Living in harmony in the wood underground: ectomycorrhizal genomics

Living in harmony in the wood underground:ectomycorrhizal genomicsFrancis Martin, Annegret Kohler and Sebastien Duplessis

The ectomycorrhizal symbiosis involving trees and soil

fungi is a process of major ecological importance in forest

ecosystems. The establishment of an effective symbiosis

encompasses a series of complex and overlapping

developmental processes in the colonizing mycelium and roots

of host trees. Regulated gene expression is an important

mechanism for controlling ectomycorrhizal symbiosis

development and functioning. Gene profiling studies led to the

identification of genes that are required for fungal attachment,

plant defense, and symbiosis-related metabolism. They

showed that changes in morphology associated with

mycorrhizal development were accompanied by changes in

transcript patterns, but no ectomycorrhiza-specific genes were

detected. Comparison of the genomes of pathogenic and

saprobic fungi with the recently released ectomycorrhizal

Laccaria genome is providing crucial insights into the genetic

makeup of plant–fungus interactions.

Addresses

UMR 1136 INRA/UHP, Interactions Arbres/Micro-Organismes, IFR 110,

Centre INRA de Nancy, 54280 Champenoux, France

Corresponding author: Martin, Francis ([email protected])

Current Opinion in Plant Biology 2007, 10:204–210

This review comes from a themed issue on

Genome studies and molecular genetics

Edited by Stefan Jansson and Edward S Buckler

Available online 8th February 2007

1369-5266/$ – see front matter

# 2007 Elsevier Ltd. All rights reserved.

DOI 10.1016/j.pbi.2007.01.006

IntroductionMycorrhizal symbioses — the union of roots and soil fungi

— are widespread: boreal, temperate, montane and trop-

ical forests all have them, as do grasslands and tundras.

Within days of their emergence in the upper soil profiles,

up to 95% of short roots of most terrestrial plants are

colonized by mycorrhizal fungi. The fungal symbionts

send out extensive webs of fine threads of mycelia, which

link with and extend the reach of plant roots. Host plants

are then able to harness mycorrhizal symbionts very

efficiently for their nutritional benefit. They hijack the

formidable web of saprotrophic hyphae of mycorrhizal

fungi permeating the soil horizons, litter and decaying

wood debris. The prospecting mycelium delivers soil

minerals, particularly phosphorus and nitrogen, to the


host roots; the plants reward them with energizing

photoassimilates. In addition, these fungal threads link

one plant to another, transferring nutrients not only

among fungi but also from plant to plant, shaping the

biological makeup of whole communities [1].

It is widely thought that the activity of mycorrhizal fungi

affected the evolution of early land plants [2,3]. There are

therefore important ecological benefits to be gained from

understanding the molecular evolution of mycorrhizal

symbioses. Although research over the past decade has

broadened our knowledge of the ecological roles of

mycorrhizal symbioses [1], our understanding of the

mechanisms that govern the establishment and function-

ing of arbuscular endomycorrhiza (AM) and ectomycor-

rhizal (ECM) symbioses has only recently significantly

improved. What could be the molecular basis of such a

progressive, highly organized ontogenic process? What is

the role of rhizospheric chemicals and cellular signals in

symbiosis development? How many gene networks con-

trol mycorrhiza development, as distinct from providing

the housekeeping functions of the fungal and plant cells?

This review focuses on the molecular processes involved

in the development of ECM symbiosis. Recent reviews

[4–6] summarize the progress made in understanding AM

symbiosis.

The quest for master symbiotic genes in theectomycorrhizal symbiosisEctomycorrhizal fungi are best known for their fruiting

structures (e.g. toadstools) that often grow next to tree

trunks in woodlands. Although a relatively small number

of plants (around 8000) form ECM, the ecological import-

ance of these symbioses is amplified by their wide occu-

pancy of biomes [1,3]. Through mutualistic symbioses

with ECM fungi, tree species have been able to acquire

metabolic capabilities that have allowed the utilization of

otherwise unavailable ecological niches. The mechan-

isms involved in the development of symbiosis are likely

to be similar if not identical in the numerous ectomycor-

rhizal morphotypes and in mutualistic and some bio-

trophic parasitic symbioses. The identification of these

primary genetic determinants is a daunting task. It

involves the typical gene-to-phenotype approach (i.e.

the identification of traits by characterization of gene

expression and subsequent gene inactivation). It should

be kept in mind, however, that this powerful approach

might be restricted by the fact that symbiosis develop-

ment and activity might be determined partly by complex

epistatic interactions among different genes showing

subtle quantitative variation.

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http://dx.doi.org/10.1016/j.pbi.2007.01.006

Ectomycorrhizal genomics Martin, Kohler and Duplessis 205

The pathways triggering the development of the ecto-

mycorrhizal hyphal networks (i.e. mantle sheath, apoplas-

tic Hartig net and soil fungal mats) involve a cascade of

nuclear gene expression, including the expression of

genes that encode developmental proteins, enzymes

and transporters that regulate the details of symbiosis

development [7]. These genes respond to rhizospheric

and apoplastic signals released by the plant partner,

positional information mediated by sensory molecules

and nutritional cues [7–9]. In the wake of the first tran-

script profiling of the Eucalyptus–Pisolithus symbiosis [10],

hundreds of genes that are preferentially expressed in

symbiotic tissues have been identified using cDNA

arrays, amplified fragment length polymorphism (AFLP)

or suppression subtractive hybridization (SSH) [11–14,

15��,16��]. These studies have confirmed that dramatic

alterations in gene expression take place during, and are

likely to be required for, symbiosis development; how-

ever, plant and fungal genetic switches that are necessary

for ECM development remain unidentified to date.

Legume mutants have been key to identifying the

genetic switches in AM development [4,6,17]. Impaired

genes such as those encoding the SYMRK/NORK/DMI2

receptor kinase, the DMI1 ion channel and DMI3

calcium- and calmodulin-dependent kinase are collec-

tively referred to as the ‘common’ SYM genes. These

genes define a partial overlap between the genetic pro-

grams for AM endosymbiosis and those for the nitrogen-

fixing root nodule symbiosis. The evolutionary implica-

tion is that the younger bacterial symbiosis has recruited

perception functions from the ancient AM symbiosis. It is

tempting to speculate that the recent ectomycorrhizal

symbioses (which first evolved around 180 million years

ago) have also recruited the AM symbiosis SYM genes for

signaling and the early steps of the symbiosis (e.g. intra-

radicular accommodation).

These DMI genes are found in the genome of Populustrichocarpa [18��], a tree hosting both AM and ECM

symbioses. Their inactivation using RNAi will confirm

whether or not perennial tree species and legumes have

evolved similar mechanisms to interact with mycorrhizal

fungi. Although many pieces of the puzzle remain to be

elucidated, it seems inescapable that the cross-talk

between rhizospheric metabolites, the hormonal balance

and signalling networks involving Ca2+ play important

roles in coordinating the execution of the appropriate

responses. It will be fascinating to learn more about the

multiple facets of this communication network. In this

regard, advances in the elucidation of symbiosis signalling

pathways can be accelerated by the identification of more

target genes by transcript profiling [15��,16��] and inser-

tional mutagenesis [22].

Interestingly, a quantitative trait locus (QTL) linked to

ectomycorrhizal infection rate on the male P. trichocarpa


genetic map was localized close to a locus previously

shown to be involved in the interaction between Populusand the foliar rust fungus Melampsora larici populina [20].

This evidence provides a genetic indication that the

ectomycorrhizal trait could be associated with loci and

genes that might be common to the interaction with

mutualistic root and pathogenic leaf fungi [19].

Transcript alteration in symbiotic tissueTo examine gene activity changes that are associated with

the development of the Eucalyptus–Pisolithus and Betula–Paxillus symbioses, expression profiling using cDNA arrays

were performed during the development of ectomycor-

rhiza [15��,16��]. RNAs used for cDNA array hybridiz-

ations were derived from nonmycorrhizal roots, free-

living mycelium and colonized roots collected during

the early, middle and late stages of symbiosis development.

Thus, these time points for RNA collection correspond to

the various stages of ectomycorrhiza development: i) early

hyphae–root contacts, ii) root surface colonization, mantle

formation, root penetration and subsequent Hartig net

formation, and iii) mature symbiotic organ. These inves-

tigations confirmed that changes in morphology that are

associated with mycorrhizal development were accom-

panied by changes in transcript patterns and that these

changes commenced at the time of contact between the

two partners, long before the formation of functional

ectomycorrhiza.

Clustering algorithms revealed groups of transcripts that

have both related regulation patterns and expression

amplitudes (Figure 1). Developmental reprogramming

was observed in roots and hyphae, although the magnitude

of transcriptome alteration appears to be much larger in the

mycelium (�10–20% of the analyzed transcripts) than in

root cells (�2% of the transcripts) [10,14,15��,16��]. Induc-

tion of common gene networks takes place in ectomycor-

rhizal systems, as demonstrated by the observation

that several cellular functions are similarly regulated in

the investigated symbiotic models. For example, many

cellular functions were found to be upregulated upon

symbiosis development, including fungal cell division

and proliferation, differentiation and signaling, synthesis

of cell wall and extracellular matrices, plant defense or

stress responses and primary metabolism (i.e. glycolytic

respiration, amino acid biosynthesis and the activity of

transporters).

At the different developmental stages studied, the devel-

opment of the symbioses between Pisolithus–Eucalyptus,Paxillus–Betula, Pisolithus–Populus, Laccaria–Populus, Lac-caria–Pseudotsuga and Tuber–Tilia do not induce the

expression of ectomycorrhiza-specific genes [10–14,

15��,16��]. Overall, the induction or repression rates of

the ectomycorrhiza-regulated genes were moderate and

rarely exceeded five-fold upregulation or downregulation.

An analysis of around 9500 unique transcripts (i.e. 20% of


206 Genome studies and molecular genetics

Figure 1

The main expression patterns of plant and fungal symbiosis-regulated genes during the development of the ectomycorrhizal symbiosis, as revealed by

transcript profiling studies. Transcriptional responses of fungal and root tissues progressing through the development of ectomycorrhiza were

investigated in the Betula–Paxillus and Eucalyptus–Pisolithus interactions using cDNA arrays [15��,16��]. We have derived groups of coordinately

expressed genes using hierarchical and non-hierarchical clustering algorithms. Major temporal patterns of induction or repression were observed with

distinct groups of genes that have early, middle and late transcription responses to fungal colonization (after [15��]).

the total gene set) of P. trichocarpa confirmed the lack of

host ectomycorrhiza-specific genes (A Kohler et al. unpub-

lished). The apparent lack of ectomycorrhiza-specific

genes and the moderate induction of symbiosis-regulated

genes are striking, and suggest that ontogenic and meta-


bolic programs that lead to the development of symbiosis

are driven by the differential expression of pre-existing

transcription factors and/or transduction pathways, rather

than by the expression of symbiosis-specific gene arrays.

A more complete analysis of this crucial question awaits the



completion of larger sets of ECM expression profiles on a

wider range of associations using whole-genome microar-

rays and high-throughput quantitative PCR of transcrip-

tion factors.

By comparing two closely related strains of Paxillus invo-lutus, Le Quere et al. [21] showed that loss of symbiotic

ability was associated with the lack of plant-induced gene

expression of symbiosis-regulated genes. The observed

changes in expression are likely to be due to changes in

promoter element sequences and expression levels of

transcription factors. Tunlid and coworkers also showed

that the lack of mutualism was associated with structural

changes in the products of two of the differentially

regulated genes, the gene encoding the conconamycin-

induced protein CIPC1 and that encoding the metallo-

chaperone CCHA [21]. A further challenge will be to

investigate the function of these proteins and how the

observed nucleotide substitutions alter symbiotic com-

patibility.

The ectomycorrhiza-regulated genes that have been

identified using transcriptomics are primary targets for

gene inactivation, but homologous recombination and

RNA interference procedures are not yet available for

ECM fungi. In a breakthrough study, Agrobacterium-

mediated transformation was recently used for random

insertional mutagenesis to generate mutants of the ecto-

mycorrhizal basidiomycete Hebeloma cylindrosporum that

were impaired in their symbiotic capability [22]. Light

and scanning electron microscopy observations of pine

roots inoculated with nonmycorrhizal (myc null) mutants

suggested that these mutants were blocked at early stages

of interaction, confirming that master genes are essential

for symbiosis development.

Toward the promised land: how to land andescape host surveillanceBefore contact, the hyphae of ECM fungi growing in the

rhizosphere induce an intense short-root formation, pro-

viding a means of increasing contact sites and niches for

hosting the colonizing hyphae. The molecular basis for this

coup d’etat is unknown, but it is clear that the mycobiont

alters auxin-regulated developmental pathways, meriste-

matic activity and cell shape through the action of secreted

molecules, such as auxins and hypaphorin, an indole-3-

acetic acid (IAA) antagonist [7,8,23,24]. Several ectomy-

corrhiza-regulated genes in host tissues are involved in

auxin metabolism, calcium signaling pathways and tran-

scriptional regulation, thus supporting this hypothesis

[10,14,15��,16��].

After contact, mycorrhizal fungi must be equipped to

evade or overcome the constitutive barriers and inducible

defenses of its host, and must possess the developmental

and metabolic features needed to exploit the nutritional

environment provided by that host. Some nonspecific,


broad-spectrum responses (e.g. those involving metal-

lothioneins, chitinases, glutathione S-transferases and

peroxidases) are clearly mounted in plant hosts when

ectomycorrhizal fungi approach the host roots [25] and

as they penetrate the root and digest their way through

the apoplastic space [15��,16��]. These induced defense

responses might limit the fungal invasion of root tissues.

Future research should explore the molecular mechan-

isms that orchestrate the escape of the symbionts from the

host defense system. For example, we do not know how

ECM fungi avoid clearance by the innate immune system

of the host and persist for large periods of time in host

tissues.

Novel metabolic networks for a fair tradeAs expected from an alliance aimed to better exploit the

scarce nutrients of soil horizons, symbiosis induces

dramatic changes in nutrient content and metabolic fluxes

in root and fungal tissues [26]. To survive in planta, the

developing mycobiont must express the channels, pumps

and transporters at the appropriate time, the correct

location and at the right levels [27�,28]. ECM fungi

activate and regulate the anabolic and catabolic enzymes

involved in nutrition and growth over a sustained period

to complete the symbiosis development [15��,16��]. It has

been a general observation that these metabolic altera-

tions are also accompanied by mineral and nutrient-

related changes in plant gene expression.

Owing to large expressed sequence tag (EST) sets

[12,28] and available Populus [18��] and Laccaria (http://

genome.jgi-psf.org/Lacbi1/Lacbi1.home.html) genome

sequences, several genes encoding transporters [29–

33,34�] and channels [35] have been cloned and their

expression during ECM development investigated. The

observed upregulation of several of these genes is likely to

reflect the intense metabolite fluxes occurring between the

symbiotic partners and reveal a complex interplay of fungal

and plant transporter activities. An important challenge

will be to determine how the different transporters are

reallocated at the plant–fungal interface to sustain the

intense and opposite fluxes of phosphorus and nitrogen

compounds (fungus to plant) and carbon assimilates

(plant to fungus).

An additional challenge for further research will be to

identify the ‘dispatch centre’, if any, that coordinates the

fluxes of cargo vesicle that translocate transporter proteins

to the plasma membranes of the symbiotic interfaces.

Functional specialization of the hyphal webcompartmentsThe fungal symbiont differentiates three main hyphal

networks: (i) the mantle and intraradical Hartig net of the

ectomycorrhizal tips with their mutualistic activities, (ii)

the rhizomorphic web linking the latter tissues to (iii)


http://genome.jgi-psf.org/Lacbi1/Lacbi1.home.html



fungal mats that proliferate on nutrient-rich sources

in the different soil horizons. These compartments

with contrasted metabolic activities should efficiently

solve logistics issues. In microcosms mimicking forest

soil conditions, Wright et al. [36��] and Morel et al.[37�] identified striking differential expression in the

various fungal compartments of the Betula–Paxillusassociation (i.e. mycelial patches growing on nutrient

sources, extramatrical hyphae, rhizomorphs draining

metabolites to the symbiotic tissues and ectomycorrhizal

tips). The pattern of differential expression of genes (e.g.

nitrogen-assimilating enzymes) might be influenced by

multiple factors, such as the level of nutrients within the

nutrient patches, the extent of metabolite translocation

versus assimilation within the extramatrical mycelium,

and the microenvironment in which the rhizomorph and

mycorrhizal root tips are situated. Interestingly, both

Wright et al. [36��] and Morel et al. [37�] showed that

urea was the principal nitrogen compound in hyphae, and

suggested that the urea cycle could be activated in

extramatrical mycelium of P. involutus under nitrogen-

limited conditions; it might also play a key role in both

nitrogen translocation between the hyphal webs and in

nitrogen transport between partners [27�].

These novel transcriptomics data clearly confirmed the

physiological heterogeneity and functional specialization

among the different compartments of the fungal webs

[38]. The identification of signals that coordinate these

activities is a major focus for further research. Whether

gene expression of metabolic genes is controlled by sugar-

and amino-acid-dependent regulation, as reported for

free-living mycelium [9], by symbiosis-related develop-

mental signals [7], the external microenvironment

[36��,37�] or, as is likely, by a complex blend of these

different signals is currently unknown.

What makes a good ectomycorrhizal fungus?The ECM fungi are found in many ascomycetous and

basidiomycetous clades, suggesting that this mutualistic

habit has evolved several times during the evolution of the

Mycota kingdom, probably from saprotrophic ancestors

[39].

On the genomic level, there are basically three compatible

mechanisms that can account for the multiple emergences

of and adaptations to symbiosis in fungi: differences in the

regulation of gene expression through the activity of a core

set of transcription factors; the presence of novel genes; and

gene loss and deletions [40]. The mechanism(s) involved

are likely to be identified in the coming years through

comparative genomics, because a large amount of infor-

mation from the genome sequences of fungal saprotrophs,

pathogens and symbionts is now available through the

Fungal Genome Initiative at the Broad Institute (http://

www.broad.mit.edu/annotation/fungi/fgi/) and the Com-

munity Sequencing Programme of the US Department


of Energy Joint Genome Institute (http://www.jgi.doe.gov/

CSP/index.html). There are currently 115 completed or

ongoing fungal genome projects [41,42].

In the wake of the Populus genome sequencing project

[18��], the sequencing of the genome of the ECM basi-

diomycete Laccaria bicolor was accomplished, using the

whole-genome shotgun approach, by the US Department

of Energy Joint Genome Institute (Laccaria Genome Por-

tal; [http://genome.jgi-psf.org/Lacbi1/Lacbi1.home.html])

and the Laccaria Genome Consortium, and publicly

released in July 2006.

The Laccaria genome is much larger (�65 Mb) than that

of the other fungi whose genomic sequences have been

published [41–45]. A total of around 20 000 genes encod-

ing proteins (i.e. 37% of the whole-genome sequence)

were identified using automated annotation and manual

curation. These genes contain many short introns and, as

expected from previous EST analysis [12], 50% of them

are of unknown function. Predicted genes, supporting

evidence, and structural and functional annotations are

available through interactive visualization and analysis

tools from the JGI Laccaria Genome Portal.

This genome sequence, from a major mycorrhizal clade,

reveals an organism equipped to take advantage of tran-

sient occurrences of high-nutrient niches within a bulk

low-nutrient environment. Not only the roots of the host–

plant but also dead organic matter and microscale ‘hot

spots’ of the rhizospheric soil might provide such niches.

Ongoing analysis of the Laccaria genome reveals that this

ECM basidiomycete has both saprotrophic and mutualistic

abilities (F Martin et al., unpublished). By elucidating the

genomes of close relatives that have differing saprotrophic

or symbiotic properties, such as the basidiomycetous gill

mushrooms L. bicolor and Coprinopsis cinerea, we will be

able to catalogue the genetic differences that might

underlie their different life habits. Hence, we should

achieve a deeper understanding of the processes by which

fungi colonize wood, interact with their host trees in their

ecosystem and perform vital functions in the carbon and

nitrogen cycles.

ConclusionsTranscriptomics of the ectomycorrhizal symbiosis offers

new insights into our understanding of both biotrophic

interactions and fungal and root development. The

integration of knowledge arising from whole-genome

sequencing with information provided by transcrip-

tomics and advanced functional analysis of target genes,

such as transporters, will help us understand how

fungi have learned to interact with plants in a balanced

way.

A view that is gaining increasing support among research-

ers studying plant–microbe interactions is the hypothesis


http://www.broad.mit.edu/annotation/fungi/fgi/

http://www.broad.mit.edu/annotation/fungi/fgi/

http://www.jgi.doe.gov/CSP/index.html

http://www.jgi.doe.gov/CSP/index.html



that plant fungal pathogens might have arisen by the

recruitment and exploitation of gene networks of ancient

symbiotic pathways; the symbionts themselves being

derived from saprotrophic ancestors. The gene networks

that control the saprotrophic/biotrophic phase switch,

recognition mechanisms, host penetration and in plantaaccommodation are often alike in biotrophic parasites and

mutualistic symbionts. Analysis of the molecular mech-

anisms that lead to ECM symbiosis should thus lead to a

better understanding of plant–pathogen interactions. It

will be far harder to define genes that influence symbiont

fitness. Any gene that provides the mycobiont with a

growth advantage could easily influence how beneficial a

particular strain is within a given host. Therefore, dis-

secting the molecular mechanisms of symbiosis fitness

requires both the identification of the functions of indi-

vidual genes and knowledge of how genes interact to form

complex traits, such as those expressed in a mutualistic

symbiosis. It is difficult to predict the total number of

genes involved in symbiosis and, hence, the scope for

each mycorrhizal association to be unique. There are

more than 8000 different ectomycorrhizal associations,

and each and every ectomycorrhizal type might express a

specific set of genes. Despite this, a variety of morpho-

logical and molecular common parameters can be used to

classify ectomycorrhizal symbioses into discrete molecu-

lar classes for further investigation [15��,16��]. In the

future, symbiotic molecular phenotypes might be corre-

lated to ecological phenotypes.

Finally, knowledge of the regulatory mechanisms that

allow fungal symbionts to promote plant growth in nutri-

ent-scarce environments will provide the information

needed to manage sustainable forest ecosystems in a

biosphere threatened by global climate changes.

AcknowledgementsSpecial thanks go to the former and present members of our research groupfor their great contributions to our work and for stimulating discussions.Investigations carried out in our laboratory were supported by grants fromthe INRA, Genoscope (project ForEST) and the Region Lorraine. TheLaccaria genome project was performed under the auspices of the USDepartment of Energy’s Office of Science, Biological and EnvironmentalResearch Program, the University of California, Lawrence LivermoreNational Laboratory and INRA.

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� of special interest�� of outstanding interest

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16.��

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21. Le Quere A, Eriksen KA, Rajashekar B, Schutzendubel A,Canback B, Johansson T, Tunlid A: Screening for rapidlyevolving genes in the ectomycorrhizal fungus Paxillusinvolutus using cDNA microarrays. Mol Ecol 2006, 15:535-550.

22. Combier JP, Melayah D, Raffier C, Pepin R, Marmeisse R, Gay G:Nonmycorrhizal (MycS) mutants of Hebeloma cylindrosporumobtained through insertional mutagenesis. Mol Plant MicrobeInteract 2004, 17:1029-1038.

23. Dauphin A, De Ruijter NCA, Emons AMC, Legue V: Actinorganization during Eucalyptus root hair development and itsresponse to fungal hypaphorine. Plant Biol 2006, 8:204-211.

24. Reboutier D, Bianchi M, Brault M, Roux C, Dauphin A, Rona JP,Legue V, Lapeyrie F, Bouteau F: The indolic compoundhypaphorine produced by ectomycorrhizal fungus interfereswith auxin action and evokes early responses in nonhostArabidopsis thaliana. Mol Plant Microbe Interact 2002,15:932-938.

25. Frettinger P, Derory J, Herrmann S, Plomion C, Lapeyrie F,Oelmuller R, Martin F, Buscot F: Transcriptional changes intwo types of pre-mycorrhizal roots and in ectomycorrhizas ofoak microcuttings inoculated with Piloderma croceum.Planta 2007, 225:331-340.

26. Laczko E, Boller T, Wiemken V: Lipids in roots of Pinus sylvestrisseedlings and in mycelia of Pisolithus tinctorius duringectomycorrhiza formation: changes in fatty acid and sterolcomposition. Plant Cell Environ 2003, 27:27-40.

27.�

Chalot M, Blaudez D, Brun A: Ammonia: a candidate for nitrogentransfer at the mycorrhizal interface. Trends Plant Sci 2006,11:263-266.

The data reviewed herein provide strong biochemical evidence thatammonium might play a role in nitrogen translocation between ectomy-corrhizal partners. Together with the papers by Laczko et al. [26] and Selleet al. [34�], this paper re-visits the text book view on pathways that areinvolved in nutrient exchanges in mycorrhizal symbioses.

28. Lambilliotte R, Cooke R, Samson D, Fizames C, Gaymard F,Plassard C, Tatry MV, Berger C, Laudie M, Legeai F et al.:Large-scale identification of genes in the fungus Hebelomacylindrosporum paves the way to molecular analyses ofectomycorrhizal symbiosis. New Phytol 2004, 164:505-513.

29. Jargeat P, Rekangalt D, Verner MC, Gay G, Debaud JC,Marmeisse R, Fraissinet-Tachet L: Characterisation andexpression analysis of a nitrate transporter and nitritereductase genes, two members of a gene cluster for nitrateassimilation from the symbiotic basidiomycete Hebelomacylindrosporum. Curr Genet 2003, 43:199-205.

30. Javelle A, Andre B, Marini AM, Chalot M: High-affinityammonium transporters and nitrogen sensing in mycorrhizas.Trends Microbiol 2003, 11:53-55.

31. Javelle A, Morel M, Rodriguez-Pastrana BR, Botton B, Andre B,Marini AM, Brun A, Chalot M: Molecular characterization,function and regulation of ammonium transporters (Amt)and ammonium-metabolizing enzymes (GS, NADP-GDH) inthe ectomycorrhizal fungus Hebeloma cylindrosporum.Mol Microbiol 2003, 47:411-430.

32. Wipf D, Benjdia M, Tegeder M, Frommer WB: Characterization ofa general amino acid permease from Hebelomacylindrosporum. FEBS Lett 2002, 528:119-124.

33. Grunze N, Willmann M, Nehls U: The impact of ectomycorrhizaformation on monosaccharide transporter gene expression inpoplar roots. New Phytol 2004, 164:147-155.


34.�

Selle A, Willmann M, Grinze N, Geßler A, Weiß M, Nehls U: Thehigh-affinity poplar ammonium importer PttAMT1.2 and its rolein ectomycorrhizal symbiosis. New Phytol 2005, 168:697-706.

This study shows an increased ammonium uptake capacity of mycor-rhizal Populus roots through the mycorrhiza-dependent upregulation ofan ammonium transporter. It also suggests, together with the expressionof putative ammonium exporter genes in the ectomycorrhizal fungusAmanita muscaria, that ammonium could be a major nitrogen sourcedelivered from the fungus to the plant in symbiosis. Also see annotationChalot et al. [27�].

35. Marjanovic Z, Uehlein N, Kaldenhoff R, Zwiazek JJ, Weiß M,Hampp R, Nehls U: Aquaporins in poplar: what a difference asymbiont makes! Planta 2006, 222:258-268.

36.��

Wright DP, Johansson T, Le Quere A, Soderstrom B, Tunlid A:Spatial patterns of gene expression in the extramatricalmycelium and mycorrhizal root tips formed by theectomycorrhizal fungus Paxillus involutus in associationwith birch (Betula pendula) seedlings in soil microcosms.New Phytol 2005, 167:579-596.

Using soil microcosms of increased ecological complexity, more geno-mics studies of the kind discussed herein will advance our understandingof mycorrhizal symbioses in situ. The authors investigated the geneexpression of the mycobiont in the major hyphal compartments (i.e.symbiotic root tissues, the web of rhizomorphic hyphae permeatingthe soil and the fungal patches proliferating on nutrient sources). Pre-ferentially expressed genes were identified in these various compart-ments, illustrating the physiological heterogeneity of the fungal mycelia. Itis a major touchstone for future research.

37.�

Morel M, Jacob C, Kohler A, Johansson T, Martin F, Chalot M,Brun A: Identification of genes differentially expressed inextraradical mycelium and ectomycorrhizal roots duringPaxillus involutus–Betula pendula ectomycorrhizal symbiosis.Appl Environ Microbiol 2005, 71:382-391.

Together with the work described by Wright et al. [36��], this study usessoil microcosms to investigate functional specialization among the dif-ferent compartments of the fungal webs in ectomycorrhizal symbiosis.This transcriptomics analysis shows the overlooked importance of theurea cycle in nitrogen translocation in ectomycorrhizal systems.

38. Cairney JWG, Burke RM: Physiological heterogeneity withinfungal mycelia: an important concept for a functionalunderstanding of the ectomycorrhizal symbiosis.New Phytol 1996, 134:685-695.

39. Hibbett DS, Gilbert LB, Donoghue MJ: Evolutionary instabilityof ectomycorrhizal symbioses in basidiomycetes.Nature 2000, 407:506-508.

40. Tunlid A, Talbot NJ: Genomics of parasitic and symbiotic fungi.Curr Opin Microbiol 2002, 5:513-519.

41. Galagan JE, Henn MR, Li-Jun Ma, Cuomo CA, Birren B: Genomicsof the fungal kingdom: insights into eukaryotic biology.Genome Res 2005, 15:1620-1631.

42. Xu JR, Peng YL, Dickman MB, Sharon A: The dawn of fungalpathogen genomics. Annu Rev Phytopathol 2006, 44:337-366.

43. Martinez D, Larrondo LF, Putnam N, Sollewijn Gelpke MD,Huang K, Chapman J, Helfenbein KG, Ramaiya P, Detter JC,Larimer F et al.: Genome sequence of the lignocellulosedegrading fungus Phanerochaete chrysosporium strain RP78.Nat Biotechnol 2004, 22:695-700.

44. Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D,Vamathevan J, Miranda M, Anderson IJ, Fraser JA et al.: Thegenome of the basidiomycetous yeast and human pathogenCryptococcus neoformans. Science 2005, 307:1321-1324.

45. Kamper J, Kahmann R, Bolker M, Ma L-J, Brefort T, Saville BJ,Banuett F, Kronstad JW, Gold SE, Muller O et al.: Insights fromthe genome of the biotrophic fungal plant pathogen Ustilagomaydis. Nature 2006, 444:97-101.


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Living in harmony in the wood underground: ectomycorrhizal genomics