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Biological Nitrogen Fixation


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Table of Contents

Biological Nitrogen Fixation VOLUME 1

Chapter 1. Introduction

Frans J. de Bruijn

Section 1. Focus Chapters

Chapter 2. Recent advances in Understanding Nitrogenases and How They Work

William Newton

Chapter 3. Evolution and Taxonomy of Nitrogen-fixing Organisms with emphasis on Rhizobia

Kristina Lindstrom

Chapter 4. Evolution of Rhizobium Nodulation: From Nodule Specific Genes (Nodulins) to Recruitment of Common Processes

Ton Bisseling

Chapter 5. Bioengineering Nitrogen Acquisition in Rice: Promises for Global Food Security

Herbert Kronzucker

Section 2. Chemistry and Biochemistry of Nitrogenases

Chapter 6. An Overview of Fe-S Protein Biogenesis from Prokaryotes to Eukaryotes

Mahipal Kesawat

Chapter 7. Biosynthesis of the Iron-Molybdenum Cofactor of Nitrogenase

Luis Rubio

Chapter 8. Distribution and Ecological Niches of Nitrogenases

Alexander Glazer

Section 3. Expression and Regulation of Nitrogen Fixation Genes and Nitrogenase

Chapter 9. Regulation of nif Gene Expression in Azotobacter vinelandii

Cesar Poza-Carrion, Luis Rubio

Chapter 10. Coupling of Regulation between Nitrogen and Carbon Metabolism in Nitrogen Fixing Pseudomonas stutzeri A1501

Lin Min

Chapter 11. Regulation of NItrogen Fixation and Molybdenum Transport in Rhodobacter capsulatus

Bernd Masepohl

Chapter 12. Metabolic Regulation of Nitrogenase Activity in Rhodospirillum rubrum: The Role of PII Proteins and Membrane Sequestration

Stefan Nordlund

Chapter 13. How Does the DraG-PII Complex Regulate Nitrogenase Activity in Azospirillum brasilense?

Xiao-Dan Li

Chapter 14. Fe Protein Over-expression Can Enhance the Nitrogenase Activity of Azotobacter vinelandii

Papri Nag

Chapter 15. FNR-like Proteins in Rhizobia: Past and Future

Lourdes Girard

Section 4. Taxonomy and Evolution of Nitrogen Fixing Organisms

Chapter 16. Exploring Alternative Paths for the Evolution of Biological Nitrogen Fixation

John Peters

Chapter 17. Phylogeny, Diversity, Geographical Distribution and Host Range of Legume-Nodulating Betaproteobacteria: What Is the Role of Plant Taxonomy?

Lionel Moulin, Euan James

Chapter 18. Bradyrhizobium, The Ancestor of All Rhizobia: Phylogeny of Housekeeping and Nitrogen-fixation Genes

Mariangela Hungria

Chapter 19. Interaction between Host and Rhizobial Strains: Affinities and Coevolution

Mario Aguilar

Chapter 20. Assessment of Nitrogenase Diversity in the Environment

Daniel Buckley

Section 5. Genomics of Nitrogen Fixing Organisms

Chapter 21. Genetic Regulation of Symbiosis Island Transfer in Mesorhizobium loti

Joshua Ramsay, Clive Ronson

Chapter 22. The Azotobacter vinelandii Genome: An Update

Joao C. Setubal

Chapter 23. The Genome Sequence of the Novel Rhizobial Species Microvirga lotononidis Strain WSM3557.

Julie Ardley

Chapter 24. Genome Characteristics of Frankia sp. Reflect Host Range and Host Plant Biogeography

Philippe Normand, David Benson

Chapter 25. Core and Accessory Henomes of The Diazotroph Azospirillum

Florence Wisniewski-Dye

Chapter 26. Pangenome Evolution in The Symbiotic Nitrogen Fixer Sinorhizobium meliloti

Marco Galardini

Chapter 27. Pangenomic Analysis of The Rhizobiales Using The GET_HOMOLOGUES Software Package

Pablo Vinuesa

Section 6. Physiology and Metabolism of Nitrogen Fixing Organisms

Chapter 28. Metabolism of Photosynthetic Bradyrhizobia During Root and Stem Symbiosis with Aeschynomene legumes

Benjamin Gourion

Chapter 29. A Plethora of Terminal Oxidases and Their Biogenesis Factors in Bradyrhizobium japonicum

Hauke Hennecke

Chapter 30. Rhizobial Extracytoplasmic Function (ECF) Factors and Their Role in Oxidative Stress Response of Bradyrhizobium japonicum

Hans-Martin Fischer

Chapter 31. Role of the Bacterial BacA ABC-transporter in Chronic Infection of Nodule Cells by Rhizobium

Peter Mergaert

Chapter 32. Molecular Keys to Broad Host Range in Sinorhizobium fredii NGR234, USDA257 and HH103

Wolfgang Streit

Chapter 33. Motility and Chemotaxis in the Rhizobia

Michael Hynes

Chapter 34. The Pts/Ntr System Globally Regulates ATP-dependent Transporters in Rhizobium leguminosarum

Jurgen Prell

Section 7. Nitrogen Fixing Organisms, the Plant Rhizosphere and Stress Tolerance

Chapter 35. Actinorhizal Root Exudates Alter the Physiology, Surface Properties and Plant Infectivity of Frankia

Louis Tisa

Chapter 36. Exopolysaccharide Production in Rhizobia is Regulated by Environmental Factors

Monika Janczarek

Chapter 37. Regulation of Symbiotically-Important Functions by Quorum Sensing in the Sinorhizobium meliloti-Alfalfa Interaction

Juan Gonzales

Chapter 38. Lumichrome as a Bacterial Signal Molecule Influencing Plant Growth

Felix Dakora

Chapter 39. Genes Involved in Desiccation Resistance of Rhizobia and Other Bacteria

Michael Kahn

Chapter 40. The General Stress Response in Alpha-rhizobia

Claude Bruand

Section 8. Physiology and Regulation of Nodulation

Chapter 41. The Root Hair: A Single Cell Model for Systems Biology

Marc Libault

Chapter 42. How Transcriptomics Revealed New Information on Actinorhizal Symbioses Establishment and Evolution

Valerie Hocher

Chapter 43. Molecular Biology of Infection and Nodule Development in Discaria trinervis - Frankia Actinorhizal Symbiosis

Sergio Svistoonoff

Chapter 44. Lotus japonicus Nodulates When It Sees Red

Akihiro Suzuki

Chapter 45. Out of Water of A New Model Legume: The Nod-independent Aeschynomene evenia

Jean-Francois Arrighi

Chapter 46. Phosphorus Use Efficiency for N2 Fixation in The Rhizobial Symbiosis with Legumes

Jean -Jacques Drevon

Chapter 47. Regulation of Nodule Development by Short and Long Distance Auxin Transport

Ulrike Mathesius

Chapter 48. Functional Analysis of Nitrogen-Fixing Root Nodule Symbioses Induced by Frankia: Transport and Metabolic Interactions

Alison Berry

Chapter 49. NOOT-dependent Control of Nodule Identity: Nodule Homeosis and Meristem Perturbation

Pascal Ratet

Volume 2 Section 9. Recognition in Nodulation

Chapter 50. Roles for Flavonoids in Symbiotic Root-Rhizosphere Interactions

Ulrike Mathesius

Chapter 51. Nod Factor Recognition in Medicago truncatula

Jean Jacques Bono

Chapter 52. Role of Ectoapyrases in Nodulation

Gary Stacey

Chapter 53. Role of Rhizobium Cellulase CelC2 in Root Colonization and Infection

Pedro Mateos

Chapter 54. Nod Factor-Induced Calcium Signaling in Legumes

Giles Oldroyd

Chapter 55. Signalling and Communication between Actinorhizal Plants and Frankia During the Intracellular Symbiotic Process

Claudine Franche

Section 10. Infection and Nodule Ontogeny

Chapter 56. The Role of Hormones in Rhizobial Infection

Jeremy Murray

Chapter 57. Nuclear Ca2+ Signaling Reveals Active Bacterial-Host Signaling throughout Rhizobial Infection in Root Hairs of Medicago truncatula

David Barker

Chapter 58. A Pectate Lyase Required for Plant-Cell Wall Remodelling During Infection of Legumes by Rhizobia

Allan Downie

Chapter 59. Dissecting The Roles in Outer and Inner Root Cell Layers of Plant Genes That Control Rhizobial Infection and Nodule Organogenesis

Clare Gough

Chapter 60. The Medicago truncatula NIP/LATD Transporter Is Essential for Nodulation and Appropriate Root Architecture

Rebecca Dickstein

Chapter 61. A MYB Coiled Coil Type Transcription Factor Interacts with NSP2 and Is Essential for Nodulation in Lotus japonicus

Zhongming Zhang

Chapter 62. AP2/ERF Transcription Factors and Root Nodulation

Fernanda de Carvalo-Niebel

Chapter 63. Identification of Medicago truncatula Genes Required for Rhizobial Invasion and Bacteroid Differentiation

Peter Kalo

Chapter 64. Multifacetted Roles of Nitric Oxide in Rhizobium-Legume Symbioses

Eliane Meilhoc

Chapter 65. Profiling Symbiotic Responses of Sinorhizobium fredii Strain NGR234 with RNA-seq

Xavier Perret

Chapter 66. Computational and Experimental Evidence That Auxin Accumulation in Nodule and Lateral Root Primordia Occurs by Different Mechanisms

Eva Elisabeth Deinum

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

Eva Kondorosi

Chapter 68. The Symbiosome Membrane

Penelope Smith

Section 12. Nitrogen Fixation, Assimilation and Senescence in Nodules

Chapter 69. Nodulin Intrinsic Proteins: Facilitators of Water and Ammonia Transport across the Symbiosome Membrane

Daniel Roberts

Chapter 70. Leghemoglobins with Nitrated Hemes in Legume Root Nodule

Manuel Becana

Chapter 71. The Role of 1-aminocyclopropane-1-carboxylase Enzyme in Leguminous Nodule Senescence

Neung Teaumroong

Section 13. Microbial "Omics"

Chapter 72. Pool-Seq Analysis of Microsymbiont Selection by the Legume Plant Host

Juan Imperial

Chapter 73. Contribution of the RNA Chaperone Hfq to Environmental Fitness and Symbiosis in Sinorhizobium meliloti

Jose I. Jimenes-Zurdo

Chapter 74. Biodiversity, Symbiotic Efficiency and Genomics of Rhizobium tropici and Related Species

Mariangela Hungria

Chapter 75. The Frankia alni Symbiotic Transcriptome

Philippe Normand

Chapter 76. A Comprehensive Survey of Soil Rhizobiales Using High-Throughput DNA Sequencing

Ryan Jones

Chapter 77. Gene Targeted Metagenomics of Diazotrophs in Coastal Saline Soil

Bhanavath Jha

Section 14. Plant "Omics" and Functional Genetics

Chapter 78. The Medicago truncatula Genome

Frederic Debelle

Chapter 79. Leveraging Large-Scale Approaches to Dissect the Rhizobia-Legume Symbiosis

Oswaldo Valdes-Lopez

Chapter 80. LegumeIP: An Integrative Platform for Comparative Genomics and Transcriptomics of Model Legumes

Patrick Xuechun Zhao

Chapter 81. Databases of Transcription Factors in Legumes

Lam-son Phan Tran

Chapter 82. Functional Genomics of Symbiotic Nitrogen Fixation in Legumes with a Focus on Transcription Factors and Membrane Transporters

Michael Udvardi

Chapter 83. Retrotransposon (Tnt1)-insertion Mutagenesis in Medicago as a Tool for Genetic Dissection of Symbiosis in Legumes

Michael Udvardi

Section 15. Cyanobacteria and Archaea

Chapter 84. Marine Titrogen Fixation: Organisms, Significance, Enigmas and Future Directions

Jonathan Zehr

Chapter 85. Requirement of Cell Wall Remodelling for Cell-Cell Communication and Cell Differentiation in Filamentous Cyanobacteria of the Order Nostocales

Karl Forchhammer

Chapter 86. Nitrogen Fixation in the Oxygenic Phototrophic Prokaryotes (Cyanobacteria): The Fight Against Oxygen

Enrique Flores

Chapter 87. Underestimation of Marine Dinitrogen Fixation: A Novel Method and Novel Diazotrophic Habitats

Ruth Schmitz

Section 16. Diazotrophic Plant Growth Promoting Rhizobacteria and Non-Legumes

Chapter 88. One Hundred Years Discovery of Nitrogen-Fixing Rhizobacteria

Claudine Elmerich

Chapter 89. Symbiotic Nitrogen Fixation in Legumes: Perspectives on the Diversity and Evolution of Nodulation by Rhizobium and Burkholderia Species

Ann Hirsch

Chapter 90. Agronomic Applications of Azospirillum and Other PGPR

Yaacov Okon

Chapter 91. Auxin Signaling in Azospirillum brasilense: A Proteome Analysis

Stijn Spaepen

Chapter 92. Genetic and Functional Characterization of Paenibacillus riograndensis: A Novel Plant Growth Promoting Bacterium Isolated from Wheat

Luciane Passaglia

Chapter 93. Role of Herbaspirillum seropedicae LPS in Plant Colonization

Rose Adele Monteiro

Chapter 94. Culture-independent Assessment of Diazotrophic Bacteria in Sugarcane and Isolation of Bradyrhizobium spp. from Field Grown Sugarcane Plants Using Legume Trap Plants

Anton Hartmann

Chapter 95. How Fertilization Affects the Selection of Plant Growth Promoting Rhizobacteria by Host Plants

Luciane Passaglia

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

Jan Vriezen

Chapter 97. Making the Most of High Quality Inoculants

Rosalind Deaker

Chapter 98. Rhizobiophages As Markers in The Selection of Symbiotically Efficient Rhizobia for Legumes

Felix Dakora

Chapter 99. Nitrogen Fixation with Soybean: The Perfect Symbiosis?

Mariangela Hungria

Chapter 100. Nodule Functioning and Symbiotic Efficiency of Cowpea and Soybean Varieties in Africa

Flora Pule Meulenberg

Chapter 101. Microbial Quality of Commercial Inoculants to Increase BNF and Nutrient Use Efficiency

Didier Lesueur

Chapter 102. Developed Fungal-Bacterial Biofilms Having Nitrogen Fixers: Universal Biofertilizers for Legumes and Non-legumes

H.M. Herath

Chapter 103. Phenotypic Variation in Azospirillum spp. and Other Root-Associated Bacteria

Anton Hartmann

Chapter 104. The physiological mechanisms of desiccation tolerance in rhizobia

Andrea Casteriano

Chapter 105. Food Grain Legumes: Their Contribution to Soil Fertility and Human Nutrition and Health in Africa

Felix Dakora

Chapter 106. Plant Breeding for Biological Nitrogen Fixation: A Review

Peter Kennedy

Chapter 107. LCO Applications Provide Improved Responses with Legumes and Non-legumes

Stewart Smith

Section 18 Nitrogen Fixation and Cereals

Chapter 108. The Quest for Biological Nitrogen Fixation in Cereals : A Perspective and Prospective

Frans J. de Bruijn

Chapter 109. Environmental and Economic Impacts of Biological N2 Fixing (BNF) Cereal Crops

Perrin Beatty

Chapter 110. Conservation of the Symbiotic Signalling Pathway between Legumes and Cereals: Did Nodulation Constraints Drive Legume Symbiotic Genes to Become Specialised During Evolution?

Charles Rosenberg

Chapter 111. Occurrence and Ecophysiology of the Natural Endophytic Rhizobium-rice Association, and Translational Assessment of its Biofertilizer Performance within the Egypt Nile Delta

Youssef Yanni

Section 19. Concluding Chapters

Chapter 112. The Relevance of N-fixation and N-recyling for Insect Biomass and N-balances of Ecosystems

Martin Heil

Chapter 113. Rapid Identification of Nodule Bacteria with MALDI-TOF Mass Spectrometry

Xavier Perret

Chapter 114. The Microbe-Free Plant: Fact or Artefact?

Martin Heil

About the Author

Frans J. de Bruijn received his Ph.D. (Cellular and Developmental Biology; Microbial Genetics) from Harvard University in 1983. His resume reflects an array of experiences as a teacher, researcher, board member, and he is currently Director of Research at the Laboratory for Plant-Microbe Interactions in Toulouse, France.

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