Omics Science for Rhizosphere Biology

Preface
Contents
Editors and Contributors
Chapter 1: Rhizosphere Metagenomics: Methods and Challenges
1.1 Introduction
1.2 Rhizosphere Metagenomics
1.3 Metagenomics Methods to Explore Microbial Diversities
1.3.1 Marker-Based Sequencing Method
1.3.2 Shotgun Metagenome Sequencing Method
1.3.3 Attributes to Quantify Microbial Diversity
1.3.4 Classification of Metagenomic Datasets
1.3.5 Structural Classification
1.3.5.1 Binning Strategies Based on Taxonomy
1.3.5.2 Alignment-Based Classification
1.3.5.3 Composition-Based Classification
1.3.5.4 Hybrid-Based Classification
1.3.5.5 Amino Acid-Based Taxonomic Classification
1.3.5.6 Taxonomy-Independent Binning
1.3.5.7 De Novo Assembly of Metagenomic Datasets
1.3.5.8 Contig Binning
1.3.6 Functional Classification
1.4 Milestones of Rhizosphere Metagenomics
1.5 Challenges of Rhizosphere Metagenomics
1.6 Concluding Remarks
References
Chapter 2: Metagenomic Approach in Relation to Plant-Microbe and Microbe-Microbe Interactions
2.1 Introduction
2.2 Unravelling Microbiome Interactions Through Metagenomics Approach
2.2.1 Microbe-Microbe Interactions
2.2.2 Plant-Microbe Associations
2.2.2.1 Significance of Above-Ground Microbiomes
2.2.2.2 Significance of Below-Ground Microbiomes
2.2.2.3 Benefits of Rhizosphere Microbiomes
2.3 Sampling and Experimental Design to Study Plant-Microbiomes
2.3.1 Soil Sampling
2.3.2 Isolation of DNA from Rhizosphere
2.3.3 Amplicon Sequencing
2.3.4 Shotgun Metagenomics
2.3.5 Bioinformatics Analysis
2.4 Concluding Remarks
References
Chapter 3: Metagenomics and Metatranscriptomics Approaches in Understanding and Discovering Novel Molecules in Rhizosphere Env...
3.1 Introduction
3.2 The Rhizosphere Microbiome-Who Is There?
3.3 Interaction Network, Communications, and Chemical Diversity in Rhizosphere
3.4 Omics Approaches and Microbial Dynamics in Rhizosphere
3.4.1 What Is Omics?
3.4.2 Metagenomics in Understanding and Discovery of Novel Molecules from Rhizosphere
3.4.3 Metatranscriptomics in Understanding and Discovery of Novel Molecule and Metabolic Pathways from Rhizosphere
3.5 Conclusions and Future Trends
References
Chapter 4: ``Omics´´ Approaches for Understanding Soil Suppressiveness in Agriculture
4.1 Introduction
4.2 Understanding General-Soil Suppressiveness by Employing Omics Approaches
4.3 Understanding Specific-Soil Suppressiveness by Employing Omics Approaches
4.3.1 Rhizoctonia solani
4.3.2 Fusarium oxysporum
4.3.3 Phytophthora nicotianae
4.4 Conclusions and Future Perspectives
References
Chapter 5: Rhizosphere Dynamics: An OMICS Perspective
5.1 Introduction
5.2 Recent Advances in OMICS Approaches in Rhizosphere
5.3 Challenges for Multi-OMICS Data Analysis in Rhizosphere
5.4 Current Resources for Multi-OMICS Analysis
5.5 Recent OMICS Techniques to Study Rhizosphere Dynamics
5.5.1 Metagenomics
5.5.2 Metaproteomics
5.5.3 Metatranscriptomics
5.5.4 Metametabolomics
5.6 Conclusions
References
Chapter 6: Transcriptomics Analyses and the Relationship Between Plant and Plant Growth-Promoting Rhizobacteria (PGPR)
6.1 Introduction
6.2 Plant Growth-Promoting Rhizobacteria
6.3 Beneficial Characterizations of Rhizobacteria
6.4 Interaction of Plant and Beneficial Rhizobacteria
6.5 Genes and Plant Growth Promotion
6.6 Transcriptomics Analyses
6.6.1 Isolation of RNA (Properties of Bacterial RNA)
6.6.2 RNA Amplification and the Synthesis of Bacterial cDNA
6.6.3 Expressed Sequence Tags (EST)
6.6.4 Serial and Cap Analysis of Gene Expression (SAGE/CAGE)
6.7 Methods for Investigating Gene Expression
6.7.1 Methods Based on Hybridization
6.7.1.1 Northern Blot
6.7.1.2 Microarray Method
6.7.2 Methods Based on PCR
6.7.2.1 Real-Time Quantitative PCR
6.7.2.2 Real-Time RT-PCR
6.7.3 Next-Generation Sequencing: RNA-Seq
6.7.3.1 Methods Based on Sequencing
6.7.3.2 Using RNA-Seq for the Analysis of Bacterial Transcriptomes
6.7.3.3 Bioinformatics Analysis of RNA-Seq Data
6.7.3.4 Quality Check and Data Preprocessing
FastQC
6.7.3.5 Transcriptome Assembly
6.7.3.6 Annotation and Pathway Analysis
6.8 Conclusion
References
Chapter 7: Proteomics for Understanding the Interaction Between Plant and Rhizospheric Microflora
7.1 Introduction
7.2 Proteomics
7.2.1 Gel-Based Protein Separation Techniques
7.2.1.1 Two-Dimensional Gel Electrophoresis (2-DE)
7.2.1.2 Fluorescence 2-D Difference Gel Electrophoresis (DIGE)
7.2.2 Gel-Free Proteomics
7.2.2.1 Isotope-Coded Affinity Tag (ICAT)
7.2.2.2 Isobaric Tags for Relative and Absolute Quantitation (iTRAQ)
7.2.2.3 Multidimensional Protein Identification Technology (MudPIT)
7.2.3 Mass Spectrometry (MS) for Protein Identification
7.3 Tools for Analyzing Protein-Protein Interactions and Protein Function
7.4 Metaproteomics and Its Use in Rhizosphere
7.5 Metaproteogenomics Studies in Rhizosphere
7.6 Conclusion
References
Chapter 8: A Proteomics Perspective for Understanding Rhizosphere Biology at Higher Altitudes
8.1 Introduction
8.2 Ecology of Higher Altitudes
8.2.1 Cold-Adapted Microorganisms
8.3 Synergistic Effect of Rhizosphere with Cold-Adapted Microbial Life
8.4 Microbial Community and Proteomics
8.4.1 Strategies for Rhizosphere Proteomic Studies
8.4.1.1 2-DE
8.4.1.2 2D-DIGE
8.4.1.3 LC-MS
8.4.1.4 Shotgun Proteomics
8.4.1.5 Protein-SIP
8.4.1.6 MALDI-TOF-MS
8.4.1.7 LC-ESI-MS/MS
8.4.1.8 MS/MS
8.4.1.9 Surface-Enhanced Laser Desorption/Ionization Time-of-Flight (SELDI-TOF)
8.4.1.10 Proteins and Antibody Microarray
8.4.1.11 Isotope-Coded Affinity Tags (ICAT)
8.4.1.12 Unipept 4.0
8.4.2 Microbial Potential Proteins for Plant Survival and Total Productivity
8.5 Proteomics Strategies for Crop Improvement at Higher Altitude
8.6 Conclusion and Future Perspectives
References
Chapter 9: Structural and Functional Rhizospheric Microbial Diversity Analysis by Cutting-Edge Biotechnological Tools
9.1 Introduction
9.2 What is Rhizosphere?
9.3 Rhizospheric Diversity
9.3.1 Common Rhizospheric Population
9.3.2 Plant-Microbe Interaction
9.4 Molecular Tools for Rhizospheric Microbial Diversity Analysis
9.4.1 Traditional Molecular Tools
9.4.1.1 ARDRA
9.4.1.2 DGGE
9.4.1.3 RISA
9.4.2 Omics-Based Rhizospheric Microbial Diversity
9.4.2.1 Metagenomics (Using all NGS platforms)
9.4.2.2 Functional Metagenomics
9.4.2.3 Metatranscriptomics
9.4.2.4 Metaproteomics
9.4.2.5 Metabolomics
9.5 Pros and Cons of the Omics-Based Approach
9.6 Future Prospects
References
Chapter 10: Rhizosphere Fingerprints: Novel Biomolecules Via Meta-Omics Technology
10.1 Introduction
10.2 Plant-Microbe Interactions
10.3 Key Barriers During Interactions
10.4 Chemical Communication in Rhizospheres Via Secretion of Signaling Molecules
10.4.1 Plant to Plant
10.4.2 Bacteria to Bacteria
10.4.3 Plant to Bacteria
10.4.4 Bacteria to Plant
10.5 Overview of Rhizosphere Defense
10.6 Meta-Omics Technology
10.7 Conclusion and Future Aspect
References
Chapter 11: Rhizosphere Virology and Plant Health
11.1 Introduction
11.2 Virus Particles Enter the Host Plants Through Their Roots
11.2.1 Nematode-Transmitted Viruses
11.2.2 Fungi-Transmitted Viruses
11.2.3 Plasmodiophorids-Transmitted Viruses
11.2.4 Viral Transport to Aerial Parts
11.3 RNAi-Based Signalling Mechanisms
11.4 R-Gene-Mediated Defence Responses
11.5 Viral Replication Inside the Host and Associated Damages
11.6 Signalling Events in Plant Defence Against Viral Attack
11.6.1 Contribution of Cyclins, CDKs, Chaperones, and Other Enzymes During Viral Infection
11.6.2 Systemic Acquired Resistance in Plant Against Viral Infection
11.6.3 Phytohormones-Mediated Defence Against Viral Attack
11.6.4 Volatile Organic Compounds and Plant-Virus Interactions
11.7 Conclusion
References
Chapter 12: Long Sequencing Tools for Rhizosphere Study
12.1 Introduction to Rhizosphere
12.2 Introduction to NGS Technology
12.2.1 The First Generation of Sequencing
12.2.2 The Next Generation of Sequencing
12.2.2.1 Sequencing by Synthesis
12.2.2.2 Roche 454 Pyrosequencing
12.2.2.3 Illumina
12.2.2.4 Ion Torrent
12.2.2.5 Sequencing by Ligation
12.2.2.6 SOLiD
12.2.3 Single-Molecule Sequencing
12.2.3.1 Pacific Biosciences (PacBio) Single Molecule Real-Time (SMRT) Sequencing
12.2.3.2 Nanopore DNA Sequencing
12.3 Application of NGS in Rhizosphere Study
12.4 Computational Tools for Metagenomics Study
12.5 Future Aspects
References
Chapter 13: Rhizoengineering: A Strategy to Enhance Soil and Crop Productivity
13.1 Introduction
13.2 Significance of Rhizosphere Biology in Agriculture
13.3 Rhizoengineering
13.4 Rhizoengineering and Its Types
13.4.1 Rhizosphere Modification Through Plant Engineering
13.4.2 Rhizosphere Modification Through Microbiome Engineering
13.4.3 Rhizoengineering Through Soil Engineering
13.5 Factors Influencing Rhizosphere Functioning
13.5.1 Role of Rhizodeposits in Rhizosphere Biology and Functioning
13.5.2 Soil Microbiome and Rhizosphere Functioning
13.5.3 Soil and Crop Management
13.6 Role of Microbial Biofilms and in Rhizoengineering
13.7 Conclusion and Future Outlook
References
Chapter 14: Endospheric Microbiome-Assisted Alteration in the Metabolomic Profiling of Host towards Abiotic Stress Mitigation
14.1 Introduction
14.2 Endophytes and Their Potential Roles
14.2.1 As Plant Growth Promoters
14.2.2 Endophytes in Mitigation of Abiotic Stress
14.2.2.1 Regulation of Relative Water Content
14.2.2.2 Antioxidant Enzymes
14.2.2.3 Production of Phytohormones
14.3 Endophytes and Sustainable Agriculture
14.4 Metabolomics Approach for Amelioration of Abiotic Stress
14.5 Deciphering Host Endophyte Interaction Through Metabolomics
14.6 Metabolomic Profiling
14.7 Conclusions
References