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This book reviews the history and development of rhizobial ecology (diversity, function and interactions with the biotic and abiotic environments), evolution (genome diversification, systematics of symbiotic genes) and application. Further, it describes the new concept of rhizobia, the latest systematic methods, biogeographic study methods, and genomic studies to identify the interactions between rhizobia, legumes and environments. To enable readers to gain a comprehensive understanding of rhizobial biogeography, the book provides effective protocols for the selection and application of high-efficiency rhizobial inoculants. In addition, it presents standard and modern methods used in studies on rhizobial ecology and evolution in dedicated appendices, making it a unique and valuable handbook for researchers.

Ecology and Evolution of Rhizobia: Principles and Applications

Preface

Wen Xin Chen

Unit 1. General description of rhizobia

En Tao Wang

Chapter 1. Symbiosis between rhizobia and legumes

Section 1. Symbiosis of rhizobia and legumes

Rhizobia

Rhizobia-legume symbiosis

Section 2. Importance of rhizobia and rhizobial research

History of rhizobial studies

Ecological and economic importance of rhizobia

Model of microbe-plant interaction

Concluding remarks and perspectives

References

Unit 2. Diversity and evolution of rhizobia

En Tao Wang, Chang Fu Tian, and J. Peter W. Young

Chapter 2. History of rhizobial taxonomy

Section 1. Bacterial diversity and taxonomy

Classification, identification and nomenclature.

Section 2. History of studies on rhizobial diversity and taxonomy

Cross-nodulation groups

Numerical taxonomy

DNA/DNA hybridization

Polyphasic taxonomy

Chapter 3. Current Systematics of rhizobia

Section 1. Current methodology for studying diversity and taxonomy

Sampling strategies: how many strains to sample

Recommended genes for studying phylogeny and genomic diversity

Current criteria for identification and description of novel species

Section 2. Phylogeny and systematics of rhizobia.

Section 3. Alpha-rhizobia.

Section 4. Beta-rhizobia.

Chapter 4. Genomics and evolution of rhizobia

Section 1. The general organization of rhizobial genomes.

Replicons: chromosome, chromid, and plasmid.

Symbiosis plasmid and symbiosis island.

Section 2. Evolution of core and accessory genes.

Characteristics of core and accessory genes.

Main evolutionary forces shaping the diversity of core and accessory genes.

Concluding remarks and perspectives

References

Unit 3. Diversity and evolution of rhizobial symbiosis genes

Chang Fu Tian, Wen Feng Chen, and J. Peter W. Young

Chapter 5. Symbiosis genes: diversity and organization

Section 1. Pathways of diverse functions involved in symbiosis.

Key symbiosis genes: nodulation and nitrogen fixation genes, nod-independent rhizobia.

Symbiosis related functions: exopolysaccharides, secretion systems, and others.

Section 2. The organization of symbiosis related genes.

The distribution of symbiosis related genes in rhizobial genomes.

Chapter 6. Evolution of symbiosis genes: Vertical and horizontal gene transfer

Section 1. Interaction between the symbiosis genes and the core genome

Section 2. Horizontal transfer of symbiosis genes and their integration into the core genome

Chapter 7. Diversity of interactions between rhizobia and legumes

Section 1. Rhizobia with wide host ranges.

NGR 234, etc.

Section 2. Rhizobia associated with symbiotically specific plants.

Alfalfa, chickpea, Amorpha, etc.

Section 3. Rhizobia associated with promiscuous plants.

Soybean, Sophora, common bean, peanut.

Section 4. Rhizobial infection through root hair or crack.

Section 5. Determinate or indeterminate root nodules.

Section 6. Swollen or non-swollen bacteroids.

Concluding remarks and perspectives

References

Unit 4. Interaction of rhizobia, environments and legumes

Wen Feng Chen, and Chang Fu Tian

Chapter 8. Geographical distribution of rhizobia

Section 1. Biogeography of rhizobial species.

Specific focus on soybean, Caragana, Astragalus, broad bean, peanut, Sophora, Phaseolus vulgaris.

Section 2. Biogeography of rhizobial populations

Alfalfa rhizobia, soybean rhizobia

Chapter 9. Environmental determinants of biogeography of rhizobia

Section 1. Soil factors affecting the distribution of rhizobia.

soybean rhizobia, and Astragalus rhizobia.

Section 2. Effects of agricultural practices on distribution of rhizobia.

wild vs. cultivated legumes.

Chapter 10. Effects of host plants on biogeography of rhizobia

Section 1. Geographic distribution of legumes and rhizobia.                

Section 2. Effects of legume cultivars on rhizobial population

Chapter 11. Rhizobial genomics and biogeography

Section 1. Core genes and adaptation genes of rhizobia

Section 2. Genes related to the biogeography of rhizobia

Concluding remarks and perspectives

References

Unit 5. Agricultural applications of rhizobia and other PGPR

Wen Feng Chen

Chapter 12. Current status of rhizobial inoculants

The using of rhizobia in USA, Brazil, Argentina, Australia, China.<

Chapter 13. Screening for effective rhizobia

Section 1. Strategy to screen for effective rhizobia

Consider the environments, leguminous cultivar, levels and concentration of chemical nitrogen fertilization.

Section 2. Suggested rhizobia used for inoculants for legumes.

Section 3. Usage of microelements to enhance nitrogen fixation

Microelements, Mo, Be, Fe, fulvic acid, Nod factors.

Chapter 14. Usage of rhizobial inoculants in agriculture

Section1. Inoculating methods.

Section 2. Intercropping and crop rotation between legumes, and other measures to enhance nitrogen fixation.

Section 3. Inoculation of soybean, peanut, alfalfa, medicinal legumes.

Section 4. Combination of rhizobia with PGPR

Chapter 15. Rhizobial activity beyond nitrogen fixation

Plant growth promoting, endophytic rhizobia

Concluding remarks and perspectives

References

Unit 6 Technology and methods

En Tao Wang, Chang Fu Tian, and Wen Feng Chen

Chapter 16. Working on the taxonomy, biodiversity, ecology and evolution of rhizobia

Section 1. Sampling, isolation, purification, observation, preservation of them, Gram-staining, light and electron microscopy should be included.

Section 2. Phenotypic characterization

Application of Biolog system and determination of other features

Nitrogenase activity determination

Chlorophyll determination

Nodulation tests and proposed cross-nodulation group

Section 3. Chemical characterization

Chemical taxonomy: fatty acid methyl ester profile, quinone determination

Section 4. Genetics-based methods

DNA fingerprinting (BOX-A1R, ERIC)

MLSA (candidate genes: 16S rRNA gene, rpoB, recA, ..., nodC, nifH; evolutionary genetics statistics for mutation, recombination, and genetic differentiation), Blastn

Genomics (Phylogenomics, ANI, core genes and accessory genes)

Section 5. Ecological methods

The relationship between rhizobial distribution and environmental factors (PCA, CA, etc.).

Diversity index.

High-throughput amplicon sequencing analysis (16S rRNA gene, rpoB, nodC or nodD, nifH) in soil

Concluding remarks and perspectives

References

 

Index

Acknowledgments