Patterns, Function and Application of Seed Microbiome

Bacteria, Fungi and Viruses

1st Edition - February 6, 2025
Imprint: Academic Press
Authors: Mohammad Yaseen Mir, Javid A. Parray, Saima Hamid, Munagala S. Reddy
Language: English
Paperback ISBN:
9 7 8 - 0 - 4 4 3 - 2 4 7 7 6 - 7
eBook ISBN:
9 7 8 - 0 - 4 4 3 - 2 4 7 7 7 - 4

Patterns, Function and Application of Seed Microbiome: Bacteria, Fungi and Viruses presents the current understanding of seed and microbiota associations, emphasizing recent findin… Read more

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Patterns, Function and Application of Seed Microbiome: Bacteria, Fungi and Viruses presents the current understanding of seed and microbiota associations, emphasizing recent findings that highlight the latest insights into these interactions, and how they may ultimately influence plant ecology, health and productivity in both natural and agricultural systems. The development and dispersal of seeds and their transition to seedlings are among the most critical stages of the life cycle of plants and seed health is of crucial global importance for producing both quantity and high quality crops to feed world’s population. It is important for seeds to be produced that contain the best hybrid embryo so that it is free of diseases, includes beneficial endophytes and ensures a healthy start of a seedling. Focusing on the role of seed microbiota, their transmission and implications for producing healthier seeds as well as the relationship between the seed microbiome and primed plant resistance this book reveals the targeted use of the seed microbiome to enrich the soil biodiversity and its resilience and its resulting impact on plant health and yield. also explores the importance of nanotechnology in the development and production of crops for both improved plant production, and plant protection. It explores the different microbes that are vectored onto and within the seeds of both cultivated and non-cultivated plants, with an emphasis on the importance and roles of seed microbiomes in sustainable agriculture. It explains how to change seeds to increase microbiome vectoring; repairing damaged ones, and conserves seed microbiota. It also present seed microbiome roles for plant health and design effective microbiome engineering.

Title of Book
Cover image
Title page
Table of Contents
Copyright
Preface
Chapter 1. Diversity and dynamics of seed microbiome
1.1 Concept and history of seed microbiology
1.2 Microbes associated with seeds
1.3 Assembly and structure framework of seed microbiomes
1.4 Acquisition of microbes during seed dispersal
1.4.1 Wind and water dispersal
1.4.2 Frugivorous/granivorous seed dispersal
1.4.3 Seed-microbe interactions in the soil seed bank
1.4.4 The seed bank ecology of Pyrenophora semeniperda and Bromus tectorum
1.5 Conclusion and future perspectives
Chapter 2. Ecological role of seed microbiome
2.1 Structure and function of the seed microbiome
2.1.1 Functions of the seed microbiome
2.1.2 Seed microbiome and plant conservation
2.1.3 Seed microbiome and plant invasion
2.2 Seed microbiome diversity and transmission
2.3 Seed microbiome in natural and agricultural systems with case studies
2.3.1 Factors determine the composition of seed microbiomes
2.3.1.1 The host factors
2.3.1.2 The microbial factors
2.3.1.3 Environmental factors
2.4 Seed microbiome of medicinal plants with case studies
2.4.1 Plant growth promotion and biological control for medicinal plants
2.4.1.1 Medicinal plants and human pathogens: occurrence and possible biocontrol
2.4.2 A case study: the microbiome of medicinal plants grown on a desert farm under organic management
2.5 Future perspectives
Chapter 3. Seed endophytes: plant and soil health
3.1 Concept and importance of endophytes in seeds
3.2 Types of seed-borne endophytes
3.2.1 Bacterial endophytes
3.2.1.1 Bacteria-host interactions
3.2.1.2 Life cycle of seed endophytic bacteria
3.2.1.3 Seed colonization
3.2.1.4 Localization and transmission of endophytes
3.2.2 Seed endophytic fungi
3.2.2.1 Life cycle of seed endophytic fungi
3.3 Potential of seed endophytes in enhancing plant growth
3.3.1 Seed endophytes mitigating heavy metal toxicity/stress
3.3.2 Mechanism of the growth promotion and heavy metal stress tolerance
3.3.3 Heavy metal resistance genes conferring metal resistance
3.4 Seed endophytes and soil health
3.4.1 Endophytes for agricultural soil health
3.5 Seed endophytes as biocontrol agents
3.5.1 Screening of biocontrol agents
3.5.1.1 In vitro screening
3.6 Mechanisms of action of endophytes in various development and growth processes of plants
3.6.1 Induced systemic resistance
3.6.2 Competition for nutrient and space
3.6.3 Defense enzymes
3.6.4 Antibiosis
3.6.5 Siderophores production
3.6.6 Application of microbial endophytes in plant disease management
3.6.7 Microbial biocontrol agents such as generally recognized as safe and qualified presumption of safety organisms
3.6.8 Direct mechanisms of plant protection from pathogens
3.6.9 Antibiotics produced by endophytes
3.6.10 Lytic enzymes secretion
3.6.11 Production of phytohormone
3.6.12 Phosphate solubilization
3.6.13 Siderophore production
3.6.14 Indirect mechanisms of plant protection from pathogens
3.6.15 Induction of plant resistance
3.6.16 Plant secondary metabolites stimulation
3.6.17 Promotion of plant growth and physiology
3.6.18 Hyperparasites and predation
3.7 Future perspectives
Chapter 4. Role of bacteria, fungi, and viruses in stress regulation
4.1 Microbial diversity and their role in stress regulation
4.2 ACC deaminase production: Role in stress tolerance
4.3 ACC deaminase in plant growth-promoting microorganisms
4.3.1 ACC deaminase in rhizospheric bacilli
4.3.2 ACC deaminase in endophytic bacilli
4.3.3 Synergy between ACC deaminase and other saline stress tolerance mechanisms
4.4 Role of seed microbiome to improve drought tolerance: Mechanisms and perspectives
4.4.1 Plant microbiome as emerging barrier for drought stress in plants
4.4.2 Microbes as modulators in plant drought stress resilience
4.4.3 Quorum sensing and its links with biopriming-induced plant stress responses
4.4.4 Importance of bio-priming in the context of abiotic stress management in plants
4.4.5 Specific cellular behaviors in seed bio-priming
4.5 Stress resilience as induced by biopriming and underlying mechanisms
4.5.1 Signaling and transcription factors
4.6 Epigenetic reprogramming
4.7 Conclusion and future perspectives
Chapter 5. Seed and microbiome interaction: Plant growth
5.1 Microbiology of spermosphere, rhizosphere, and anthosphere
5.1.1 Spermosphere
5.1.2 In space
5.1.3 In time
5.1.4 By the exudate composition
5.1.5 Origin of microbial communities in the spermosphere
5.1.6 Beneficial effects on seed germination
5.1.7 How can the spermosphere be studied?
5.1.8 Seed exudate characterization
5.1.9 Rhizosphere
5.1.10 Plant–microbe interactions in the rhizosphere
5.1.11 Mechanisms of plant–microbe interactions in rhizosphere
5.1.12 Quorum sensing
5.1.13 Volatile
5.1.14 Plant-mediated signaling
5.1.15 Factors affecting plant–microbe interactions
5.1.16 Anthosphere
5.1.17 Anthosphere microbiome and their composition
5.1.18 Abiotic and biotic determinants of microbial colonization
5.1.19 Plant–microbe-pollinator triangle
5.2 Characterization of seed microbial communities
5.2.1 Characterization and metabolism effect of seed endophytic bacteria associated with peanut
5.3 Plant growth promotion by phytohormone synthesis
5.3.1 Auxins
5.3.2 Cytokinins
5.3.3 Abscisic acid
5.3.4 Gibberellic acid
5.3.5 Salicylic acid
5.3.6 Root-associated phytohormone-producing microbes
5.3.7 Microbial phytohormones in plant stress tolerance
5.4 Monitoring soil quality in agriculture through soil–plant–microbiota crosstalk
5.4.1 The relationship between soil quality and agricultural productivity
5.4.2 Soil–plant–microbiota crosstalk
5.5 Future perspectives
Chapter 6. Seed pathology and the epidemiology of seed-borne diseases
6.1 Recent innovations in seed pathology
6.2 Nucleic acid-based methods in epidemiology research
6.3 Markers in seed-borne pathogens
6.4 Seed treatment outlook and its effect on plant physiology
6.5 Standards and uniformity for seed health tests
6.5.1 Conventional methods
6.5.1.1 Direct examination
6.5.1.2 Seed washing test
6.5.1.3 NaOH seed soak method
6.5.1.4 Embryo count method
6.5.1.5 Incubation test
6.5.1.6 Seedling grow-out test
6.5.1.7 Immunoassay methods
6.5.1.8 Molecular/nucleic acid-based diagnostic methods
6.6 Conclusion and future prospective
Chapter 7. Seed microbiome genomics
7.1 Introduction
7.2 Holobiont—a heritable unit of selection
7.2.1 Phenotype and fitness variation associated with variation in microbial symbionts
7.2.2 Heritability of symbiont presence
7.3 Selection breeding and plant genome
7.3.1 Microbiome offers genetic variability to plants
7.4 Ecological selection of plant microbiome
7.5 Host genome and its microbiome
7.6 Copropagating the coevolved
7.7 Conclusion and future prospective
Chapter 8. Seed microbiome engineering
8.1 Introduction
8.2 Engineering microbiomes
8.2.1 Host-mediated and multi-generation microbiome selection
8.2.2 Inoculation into the soil and rhizosphere
8.2.3 Inoculation into seeds or seedlings
8.2.4 Tissue atomization
8.3 Applications of agriculturally important microbes
8.3.1 Role of microbial biotechnology in agriculture
8.4 Product development strategies
8.4.1 Microbial gene pool from diverse ecological niches with specific microbiome services
8.4.2 Biocontrol ability ISR/SAR antimicrobial compounds defense hormones
8.4.3 Implication of phytohormones
8.4.4 Biostimulation capability nitrogen fixation phosphate solubilization 1-aminocyclopropane-1-carboxylate deaminase antioxidants decomposing
8.4.5 Non-GMO approach delivery system development
8.5 Formulation, adaptation strategies and challenges
8.6 Conclusion and future prospective
Chapter 9. Plant and seed microbiota and their main drivers
9.1 Introduction
9.2 Habitat-specific and species-specific microbial signatures
9.3 Soil and seed microbiomes to maintain microbial diversity
9.4 Biotechnological solutions for sustainable agriculture
9.4.1 Role of bacteria, cyanobacteria, and fungi in agriculture
9.5 Conclusion
Chapter 10. Nanotechnology of seed microbiome for improving crop productivity
10.1 Introduction
10.2 Manipulation in soil microbiome via nanotechnology for soil health improvements
10.2.1 Seed germination with nanofertilizer
10.3 Sustained release nanocarrier systems
10.3.1 New technologies for controlled release in agriculture
10.3.1.1 Nanoparticles
10.4 Improving crop quality and production
10.4.1 Nanofertilizers
10.4.2 Macronutrient fertilizers
10.4.3 Nanostimulator for plant growth
10.4.4 Plant uptake of nutrients and their subsequent movement
10.4.5 Nanopesticide
10.4.6 Nanoinsecticides
10.4.7 Nanofungicides
10.4.8 Nanonematicides
10.4.9 Enhancement of shelf-life of crops by nanomaterials
10.4.10 Nanofilms
10.4.11 Nanopackaging
10.5 Conclusion and future perspectives
Chapter 11. Modeling and analysis techniques: seed microbiome
11.1 Phytohormonal or biochemical modulation of seed microbiota
11.2 Computational modeling of seed microbiome
11.2.1 Integrating machine learning and GEMs to study interspecies microbial interactions
11.3 Meta-analysis study of different seed microbiomes
11.4 Advances in constraint-based modeling of seed microbial communities
11.4.1 Principles of constraint-based reconstruction and analysis
11.4.2 Current applications of constraint-based modeling
11.4.2.1 Interactions in synthetic communities
11.5 Conclusion and future prospective
Index

Mohammad Yaseen Mir

Dr. Mohammad Yaseen Mir, Department of Education J&K earned his M.Phil and a Ph.D in Botany with a specialization in plant biotechnology on the topic “Role of elicitors for in vitro induction of secondary metabolites in suspension cultures of Artemisia amygdalina D.” from the University of Kashmir, India. He was awarded Doctorate Merit Scholarship by University of Kashmir to pursue his Ph.D programme is also subject course expert for Environmental science Approved CEC-Moocs by MHRD GoI New Delhi. He has previously worked as a senior researcher in Research project funded by Ministry of Environment, Forest & Climate Change (MoEF & CC), Government of India along with G.B. Pant National Institute of Himalayan Environment & Sustainable Development under National Mission on Himalayan Studies (NMHS).

Affiliations and expertise

University of Kashmir, India

Javid A. Parray

Javid A Parray is currently teaching at the Department of Environmental Science, GDCEidgah, affiliated with Cluster University, Srinagar. His research interests include ecological and agricultural microbiology, climate change, microbial biotechnology, and environmental microbiomes. He has also done his Post Doctorate Research from the University of Kashmir. Dr Parray was also awarded a Fast Track Young Scientist Project by SERB – DST, GoI New Delhi. Dr Javid was also awarded “Emerging scientist year Gold Medal” for the year 2018 by the Indian Academy of Environmental Science. Dr Parray is the course coordinator for the UG- Programmes for CeC-MOOCS Swayam in Environmental Science. Dr Parray is an expert review member in the field of environmental science in the CSTT, Ministry of Education, GoI New Delhi.

Affiliations and expertise

Assistant Professor and Head of the Department of Environmental Science, Govt. SAMDegree College - Budgam, India

Saima Hamid

Dr.Saima Hamid is a Program Officer in EIACP with Government of India. She holds a Doctorate as well as Master's Degree in Environmental Science from the University of Kashmir, India. Her research area includes Plant molecular biology, stress adaptations, bioactive compound isolation and characterization, climate change and microbial biotechnology. She has published in highly reputed and peer-reviewed journals. She is the Co-founder of CERD Foundation, Research and Educational Non-profitable Charitable Trust that aims and encourages to develop communities with scientific temperament towards education and research in the society. We offer platform and access to the resources for multiple programs: research projects, seminars, conferences, awareness camps, relief works and public policies etc. She is also a member of various international organisations that focus on plant adaptations and climate change and has presented at international forums. She was awarded Doctorate Merit scholarship by University of Kashmir to pursue the Ph.D program.

Affiliations and expertise

Department of Ecology and Remote Sensing, Government of India, India

Munagala S. Reddy

Dr. Reddy, Department of Entomology & Plant Pathology, Auburn University, USA. holds a Ph. D. in Integrated Pest Management with a specialization in Biological Control and PGPR from the Department of Biological Sciences, Simon Fraser University. He completed Post Doctoral training in the Department of Botany at the University of Toronto,. He worked as a Senior Scientist and R & D Global Manager for industries such as ExxonMobil, Agrium, Cominco fertilizers, Allelix etc. conducting multi-disciplinary, comprehensive research in the area of biological control of soil-borne diseases, IPM, biofertilizers & biofungicides (PGPR), induced systemic resistance, organic agriculture. He collaborated on several commercial biofertilizers and biofungicides for sustainable agriculture. He has published extensively and participated in successfully organizing International PGPR Workshops, and established a non-profit Asian PGPR Society of Sustainable Agriculture to enable various agricultural disciplines to meet regularly in Asian Countries and discuss teaching, research and commercialization of PGPR’s.

Affiliations and expertise

Auburn University Asian PGPR Society of Sustainable Agriculture, USA

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Patterns, Function and Application of Seed Microbiome

Bacteria, Fungi and Viruses

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Mohammad Yaseen Mir

Javid A. Parray

Saima Hamid

Munagala S. Reddy

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