Mycorrhiza: State of the Art, Genetics and Molecular Biology, Eco-Function, Biotechnology, Eco-Physiology, Structure and Systematics

798 Pages·2008·7.59 MB·English

by  E. Mohammadi Goltapeh

Mycorrhiza
Third Edition
Ajit Varma
Editor
Mycorrhiza
State of the Art, Genetics and Molecular
Biology, Eco-Function, Biotechnology,
Eco-Physiology, Structure and Systematics
Third Edition
Editor
Professor Dr. Ajit Varma
Director, Amity Institute of Microbial Technology (AIMT)
Vice President (International)
Amity Science, Technology & Innovation Foundation (ASTIF)
Amity University Uttar Pradesh
Block ‘A’, Ground Floor, Sector 125
Noida, UP 201303
India
E-mail: [email protected]
ISBN 978-3-540-78824-9 e-ISBN 978-3-540-78826-3
DOI: 10.1007/978-3-540-78826-3
Library of Congress Control Number: 2008923753
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Foreword
Terrestrial ecosystems are driven by microbial guildes. We are, however, severely
hampered by our limited understanding of the diversity and function of such micro-
bial ecosystems. Growing on mineral particles and decaying organic matter, and liv-
ing in the vicinity of or within plant roots, are a cast of hundreds of competing
versatile and diverse fungal species, including soil decomposers, pathogens, endo-
phytes and obligate symbionts (Frankland 1998). Amongst the extensive intermin-
gling webs of hyphae permeating the soil, those of mycorrhizal fungi play a crucial
role in ecosystem sustainability through their role in biogeochemical cycles. These
mycorrhizal species are no marginal oddity, having been shown to account for half
of the fungal species in most temperate, montane and boreal forests. The hyphae of
mycorrhizal fungi and plant short roots form a novel composite organ, the so-called
mycorrhiza, which is the site of nutrient and carbon transfer between the two symbi-
otic partners. This mutualistic interactions allow terrestrial plants to grow efficiently
in suboptimal environments (Read and Perez-Moreno 2003). They are key drivers of
ecosystem function, receiving 15–25% of carbon net productivity and providing most
of the host plant nitrogen and phosphorus. The symbiotic relationship between roots
and these fungi is undoubtly one of the most prevalent associations in all terrestrial
ecosystems. Knowing which processes these soil fungi are responsible for, and how,
is thus increasingly important for understanding the inputs and outputs in forest eco-
systems under global change. In this book, many of those at the forefront of the
research field integrate and comment on recent developments and ideas on the
molecular biology, physiology, and ecology of the mycorrhizal symbioses. All of the
major types of mycorrhiza are considered. By taking a broad perspective, they show
how new information on mycorrhizal fungi, but also on interactions involving endo-
phytes, nitrogen-fixing bacteria and mycorrhiza helper bacteria, may contribute to
concepts and ideas of biology and ecology as a whole. Just as important, they con-
tribute to further invigoration of mycorrhizal research by illuminating the field with
new ideas and concepts, derived in part from other fields of plant biology and mycol-
ogy. Attempts to improve productivity of ecosystems by inoculation with more effec-
tive fungal symbionts are also described.
The work described here confirms that the ecological performance of mycor-
rhizal fungi is a complex phenotype affected by many different traits and by envi-
ronmental factors. In this Foreword, I will look to future challenges that lie ahead.
v
vi Foreword
Understanding the complexity of the interactions between mycorrhizal symbionts
and how this mutualistic association adapts and responds to changes in the biologi-
cal, chemical and physical properties of the rhizosphere remains a significant chal-
lenge for plant and microbial biologists. Identification of the primary determinants
controlling the symbiosis development and its metabolic activity (e.g., phosphorus,
nitrogen and water acquisition) will open the door to understanding the ecological
fitness of the ectomycorrhizal symbiosis. Without any doubt, anatomical features of
the mycorrhizal mycelial network (e.g., extension of the extramatrical hyphae)
resulting from the symbiosis development is of paramount importance to the meta-
bolic and ecophysiological fitness of the mature mycorrhiza.
In the past decade, research in the field has strongly benefited from approaches
aimed at the elucidation of the molecular mechanisms of mycorrhiza developmental
processes and key concepts and principles have been elaborated (Section II of this
book; see also Harrison 2005; Paszkowski 2006; Martin et al. 2007). The genomics
era for mycorrhizas is not yet in full swing, but it is clear from recent studies, high-
lighted in the reviews in this book, that functional genomics have already made
significant contributions to our understanding of developmental and metabolic
mechanisms leading to the formation and functioning of mycorrhizas. What will
the future bring? We are likely to see imminent advances in understanding of the
molecular and cellular mechanisms of the coordinated regulation of developmental
and metabolic gene expression in symbiotic partners, although the equally impor-
tant mechanisms that modulate cell growth rates and shape during mycorrhiza
development have not generated a similar intensity of interest. With the genome of
the ectomycorrhizal Laccaria bicolor in hand (Martin et al. 2008), and genomes
of the ectomycorrhizal ascomycete Tuber melanosporum and the endomycorrhizal
Glomus intraradices on the way, we should see rapid progress in elucidating the
molecular processes involved in mycorrhizal interactions. The genome sequence of
these mycobionts, their analysis, associated genomics and bioinformatics tools
provide an unprecedented opportunity to identify the key components of organ-
ism–environment interactions that modulate ecosystem responses to global change
and increased nutrient input needed for faster growth of biomass feedstock. The
immediate benefit of these genomic and genetic resources is the increased precision
with which mycorrhizasts can characterize the gene networks controlling the devel-
opmental pathways in fungal symbionts. Alternatively, these genomes will facilitate
whole-genome transcript profiling for further characterization of the repertoire of
symbiosis-regulated genes – from the well-understood protein-coding genes to the
more elusive DNA motifs that regulate gene expression. We should be able to
answers such questions as: What is the role of rhizospheric chemicals and cellular
signals in symbiosis development? How many gene networks control mycorrhiza
development, as distinct from providing the housekeeping functions of the fungal
and plant cells? What could be the molecular basis of such a progressive, highly
organized ontogenic process? The genetic mechanism of symbiosis, which contributes
to the delicate ecological balance in healthy forests, also provides insights into
plant health that may enable more efficient carbon sequestration and enhanced
phytoremediation – using plants to clean up environmental contaminants. We now
Foreword vii
have the opportunity to gain fundamental insights into plant development and
growth as related to their intimate interaction which symbiotic fungi. These
genome-based studies will hopefully spur work on in situ functions of mycorrhizal
individuals (genets), populations and communities through ecological genomics.
The aim of ecological genomic studies is to identify the genes and genetic pathways
that underlie important ecological responses and interactions, determine the extent to
which those genes and pathways exhibit functional variation in nature and characterize
the ecological and evolutionary consequences of that variation (Ungerer et al. 2008).
Another goal of ecological genomic research is to understand how genomes interact
at higher levels of organization, for example, is there a ‘community mycorrhizal
(meta)genome’ and, if so, can we understand how it functions? When considering the
mutualistic interaction of mycorrhizal fungi with their hosts and the impact of the
environmental factors on the fitness of the symbiosis, we would like to identify the
gene networks and gene functions that matter most in a given ecological interaction.
The prerequisite of such studies is the acquisition of census of mycorrhizal fungi in
their patchy soil environment. During the past decade, PCR-based molecular methods
and DNA-sequencing have been routinely used to generate census of mycorrhizal
fungi in numerous ecosystems, and the application of these genotyping methods has
provided detailed insights into the complexity of mycorrhizal fungal communities and
populations, and offers exciting prospects for elucidation of the processes that struc-
ture mycorrhizal fungal communities (Horton and Bruns 2001). These tools have
managed to reveal the tremendous diversity of mycorrhizal fungi interacting with their
host in space and time, but also how different environmental factors and land usage
could alter the composition of these soil fungal communities. Applied to species sur-
vey, the use of DNA arrays is likely to bring typing of hundreds of individuals, or even
entire populations, into the realm of practical reality. If mycorrhizasts follow the tracks
of their plant or bacterial geneticist fellows, environmental soil samples will also be
probed with hundreds to thousands of different protein-coding gene probes (e.g.,
GeoChip functional gene arrays; He et al. 2008) to tackle ecological questions such as
regulation of nutrient acquisition by extramatrical mycorrhizal hyphae. Single nucle-
otide polymorphisms (SNPs) and high-density DNA oligoarrays of model mycorrhizal
species, such as L. bicolor, and its sequenced host tree, Populus trichocarpa, usher in
the possibility of determining allelic imbalance at hundreds of symbiosis-regulated
loci from hundreds of DNA samples, allowing the contemplation of genome-wide
association studies (Zhu and Salmeron 2007) to determine the genetic contribution to
this complex polygenic processes. A combination of the analysis of community/popu-
lation composition of mycorrhizal fungi by high-throughput DNA genotyping with in
situ assessment of function by transcript profiling will have a substantial effect on the
kinds of questions that can be addressed in ecology, particularly for model symbionts
where genome sequences and transcriptome have been released (e.g., Laccaria,
Pisolithus, Hebeloma, Glomus, Medicago and Populus). This book is therefore not the
last word on mycorrhizal research; it is a description of where we stand, how we got
here and perhaps a view of where we might be headed.
Francis Martin
viii Foreword
References
Frankland JC (1998) Fungal succession – unravelling the unpredictable. Mycol Res 102:1–15
Harrison M (2005) Signaling in the arbuscular mycorrhizal symbiosis. Annu Rev Microbiol
59:19–42
He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, Chong SC, Huang Z, Wu W, Gu B, Jardine P,
Criddle C, Zhou J (2007) GeoChip: a comprehensive microarray for investigating biogeo-
chemical, ecological and environmental processes. Int Soc Microb Ecol J 1:67–77
Horton TR, Bruns TD (2001) The molecular revolution in ectomycorrhizal ecology: peeking into
the black-box. Mol Ecol 10:1855–1871
Martin F, Kohler A, Duplessis S (2007) Living in harmony in the wood underground: ectomycor-
rhizal genomics. Curr Opin Plant Biol 10:204–210
Martin F, Aerts A, Ahrén D, Brun A, Danchin EGJ, Duchaussoy F et al. (2008) Symbiosis insights
from the genome of the mycorrhizal basidiomycete Laccaria bicolor. Nature 452:88–92
Paszkowski U (2006) A journey through signaling in arbuscular mycorrhizal symbioses 2006.
New Phytol 172:35–46
Read DJ, Perez-Moreno J (2003) Mycorrhizas and nutrient cycling in ecosystems – a journey
towards relevance? New Phytol 157:475–492
Ungerer MC, Johnson LC, Herman MA (2008) Ecological genomics: understanding gene and
genome function in the natural environment. Heredity 100:178–183
Zhu T, Salmeron J (2007) High-definition genome profiling for genetic marker discovery. Trends
Plant Sci 12:196–202
Preface
It has been a pleasure to edit this book, primarily due to stimulating discussions with
a large number of eminent scientists working on mycorrhizal science and other root
endophytes, students and fellow colleagues. The first and second editions were jointly
edited with Professor Dr. Berthold Hock, Technical University, München, Germany,
and published in 1995 and 1999, respectively. This third edition falls into a time
period exceptionally rapid growth in mycorrhizal research. Therefore, the editor has
been most pleased with the decision of Springer-Verlag to revise and update and to
incorporate the remarkable advances experienced in mycorrhizal field.
A vast expansion of interest in mycorrhiza, resulting in public awareness that the
productivity of plants and the quality of leaves, flowers, fruits and seeds are deter-
mined by the activities of root systems and their associated physical, chemical and
biological environment, is manifest worldwide. Symbiotic fungi have become
important subjects of tests to evaluate some of the new opportunities being devel-
oped in biotechnology. While these fungi have been used to stabilize eroded soils
and the forests since the turn of century, the novelty in recent years has been
increased recognition that biological processes can be manipulated genetically,
opening up numerous unexplored opportunities for the optimization of plant
productivity in both managed and natural ecosystems, while minimizing the risks
of environmental damage. The book contains the current state of knowledge and
theories on the structure, function, molecular biology and biotechnological applica-
tions of mycorrhizas. It will thus be of interest to a diverse audience of researchers
and instructors, especially biologists, biochemists, agronomists, foresters, horticul-
turists, mycologists, soil scientists, ecologists, plant physiologists, microbiologists
and landscape architects.
In planning this book, invitations for contributions were extended to leading
international authorities working with symbiotic fungi. I would like to express my
sincere appreciation to each contributor for his/her work, patience and attention to
detail during the entire production process. It is hoped that the reviews, interpreta-
tion and concepts proposed by the authors will stimulate further research, as the
information presented tends to highlight both the need for further work in this
challenging field and the lack of agreement on some fundamental issues.
The encouragement and inspiration received from the Dr. Ashok K Chauhan,
Founder President, Ritnand Balved Education Foundation, Sri Atul Chauhan,
ix
x Preface
Chancellor, Amity University Uttar Pradesh, and Sri Aseem Chauhan, Chancellor,
Amity University Rajasthan need special mention. I am indebted to Dr. Dieter
Czeschlik for his continued interest and Ursula Gramm for active help. I wish to
acknowledge the help and support given to me by my students, faculty colleagues,
family members and friends for their constant encouragement.
Amity University Ajit Varma
Uttar Pradesh, India
April 2008