Table Of ContentSoil Biology
Volume 15
Series Editor
Ajit Varma, Amity Institute of Microbial Sciences,
Amity University Uttar Pradesh, Noida, UP, India
Volumes published in the series
Applied Bioremediation and Phytoremediation (Vol. 1)
A. Singh, O.P. Ward (Eds.)
Biodegradation and Bioremediation (Vol. 2)
A. Singh, O.P. Ward (Eds.)
Microorganisms in Soils: Roles in Genesis and Functions (Vol. 3)
F. Buscot, A. Varma (Eds.)
In Vitro Culture of Mycorrhizas (Vol. 4)
S. Declerck, D.-G. Strullu, J.A. Fortin (Eds.)
Manual for Soil Analysis – Monitoring and Assessing Soil
Bioremediation (Vol. 5)
R. Margesin, F. Schinner (Eds.)
Intestinal Microorganisms of Termites and Other Invertebrates (Vol. 6)
H. König, A. Varma (Eds.)
Microbial Activity in the Rhizosphere (Vol. 7)
K.G. Mukerji, C. Manoharachary, J. Singh (Eds.)
Nucleic Acids and Proteins in Soil (Vol. 8)
P. Nannipieri, K. Smalla (Eds.)
Microbial Root Endophytes (Vol. 9)
B.J.E. Schulz, C.J.C. Boyle, T.N. Sieber (Eds.)
Nutrient Cycling in Terrestrial Ecosystems (Vol. 10)
P. Marschner, Z. Rengel (Eds.)
Advanced Techniques in Soil Microbiology (Vol. 11)
A. Varma, R. Oelmüller (Eds.)
Microbial Siderophores (Vol. 12)
A. Varma, S. Chincholkar (Eds.)
Microbiology of Extreme Soils (Vol. 13)
P. Dion, C.S. Nautiyal (Eds.)
Secondary Metabolites in Soil Ecology (Vol. 14)
P. Karlovsky (Ed.)
Chandra Shekhar Nautiyal • Patrice Dion
Editors
Molecular Mechanisms
of Plant and Microbe
Coexistence
Foreword by V.L. Chopra
Editors
Professor Dr. Chandra Shekhar Nautiyal Professor Dr. Patrice Dion
National Botanical Research Institute Département de phytologie
Rana Pratap Marg Pavillon Charles-Eugène Marchand
Lucknow 226001 1030, avenue de la Médecine
India Université Laval
[email protected] Québec (Québec) G1V 0A6
Canada
[email protected]
ISBN 978-3-540-75574-6 e-ISBN 978-3-540-75575-3
DOI:10.1007/978-3-540-75575-3
Soil Biology ISSN: 1613–3382
Library of Congress Control Number: 2008923850
© 2008 Springer-Verlag Berlin Heidelberg
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SCIENCE OF LIFE
Pollens of fl owers, sperms of animals
Coded with messages internal
Busy in the acts of creation
Millions perish in action
The few successes are the great Creations!
Also succeed microbes many
Which disrupt the inner harmony
Of organisms big and mighty!
Bodies, anti bodies, biochemical wars
Evolutionary wisdom of immune systems
Nature’s beauty opens one petal
For the researcher with knowledge tool
One by one petals open
Trillions more waiting to be seen
Y.S. Rajan
Foreword
Coexistence between microorganisms and plants has moulded civilization from the
time humans began to rely extensively on cultivated crops for food. It is becoming
increasingly clear that microbes are the basic of the biosphere. The interactions of
plant roots with soil microorganisms are spatially and temporally complex. These
interactions are fundamental to soil carbon dynamics and availability of inorganic
and organic N to plants. The primary source of mineral nutrients for plants is the
decomposition of organic matter by soil microbes.
Molecular Mechanisms of Plant and Microbe Coexistence reflects on the world of
microbes in the soil that cause a soil to become biologically alive to enable plants to
withstand better the rigors of life. For these reasons, our challenge is to understand
the molecular processes that are crucial for establishing successful plant-microbe
coexistence. This will not only lead to new scientific discoveries, but will provide the
bases for new strategies for combating infectious diseases, producing novel and
environment friendly, microbial inoculants for protecting plants from disease, for
promoting healthy growth and ensuring precise regulation of nutrient supply to plants.
The book has assembled contributions from leading authorities of varied back-
grounds on topics relating to interactions between plant and microbe coexistence
research and dealing with contemporary scientific findings and cutting-edge tech-
nologies. Studying plant-microbe associations is important for all of these
practical reasons and also for the goal of improved agricultural productivity.
Exploitation of beneficial plant-microbe coexistence in the rhizosphere can pro-
mote plant health and have significant implications for low input sustainable
agriculture. A major difficulty faced by plant biologists and microbiologists is
that many groups of microbes that inhabit rhizosphere are not cultivable in the
laboratory. Recent developments in molecular biology are shedding light on
microbial diversity of rhizosphere. Understanding the complexity of this environ-
ment and how the microbial communities adapt and respond to alterations in the
physical, c hemical and biological properties of the rhizosphere remains a signifi-
cant c hallenge for plant and microbial biologists. Contributors have focused on
recent and exciting findings in the biology of plant and microbe coexistence and
vii
viii Foreword
s peculated on the technical and conceptual developments that will drive innova-
tive research to open new vistas.
The practical utility of understanding plant-microbe coexistence is obvious.
Genomic technologies can elucidate the role of novel genes in plant-microbe
c oexistence in the rhizosphere. The understanding of the molecular signaling
processes and the functions they regulate within the rhizosphere will play a pivotal
role in promoting beneficial plant and microbe coexistence, in overcoming existing
limitations, and in designing strategies for the generation of novel inoculant
consortia with applications in sustainable environmental biotechnology. The avail-
ability of new and powerful technologies for studying plant microbial coexistence
in the soil guarantees a better understanding of these processes, which will not only
facilitate their successful applications in biotechnology but will also provide new
insights into sustaining plant and animal productivity, maintaining or enhance water
and air quality, and supporting human health and habitation.
I sincerely hope that this volume will be of great interest to a wide spectrum of
biologists.
Member of Planning Commission V.L. Chopra
Government of India
Yojna Bhavan, Sansad Marg
New Delhi 110001
India
Preface
The coexistence of plant and microbes has had major effects on the development
of civilization since humans began to rely extensively on cultivated crops for food,
soon after the emergence of agriculture, dating back to about 10,000 years before
the present (BP). The refinement of our knowledge on this system is brought about
by the interaction between existing social values and the integrity of our measuring
tools- with interplay of scientific and philosophical rationale. Thus, the wisdom
gained and practices adopted have been passed down through generations.
The ecological competence of traditional farmers is now reflected in the resur-
gence of organic agriculture. The available ancient literature includes the four
Vedas, Susruta Samhita, Charaka Samhita, Krishi-Parashara, and Surapala’s
Vriskshayurveda. This literature is most likely to have been composed between
8000 and 1000 BP. Indeed, ancient civilizations often worshipped the soil as the
foundry of life itself. We are becoming increasingly aware that microbes are the
basis of the biosphere. The interactions of plant roots with soil microorganisms are
spatially and temporally complex; however, it is becoming increasingly apparent
that these interactions are fundamental to soil carbon dynamics and the availability
of inorganic and organic N to plants. The primary source of mineral nutrients for
plants is the decomposition of organic matter by humble soil microbes. The
present book on molecular mechanisms of plant and microbe coexistence thus
reflects upon the world of microbes in the soil that cause a soil to become biologi-
cally alive and assist other organisms in withstanding the rigors of life. We know
that microbes inhabitated the Earth long before multicellular life appeared and
diversified. Following their appearance, multicellular plants and animals c oexisted,
interacted and coevolved with microbes. The evolution and activity of all plants
and animals has thus been influenced by microorganisms, often as a result of
i ntimate interactions.
We are at a time when the confluence of technological advances and the explo-
sion of knowledge on plant-microbe coexistence will enable significant advances
over the next decade. Thus, mechanisms controlling the multiple interactions
between plant roots, other organisms and the soil environment are currently
ix
x Preface
a rousing great scientific interest. As plant and microbe coexistence research is a
true interdisciplinary field of biological and soil sciences, the volume deals with
new scientific findings and cutting-edge technologies, including molecular
biological and functional genomic approaches. The present book has been organ-
ized in four sections, covering molecular mechanisms of plant and microbe coexist-
ence from the point of view of populations, genomes, molecules and methods,
respectively. Opening the first section, Chap. 1 provides an overview of plant-asso-
ciated soil microorganisms and places the other book chapters into perspective.
Chapter 2 deals with the role of microbial diversity in enhancing soil and plant
health. Chapter 3 seeks to examine the structure of soil microbial communities in
the light of evolution. Particular emphasis is placed on the defining role of plant-
microbe mutualistic symbioses. Chapter 4 deals with new techniques, based on the
genomics of rhizosphere colonization that offer opportunities for greatly expanding
our knowledge of signaling, recognition and interaction in the root zone. Chapter 5
describes how the arbuscular mycorrhizal fungi, by maintaining belowground
endosymbiosis with the roots of vascular land plants, influence the interactions
between their host plant and aboveground insects.
The second section of the book describes the molecular processes that are
crucial in establishing successful plant-microbe coexistence. Chapter 6 relates to
macromolecular structure and evolutionary genomics, examining how these relate
to the evolution of function in transcript RNA and protein molecules. This
approach, involving the definition of rooted phylogeny of proteomes and fold
architectures, is leading to fundamental understandings on genome coexistence.
Chapter 7 highlights the main features of the currently known complete genomes
of nitrogen-fixing symbiotic rhizobia, comparisons between these genomes
revealing their evolution. Chapter 8 discusses the pathogen stress-induced epige-
netic changes occurring in plants as a result of the production of a plant-derived
signal, named the systemic recombination signal (SRS), which triggers the desta-
bilization of the somatic and meiotic cell genomes and leads to heritable changes
in response to stress. Functional genomics and proteomics are two rapidly expand-
ing research areas. Chapter 9 deals eloquently with recent advances in functional
genomics and proteomics of plant-associated microbes which will form the basis
for new microbial inoculant-based strategies to combat infectious plant diseases
promote plant growth and regulate nutrient supply to plants. Chapter 10 discusses
how recent advances in molecular genetics will contribute to our knowledge of
biocontrol process, and suggest new avenues for solving intriguing problems that
the biocontrol industry faces, like inconsistency in performance of Trichoderma
spp. under field conditions.
The third section relates to studies indicating a significant role for signaling in
successful plant-microbe coexistence. Dedicated studies are needed to unravel the
function and mechanism of signaling during the different stages of plant-microbe
coexistence. Many Gram-negative, plant-associated bacteria use N-acyl homoserine
lactone (AHL)-mediated quorum sensing to regulate traits involved in symbiotic,
pathogenic or surface-associated relationships with their corresponding host plant.
Chapter 11 presents an overview of the diverse phenomena regulated by quorum
Preface xi
sensing in representative groups of these bacteria and illustrates the regulatory
complexity often associated with these signaling networks. Chapter 12 then
s ynthesizes eloquently the information available on the various types of signaling
interactions that occur in the rhizosphere between microorganisms and plants. The
investigation of host proteins interacting with viral proteins is a very promising
approach to dissect the molecular basis of viral infections and to understand how
viruses integrate in the complex structural and regulatory networks controlling
plant growth; these plant-viral relationships are examined in Chap. 13. Given the
major effects of rhizodeposition on composition and activities of microbial
communities inhabiting rhizosphere soil, Chap. 14 discusses the state-of-the-art of
studies on microbial activity and microbial diversity in the rhizosphere soil.
The fourth section explores questions related to the extent of diversity within
naturally occurring microbial communities and addresses the challenge of studying
as yet uncultivable prokaryotes. Techniques as described in methods-based Chaps.
15–18 offer opportunities for greatly expanding our knowledge of interaction of
various eukaryotes in the root zone. Chapter 15 sets in motion as an example
siderotyping as a particularly promising method for the characterization and identi-
fication at the species level of fluorescent and non-fluorescent Pseudomonas.
Offering simplicity and rapidity of execution, siderotyping could advantageously
replace a phenotypic numerical analysis. Chapter 16 deals with recent advances
towards understanding oomycetes, which have been facilitated by the development
of genomics databases and proteomics-based strategies. These new tools have use-
fully complemented traditional methods of gene cloning and classical genetics.
Advanced molecular methods that can be used to analyze rhizosphere and soil-
derived nucleic acids have been described in Chap. 17, along with examples where
the use of these approaches has contributed significantly to our understanding of
microbial life in soil and of microbial interactions with plants. Chapter 18 concen-
trates on in-depth morphotyping and molecular methods to characterize the ecto-
mycorrhizal fungi. It is anticipated that these methods will allow us to understand
the interplay of genes and functions in an ecosystem.
We could not have completed this book without the unflinching cooperation of
our invaluable contributors who are authorities from varied background and,
despite being heavily occupied, were always willing to accede to our demands to
focus on exciting sub disciplines via simple schematic diagrams or at times even
sharing their unpublished work. While editing the chapters we have taken care that
personal style of the contributors is not influenced by our own. Without the legen-
dary elephantine cool patience and composed posture of Professor Ajit Varma,
Series Editor, this book could have remained indefinitely as an idea in our minds.
We wish to thank Dr. Dieter Czeschlik and Dr. Jutta Lindenborn, Springer
Heidelberg, for excellent feedback and professional support throughout the book
preparation process. Jutta deserves special recognition of her very kind and
s upportive nature. Our thanks are also extended to Puneet S. Chauhan for help in
compiling the chapters and those who have participated in the production of this
book, whose indispensable help has significantly improved the quality of individual
chapters and of the book as a whole, but the mistakes that are left remain our
