Table of Contents
Cover
Title Page
Copyright
Dedication
Preface
References
Acknowledgments
Contributors
Volume 1
Chapter 1: Introduction
1.1 Free-Living Diazotrophs
1.2 Symbiotic Nitrogen-Fixing Bacteria
1.3 Associative Nitrogen-Fixing Bacteria
1.4 Outline of This Book
References
Section 1: Focus Chapters
Chapter 2: Recent Advances in Understanding Nitrogenases and How They Work
2.1 Introduction: Two Types of Nitrogenases Exist
2.2 Occurrence and Relationships among the Group-1 Nitrogenases
2.3 Overview of Properties of Mo-Nitrogenase
2.4 Overview of Properties of V-Nitrogenase and Fe-Nitrogenase
2.5 Structures of the Nitrogenase Component Proteins and their Complexes
2.6 Structures of the MoFe-Protein Prosthetic Groups
2.7 How are Substrates Reduced?
2.8 Where are the Binding Sites for Substrates and Inhibitors?
2.9 How are Electrons and Protons Delivered?
2.10 Some Concluding Remarks
References
Chapter 3: Evolution and Taxonomy of Nitrogen-Fixing Organisms with Emphasis on Rhizobia
3.1 Introduction
3.2 Materials and Methods
3.3 Results
3.4 Discussion
Note
Acknowledgments
References
Chapter 4: Evolution of Rhizobium Nodulation: From Nodule-Specific Genes (Nodulins) to Recruitment of Common Processes
4.1 Nodule Formation in a Nutshell
4.2 Signaling in Symbiosis
4.3 The Indeterminate Nodule
4.4 Signaling Inside the Nodule
4.5
Rhizobium
Symbiosis in
Parasponia
4.6 Actinorhizal N-Fixing Symbiosis
4.7 Arbuscular Mycorrhizal Symbiosis
4.8 Interactions with (Biotrophic) Pathogens
4.9 The Evolution of the
Rhizobium
Nodule Symbiosis
References
Chapter 5: Bioengineering Nitrogen Acquisition in Rice: Promises for Global Food Security
5.1 Introduction
5.2 Primary Nitrogen Uptake and Nitrogen-Use Efficiency: Gene Candidates and Caveats
5.3 The Carbon–Nitrogen Interface and N-Transfer: Removing Enzymatic Bottlenecks
5.4 Nitrogen Fixation: The Holy Grail
5.5 Concluding Remarks
References
Section 2: Chemistry and Biochemistry of Nitrogenases
Chapter 6: An Overview on Fe–S Protein Biogenesis from Prokaryotes to Eukaryotes
6.1 Introduction
6.2 Source of Iron and Sulfur
6.3 Structures and Properties of Fe–S Clusters
6.4 Formation of Fe–S CLUSTERS
6.5 Diverse Functionsof Fe–S Proteins
6.6 Fe–S Cluster Biosynthesis in Prokaryotes
6.7 ISC Assembly Machinery
6.8 The SUF Machinery in Bacteria and Plastids
6.9 F–S Protein Assembly in Eukaryotes
6.10 Mitochondrial Isc Assembly Machinery
6.11 Mitochondrial ISC Export System
6.12 CIA Assembly Apparatus
6.13 Conclusion
Acknowledgments
References
Chapter 7: Biosynthesis of the Iron-Molybdenum Cofactor of Nitrogenase
7.1 Introduction: Dinitrogenase and APO-Dinitrogenase
7.2 NifU and NifS
7.3 NifB: From Simple [Fe–S] Clusters to the Core of FeMo-co
7.4 NifQ: Directing Mo to FeMo-co Synthesis
7.5 NifV and the Incorporation of Homocitrate into FeMo-co
7.6 NifEN: A Node in the FeMo-co Biosynthetic Pathway
7.7 NifH: Nitrogenase Moonlighting Protein
7.8 Metallocluster Carrier (Escort) Proteins
7.9 Conclusion
Acknowledgments
References
Chapter 8: Distribution and Ecological Niches of Nitrogenases
8.1 Introduction
8.2 Alternate Nitrogenases and the Metal Content of the Cofactor
8.3 Distinguishing FeFe-Nitrogenase from VFe-Nitrogenase
8.4 Why Three Nitrogenases?
8.5 Rhodopseudomonas palustris CGA009 and Closely Related Strains
8.6 Control of Expression of Nitrogenase
8.7 Global Diversity of Nitrogen-Fixing Organisms
8.8 Isolation of Diazotrophs Containing Mo-Independent Nitrogenases
8.9 Coincidentally Discovered Novel Genera and Species with Alternate Nitrogenases
8.10 Estimates of Current Global Nitrogen Fixation
8.11 Concluding Remarks
References
Section 3: Expression and Regulation of Nitrogen Fixation Genes and Nitrogenase
Chapter 9: Regulation of nif Gene Expression in Azotobacter vinelandii
9.1 Introduction:
Azotobacter vinelandii
as Paradigm of Nitrogen-Fixing Bacteria
9.2 Methodologies Used to Study Regulation of
nif
Gene Expression in
A. vinelandii
9.3
nif
Genes
9.4 The NifA-NifL-GlnK System: A Dynamic Signal Integrating System that Modulates
nif
Gene Expression
9.5 Perspectives
Acknowledgments
References
Chapter 10: Regulatory Coupling of Nitrogen and Carbon Metabolism in Nitrogen-Fixing Pseudomonas stutzeri A1501
10.1 Introduction
10.2 Global Regulatory Networks Controlling Nitrogen Fixation And Nitrogen Source Utilization in Diazotrophic Proteobacteria
10.3 The Nitrogen Regulatory Cascade in
P. stutzeri
A1501
10.4 Catabolite Repression of Carbon Sources Utilization in
Pseudomonas
10.5 Catabolite Repression Control: Properties of A
crc
Mutant Strain of
P. stutzeri
A1501
10.6 Catabolite Repression Control: Transcriptome Analysis
10.7 Catabolite Repression: The CbrA–CbrB System IN
P. stutzeri
A1501
10.8 CbrAB and NtrBC Overlapping Functions in
P. stutzeri
A1501
10.9 Small Regulatory Noncoding RNAs
10.10 Identification of ncRNA in the Genome of
P. stutzeri
A1501
10.11 Concluding Remarks
Acknowledgments
References
Chapter 11: Regulation of Nitrogen Fixation and Molybdenum Transport in Rhodobacter capsulatus
11.1 Introduction
11.2 Transcriptional Activation of Nitrogen Fixation Genes
11.3 Ammonium Inhibition of Nitrogen Fixation
11.4 Molybdenum Repression of Fe-Nitrogenase and Mo Transport
Acknowledgments
References
Chapter 12: Metabolic Regulation of Nitrogenase Activity in Rhodospirillum rubrum: The Role of PII Proteins and Membrane Sequestration
12.1 Introduction
12.2 The “Switch-Off” Effect at the Molecular Level
12.3 The DraT and DraG Proteins
12.4 Regulation of DraT and DraG Activities
12.5 DraT and DraG in Other Organisms
12.6 Concluding Remarks
Acknowledgment
References
Chapter 13: How Does the DraG–PII Complex Regulate Nitrogenase Activity in Azospirillum brasilense?
13.1 Introduction
13.2 Reversible ADP-Ribosylation Regulates Nitrogenase Activity in
A. brasilense
at a Posttranslational Level
13.3 P
II
Proteins Regulate DraT and DraG Activity
13.4 Conclusions
Acknowledgments
References
Chapter 14: Fe Protein Overexpression Can Enhance the Nitrogenase Activity of Azotobacter vinelandii
14.1 Introduction
14.2 Methods
14.3 Results
14.4 Discussion
14.5 Conclusion
Acknowledgments
References
Chapter 15: FNR-Like Proteins in Rhizobia: Past and Future
15.1 Introduction
15.2 Regulation of the
R. etli fix
Genes: An Overview
15.3 Novel Elements in the Regulatory Cascade of
fix
Genes in
Rhizobium etli
15.4 NnrR Links the Low-Oxygen and N-Oxide Response in
Rhizobium etli
15.5 Conserved Functional Features in FNR-Related Proteins of
R. etli
15.6 Prediction of DNA-Binding Specificity Using Three-Dimensional Models of FNR-Related Proteins of
R. etli
15.7 Prediction of FNR-Related Targets in the Genome of
R. etli
CFN42
15.8 Concluding Remarks
Acknowledgments
References
Section 4: Taxonomy and Evolution of Nitrogen Fixing Organisms
Chapter 16: Exploring Alternative Paths for the Evolution of Biological Nitrogen Fixation
16.1 Introduction
16.2 How Ancient isBiological Nitrogen Fixation?
16.3 What are the Most Deeply Rooted Organisms that Harbor Nitrogenase and Presumably Fix Nitrogen?
16.4 Are Alternative Nitrogenases Evolutionary Ancestors of Mo-Nitrogenase?
16.5 What is the Nature of the Metal Complement of “Uncharacterized Nitrogenases”?
16.6 Is There an Evolutionary Relevance to Nitrogenase Promiscuity?
16.7 What is the Evolutionary Origin of Nitrogenase?
Acknowledgments
References
Chapter 17: Phylogeny, Diversity, Geographical Distribution, and Host Range of Legume-Nodulating Betaproteobacteria: What Is the Role of Plant Taxonomy?
17.1 Introduction
17.2 Burkholderias are Highly Diversified Symbionts of Legumes
17.3 Origin and Diversity of
Cupriavidus
Legume Symbionts
17.4 New Rhizobial Taxa in the Beta and Gamma Subclasses of Proteobacteria?
17.5 Has
Mimosa
Coevolved with Its Symbionts?
17.6 Is There Evidence of Coevolution Between Legumes in the Tribe Mimoseae and Their
Burkholderia
Symbionts?
17.7 Conclusion
Acknowledgments
References
Chapter 18: Bradyrhizobium, the Ancestor of All Rhizobia: Phylogeny of Housekeeping and Nitrogen-Fixation Genes
18.1 Introduction
18.2 State of The Art of The Genus
Bradyrhizobium
18.3 Described Species of
Bradyrhizobium
18.4 Phylogeny Based on The Analysis of Ribosomal Genes
18.5 The Use of The Multilocus Sequence Analysis (MLSA) Approach to Define Taxonomy and Phylogeny of
Bradyrhizobium
18.6 Phylogeny of Nodulation and Nitrogen-Fixation Genes in
Bradyrhizobium
18.7 Concluding Remarks
Acknowledgments
References
Chapter 19: Interaction between Host and Rhizobial Strains: Affinities and Coevolution
19.1 Introduction
19.2 Nod Factor Recognition
19.3 Mechanisms Using Plant Immune Responses
19.4 The Symbiotic Interaction of
Phaseolus vulgaris
in the Regions of Host Diversification
19.5 The Need of Factors Other Nod Factor for Specificity in Nodulation
19.6 Conclusions
Acknowledgments
References
Chapter 20: Assessment of Nitrogenase Diversity in the Environment
20.1 Introduction
20.2 Databases Available for
nifH
20.3 Description of the
nifH
Database
20.4 Defining
nifH
Diversity
20.5 Phylogenetic Diversity
20.6 Environmental Diversity
20.7
nifH
Primer Assessment
20.8 Conclusions
Acknowledgments
References
Section 5: Genomics of Nitrogen Fixing Organisms
Chapter 21: Genetic Regulation of Symbiosis Island Transfer in Mesorhizobium loti
21.1 Discovery and Field Transfer of the
Mesorhizobium loti
Symbiosis Island
21.2 Integration and Excision of the Symbiosis Island
21.3 Symbiosis Island Transfer is Regulated by Quorum Sensing
21.4 Quorum Sensing Induces a Novel Activator of Symbiosis Island Excision and Transfer
21.5 The qs Circuit is Controlled by an Antiactivator
21.6 A Molecular Switch Controls the Production of the Antiactivator
21.7 Concluding Remarks
References
Chapter 22: The Azotobacter vinelandii Genome: An Update
22.1 Introduction
22.2 Materials and Methods
22.3 Results and Discussion
22.4 Conclusion
Acknowledgments
References
Chapter 23: The Genome Sequence of the Novel Rhizobial Species Microvirga lotononidis Strain WSM3557T
23.1 Introduction
23.2 Methods
23.3 Results and Discussion
23.4 Conclusions
Acknowledgments
References
Chapter 24: Genome Characteristics of Frankia sp. Reflect Host Range and Host Plant Biogeography
24.1 Introduction
24.2 Genomes Obtained and Underway
24.3 Link with Host Range
24.4 Conclusion
Acknowledgments
References
Chapter 25: Core and Accessory Genomes of the Diazotroph Azospirillum
25.1 Introduction
25.2 Concluding Remarks
Acknowledgments
References
Chapter 26: Pangenome Evolution in the Symbiotic Nitrogen Fixer Sinorhizobium meliloti
26.1 Introduction
26.2 The Open Pangenome of
S.meliloti
Agrees with the Species Lifestyle
26.3 Replicon Diversity: The Chromid has an Important Role in Intraspecies Differentiation
26.4 Ancient Versus Recent: Different Timing of HGT Events
26.5 Replicon-Specific Features of the
S
.
meliloti
Pangenome
26.6 Conclusions and Future Perspectives
References
Chapter 27: Pangenomic Analysis of the Rhizobiales Using the GET_HOMOLOGUES Software Package
27.1 Introduction
27.2 Methods
27.3 Results and Discussion
27.4 Conclusions and Perspectives
Acknowledgments
References
Section 6: Physiology and Metabolism of Nitrogen Fixing Organisms
Chapter 28: Metabolism of Photosynthetic Bradyrhizobia during Root and Stem Symbiosis with Aeschynomene Legumes
28.1 Introduction
28.2 Photosynthesis and Symbiosis
28.3 The Calvin Cycle and Symbiosis
28.4 Additional Aspects of Bacteroid Central Metabolism
28.5 Plant Control of Bacteroid Morphotypes
28.6 Conclusions
Acknowledgments
References
Chapter 29: A Plethora of Terminal Oxidases and Their Biogenesis Factors in Bradyrhizobium japonicum
29.1 Introduction
29.2 The Diversity of Terminal Oxidases in
B. japonicum
29.3 The Heme-copper Oxidases
29.4 Two Cytochrome
bd
-Family Members
29.5 Factors Involved in the Biogenesis of Cytochromes
aa
3
and
cbb
3
29.6 Future Perspectives
Acknowledgments
References
Chapter 30: Rhizobial Extracytoplasmic Function (ECF) σ Factors and Their Role in Oxidative Stress Response of Bradyrhizobium japonicum
30.1 Gene Regulation Mediated by σ Factors
30.2 Diversity and Common Features of ECF σ Factors
30.3 σ Factors in Rhizobia
30.4 Diversity and Sources of Reactive Oxygen Species (ROS)
30.5 ROS in the
Rhizobium
–Legume Symbiosis
30.6 ROS Detoxification in the
Rhizobium
–Legume Symbiosis
30.7 Reactive Oxygen Species (ROS)-Inducible ECF σ Factors of
Bradyrhizobium japonicum
30.8 Paralogs and Orthologs of EcfF and EcfQ
Acknowledgments
References
Chapter 31: Role of the Bacterial BacA ABC-Transporter in Chronic Infection of Nodule Cells by Rhizobium Bacteria
31.1 Introduction
31.2
BacA
is Required in Legumes Forming E- or S-morphotype Bacteroids But Not in Other Legumes
31.3
BacA
Provides Protection Against NCR Peptides
in vitro
and in Nodules
31.4
BacA
Homologs are Required in Pathogens for Chronic Infection
31.5 BacA is an ABC Transporter. But what Does it Transport?
31.6 General Envelope Stress Response Function of BacA/SbmA?
31.7 Conclusion
Acknowledgments
References
Chapter 32: Molecular Keys to Broad Host Range in Sinorhizobium fredii NGR234, USDA257, and HH103
32.1 Introduction
32.2 Key Traits of the Alphaproteobacteria
Sinorhizobium fredii
NGR234, USDA257, AND HH103
32.3 Molecular Keys to Broad Host Range in
S. fredii
NGR234, USDA257, and HH013
Acknowledgments
References
Chapter 33: Motility and Chemotaxis in the Rhizobia
33.1 Introduction
33.2 The Enteric Model System of Chemotaxis and Motility
33.3 Flagellation and Flagellar Rotation in Rhizobia
33.4 Flagellar Genes and Their Genetic Organization in Rhizobia
33.5 Characterization of Rhizobial Flagellins
33.6 Chemotaxis
33.7 Regulation of Chemotaxis and Motility Genes
References
Chapter 34: The PTSNtr System Globally Regulates ATP-Dependent Transporters in Rhizobium leguminosarum
34.1 Introduction
34.2 Results and Discussion
34.3 Conclusions
Glossary
References
Section 7: Nitrogen Fixing Organisms, the Plant Rhizosphere and Stress Tolerance
Chapter 35: Actinorhizal Plant Root Exudates Alter the Physiology, Surface Properties, and Plant Infectivity of Frankia
35.1 Introduction
35.2 Materials and Methods
35.3 Results and Discussion
Acknowledgments
References
Chapter 36: Exopolysaccharide Production in Rhizobia Is Regulated by Environmental Factors
Introduction
36.1 Chemical Structures of Rhizobial Exopolysaccharides
36.2 Genetic Control of EPS Synthesis
36.3 Regulation of EPS Synthesis in Rhizobia
36.4 Conclusions
Acknowledgment
References
Chapter 37: Regulation of Symbiotically Important Functions by Quorum Sensing in the Sinorhizobium meliloti–Alfalfa Interaction
37.1 Introduction
37.2 Quorum Sensing In Gram-Negative Bacteria
37.3 The ExpR/Sin Quorum-Sensing System In
Sinorhizobium meliloti
37.4 The Tra Quorum-Sensing System in
Sinorhizobium meliloti
37.5 Other LuxR Homologs in
S. meliloti
37.6 Conclusion
Acknowledgments
References
Chapter 38: Lumichrome: A Bacterial Signal Molecule Influencing Plant Growth
38.1 Introduction
38.2 Components of Rhizobial Exudates and Their Effects on Plants
38.3 Lumichrome: A Rhizobial Signal Molecule Involved in Plant Development
38.4 Effect of Lumichrome on Plant Growth and Productivity
38.5 Effect of Environmental Factors on the Synthesis and Release of Lumichrome by Rhizobia and Nodule Endophytes
38.6 Ecological Significance of Rhizobial Exudation of Lumichrome and Riboflavin in the Rhizosphere
38.7 Conclusion
Acknowledgments
References
Chapter 39: Genes Involved in Desiccation Resistance of Rhizobia and Other Bacteria
39.1 Introduction
39.2 Desiccation of Rhizobia
39.3 Desiccation Resistance Genes in Nonrhizobia
39.4 Desiccation Resistance Genes in Rhizobia
39.5 Summary
References
Chapter 40: The General Stress Response in Alpha-Rhizobia
40.1 Introduction
40.2 σ
EcfG
, the Major Regulator of the General Stress Response
40.3 Functions of the σ
EcfG
-Dependent General Stress Response
40.4 Conclusions and Future Prospects
Acknowledgments
References
Section 8: Physiology and Regulation of Nodulation
Chapter 41: The Root Hair: A Single Cell Model for Systems Biology
41.1 Introduction
41.2 The Root Hair Symbiotic Pathway
41.3 Systems Biology Approach to Elucidate the Molecular Response of Root Hair Cells in Response to Rhizobia
41.4 Transcriptomic Approach to Unravel the Complexity of the Root Hair Cell Response to Rhizobia
41.5 Characterization of the Soybean Root Hair Proteome, Phosphoproteome, and Metabolome
41.6 Upcoming Challenges in Root Hair Cell Systems Biology
References
Chapter 42: How Transcriptomics Revealed New Information on Actinorhizal Symbioses Establishment and Evolution
42.1 Introduction
42.2 Conclusion and Future Directions
Acknowledgments
References
Chapter 43: Molecular Biology of Infection and Nodule Development in Discaria trinervis–Frankia Actinorhizal Symbiosis
43.1 Introduction
43.2 Conclusion
Acknowledgments
References
Chapter 44: Lotus japonicus Nodulates When It Sees Red
44.1 Introduction
44.2 Results and Discussion
References
Chapter 45: Out of Water of a New Model Legume: The Nod-independent Aeschynomene evenia
45.1 Introduction
45.2 Conclusions
Acknowledgments
References
Chapter 46: Phosphorus Use Efficiency for N2 Fixation in the Rhizobial Symbiosis with Legumes
46.1 Introduction
46.2 Methods
46.3 Results and Discussion
46.4 Conclusion
References
Chapter 47: Regulation of Nodule Development by Short- and Long-Distance Auxin Transport Control
47.1 Introduction
47.2 Conclusions and Perspectives
Acknowledgments
References
Chapter 48: Functional Analysis of Nitrogen-Fixing Root Nodule Symbioses Induced by Frankia: Transport and Metabolic Interactions
48.1 Introduction
48.2 Conclusions
Acknowledgments
References
Chapter 49: NOOT-Dependent Control of Nodule Identity: Nodule Homeosis and Merirostem Perturbation
49.1 Introduction
49.2 The Nodule Root Originates from Nodule Vasculature
49.3 Is NOOT Necessary to Delimit Domains in the Symbiotic Organ?
49.4 NOOT-Like Structures can be Triggered by Environment or Mutant Rhizobia
49.5 Are NOOT and COCH Involved in Nodule Immunity?
49.6 Conclusions
49.7 Perspectives
Acknowledgments
References
Volume 2
Section 9: Recognition in Nodulation
Chapter 50: Flavonoids Play Multiple Roles in Symbiotic Root–Rhizosphere Interactions
50.1 Introduction
50.2 Roles for Flavonoids in the
Rhizobium
-Legume Symbiosis
50.3 Flavonoids are Involved in Actinorhizal Symbioses
50.4 Flavonoids Enhance Plant Interactions with Free-Living Nitrogen-Fixing Bacteria
50.5 Roles for Flavonoids in Mycorrhizal Symbioses
50.6 Outlook
Acknowledgments
References
Chapter 51: Nod Factor Recognition in Medicago truncatula
51.1 Introduction
51.2 NFP, a Protein with Multiple Biological Functions
51.3 Nod Factor Binding Sites are Independent of NFP
51.4 The LysM-RLK LYR3: A New Player in Nod Factor Perception?
51.5 Conclusion
Acknowledgments
References
Chapter 52: Role of Ectoapyrases in Nodulation
52.1 Apyrase
52.2 Ectoapyrase Plays an Important Role in Nodulation
52.3 Possible Functions of Ectoapyrase in Nodulation Signaling
52.4 Future Perspectives
Acknowledgments
References
Chapter 53: Role of Rhizobium Cellulase CelC2 in Host Root Colonization and Infection
53.1 Introduction
53.2 Methods
53.3 Results and Discussion
53.4 Conclusions
Acknowledgments
References
Chapter 54: Nod Factor-Induced Calcium Signaling in Legumes
54.1 Introduction
54.2 Calcium Spiking
54.3 Secondary Messengers: Linking NF Recognition at the Plasma Membrane with Nuclear Calcium Spiking
54.4 Encoding Calcium Spiking: The Nuclear Envelope Machinery
54.5 Modeling Calcium Spiking
54.6 Decoding Calcium Spiking in the Nucleus
54.7 Do Calcium Spiking Signatures Encode Specificity between Nodulation and Mycorrhization?
54.8 The Calcium Influx
54.9 A Role for the Apyrase LNP in NF-Induced Calcium Signaling
54.10 The Calcium Influx is Spatially and Temporally Coincident with Other NF Responses
54.11 Calcium Signaling in Root Hairs: Lessons from Apical Growth
54.12 Concluding Remarks
References
Chapter 55: Signaling and Communication between Actinorhizal Plants and Frankia during the Intracellular Symbiotic Process
55.1 Introduction
55.2 The Presymbiotic Dialog
55.3 Plant Response to
Frankia
in the Intracellular Pathway
55.4 Plant Genes Expressed in
Frankia
-Infected Cells
55.5 Conclusions
Acknowledgments
References
Section 10: Infection and Nodule Ontogeny
Chapter 56: The Role of Hormones in Rhizobial Infection
56.1 Introduction
56.2 Strigolactones are Phytohormones and Plant-Microbe Signals
56.3 Strigolactones in Nodulation
56.4 Jasmonic Acid Acts as a Plant Hormone and a Long Distance Signal for Rhizobia
56.5 A Role in Signaling to Rhizobia
56.6 JA Inhibits NF-Signaling
56.7 JA Has a Role in the Autoregulation of Nodulation
56.8 Auxin's Role in Nodulation
56.9 Auxin and Rhizobial Infection
56.10 The Role of Gibberellins in Nodulation
56.11 GA is Needed for Nodulation Involving Crack Entry
56.12 Future Directions
References
Chapter 57: Nuclear Ca2+ Signaling Reveals Active Bacterial-Host Communication Throughout Rhizobial Infection in Root Hairs of Medicago truncatula
57.1 Introduction
57.2 Methods
57.3 Results
57.4 Discussion
Acknowledgments
References
Chapter 58: A Pectate Lyase Required for Plant Cell-Wall Remodeling During Infection of Legumes by Rhizobia
58.1 Introduction
58.2 Cell Wall Components
58.3 Infection Thread Initiation
58.4 Rhizobial Enzymes that Degrade Plant Cell Walls
Acknowledgments
References
Chapter 59: Dissecting the Roles in Outer and Inner Root Cell Layers of Plant Genes That Control Rhizobial Infection and Nodule Organogenesis
59.1 Introduction
59.2 Rhizobial Infection and Nodule Organogenesis are Coordinated Processes Occurring in Different Cell Layers of the Root
59.3 The Nod Factor Signaling Pathway
59.4 How The Epidermal Infection Process is Controlled by Nod Factor Signaling Genes
59.5 How the Cortical Programme of Nodule Organogenesis is Controlled by Nod Factor Signaling Genes
59.6 Conclusion
Acknowledgments
References
Chapter 60: The Medicago truncatula NIP/LATD Transporter Is Essential for Nodulation and Appropriate Root Architecture
60.1 Introduction
60.2
Mtnip/latd
Mutants' Phenotypes
60.3 MtNIP/LATD Protein, A Member of the NRT1(PTR) Transporter Family
60.4 MtNIP/LATD Biochemical Function(s)
60.5 Summary and Perspectives
Acknowledgments
References
Chapter 61: A MYB Transcription Factor Interacts with NSP2 and Is Involved in Nodulation in Lotus japonicus
61.1 Introduction
61.2 Methods
61.3 Results
61.4 Discussion
Acknowledgments
References
Chapter 62: AP2/ERF Transcription Factors and Root Nodulation
62.1 Introduction
62.2 The AP2/ERF Family in Plants
62.3 A Diverse Number of ERF TFs are Expressed in
M. truncatula
Nodules
62.4 Concluding Remarks
Acknowledgments
References
Chapter 63: Identification of Medicago truncatula Genes Required for Rhizobial Invasion and Bacteroid Differentiation
63.1 Introduction
63.2 Materials and Methods
63.3 Results
63.4 Discussion
Acknowledgments
References
Chapter 64: Multifaceted Roles of Nitric Oxide in Legume–Rhizobium Symbioses
64.1 Introduction
64.2 NO: Positive/Signaling Roles on Symbiosis Establishment and Nodule Functioning
64.3 NO Level in Legume Nodules: A Matter of Balance
64.4 Concluding Remarks and Future Prospects
Acknowledgments
References
Chapter 65: Profiling Symbiotic Responses of Sinorhizobium fredii Strain NGR234 with RNA-Seq
65.1 Introduction
65.2 Methods
65.3 Results and Discussion
Acknowledgments
References
Chapter 66: Computational and Experimental Evidence That Auxin Accumulation in Nodule and Lateral Root Primordia Occurs by Different Mechanisms
66.1 Introduction
66.2 Methods
66.3 Results and Discussion
66.4 Conclusion and Outlook
Acknowledgments
References
Section 11: Transitions from the Bacterial to the Bacteroid State
Chapter 67: Bacteroid Differentiation in Legume Nodules: Role of AMP-Like Host Peptides in the Control of the Endosymbiont
67.1 Introduction
67.2 Two Nodule Types with Common Features of Symbiotic Host Cells and Different Fate of Endosymbionts
67.3 Identification of Key Plant Factors Mediating Terminal Bacteroid Differentiation
67.4 Gene Expression Analysis of NCRs
67.5 Possible Functions and Targets of NCRs
67.6 Antimicrobial Peptides in Other Symbiotic Systems
Acknowledgments
References
Chapter 68: The Symbiosome Membrane
68.1 Symbiosome Formation and Development
68.2 Transport Activity of the Symbiosome Membrane
68.3 Conclusion and Future Work
References
Section 12: Nitrogen Fixation, Assimilation, and Senescence in Nodules
Chapter 69: Nodulin Intrinsic Proteins: Facilitators of Water and Ammonia Transport across the Symbiosome Membrane
69.1 Introduction
69.2 The NIP Subfamily: Plant-Specific Channels of the Aquaporin Superfamily
69.3 Symbiosome Membrane Nodulin 26: Transport Properties
69.4 Efflux of Fixed Nitrogen from the Symbiosome
69.5 Nodulin 26, Glutamine Synthetases, and Ammonia Assimilation
69.6 Summary
Acknowledgments
References
Chapter 70: Leghemoglobins with Nitrated Hemes in Legume Root Nodules
70.1 Introduction
70.2 Methods
70.3 Results
70.4 Discussion
Acknowledgments
References
Chapter 71: The Role of 1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase Enzyme in Leguminous Nodule Senescence
71.1 Introduction
71.2 Nodule Senescence
71.3 Ethylene Stress and ACC Deaminase Enzyme Activity in Symbiosis and Nodule Senescence
71.4 Conclusion
References
Section 13: Microbial “Omics”
Chapter 72: Pool-Seq Analysis of Microsymbiont Selection by the Legume Plant Host
72.1 Introduction
72.2 Genomics of Rhizobia
72.3 Metagenomics
72.4 Soil Metagenomics and the Rhizobia
72.5 The Pool-Seq Approach to Study Rhizobial Populations
72.6 Operation of the Pool-Seq Data Analysis Pipeline
72.7 A Cautionary Note on Metagenomic Analysis of Pool-Seq Data
72.8 Discussion: Pros and Cons of Pool-Seq Analysis for the Study of Rhizobial Populations
Acknowledgments
References
Chapter 73: Contribution of the RNA Chaperone Hfq to Environmental Fitness and Symbiosis in Sinorhizobium meliloti
73.1 Introduction
73.2 The
S. meliloti
Hfq Protein
73.3 Deletion of
hfq
Results into a Pleiotropic Free-Living and Symbiotic Phenotype
73.4 A Large Regulon Explains the Phenotypic Pleiotropy of the
S. meliloti hfq
Mutants
73.5 Hfq Contributes to the Control of Symbiotic Nitrogen Fixation
73.6 Hfq and Riboregulation in
S. meliloti
Acknowledgments
References
Chapter 74: Biodiversity, Symbiotic Efficiency, and Genomics of Rhizobium tropici and Related Species
74.1 Introduction
74.2 Phylogeny and Taxonomy of
R
.
tropici
74.3 Origin and Geographic Distribution of
R. tropici
74.4 Interesting Features of
R. tropici
74.5 Genomics
74.6 Proteomics
74.7 Transcriptomics
74.8 Concluding Remarks
References
Chapter 75: The Frankia alni Symbiotic Transcriptome
75.1 Introduction
75.2 Materials and Methods
75.3 Results
75.4 Conclusion
Acknowledgments
References
Chapter 76: A Comprehensive Survey of Soil Rhizobiales Diversity Using High-Throughput DNA Sequencing
76.1 Introduction
76.2 Methods
76.3 Results
76.4 Discussion
76.5 Conclusion
Acknowledgments
References
Chapter 77: Gene-Targeted Metagenomics of Diazotrophs in Coastal Saline Soil
77.1 Introduction
77.2 Materials and Methods
77.3 A Case Study: Diversity and Abundance of
nifH
Gene in Coastal Saline-Alkaline Soil
77.4 Conclusion
Acknowledgment
References
Section 14: Plant “Omics” and Functional Genetics
Chapter 78: The Medicago truncatula Genome
78.1 Introduction
78.2 A Reference Annotated Genome Sequence for
Medicago truncatula
A17
78.3
M. truncatula
Genome Organization and Evolution
78.4 Natural Variation in
Medicago
Genomes
78.5 The
M.
truncatula
Genome and Functional Genomics
78.6 Two Case Studies: Gene Families with Remarkable Diversification in
Medicago
78.7
M. truncatula
Genome and Translational Genomics
References
Chapter 79: Leveraging Large-Scale Approaches to Dissect the Rhizobia–Legume Symbiosis
79.1 Introduction
79.2 Availability of Genome Sequence: A Milestone for Large-Scale Analysis
79.3 Transcriptional Responses During the Legume–Rhizobia Interaction
79.4 MicroRNAs Participate in The Control of The legume–Rhizobia Interaction
79.5 Protein Phosphorylation: Another Level of Regulation in The Legume–Rhizobia Interaction
79.6 Conclusions
Acknowledgments
References
Chapter 80: LegumeIP: An Integrative Platform for Comparative Genomics and Transcriptomics of Model Legumes
80.1 Introduction
80.2 Overview of Data Repositories
80.3 Platform Structure and Web Interface
80.4 Demonstrations of the Utility of LegumeIP
80.5 Conclusions and Future Perspectives
References
Chapter 81: Databases of Transcription Factors in Legumes
81.1 Introduction
81.2 Species-Specific Databases for Legume TFs
81.3 Integrative Databases for Legume TFs
81.4 Conclusions
Acknowledgments
References
Chapter 82: Functional Genomics of Symbiotic Nitrogen Fixation in Legumes with a Focus on Transcription Factors and Membrane Transporters
82.1 Introduction
82.2 Current Knowledge on the Transcriptional Control of SNF in Legumes
82.3 Functional Studies on Membrane Transporters Involved in SNF
82.4 Essential Resources for Functional Analysis of Symbiotic Genes in
Medicago
82.5 Strategies of candidate gene selection for reverse genetic studies
82.6 Re-Annotation of Nodule-induced TF and TRs
82.7 Nodule Developmental Spatiotemporal Gene Expression Pattern
82.8 Selection of Transcription Factors and Transporters for Reverse Genetic Screening
82.9 Zinc-Finger Proteins in Nodule Development
82.10 SNF-Associated Transporters Targeted by
Tnt1
Insertional Mutagenesis
82.11 Considerations Associated with the Use of the
Tnt1
-Insertion Mutant Population
82.12 Conclusion
Acknowledgments
References
Chapter 83: Retrotransposon (Tnt1)-Insertion Mutagenesis in Medicago as a Tool for Genetic Dissection of Symbiosis in Legumes
83.1 Introduction
83.2 Genomic, Transcriptomic, and Mutant Resources for the Functional Dissection of Legume Symbioses
83.3 Isolation of
Tnt1
-Insertion Mutants with Defects in Nodule Development and Symbiotic Nitrogen Fixation
83.4 Discussion
Acknowledgments
References
Section 15: Cyanobacteria and Archaea
Chapter 84: Marine Nitrogen Fixation: Organisms, Significance, Enigmas, and Future Directions
84.1 Introduction
84.2 N
2
Fixation, Marine Habitats, and Cyanobacteria
84.3 Why IS N
2
Fixation in the Open Ocean Interesting?
84.4 N
2
Fixation in the Sea
84.5 What are the N
2
Fixation Rates of the Oceans?
84.6 Oceanic N
2
-Fixing Microorganisms and Changes in Paradigms
84.7 Other Knowledge Gaps
84.8 Concluding Remarks
Acknowledgments
References
Chapter 85: Requirement of Cell Wall Remodeling for Cell–Cell Communication and Cell Differentiation in Filamentous Cyanobacteria of the Order Nostocales
85.1 Introduction
85.2 Requirement for Cell Wall Modification During Heterocyst Differentiation and Diazotrophic Growth
85.3 The PG Layer of Filamentous Cyanobacteria
85.4 The Nanopore Array of Septal Murein
Acknowledgments
References
Chapter 86: Nitrogen Fixation in the Oxygenic Phototrophic Prokaryotes (Cyanobacteria): The Fight Against Oxygen
86.1 Cyanobacteria and Nitrogen Fixation
86.2 Phylogenetic Analysis
86.3 Strategies of Nitrogen Fixation
86.4 Nitrogen Fixation in Heterocyst-Forming Cyanobacteria
86.5 Concluding Remarks
Acknowledgments
References
Chapter 87: Underestimation of Marine Dinitrogen Fixation: A Novel Method and Novel Diazotrophic Habitats
87.1 Introduction
87.2 Comparing N
2
-Fixation Rates Calculated Using the Two Methods
87.3 Presence, Distribution, and Expression of the Key Functional Gene for Nitrogenase Reductase (
nifH
) in Novel Habitats
87.4 Discussion and Conclusion
Acknowledgments
References
Section 16: Diazotrophic Plant Growth Promoting Rhizobacteria and Nonlegumes
Chapter 88: One Hundred Years Discovery of Nitrogen-Fixing Rhizobacteria
88.1 Discovery of Symbiotic and Non-Symbiotic Nitrogen Fixation
88.2
Azotobacter
and Other Related Nitrogen-Fixing Bacteria
88.3 Contribution of
Azotobacter
to Soil Fertility
88.4
Azotobacteraceae
and the Classification in
Proteobacteria
88.5
Azospirillum
History
88.6 About Progress in Isolation, Identification, and Quantification
88.7 Diversity of Nitrogen-Fixing Root-Associated Bacteria: Root Colonizers and Endophytes
88.8 Concluding Remarks
Acknowledgments
References
Chapter 89: Symbiotic Nitrogen Fixation in Legumes: Perspectives on the Diversity and Evolution of Nodulation by Rhizobium and Burkholderia Species
89.1 Introduction
89.2 The Legumes
89.3 The Rhizobia
89.4 The Betarhizobia
89.5 The Root-Nodulating
Burkholderia
Species
89.6 Regarding the Evolution of Nodulating
Burkholderiaceae
and
Rhizobiaceae
89.7 Final Comments and Perspectives
Acknowledgments
References
Chapter 90: Agronomic Applications of Azospirillum and Other PGPR
90.1 Introduction and Discussion
Acknowledgments
References
Chapter 91: Auxin Signaling in Azospirillum brasilense: A Proteome Analysis
91.1 Introduction
91.2 Methods
91.3 Results and Discussion
91.4 Conclusion
Acknowledgments
References
Chapter 92: Genetic and Functional Characterization of Paenibacillus riograndensis: A Novel Plant Growth-Promoting Bacterium Isolated from Wheat
92.1 Introduction
92.2 Genetic and Functional Characterization of
Paenibacillus riograndensis
92.3 Other Features of
P. riograndensis
Species
Acknowledgments
References
Chapter 93: Role of Herbaspirillum seropedicae LPS in Plant Colonization
93.1 LPS Biosynthesis Mechanism in
H. seropedicae
93.2 LPS Biosynthesis Regulation in
H. seropedicae
93.3 LPS as a Bacterial Protection Barrier
93.4 LPS as an Anchoring Site for Binding Root Lectins
93.5 Conclusion
References
Chapter 94: Culture-Independent Assessment of Diazotrophic Bacteria in Sugarcane and Isolation of Bradyrhizobium spp. from Field-Grown Sugarcane Plants Using Legume Trap Plants
94.1 Introduction
94.2 Materials and Methods
94.3 Results
94.4 Discussion
Acknowledgments
References
Chapter 95: How Fertilization Affects the Selection of Plant Growth Promoting Rhizobacteria by Host Plants
95.1 Introduction
95.2 The Effect of Fertilizers on the Use of PGPR
95.3 Conclusions
Acknowledgments
References
Section 17: Field Studies, Inoculum Preparation, Applications of Nod Factors
Chapter 96: Appearance of Membrane Compromised, Viable but Not Culturable and Culturable Rhizobial Cells as a Consequence of Desiccation
96.1 Introduction and Discussion
96.2 The Membrane-Compromised (MC) Fraction
96.3 The Viable But Nonculturable (VBNC) Fraction
96.4 The Culturable Fraction (CFU)
Acknowledgments
References
Chapter 97: Making the Most of High Quality Legume Inoculants
97.1 Introduction
97.2 What is Inoculant Quality?
97.3 Development of Legume Inoculant Standards
97.4 Quality and Shelf Life of Australian Legume Inoculants
97.5 Quality of Peat Inoculants
97.6 Quality of Granular and Freeze-Dried Inoculants
97.7 Contamination in Legume Inoculants
97.8 Inoculum Potential and Inoculant Efficacy
97.9 Soil Versus Seed Inoculation
97.10 Quality of Commercially Inoculated [Preinoculated] Legume Seed
97.11 Conclusions
References
Chapter 98: Rhizobiophages as a Marker in the Selection of Symbiotically Efficient Rhizobia for Legumes
98.1 Introduction
98.2 Phage Typing
98.3 Materials and Methods
98.4 Results and Discussion
98.5 Symbiotic Response of Phage-Typed
Rhizobium
with Host Plant
98.6 Conclusion
References
Chapter 99: Nitrogen Fixation with Soybean: The Perfect Symbiosis?
99.1 Introduction
99.2 Concluding Remarks
Acknowledgments
References
Chapter 100: Nodule Functioning and Symbiotic Efficiency of Cowpea and Soybean Varieties in Africa
100.1 Introduction
100.2 Conclusion
Acknowledgment
References
Chapter 101: Microbial Quality of Commercial Inoculants to Increase BNF and Nutrient Use Efficiency
101.1 Introduction
101.2 Materials and Methods
101.3 Results and Discussion
Acknowledgment
References
Chapter 102: Developed Fungal-Bacterial Biofilms Having Nitrogen Fixers: Universal Biofertilizers for Legumes and Non-Legumes
102.1 Introduction
102.2 Methodology
102.3 Results
102.4 Discussion
102.5 Conclusions
Acknowledgments
References
Chapter 103: Phenotypic Variation in Azospirillum spp. and Other Root-Associated Bacteria
103.1 Introduction
103.2 Phenotypic Variation in
Azospirillum
Under Normal Growth Conditions
103.3 Phenotypic Variation in
Azospirillum
Under Starvation and Stress Conditions
103.4 Genomic Rearrangements Associated with Phenotypic Variation in
Azospirillum
103.5 Occurrence of Phenotypic Variation in Natural Environments and Potential Impact on Rhizosphere Competence and Plant Growth-Promoting Properties of
Azospirillum
103.6 Phenotypic Variation in Non-Diazotrophic Root-Associated Bacteria
103.7 Conclusions
References
Chapter 104: The Physiological Mechanisms of Desiccation Tolerance in Rhizobia
104.1 Introduction
104.2 Methods
104.3 Results
104.4 Discussion
104.5 Conclusion
Acknowledgments
References
Chapter 105: Food Grain Legumes: Their Contribution to Soil Fertility, Food Security, and Human Nutrition/Health in Africa
105.1 Introduction
105.2 N
2
Fixation and N Contribution by Food Grain Legumes in Cropping Systems
105.3 N
2
-Fixing Efficiency and Mineral Accmulation in Grain Legumes
105.4 Contribution of Legume Symbiosis to Food Security and Enhanced Human Nutrition/Health
Acknowledgment
References
Chapter 106: Plant Breeding for Biological Nitrogen Fixation: A Review
106.1 Introduction
106.2 Potential Traits and Breeding Strategies that Confer Enhanced Fixation
106.3 Conclusion
References
Chapter 107: LCO Applications Provide Improved Responses with Legumes and Nonlegumes
107.1 Introduction
107.2 Methods
107.3 Results
107.4 Root Hair Deformation
107.5 Germination and Emergence
107.6 Nodulation
107.7 Nod Factor: Myc Factor Cross Talk
107.8 Enhanced Root Development
107.9 Early Growth
107.10 Foliar Application
107.11 Yield Enhancement
107.12 Discussion
References
Section 18: Nitrogen Fixation and Cereals
Chapter 108: The Quest for Biological Nitrogen Fixation in Cereals: A Perspective and Prospective
108.1 Introduction
108.2 Past Investigations (Perspective)
108.3 More Recent Investigations (Perspective and Prospective)
Acknowledgments
References
Chapter 109: Environmental and Economic Impacts of Biological Nitrogen-Fixing (BNF) Cereal Crops
109.1 Introduction
109.2 Discussion
109.3 Conclusions
Acknowledgments
References
Chapter 110: Conservation of the Symbiotic Signaling Pathway between Legumes and Cereals: Did Nodulation Constraints Drive Legume Symbiotic Genes to Become Specialized during Evolution?
110.1 Introduction
110.2 Perception of the Symbiotic Signals
110.3 Generation of Calcium Spiking
110.4 Decoding of the Calcium Spiking
110.5 Symbiotic Transcription Factors
110.6 Discussion
References
Chapter 111: Occurrence and Ecophysiology of the Natural Endophytic Rhizobium–Rice Association and Translational Assessment of Its Biofertilizer Performance within the Egypt Nile Delta
111.1 Introduction
111.2 Methodology
111.3 Take-Home Lessons of This Research Program
Acknowledgment
References
Section 19: Accessory Chapters
Chapter 112: N Fixation in Insects: Its Potential Contribution to N Cycling in Ecosystems and Insect Biomass
112.1 Introduction
112.2 Nitrogen Acquisition by Insects
112.3 Why Endosymbionts Reside in Insects?
112.4 Bacterial Communities Associated with Insects
112.5 Nitrogen Fixation and Recycling as Support for Insect Nutrition
112.6 The Importance of N Fixation by Insects in Ecosystems
112.7 Conclusions
Acknowledgments
References
Chapter 113: Rapid Identification of Nodule Bacteria with MALDI-TOF Mass Spectrometry
113.1 Introduction
113.2 From DNA- to Protein-Based Molecular Signatures for Rhizobia
113.3 Methods
113.4 Results and Discussion
Acknowledgments
References
Chapter 114: The Microbe-Free Plant: Fact or Artifact
114.1 Introduction
114.2 Phenotypic Effects of Endophytes
114.3 Mechanisms: What Do We Know?
114.4 The Potential of Endophytes in Biocontrol
114.5 Endophyte or Pathogen: Who Controls?
114.6 Summary and Outlook
References
Index
End User License Agreement
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Guide
Cover
Table of Contents
Preface
Preface
Begin Reading