4.1 Nitrogen
9.4.2 Phosphorus
9.4.3 Potassium
9.4.4 Mycorrhization
9.5 Final Remarks
Acknowledgments
References
Chapter 10 The Impact of Drought on Plant Metabolism in Quercus Species - From Initial Response to Recovery
10.1 Introduction
10.2 Primary Metabolic Pathways and Metabolite Levels
10.2.1 Changes in Leaf Metabolism with Drought Stress Intensity
10.2.2 Variation Among Organs - Mobilization of Carbohydrates as a Mechanism of Drought Acclimation
10.3 Secondary Metabolic Pathways and Metabolite Levels
10.4 The Transport of Metabolites within the Plant - Transport Rates and Sap Composition
10.5 The Release of Metabolites Outside the Plant
10.5.1 Root Exudates
10.5.2 Volatile Organic Compounds
10.6 Conclusions
References
Further Reading/Resources
Chapter 11 Metabolomics of Forest Tree Responses to Fluctuations of Temperature and Elevated Atmospheric CO2
11.1 Introduction
11.2 Metabolic Response of Trees to Temperature Changes
11.3 Temperature Effect on Primary Metabolism
11.3.1 Carbohydrates and Photosynthesis
11.3.2 Respiratory Metabolism
11.3.3 Amino Acids and Proteins
11.4 Temperature Effect on Secondary Metabolism
11.4.1 Oxidative Stress
11.4.2 Phenylpropanoid Pathway
11.4.3 Lignin and Cell Wall
11.4.4 Disease Response to Abiotic (Heat) Stress
11.5 Effects of Elevated CO2 on Tree Metabolism
11.5.1 CO2 Fixation in Plants and Climate Predictions about Atmospheric CO2
11.5.2 Elevated CO2 and Plant Metabolism
11.5.3 Elevated CO2 and Tree Metabolism
11.6 CO2 Effects on Isoprene Emissions
11.7 CO2 and Plant Productivity
11.8 Acclimation After a Long Period of CO2 Exposure
11.9 The Interactive Effect of Elevated CO2 and High Temperature in Trees
11.10 Conclusions and Future Perspectives
Acknowledgments
References
Chapter 12 Integration of Primary Metabolism with Physiological and Anatomical Data to Assess Dutch Elm Disease Susceptibility in Three Elm Species - A Case Study
12.1 Impacts of Dutch Elm Disease on Plant Metabolism and Its Modulation by Climate
12.2 Material and Methods
12.2.1 Plant Material and Experimental Design
12.2.2 O. novo-ulmi Inoculation
12.2.3 Measurements
12.2.3.1 Stomatal Conductance
12.2.3.2 Crown Wilting
12.2.3.3 Primary Metabolites
12.2.3.4 Xylem Anatomy
12.2.4 Data Analysis
12.3 Results
12.3.1 Drought Effects on Stomatal Conductance, Xylem Anatomy, and Primary Metabolism
12.3.2 Impact of O. novo-ulmi on Crown Wilting, Xylem Anatomy, and Primary Metabolism
12.4 Discussion
12.4.1 No Legacy Effect of Two-Year Moderate Drought on Primary Metabolism
12.4.2 Early Re-organization of Primary Metabolism upon Inoculation with O. novo-ulmi Is Moderate and Species- and Organ-Specific
12.4.3 Drought Affects the Primary Metabolic Response of U. minor Branches to O. novo-ulmi
12.4.4 High DED Susceptibility of U. laevis Was Accompanied by No Change in Stem or Branch Primary Metabolite Concentrations Soon After O. novo-ulmi Inoculation
12.5 Conclusions
Acknowledgments
References
Further Reading/Resources
Chapter 13 Metabolomics of Pinus spp. in Response to Pinewood Nematode Infection
13.1 Introduction
13.2 Mass Spectrometry-Based Metabolite Responses to Pinewood Nematode Infection
13.2.1 Primary Metabolism
13.2.2 Secondary Metabolism
13.2.2.1 Phenolic Compounds
13.2.2.2 Volatile Organic Compounds and Essential Oils
13.3 Disease Management
13.3.1 Phytohormones
13.3.1.1 Ethylene
13.3.1.2 Jasmonates
13.3.1.3 Salicylates
13.3.2 Chitosan
13.3.3 Agronanochemicals
13.4 Conclusions and Future Perspectives
References
Index
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