Doyle Mckey

Régis Courtecuisse

Jacques Fournier

Christian Lechat

Gérald Gruhn

Stephane Welti

Cony Decock

Terry Henkel

Maria-Alice Neves

Emmanuelle Cam

Christophe Thébaud

Elisabeth Jamet

How would you transmit your passion" was a question from a colleague, during my application for the Maître de conference position in Toulouse. At that time, I replied that bringing students to the field was the key. I would perhaps answer differently today, and mention that meeting passionate people can be contagious too. Through this synthesis, I have tried to tell how interactions, through scientific collaborations with great colleagues -often crazy about the field and dispersed all around the world-have built my research. However, my research has also evolved through coffee-breaks, mushroom, or salad-picking walks, creative dinners, wine tasting, gliding, with many other friends, scientific or not, and I already apologize for not naming all of you. Today, I feel deeply lucky, to teach ecology and evolution, to enthuse students about symbioses, fungi and wine making, and share my interest for forests all around the world. I must thank my parents first, for letting me grow so close to the forest and discover the taste for freedom, travels and passions. I cannot thank Marc-André Selosse enough for his education during my PhD, his constant support and his friendship. His methods still inspire my creative teachings

6

PhD and anterior research topics Articles during my PhD Consiglio et al., 2007 ;Roy et al., 2008 ;Roy et al., 2009a ;2009b ;Selosse and Roy, 2009 ;Pedersen et al., 2009 Between PhD andMCF position Selosse et al., 2010 ;Tranchida-Lombardo et al., 2010 ;Richard et al., 2011 On PhD topic during my MCF position Hynson et al., 2013 ;Kohout et al., 2013a ;2013b ;Roy et al., 2013b ;[START_REF] Tesitelova | [END_REF]Gonneau et al., 2014 ;Roy et al., 2014 ;Shefferson et al., 2016 ;2018. Before my recruitment at UPS in 2010, I was already familiar with plant-fungi symbioses. I was fascinated by symbioses early in my scholarship, thanks to naturalist books and observations. My first practical stage in Erasmus at La Sapienza (Roma, Italy) focused on lichens, and I worked in Master 1 (Magistère ENS Lyon) on Medicago truncatula and its bacteria. Marc-André Selosse supervised my M2 (DEA Ressources Phytogénétiques et Interactions Biologiques) at CEFE (Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier) on a very generalist symbiosis, between Laccaria bicolor and its diverse hosts, such as oaks, beech and pines (Roy et al., 2008). I discovered fungal taxonomy at CEFE, and began using my skills in molecular biology to help taxonomists and describe new fungi species (Consiglio et al., 2007). Marc-André Selosse also supervised my PhD at CEFE, on the evolution of mycoheterotrophy in orchids, and more specifically in the tribe Neottieae.

Orchids produce the smallest seeds among plants, and rely on fungi for their germination. Circa 200 species of orchids look parasitic, as they have lost their photosynthetic pigments or capacity [START_REF] Leake | The biology of myco-heterotrophic ('saprophytic') plants[END_REF]. Thanks to the development of barcoding and the use of isotope labelling, studies in the 2000's identified the organic carbon source of these non-photosynthetic orchids, and in temperate regions, specific fungi were identified in orchids' roots [START_REF] Selosse | Communities and populations of sebacinoid basidiomycetes associated with the achlorophyllous orchid Neottia nidus-avis (L.) LCM Rich. and neighbouring tree ectomycorrhizae[END_REF]. Interestingly, those fungi were also associated with trees, and the organic carbon was indeed produced by trees, transferred to their symbiotic fungi and later received by the orchids. The tribe Neottieae is well represented in temperate forests and in tropical South-East Asia. Previous data have revealed specific but diverse fungi associated with Neottieae species and my PhD aimed at understanding the evolution of these interactions, and how orchids could become heterotrophic on fungi, i.e. mycoheterotrophic.

At the beginning of my PhD, my hypothesis was that specific interactions with fungi were acquired before the loss of photosynthetic ability. I expected convergent evolution in temperate and tropical ecosystems, but coevolution with distinct fungi depending on the orchid species. I spent 4 months in South-East Asia searching for rare mycoheterotrophic orchids, and have revealed that Aphyllorchis montana and A. caudata are associated with very diverse fungi (Roy et al. 2009a), while Cephalanthera exigua is very specific (Pedersen et al., 2009). In temperate region, I confirmed that specificity was the rule, for another rare orchid, Epipogium aphyllum (Roy et al., 2009b). To study closely related species of Neottieae, I followed several populations of green orchids, among which albino individuals are rarely observed. Such albino are scattered in populations (Tranchida-Lombardo et al., 2010) and are able to survive and reproduce. By measuring functional and reproductive traits for three years on two main populations, I showed that albino suffer from drought stress, lower germination rate and low seed viability, as compared to green individuals (Roy et al., 2013b). On the other hand, their ability to survive underground could explain the high number of albino individuals (maximum of 30% of albino individuals, Shefferson et al., 2016 ; 2018). In co-supervising the master 2 internship of Cédric Gonneau with Marc-André Selosse, we conducted experiments to test how Epipactis species could survive with less light, and if fungal resources could be limited. We confirmed that Epipactis are partly mycoheterotrophic and that photosynthesis is useful mainly for fruiting (Gonneau et al., 2014). All these clues on Neottieae show that mycoheterotrophy is widespread, among species and ecosystems, and reveal that full mycoheterotrophy could evolve from partial mycoheterotrophy, but that specific interactions are not necessary (Selosse and Roy, 2009).

I contributed to larger syntheses on this peculiar trophic mode (Hynson et al., 2013) and the need for molecular tools to study them, especially in the tropics (Selosse et al., 2010). Moreover, I spent part of my time, during my PhD, working with "amateurs" and local societies, and sharing the results of my PhD in French journals such as Pour la Science (Roy and Selosse, 2010 ; Selosse and Roy, 2012). After my PhD, I maintained collaborations on orchids for example with colleagues in Czech Republic (Kohout et al., 2013a ; 2013b ; Tesitelova et al., 2013). Today, I still publish for a broad audience in France (Roy et al., 2014 ; Roy, 2018) and abroad (Roy and Kuyper, in prep), but I have developed my career on symbiotic fungi of trees and worked at community level.

After my PhD, I spent only 6 months in post-doc with Franck Richard (CEFE) and Alain Franc (INRA Pierroton), working on symbiotic fungi of oaks and their response to drought stress. I contributed to the DNA extractions, barcode sequencing and analysis, and community analyses. Fungal communities were highly variable but apparently resistant to drought stress (Richard et al., 2011). The contract was short (end of a European project) and I got my position at Université Paul Sabatier (UPS) right after. This short contract was a great opportunity to be trained with community level analysis on symbiotic fungi, and discover their below-ground diversity. Moreover, I still work with Franck Richard (Roy et al., submitted) and colleagues in CEFE, and have begun interacting with colleagues in forestry thanks to this post-doctoral experience.

8 As with all macro-organisms, plants are always surrounded by and associated with a diverse community of microorganisms, and indeed, it is hard to find a leaf which is not colonized by a fungus nor a root which is not associated with below-ground mycelium [START_REF] Rodriguez | Fungal endophytes: diversity and functional roles[END_REF]. Plant-fungi interactions have even been detected in the first terrestrial plants of the Rhynia chert, 407 million years ago [START_REF] Strullu-Derrien | The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics[END_REF]. As in all biotic interactions, the result of these interactions follows a continuum between positive and negative interactions, and vary depending on soil conditions and partner identities [START_REF] Hoeksema | A meta-analysis of context-dependency in plant response to inoculation with mycorrhizal fungi[END_REF]. I am particularly fascinated by plant-fungal interactions, and have worked on two widespread interactions: mutualist fungi that colonize tree roots (ectomycorrhizal fungi, EMF) and fungi that grow within tree leaves and behave rather like commensals (endophytic fungi, EF; Fig 1).

Around 85% of plant species are documented as being associated with mycorrhizal fungi [START_REF] Brundrett | Mycorrhizal associations and other means of nutrition of vascular plants: understanding the global diversity of host plants by resolving conflicting information and developing reliable means of diagnosis[END_REF][START_REF] Brundrett | Evolutionary history of mycorrhizal symbioses and global host plant diversity[END_REF]. These fungi colonize their host plant roots, and form a relatively stable symbiosis in which the plant provides photosynthesis-derived sugars in return for water and nutrients [START_REF] Smith | Mycorrhizal symbiosis[END_REF]. Among fungi, Glomeromycota and Mucoromycotina were the first to interact with plant roots [START_REF] Bidartondo | The dawn of symbiosis between plants and fungi[END_REF][START_REF] Strullu-Derrien | Fungal associations in Horneophyton ligneri from the Rhynie Chert (c. 407 million year old) closely resemble those in extant lower land plants: novel insights into ancestral plant-fungus symbioses[END_REF][START_REF] Rimington | Fungal associations of basal vascular plants: reopening a closed book?[END_REF]. Their interactions result in endomycorrhiza, which are observable on most herbaceous plants and tropical trees. Later during the course of fungal evolution, several linages acquired the ability to interact with plant roots and form a symbiosis materialized by an organ, made of both plant and fungi cells: the ectomycorrhiza (Fig 1). Ectomycorrhizal plants are documented in 335 genera and 8500 species, with recent articles suggesting that many more hosts await detection, especially in the tropics [START_REF] Tedersoo | Evolution of ectomycorrhizal symbiosis in plants[END_REF]. Ectomycorrhizal fungi have been assigned to 236 genera and circa 20.000-25.000 species [START_REF] Comandini | Measuring and estimating ectomycorrhizal fungal diversity: a continuous challenge[END_REF], which is relatively little compared to the 2.2 to 3.8 million species thought to exist [START_REF] Hawksworth | Fungal diversity revisited: 2.2 to 3.8 Million Species[END_REF]. The ability to form EM mutualisms has been selected independently in several lineages, probably from saprophytic or endophytic ancestors [START_REF] Shah | Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors[END_REF]. As a result, EMF consist of phylogenetically diverse fungi, that have undergone distinct evolutionary trajectories and phylogeographic events.

Today, most temperate trees (Pinaceae, Fagaceae) and some tropical trees (Dipterocarpaceae, some tropical Fabaceae and Myrtaceae, and other families) are associated with EMF [START_REF] Brundrett | Evolutionary history of mycorrhizal symbioses and global host plant diversity[END_REF], but this general rule has many exceptions. [START_REF] Soudzilovskaia | Global patterns of plant root colonization intensity by mycorrhizal fungi explained by climate and soil chemistry[END_REF]2017) have shown that rare cases of EM plants are also reported in the tropics. Despite a significant sampling bias in the Neotropics (tropical region of American continent), Tedersoo et al. (2012;[START_REF] Wanted | to learn molecular biology before starting a PhD. She was interested in ectomycorrhizal fungi, especially Russulaceae. She applied for a Brazilian Grant ("Sandwich") and stayed for 10 months in Toulouse in[END_REF]Fig 2) and [START_REF] Brundrett | Evolutionary history of mycorrhizal symbioses and global host plant diversity[END_REF] have also shown that ectomycorrhizal symbiosis is more widespread in temperate regions and in tropical monodominant forests. Indeed, tree monodominance is partly explained by the ability of EMF to benefit mainly their hosts population and to limit the accessibility of inorganic N to other plants [START_REF] Mcguire | Common ectomycorrhizal networks may maintain monodominance in a tropical rain forest[END_REF]Corrales et al., 2016). Moreover, most EMF families probably emerged in temperate regions and dispersed later in the tropics [START_REF] Tedersoo | Global diversity and geography of soil fungi[END_REF]. Nevertheless, phylogenetic studies on widespread ectomycorrhizal lineages have suggested a tropical origin for some lineages such as Inocybaceae [START_REF] Matheny | Out of the Palaeotropics? Historical biogeography and diversification of the cosmopolitan ectomycorrhizal mushroom family Inocybaceae[END_REF], Russulaceae [START_REF] Alexander | Ectomycorrhizas ? out of Africa?[END_REF] and Clavulinaceae [START_REF] Kennedy | Scaling up: examining the macroecology of ectomycorrhizal fungi[END_REF]. (Tedersoo et al. 2012); B, distribution of confirmed EM hosts [START_REF] Soudzilovskaia | Global patterns of mycorrhizal distribution and their environmental drivers[END_REF]

and C, location of sampling sites for Alnus-EMF (green) and neotropical EMF (red).

Taxonomists regularly reveal new species of fungi in the tropics, including ectomycorrhizal species [START_REF] Hawksworth | Global species numbers of fungi: are tropical studies and molecular approaches contributing to a more robust estimate?[END_REF][START_REF] Truong | How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity[END_REF]) and more rarely, genera [START_REF] Sánchez-García | Guyanagarika, a new ectomycorrhizal genus of Agaricales from the Neotropics[END_REF].

A fundamental question therefore emerges from these observations: are EMF really so rare in non-monodominant forests of the Neotropics? And if so, what factors could explain their rarity and low density in Neotropical forests? I have spent the past few years working with taxonomists to describe ectomycorrhizal species outside of monodominant forests in the Neotropics (Fig 2C), to fill this gap of knowledge on their diversity and distribution, and question their rarity (axis 1). This first axis led me to a second topic, focusing on a distinct trait amongst plant-fungi mutualisms: their specialization. Specialization in plant-fungi mutualisms: puzzling cases and new questions?

Articles Roy et al. 2013 ;Hynson et al., 2013 ;Kohout et al., 2013a ;Kohout et al., 2013b ;Těšitelová et al., 2013 ;Gonneau et al., 2014 ;Gladieux et al., 2015 ;Roy and Selosse, 2015 In most host-symbiont coevolutionary dynamics, specialization is often expected to occur, yet plant-fungi mutualism is on the contrary relatively generalist. Indeed, numerous studies have revealed a high proportion of fungi having multiple hosts in temperate ecosystems [START_REF] Horton | Multiple-host fungi are the most frequent and abundant ectomycorrhizal types in a mixed stand of Douglas fir (Pseudotsuga menziesii) and bishop pine (Pinus muricata)[END_REF][START_REF] Cullings | Ectomycorrhizal Specificity Patterns in a Mixed Pinus contorta and Picea engelmannii Forest in Yellowstone National Park[END_REF][START_REF] Kennedy | There is high potential for the formation of common mycorrhizal networks between understorey and canopy trees in a mixed evergreen forest: Mycorrhizal networks in mixed evergreen forest[END_REF][START_REF] Ishida | Host effects on ectomycorrhizal fungal communities: insight from eight host species in mixed conifer?broadleaf forests[END_REF][START_REF] Twieg | Ectomycorrhizal fungal succession in mixed temperate forests[END_REF]Roy et al., 2008), and only exceptions have contradicted this rule [START_REF] Bruns | Host specificity in ectomycorrhizal communities: what do the exceptions tell us?[END_REF][START_REF] Smith | Are true multihost fungi the exception or the rule? Dominant ectomycorrhizal fungi on Pinus sabiniana differ from those on co-occurring Quercus species[END_REF]. This ability to associate with several hosts is expected to lead to positive interactions (so-called facilitation) between plant species [START_REF] Molina | Mycorrhiza specificity: its role in the development and function of common mycelial networks[END_REF], and eventually to the formation of a common mycorrhizal network (CMN, [START_REF] Newman | Relationship between mycorrhizal infection and diversity in vegetation: evidence from the Great Smoky Mountains[END_REF][START_REF] Simard | Net transfer of carbon between ectomycorrhizal tree species in the field[END_REF]. Indeed, shared mycorrhizal fungi have been shown to transfer organic carbon, nutrients or water between plants and the functioning of such networks can have deep consequences for plant-plant interactions [START_REF] Simard | Net transfer of carbon between ectomycorrhizal tree species in the field[END_REF][START_REF] Simard | Mycorrhizal networks: mechanisms, ecology and modelling[END_REF] ; Roy and Selosse, 2015). For example, during my PhD, I studied orchids that were even dependent on such networks, the so-called mycoheterotrophic (Hynson et al., 2013) and mixotrophic orchids (Selosse and Roy, 2009 ; Roy et al., 2013b ; Gonneau et al., 2014). However, exceptions do exist, and most mycoheterotrophic orchids [START_REF] Taylor | Mycorrhizal specificity and function in myco-heterotrophic plants[END_REF] ; Roy et al., 2009a), trees of the genus Alnus [START_REF] Molina | Ectomycorrhizal specificity in the genus Alnus[END_REF] and Neotropical trees [START_REF] Tedersoo | Low diversity and high host preference of ectomycorrhizal fungi in Western Amazonia, a Neotropical biodiversity hotspot[END_REF] have often few, and specialized interactions (Fig 3).

12 (Roy et al., 2013a, Polme et al., 2013) 38 species on 34 host individuals in Ecuador (Tedersoo et al., 2009) Figure 3:Left, Alnus stand in Corsica, right, inselberg covered by a low canopy forest in French Guiana [START_REF] Bruns | Host specificity in ectomycorrhizal communities: what do the exceptions tell us?[END_REF] have already shown how exceptions are puzzling and raise questions, for example on the benefit of networks. [START_REF] Kennedy | Interspecific mycorrhizal networks and non-networking hosts: exploring the ecology of the host genus Alnus[END_REF], focusing on the genus Alnus, have suggested several hypotheses to explain the specialization of its EMF, all linked with the ability of alders to associate with nitrogen-fixing bacteria of the genus Frankia. Indeed, [START_REF] Huggins | Unlocking environmental keys to host specificity: differential tolerance of acidity and nitrate by Alnus-associated ectomycorrhizal fungi[END_REF] have experimentally demonstrated that specific EMF associated with alders are able to grow at a low pH, a consequence of Frankia presence and acidification in roots. As an association with specialized EMF might be advantageous to avoid losing nitrogen in a common mycorrhizal network, [START_REF] Kennedy | Interspecific mycorrhizal networks and non-networking hosts: exploring the ecology of the host genus Alnus[END_REF] have suggested that plant to plant competition could also select for more specialized interactions. Another hypothesis instead relates to exchanges between Alnus and EMF: sanctions, adaptation to host metabolism or even nitrogen rewards which could select for more specialized and adapted EMF. From a more theoretical point of view, modelers are also interested in specialization, and show that isolation and environment or spatial heterogeneity, could play an important role in coevolutionary dynamics [START_REF] Brown | Evolution in heterogeneous environments: Effects of migration on habitat specialization[END_REF]Fussman et al., 2007;[START_REF] Mezquida | Habitat area and structure affect the impact of seed predators and the potential for coevolutionary arms races[END_REF]. Geological events, such as glaciations, have also contributed to the isolation of several symbioses such as Alnus-EMF mutualism, and the question remains as to how far those past events have also shaped Alnus specialization. Through several projects in Europe, I have therefore tried to investigate the extent to which biogeography could contribute to explain the actual pattern of diversity and specialization observed on Alnus EMF (axis 2a).

Only a few EM hosts are mentioned in the Neotropics [START_REF] Sulzbacher | Ectomycorrhizal fungi from southern Brazil-a literature-based review, their origin and potential hosts[END_REF][START_REF] Corrales | Ectomycorrhizal associations in the tropics -biogeography, diversity patterns and ecosystem roles[END_REF], representing 0.004% of Neotropical tree species. Interestingly, there are numerous examples of non-monodominant trees and lianas associated with highly specialized EMF [START_REF] Tedersoo | Low diversity and high host preference of ectomycorrhizal fungi in Western Amazonia, a Neotropical biodiversity hotspot[END_REF], often among Caryophyllales. Like Alnus populations, these hosts are often isolated in Neotropical forests and occur at low density. In French Guiana, few EMF hosts are recorded according to botanists and root observations (Table 1; [START_REF] Béreau | First observations on the root morphology and symbioses of 21 major tree species in the primary tropical rain forest of French Guyana[END_REF]Béreau et al., 1997).

Contrary to the case of Alnus-EMF interactions, fewer hypotheses have been formulated to explain their specialization. Moreover, as EM hosts are relatively rare, sampling bias can occur and may lead to an apparent specialization [START_REF] Tedersoo | Low diversity and high host preference of ectomycorrhizal fungi in Western Amazonia, a Neotropical biodiversity hotspot[END_REF]. In French Guiana, EMF do occur, and EM hosts can locally co-occur in low canopy forests. Such a distribution raises questions as to the possible sharing of EMF between tree species in Neotropical forests, and the occurrence of a CMN. In monodominant EM forests, Corrales et al. (2016) recently showed that Oreomunnea mexicana (Juglandaceae) did not exchange or receive nutrients through a common mycorrhizal network, while [START_REF] Smith | Ectomycorrhizal fungal diversity and community structure on three co-occurring leguminous canopy tree species in a Neotropical rainforest[END_REF] detected a high proportion of multihost EMF in Guyana. Such contrasted results raise questions about EM habits in the tropics and I have therefore investigated if specialization can be an artefact due to the low density of tree hosts, and if networks could occur between co-existing EM hosts in French Guiana (axis 2b).

14 [START_REF] Tedersoo | Global diversity and geography of soil fungi[END_REF] and endophyte community diversity (B, from Vacher et al., 2016a).

MAP : Mean annual precipitation

Changing scales to study community ecology of complex mutualisms

Recent global analyses of soil fungal communities have highlighted the main factors shaping these complex systems [START_REF] Tedersoo | Global diversity and geography of soil fungi[END_REF]. Such analyses have been made possible by the rise of environmental DNA and next generation sequencing (NGS). Analyses based on these techniques have allowed demonstration of a strong correlation between fungal richness and numerous factors including a latitudinal gradient, mean annual precipitation, Ca concentration in soils and plant species richness, together with indirect effects of fire, soil pH and total P (Fig 4A). For EMF, the host plant remains a key parameter to explain their species richness, together with abiotic parameters such as pH and soil granulometry (Tedersoo et al., 2012). Moreover, the impact of climate can be detected not only on EMF richness, but also on EMF colonization rate [START_REF] Soudzilovskaia | Global patterns of mycorrhizal distribution and their environmental drivers[END_REF]. More local studies have revealed other important drivers, such as the host plant's genetic variability (Těšitelová et al., 2013).

While literature is rich with regards to niche-based processes shaping fungal communities, neutral processes are often overlooked, and a large part of community variability remains unexplained. Following the scheme of [START_REF] Vellend | Conceptual synthesis in community ecology[END_REF]), Vacher et al. (2016a) have investigated how speciation, drift, selection and dispersal shape endophytic communities (Fig 4B). Selection has been particularly studied on endophyte communities, notably the role of climatic condition [START_REF] Galès | Needles of Pinus halepensis as Biomonitors of Bioaerosol Emissions (AC Singer[END_REF] and plant traits [START_REF] Kembel | Plant traits and taxonomy drive host associations in tropical phyllosphere fungal communities[END_REF]. This framework is rarely applied to EMF communities, and is of particular interest to understand EMF specialization. Indeed, such interactions could also be selected by drift in case of isolation, by a low migration rate or by local speciation (Fig 5). Migrations of EMF are particularly limited over large distance, as illustrated by their low number of invasive species (Gladieux et al., 2015). Following this framework, through axes 1 and 2, I have investigated if a limited regional diversity may explain the high specialization of Neotropical EMF. Through axis 2, I have investigated how past migrations could shape the high specialisation of alder EMF. Therefore, two missing factors remain to be tested to understand those cases of specialisation: neutral processes and biotic interactions between fungi and eventually other micro-organisms.

Biotic interactions may prove important in shaping fungal communities and species distributions, but most studies only consider interactions with plants, not with other organisms (Fig 4A). [START_REF] Koide | Evidence of species interactions within an ectomycorrhizal fungal community[END_REF] were the first to reveal negative interactions between EMF, modulated by soil chemistry. [START_REF] Kennedy | Root tip competition among ectomycorrhizal fungi: are priority effects a rule or an exception?[END_REF] have detected priority effects between fungi, suggesting again negative interactions. [START_REF] Kennedy | Ectomycorrhizal fungi and interspecific competition: species interactions, community structure, coexistence mechanisms, and future research directions: Tansley review[END_REF] produced a synthesis on the importance of competition between EMF and highlighted the priority effect. While experimental tests on interactions are rarely done, one option is to consider putative interactions based on co-occurrence, and study ecological networks. [START_REF] Bahram | Network perspectives of ectomycorrhizal associations[END_REF] reviewed our knowledge of EM ecological networks and concluded that their topology is often non-nested and variable across ecosystems. Taudière et al. (2015) were perhaps the first to study ecological networks between plants mediated by fungi, and to integrate neutral processes in their tests. Their study of Corsican trees also showed that Alnus species were less connected to other trees (i.e. associated with more specialized fungi) than neutral processes would predict. The analysis of ecological networks allows a comparison with null predictions and brings quantitative measures to describe EMF specialization and fungi to fungi interactions. I have begun using ecological networks to investigate variations of Alnus-EMF specialization, at both local and global scales (axis 3a).

16

Figure 5 : What are the processes shaping interactions and their specialization within a community? Evolutionary processes can be involved (triangles), and direct and indirect interactions can reinforce selection (arrows). Moreover, a low alpha and gamma diversity may reduce the number of possible interactions. To investigate all factors shaping this specialized association, I also tested how interaction with Frankia could shape Alnus-EMF interaction.

These questions on fungi-fungi interactions are intimately linked to forest dynamics and plantplant interactions. [START_REF] Bever | Rooting theories of plant community ecology in microbial interactions[END_REF] discussed how plant-fungi interactions may shape plantplant interactions, and concluded that changes in abundance and contrasted feedbacks may contribute to explain facilitation processes in ecosystems. The role of EMF in facilitation processes is often assumed and has been well illustrated through the nurse plant effect [START_REF] Dickie | Shared ectomycorrhizal fungi between a herbaceous perennial (Helianthemum bicknellii) and oak (Quercus) seedlings[END_REF][START_REF] Nara | Ectomycorrhizal networks and seedling establishment during early primary succession[END_REF][START_REF] Richard | Facilitated establishment of Quercus ilex in shrub-dominated communities within a Mediterranean ecosystem: do mycorrhizal partners matter?[END_REF].

In boreal forests, where EMF are diverse and abundant [START_REF] Taylor | A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning[END_REF], climate change is extending tree distributions northwards [START_REF] Woodall | An indicator of tree migration in forests of the eastern United States[END_REF]) and changing ecosystem dynamics. Specifically, at the ecotone between spruce-dominated forest to the north and mixed boreal forest to the south, firs are extending their northern distribution [START_REF] Messaoud | Reproductive potential of balsam fir (Abies balsamea), white spruce (Picea glauca), and black spruce (P. mariana) at the ecotone between mixedwood and coniferous forests in the boreal zone of western Quebec[END_REF]). In the spruce forest, patches of aspen are scattered, and firs are mainly growing under this broad-leaf tree, while regeneration seems limited under black spruce [START_REF] Arbour | Effect of increased Populus cover on Abies regeneration in the Picea-feathermoss boreal forest: Effect of increased Populus cover on Abies regeneration[END_REF]. Both forest types grow on the same substrate, under the same climatic conditions, and all these trees are also associated with EMF. Nevertheless, these questions of community ecology are difficult to answer with EMF fungi. Studying interactions in root or soil cores is possible but requires a reduced study scale, as suggested by [START_REF] Bogar | Processes Maintaining the Coexistence of Ectomycorrhizal Fungi at a Fine Spatial Scale[END_REF]. Within roots, EMF and mycorrhizal fungi often live with diverse endophyte fungi (e.g. in orchid roots, Kohout et al., 2013aKohout et al., , 2013b)). Within leaves, endophytic fungi can also co-occur, and colonize spaces between plant cell walls [START_REF] Rodriguez | Fungal endophytes: diversity and functional roles[END_REF]. Their effect on plant can be neutral, positive or negative, depending often on host plant fitness and environmental conditions [START_REF] Lindow | Microbiology of the Phyllosphere[END_REF]. Interestingly, because these diverse interactions all occur at a very small scale, the leaf, and this organ can therefore be sampled to study interactions, not only with the plants, but also between fungi within the leaf. In a study of endophyte global distribution, Arnold and Lutzoni (2009) have showed that their diversity was higher in tropical tree leaves, suggesting a hot spot for such fungi. Among the hypotheses proposed to explain this, the diversity of hosts, and the higher levels of photosynthetic activity in tropical leaves over a year as compared with temperate leaves, have been suggested. However, neutral processes have been neglected in explanation of the diversity of endophytic communities, despite the fact that tropical forests and their host diversity have been the key stone of the neutral theory of biodiversity (Hubbell, 2001;[START_REF] Chave | Neutral theory and community ecology: Neutral theory and community ecology[END_REF]. Through projects with chemists interested in interactions between micro-organisms within leaves, and the post-doc project of J. Donald, we have investigated how neutral processes, and host diversity, could shape the diversity of endophyte fungi and their interactions within leaves (axis 3c).

18 PAST/PRESENT RESEARCH Axis 1 : Diversity and distribution of EMF fungi in the Neotropics Projects FUNGUY, DIADEMA, DIAMOND, LONGTIME Articles [START_REF] Henkel | Cantharellaceae of the Guiana Shield: New species of Craterellus, and new distribution records for Cantharellus guyanensis and Craterellus excelsus[END_REF][START_REF] Roy | Diversity and distribution of ectomycorrhizal fungi from Amazonian lowland white-sand forests in Brazil and French Guiana[END_REF][START_REF] Roy | De la scientificité à la une gestion créative multidimensionnelle : échanges de savoirs autours des plantes rencontrées dans le vignoble gaillacois[END_REF]Hoeksema et al., 2018;Buyck et al., 2017;De Crop et al. 2017;Barbosa-Silva et al., 2017;[START_REF] Crous | Fungal Planet description sheets: 625-715[END_REF][START_REF] Gruhn | The genus Resinicium in French Guiana and the West Indies: a morphological and molecular survey, revealing Resinicium grandisporum sp[END_REF], 2018, Roy et al., 2018 ;Accioly et al., 2019 The Neotropics refer to South and Central America, and include from tropical to temperate environments (Antonelli and San Martin, 2011). Neotropical forests at low elevation have several peculiarities, compared to other tropical forests, and show a higher tree diversity, and less mono-dominance [START_REF] Ter Steege | Hyperdominance in the Amazonian tree flora[END_REF]. Moreover, EMF hosts are rare and occur at low density, except in the Guyana highlands [START_REF] Henkel | Ectomycorrhizal fungi and their leguminous hosts in the Pakaraima Mountains of Guyana[END_REF][START_REF] Henkel | Monodominance in the ectomycorrhizal Dicymbe corymbosa (Caesalpiniaceae) from Guyana[END_REF]. Soil and root sampling in Neotropical forests have confirmed this trend and have allowed detection of only few EM hosts [START_REF] Mcguire | Common ectomycorrhizal networks may maintain monodominance in a tropical rain forest[END_REF], Bâ et al., 2016). All these data have contributed to shape our understanding of the actual diversity pattern of EMF symbiosis in the Neotropics [START_REF] Soudzilovskaia | Global patterns of mycorrhizal distribution and their environmental drivers[END_REF], beside a strong sampling bias in the Amazon (Fig 2, Table 1).

Nevertheless, during my first visit to French Guiana I found an unexpected diversity of EMF, including Cantharellus guyanensis (Henkel et al., 2013). This first visit was fundamental in my career. By interacting with taxonomists, and by digging through local herbaria collections, I realised that many cases of EMF had already been reported (Fig 6A). Cantharellus guyanensis was not a newly described species, as it had been collected between 1835 and 1849 by Montagne and Leprieur (Montagne, 1850;Fig 6B). Interestingly, this species had been undetected for more than a century, while our research with taxonomists revealed its wide distribution, from South of Brazil to North of Colombia (Henkel et al., 2013). Thanks to a visit to Manaus herbarium, I had access to Rolf Singer's herbarium, and realised that boxes of specimens were still waiting for a further description. With Ricardo Braga-Neto (PhD, INPA, Brazil), we investigated if genus-level records could provide more records of species for EMF and allow for expanded outlines of distribution for EMF in Brazil. By searching in records of herbarium samples collected over the last century in Brazil, we detected 2268 records (search on species link project, http://splink.cria.org.br/). With the help of taxonomists, we were able to sort duplicates and incorrect assignments, and rejected half of the records. We revealed that EMF fungi could occur all over Brazil, but remain rarely and only recently observed (Fig 6C). Indeed, only 1066 observations were recorded over a century, and each species was observed on average 2.33 times (Roy et al. 2016).

There is a gap between the distribution of EMF outlined by ecologists and taxonomists, with taxonomists rapidly increasing the number of described EMF species (Fig 6A), and also the number of habitats where EMF could be detected, such as the restinga (dry forests) in Brazil [START_REF] Sulzbacher | Hypogeous sequestrate fungi in South America-how well do we know them?[END_REF]. To increase communication between fields, sequencing specimens is key: it allows detecting EMF sequences in soil and reciprocally permits taxonomists to extend species distributions and describe fungal ecology (Truong et al., 2017, Box 1). Since 2016, I have contributed to this end by organizing symposia, linking taxonomists and ecologists, and building an integrative discussion on EMF distribution (Roy et al., 2017b). Colleagues working on EMF in the Neotropics are now organized in a network (Fig 7A, Bueno et al., 2017), and all agree that taxonomists are leading the way to find more habitats and better understand EMF distribution and ecology.

20

Figure 7: A, network of colleagues working on mycorrhizal symbiosis in South America [START_REF] Bueno | Think globally, research locally: contrasting patterns of mycorrhizal symbiosis in South America[END_REF]; B, sites where fruiting bodies were inventoried in French Guiana (Jaouen et al., submitted), blue lines represent the precipitation gradient, C to E, habitats studied in French Guiana and F, proportion of observations (number of specimens) per trophic mode, including EMF (Schimann et al., submitted). In French Guiana, mycology has a long history, with Montagne and Leprieur collecting and describing 255 species as far back as 1850, among of which two were EMF [START_REF] Montagne | Cryptogamia Guyanensis seu Plantarum cellularium in Guyana gallica annis 1835-1849 a cl. Leprieur collectarum enumerato universalis[END_REF]. Up until recently, the checklist of fungi in French Guiana [START_REF] Courtecuisse | Check-list of fungi from French Guiana[END_REF] included more taxa (625) and 7 additional EMF (Fistulinella venezuelae and Fistulinella spp., Lactarius epitheliosus, Russula hygrophytica, R. moyersoni, R. violaceotunicata and Tricholoma crissum).

To advance knowledge about EMF, but also on French Guiana fungi in general, with my colleague Heidy Schimann at ECOFOG (Kourou), we have hosted mycologists from abroad, deposited fungi in herbaria, and exchanged specimens. This work has led to several new descriptions (Barbosa-Silva et al., 2017; Crous et al., 2017; Gruhn et al., 2017, 2018, Accioly et al., 2019), projects funded by the LABEX CEBA and more recently by the Atlas de la Biodiversité Communale de Saül (ABC). Most specimens are already deposited at Paris national herbarium and a database has been built, now containing 9115 records, of which 5219 are already in the GBIF database (https://www.gbif.org/dataset/ca0dfc4e-6a98-4b1b-b010-c6ce894a72f1, Jaouen et al., submitted). Moreover, the checklist of fungi in French Guiana is now updated by the INPN and reports 2798 species (Taxref v12.0, Gargominy et al., 2018).

Since my research questions have also been centred on community ecology, together with Heidy Schimann I have set up a protocol to replicate our inventories and study, not only for the species distribution but also for fungal diversity across all French Guiana habitats (Fig 7B to 7E,Schimann et al.,submitted). Indeed, Neotropical forests in French Guiana follow a pedohydrological [START_REF] Epron | Spatial variation of soil respiration across a topographic gradient in a tropical rain forest in French Guiana[END_REF][START_REF] Quesada | Soils of Amazonia with particular reference to the RAINFOR sites[END_REF] and topolographical gradient [START_REF] Guitet | Landform and landscape mapping, French Guiana (South America)[END_REF], from seasonally flooded forests to hilltop forests (so-called "plateau"). Slopes also host typical low-canopy forests. The soil is also particularly important, as terra-firme forestswhich represent 97% Amazonian soils -show a higher diversity and biomass than white-sand forests [START_REF] Baraloto | Disentangling stand and environmental correlates of aboveground biomass in Amazonian forests[END_REF]. Rolf Singer has spent part of his career studying white sand forests and has suggested that EM symbioses might be an adaptation to survive on these extremely poor soils [START_REF] Singer | Litter decomposition and ectomycorrhiza in Amazonian forests. 1. A comparison of litter decomposing and ectomycorrhizal basidiomycetes in latosol-terra-firme rain forest and white podzol campinarana[END_REF]. During a teaching trip to the Amazon, we revisited his sites as well as 9 white-sand plots in French Guiana and Brazil, to show that white sands are indeed generally colonized by EMF (Roy et al. 2016). In French Guiana, through several projects of the LABEX CEBA, we have also visited plots on terra-firme, slopes and white sands, including some close to inselbergs (i.e. ancient granite outcrops) isolated in the forests [START_REF] Porembski | Tropical inselbergs: habitat types, adaptive strategies and diversity patterns[END_REF] to investigate if, like tree communities, fungal communities would differ across those habitats. These inventories revealed that forests on slopes were generally richer in EMF than other sites, even on terra-firme (Fig 7F, Schimann et al., submitted).

For fungi in general, our inventories showed a higher similarity between fungal communities on slopes and plateau compared to flooded forests, together with a strong coupling with plant communities (Schimann et al., submitted) and earthworm communities (Vleminckx et al., submitted). All the data collected in Brazil (Fig 8A ) and French Guiana are now integrated with other records from the Neotropics to investigate, through spatial modelling, which factors (tree diversity, topography, climate) could explain their distribution (Fig 8B, Braga-Neto et al., in prep).

22 (Crous et al., 2018) A B

While my research has helped to record the distribution of EMF in the Neotropical lowlands, their rarity remains undeniable and is interesting per se. Indeed, each sampling has revealed new species to describe (Fig 9A, Crous et al., 2018), even in widely distributed families such as the Russulaceae. Such a pattern may signal speciation events in the Neotropics, and I have built collaborations to integrate Russulaceae sequences into large phylogenies in order to test this hypothesis. During Jan Hackel's master 2 internship and with colleagues from Ghent herbarium, we revealed new species and lineages within Lactifluus phylogeny (Fig 10, De Crop et al., 2017).

In the lesser Antilles, we have revealed numerous endemic species and a recent diversification (Delgat et al. submitted). At a larger scale, Russulaceae have undergone a complex evolution, with possible long-distance dispersal from Africa, migration along the Andes, and possible vicariance for species associated with Nothofagus (Hackel et al., in prep). In another EMF family, the Cantharellaceae, together with T. Henkel and B. Buyck, I have detected both widespread species like Cantharellus guyanensis (Henkel et al., 2013), and endemic species in the lesser Antilles, such as Cantharellus coccolobae (Buyck et al., 2016). Moyersoen has suggested that dispersal could be an important mechanism of radiation of EMF in South America [START_REF] Moyersoen | Dispersion, an important radiation mechanism for ectomycorrhizal fungi in Neotropical lowland forests? In: Tropical forests[END_REF]. As favourable habitats are relatively isolated (such as the white sands), this hypothesis could be true, and would be investigated with phylogenomic tools [START_REF] Looney | Russulaceae: a new genomic dataset to study ecosystem function and evolutionary diversification of ectomycorrhizal fungi with their tree associates[END_REF]. Moreover, for these mutualist lineages, coevolution with their host may also lead to speciation [START_REF] Looney | Into and out of the tropics: global diversification patterns in a hyperdiverse clade of ectomycorrhizal fungi[END_REF], as observed for the very specific lineages associated with Alnus (Rochet et al. 2011; Hackel et al., in prep).

If speciation has occurred, why are EMF represented by so few species in the Neotropical lowlands today, while plants, birds, mammals, insects are so diverse in this region (Antonelli and San Martin, 2011)? They occur at low densities nearly everywhere, and in lowland forests they could represent 11% of fruiting bodies (based on Jaouen et al., submitted) and a minor proportion of soil sequences [START_REF] Tedersoo | Global diversity and geography of soil fungi[END_REF]. [START_REF] Corrales | Ectomycorrhizal associations in the tropics -biogeography, diversity patterns and ecosystem roles[END_REF] produced a synthesis on EMF distribution and ecology in the tropics, but focused on mono-dominant forests. Based on studies of French Guiana forests, we can now propose several hypotheses to explain their widespread distribution at low density, linked with EMF and EM host biogeography, and the constraints shaping EMF communities (Roy and Verbruggen, in prep).

Compared to the distribution of EMF worldwide, the Neotropics only host a subset of EMF lineages and only one genus is endemic to the Guyana, Guyanagarika [START_REF] Sánchez-García | Guyanagarika, a new ectomycorrhizal genus of Agaricales from the Neotropics[END_REF]. Molecular dating of divergences within the Russulaceae tree suggests several independent speciation events around 50 million years ago (Hackel et al., in prep), a relatively recent period as compared to the emergence of EMF lineages [START_REF] Hibbett | The relative ages of ectomycorrhizal mushrooms and their plant hosts estimated using Bayesian relaxed molecular clock analyses[END_REF]. During this period, the landscape was completely different, probably dryer, as the Amazonian basin formed more recently, ca. 23 million years ago [START_REF] Hoorn | Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity[END_REF]. Radiations of palms, which characterise Amazonian forests and flooded habitats, were even more recent, dated 8 million years ago [START_REF] Roncal | Cenozoic colonization and diversification patterns of tropical American palms: evidence from Astrocaryum (Arecaceae)[END_REF], illustrating how young Amazonian landscapes are. Prior to this, 50 millions years ago, dry forests and savannas were probably more extensive and represented favourable EMF habitats, or at least represent similar conditions to white-sand forests and slopes. With the recent functioning of the Amazon, ECM-favourable habitats such as whitesand forests may have been isolated and or may have disappeared. They currently represent only 3% of Amazonian forests. French Guiana (violet). Pictures illustrate representative species from French Guiana for Albati (B) and Gymnocarpi (C) sections (De Crop et al., 2017). Among the peculiarities of Amazonian forests, we note that EM hosts are neither monodominant nor do they systematically occur at low densities. Moreover, they do not belong to widely distributed families or lineages that are highly mycorrhizal. Among Polygonaceae, only Coccoloba and Polygonum are EM hosts, and not in all habitats. Moreover, [START_REF] Béreau | First observations on the root morphology and symbioses of 21 major tree species in the primary tropical rain forest of French Guyana[END_REF] and Béreau et al. (1997) showed a relatively low colonization of Coccoloba roots in French Guiana. Among Nyctaginaceae, only Pisonia, Guiapira, and Neea are EM, and despite recent clues, not all Caryophyllales nor Fabaceae are indeed EM hosts [START_REF] Alvarez-Manjarrez | Caryophyllales are the main hosts of a unique set of ectomycorrhizal fungi in a Neotropical dry forest[END_REF]. Those associations may have evolved in the Neotropics, potentially dispersed by seeds over long distances (Sené et al., 2018). The phylogenetic diversity of hosts, and their variable mycorrhization, may suggest a recent acquisition of EM interactions for plants in the Neotropics.

There is therefore a need to date the emergence of EM interactions in the Neotropics, based on plant phylogenies. Radiations of Coccoloba are fairly recent and dated to between 17 and 27 million years ago [START_REF] Schuster | Age estimates for the buckwheat family Polygonaceae based on sequence data calibrated by fossils and with a focus on the Amphi-Pacific Muehlenbeckia[END_REF], which may support this hypothesis. Inversely, Gnetum are EM worldwide [START_REF] Singer | Litter decomposition and ectomycorrhiza in Amazonian forests. 1. A comparison of litter decomposing and ectomycorrhizal basidiomycetes in latosol-terra-firme rain forest and white podzol campinarana[END_REF][START_REF] Onguene | Mycorrhizal associations in the rain forest of South Cameroon[END_REF]Tedersoo and Polme, 2012;[START_REF] Bâ | Ectomycorrhizal symbiosis of tropical African trees[END_REF]. Their distribution and EM habit might be more ancient than other EM associations in the Neotropics, as Gnetum belongs to gymnosperms.

The current distribution of EMF in low forests raises questions about their physiology and interactions with tree roots. [START_REF] Singer | Litter decomposition and ectomycorrhiza in Amazonian forests. 1. A comparison of litter decomposing and ectomycorrhizal basidiomycetes in latosol-terra-firme rain forest and white podzol campinarana[END_REF] have suggested that EMF may be advantageous for plants on white sands and poor soils, where phosphorus may be more limited. [START_REF] Corrales | Ectomycorrhizal associations in the tropics -biogeography, diversity patterns and ecosystem roles[END_REF] have reviewed the importance of EMF in mono-dominant forests and have suggested that tannins and C/N ratios may also limit mineralization and favour EMF.

During the master 2 of Benjamin Durrington, we worked on the distribution of EMF along natural gradients in French Guiana (Fig 11A). Roots had been previously collected from soil cores by E. Verbruggen and his team (Fig 11B), and we aimed to test if phosphorus and nitrogen are key determinants of EMF distribution. We hypothesized that poor soils would favour EMF symbioses. By using NGS sequencing of ITS1, we detected only a few EMF (89 Operational Taxonomic units out of 6224 OTUs) but in 14 plots out of 22 (Fig 11C). We showed that nitrogen had a negative effect on their diversity, and that sandy soils tended to have less EMF (Durrington et al., in prep). Interestingly, the number of EMF OTUs was positively correlated with the number of tree species known as endomycorrhizal, associated with endomycorrhizal fungi. These results partly support the hypothesis that poor soils would host more EMF, and confirm their wide distribution at low densities.

This pattern raises another question: what if the low density observed for each EMF species was the result of processes shaping the low density of each tropical tree species? Indeed, Neotropical forests are well-known for their high diversity and the low density of tree species. [START_REF] Janzen | Herbivores and the number of tree species in tropical forests[END_REF] and [START_REF] Connell | On the role of natural enemies in preventing competitive exclusion in some marine animals and in rain forest trees[END_REF] both observed that the low density of individual spcies resulted from a local and negative effect of density on seedling growth and survival. They hypothesized that natural enemies, host specific, may cause such an effect. This "Janzen-Connell" hypothesis has been tested through different approaches, and natural enemies could indeed be fungi [START_REF] Bagchi | Testing the Janzen-Connell mechanism: pathogens cause overcompensating density dependence in a tropical tree[END_REF][START_REF] Mangan | Negative plant-soil feedback predicts tree-species relative abundance in a tropical forest[END_REF]. More recently, [START_REF] Levi | Tropical forests can maintain hyperdiversity because of enemies[END_REF] have highlighted how important enemies are for plant communities in the Neotropics, and [START_REF] Peay | Strong coupling of plant and fungal community structure across western Amazonian rainforests[END_REF] illustrated the strong links between plant and fungi diversity. Thus, EMF may occur at low density in relationship with their host distribution, but on the other hand, interactions with other organisms and local fungi may also reduce their density. 29

Through repeated observations in the field, I have always been amazed by the poor state of fruiting bodies, and numerous traces of mycophagy. Though our inventories with Heidy Schimann, I have tried to systematically report those signs, and indeed 39.1% of the specimens showed signs of mycophagy (over 10514 specimens, Fig 12). Mycophagy is reported in the Neotropics to be caused by rodents [START_REF] Mangan | Seasonal dispersal of arbuscular mycorrhizal fungi by spiny rats in a Neotropical forest[END_REF][START_REF] Trierveiler-Pereira | Mycophagy by small mammals: new and interesting observations from Brazil[END_REF] and tortoises (personal observations), potentially reducing fruiting-body lifespans, and possibly the local density of fruiting bodies.

Finally, the low density of fruiting bodies and possibly the low diversity of EMF can also be related to their host biomass. Indeed, most EM hosts outside of monodominant forests are lianas or shrubs. Unfortunately, hosts with a diameter at breast height (DBH) below 8 cm are not counted in most inventories. As a result, EM host distributions are highly likely to be underestimated. Through the LONGTIME project, I have had the opportunity to investigate soil communities in liana forest, pristine forests and "cambrousses" (vegetation dominated by herbs) in French Guiana (at Nouragues reserve). During Nina Gazal's master 2, we revealed that EMF were present in every habitat, especially in cambrousses, and in lianas forests (Gazal et al., submitted). Mycologists have under-explored those sites, but EMF specimens are recorded, such as a dense population of Cantharellus guyanensis. Coccoloba are frequent in liana forests and around cambrousses and can be potential hosts for these EMF.

As lianas are diverse and abundant in low-canopy forests, through Alexandre Ramon's master thesis and with Hans Verbeeck, I have investigated if lianas and small hosts may host more EMF in liana forests. Fine roots were collected from two sites on white sands, and two sites on terrafirme in French Guiana. Roots were harvested on small trees (< Therefore, small trees and lianas cannot be confirmed as EM hosts here (Ramon et al., in prep).

The low number of EM sequences contradicts our hypothesis, and confirms that EM hosts are relatively rare in French Guiana forests, even in liana forests where EM fungi are observed.

These studies on the distribution of EMF in the tropics are extremely descriptive, but necessary to guide future samplings, which should be more focused on soil and mycorrhiza than on fruiting bodies. One important aim of all those specimen collections and descriptions is the sequencing of barcodes, to better assign short sequences from metabarcoding. Metabarcoding refers to the next generation sequencing (NGS) of environmental DNA [START_REF] Taberlet | Environmental DNA: For biodiversity research and monitoring[END_REF]. The extraction of extracellular DNA and metabarcoding have permitted the production of millions of sequences from very diverse samples of materials such as water and soil. Such methods are "cheap, fast and reliable" [START_REF] Zinger | Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA[END_REF] and reduce the sampling time, as compared to methods based on fungal cultures or sequencing of EM root tips. However, various chimeras can occur, and methods are sensitive enough to amplify a high number of contaminants [START_REF] Nguyen | Parsing ecological signal from noise in next generation amplicon sequencing[END_REF]. As such, technical controls are included, PCRs are replicated, yet chimeras can still be sequenced, and may be difficult to remove from the datasets.

30 Assigning sequences to a given family or genus is a good way to eliminate dubious sequences and link biodiversity patterns to other studies or to functional traits. Several methods are available, from BLAST (Basic Local Alignment Search Tool, Altschul et al., 1990) to methods positioning sequences in classifications (ecotag, [START_REF] Boyer | obitools: a unix-inspired software package for DNA metabarcoding[END_REF] and larger phylogenies [START_REF] Berger | Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood[END_REF][START_REF] Berger | PaPaRa 2.0: a vectorized algorithm for probabilistic phylogeny-aware alignment extension[END_REF]. All these methods try to compare short sequences with a database of barcodes, such as Genbank (http://www.ncbi.nlm.nih.gov/) or UNITE (http://unite.ut.ee/; [START_REF] Kõljalg | UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi[END_REF].

Whatever the method, assignation may be strongly biased by gaps in the database [START_REF] Nilsson | Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective[END_REF] and this is particularly true for Neotropical fungi. When I began working with such techniques in French Guiana, only 8% of the fungal sequences (from soil) were assigned to a taxonomic level. This was a particularly low proportion, and probably linked to the low number of sequences deposited in public databases such as Genbank (in 2011, only 4 sequences of fungi were available). Moreover, the sequences of the internal transcribed spacer of the ribosomal DNA (ITS, [START_REF] Gardes | ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts[END_REF], a barcode for fungi, revealed very low similarity to databases (Fig 14A). As a result, BLAST may be of poor quality even for soil sequences, while they could belong to true fungi and not chimeras. Moreover, position in classifications may be basal (as for Cantharellus guyanensis within Cantharellaceae, Henkel et al., 2013), and such fungi may be assigned to the root of fungi, instead of being positioned within a fungal family.

The FUNGUY and FLAG projects have aimed at collecting specimens with the help of taxonomists and at sequencing ITS barcodes to improve the assignment of environmental sequences (Fig 14 B-I). Part of the DIADEMA and DIAMOND projects also aim at sequencing barcodes, using NGS on specimens to reduce the price of sequencing, and applying the same methods for both specimens and environmental DNA. Short barcodes were even easier to produce for old herbarium specimens, such as collections from R. Singer (Hackel et al., in prep). However, some specimens revealed several ITS that cannot be attributed only to contaminants, mainly in Xylariaceae, Geastraceae, Lepiotaceae, Gomphaceae, and Clavulinaceae. Within fungal genomes, ITS are already present in multiple copies (circa 50), but their polymorphism are usually low within an individual. Multiple and distinct copies could indicate a contaminant, or multiple genomes, for example in dikaryotic organisms. Jaouen et al. (submitted) analysed short sequences of ITS barcodes produced from specimens, and developed tests to investigate this polymorphism. Such barcodes are now beginning to be deposited in Genbank (771 barcodes, Jaouen et al. submitted), to fill the gap of public databases on fungi in French Guiana.

Sequencing all collected specimens and beginning to deposit sequences in public databases have greatly improved sequences assignation. Moreover, linking specimens with environmental sequences has enabled the opening of the black box [START_REF] Horton | The molecular revolution in ectomycorrhizal ecology: peeking into the black-box[END_REF] to understand EMF ecology and specialization in the Neotropics. Roy et al. (2013) and C, Distribution of chloroplast haplotypes in Alnus leaves, from Gryta et al. (2017).

Axis 2 : Drivers of EMF specialization Projects EC2CO, ARC, DROUGHT, MYCOTIN, NEBEDIV Articles Roy et al., 2013a;[START_REF] Roy | De la scientificité à la une gestion créative multidimensionnelle : échanges de savoirs autours des plantes rencontrées dans le vignoble gaillacois[END_REF]Schwob et al., 2017;Gryta et al., 2017;Sene et al., 2017;Buyck et al., 2017;Pozzi et al., 2018 ;Hoeksema et al., 2018. Specialization is a common pattern observed in plant-parasite interactions, where partners are involved in an arm-race or a 'red queen' coevolutionary dynamic [START_REF] Thompson | The coevolutionary process[END_REF]Kawecki, 1998). However, theoreticians have tried to find other models to understand the nonspecialization observed in plant-EMF mutualism (such as the slow red King; [START_REF] Bergstrom | The Red King effect: evolutionary rates and the division of surpluses in mutualisms[END_REF]. Indeed, even the most specialized fungi are associated with generalist hosts, and the term "preferences" is more realistic than "specialization" [START_REF] Dickie | Host preference, niches and fungal diversity[END_REF][START_REF] Molina | Mycorrhiza specificity: its role in the development and function of common mycelial networks[END_REF]. I have always been interested in the exceptions -i.e., the more specific associations among mycorrhizal symbioses -as they contribute to understanding the ecological advantages of more generalist strategies.

a. Revisiting Alnus-EMF specialization

Alnus-EMF fungi are well known for their specialization, initially demonstrated experimentally [START_REF] Molina | Ectomycorrhizal specificity in the genus Alnus[END_REF]. When I began working on alders, investigations of their below-ground communities with molecular tools had already confirmed this high specificity, but only on a single host at a time. My first study intended to determine the base of this specificity, thanks to sampling already achieved by the team at EDB. We showed that the five species and subspecies of alders in France were associated mainly with specialized fungi, such as Alnicola spp. and Tomentella spp., often sharing their partners with other Alnus species (Fig 15A). The soil chemistry and climate contributed to explain the diversity of EMF recorded on Alnus roots (Fig15B, Roy et al., 2013a), and this trend was confirmed at larger scale [START_REF] Põlme | Biogeography of ectomycorrhizal fungi associated with alders (Alnus spp.) in relation to biotic and abiotic variables at the global scale[END_REF]. This bloom of articles on Alnus-fungi mutualism also revealed interesting exceptions among mycorrhizal symbioses, particularly in locations where Alnus populations were isolated, as compared with the extended distribution of some species such as Alnus glutinosa [START_REF] Chen | Phylogenetics and biogeography of Alnus (Betulaceae) inferred from sequences of nuclear ribosomal DNA ITS region[END_REF]. For example, on A. subcordata roots in Iran, the EMF diversity was higher than elsewhere, and included generalist fungi such as Tuber and Inocybe spp.

As Alnus pollen is easily recognizable in sediments, its phylogeography has been intensely studied in the temperate region and in Europe, revealing southern and northern glacial refugia [START_REF] King | Chloroplast DNA phylogeography of Alnus glutinosa (L.) Gaertn[END_REF][START_REF] Douda | Migration patterns of subgenus Alnus in Europe since the Last Glacial Maximum: a systematic review[END_REF][START_REF] Havrdová | Higher genetic diversity in recolonized areas than in refugia of Alnus glutinosa triggered by continent-wide lineage admixture[END_REF]Mandak et al., 2015;2016). Corsica is recognized as a glacial refugium for several trees, including alders. While isolation could have selected for more intimate interactions, another hypothesis based on the distribution of alder's genetic diversity can also be proposed (Fig 15C, Gryta et al. 2017). Indeed, hypogeous fungi, which disperse at shorter scales than epigeous fungi [START_REF] Douhan | Population genetics of ectomycorrhizal fungi: from current knowledge to emerging directions[END_REF], may not have recolonized Europe after the last glaciation. If alder populations had been maintained in glacial refugia, they would have retained more diversity. I have therefore launched several projects to test if glacial refugia can host a higher diversity of EMF associated with alders, and if isolation can lead to more specialized interactions. I have also worked with colleagues on Frankia to understand if these hypotheses can apply to a more obligate symbiont. Perhaps because each glacial refugium has undergone a different history (Fig 16A), our results are distinct from one refugium to another. In Georgia, where the largest alder populations are found today, we have detected a high diversity of EMF, but rather in isolated populations than in the glacial refugium (Roy et al., 2017). In Corsica, the diversity is higher on A. cordata roots, but not on A. glutinosa ones (Pozzi et al., 2018). Moreover, very generalist fungi are detected as well. In the Carpathians, endemic hypogeous fungi are detected, but the global diversity is not higher than in recolonized areas. Finally, for A. alnobetula ssp. alnobetula in the Black Forest, a low elevation refugium in Germany [START_REF] Kamruzzahan | Is Alnus viridis'a' glacial relict in the Black Forest?[END_REF], EMF diversity is extremely low. Therefore, our analyses of EMF distribution do not support a consistent pattern of higher EMF diversity in refugia. Conversely, Frankia distribution is more intimately linked to the biogeography of alder, and shows a high endemism in Corsica and Georgia (Roy et al., 2017; Pozzi et al., 2018). Interestingly, [START_REF] Vercken | Glacial refugia in pathogens: European genetic structure of anther smut pathogens on Silene latifolia and Silene dioica[END_REF] have also revealed that Microbotryum caryophyllacearum, an obligate pathogen of Caryophyllaceae, has probably followed its host along post-glacial migrations. It is probably easier to detect such trends at the species level, and the sampling done at the community level can now be used to investigate the distribution of specific lineages, such as the EMF genus Alpova.

Investigating specialization was initially done by identifying generalist or specialist species, welldescribed by taxonomists, and indeed, we had expected to detect endemic species within Alnicola or Alpova lineages. Our markers have probably not been variable enough to detect recent differences between populations, and microsatellites would be more useful. Nevertheless, the large amount of data for alder communities can be also used to describe EMF species specialization with metrics. By comparing all sequences available for alder symbionts (3816 on ITS) with Adrien Taudière, I have investigated EMF distribution among 29 alder species worldwide, measured their number of hosts (degree), and computed several specialization indices. I have searched for indices not biased by sequence number, and chose "Blüthgen d," which compares specialisation to a random distribution (Fig 16B; [START_REF] Blüthgen | What do interaction network metrics tell us about specialization and biological traits[END_REF]. By computing a mean Blüthgen d for EMF communities, I have revealed that EMF communities in European refugia were indeed characterized by a higher d, and therefore were more specialized than communities in recently colonized areas (Fig 16C; Roy et al., submitted). Interestingly, EMF communities in Asia, which is the postulated center of origin of alders, are also more specialized (Fig 16D), suggesting more links between alder phylogeography and EMF specialization at the community level.

Taken together, the results from refugia illustrate variations of EMF specialization at the community level. The spatially variable specialization has been a keystone of the geographic mosaic theory of coevolution [START_REF] Thompson | The geographic mosaic of coevolution[END_REF]. [START_REF] Hoeksema | Geographic structure in a widespread plant-mycorrhizal interaction: pines and false truffles[END_REF] have detected geographic variations of EMF-Pinus interactions and [START_REF] Piculell | Interactions of biotic and abiotic environmental factors in an ectomycorrhizal symbiosis, and the potential for selection mosaics[END_REF] have suggested that interactions between abiotic and biotic factors may result in a selection mosaic. The specialization of alder-EMF interactions is definitely high, but probably follows the same pattern, as suggested by the importance of abiotic factors in the crossing experiment (Schwob et al., 2018). Several clues also suggest that geography could affect Alnus-EMF interaction, especially in isolated locations. For example, during M. Nagati's master 2, we were also able to sequence the EMF associated with isolated populations of Alnus maritima in the USA. Indeed this species shows disjunct populations [START_REF] Schrader | Seed germination and seedling growth of Alnus maritima from its three disjunct populations[END_REF] and has a low regeneration rate, especially by seed [START_REF] Rice | Is seedling establishment very rare in the Oklahoma seaside alder, Alnus maritima ssp. oklahomensis? Oklahoma Native Plant Record[END_REF]. The EMF communities are of low diversity (16 OTUs over 4 populations) and reveal numerous Helotiales. (Fernandez et al., in prep).

Specialized lineages are represented only by one Alnicola and by Lactarius omphaliformis, which suggests a loss of several partners, as compared with other alders. Reciprocally, [START_REF] Bogar | Testing the co-invasion hypothesis: ectomycorrhizal fungal communities on Alnus glutinosa and Salix fragilis in New Zealand[END_REF] have detected possible host shifts of Alnicola in New Zealand.

To summarize, alder-EMF interactions are definitely more specialized than other EM interactions (Taudière et al., 2015), but investigations in glacial and Tertiary refugia have revealed important variations of specialization. Thanks to the use of metrics to characterize EMF specialization at the community level, and the development of new genetic markers for alders (Gryta et al., 2017), it is now possible to investigate further the interactions between host biogeography and EMF specialization.

b. Specialization of EMF in Neotropical forests

While the isolation of Alnus populations remains an exception in the temperate zone, Neotropical trees and EMF are often isolated, and this distribution could also shape their specialization. In Yasuni National Park, [START_REF] Tedersoo | Low diversity and high host preference of ectomycorrhizal fungi in Western Amazonia, a Neotropical biodiversity hotspot[END_REF] showed, for the first time, a comparison of EMF communities associated with Neotropical trees, and demonstrated their specificity. At that time, the sampling was relatively reduced, with 100 sequences produced over 26 trees. With an increased sampling of roots of co-occurring Fabaceae, [START_REF] Smith | Ectomycorrhizal fungal diversity and community structure on three co-occurring leguminous canopy tree species in a Neotropical rainforest[END_REF] have concluded that all fungi are shared between Aldina and Dicymbe (Fabaceae) in Guyana. In French Guiana, EM hosts occur at low densities, such as the genus Coccoloba, Guapira and Neea. Their abundance is higher on slopes and low-canopy forests as is the abundance of EMF based on fruiting-bodies. As these symbioses are relatively rare in non-monodominant forests, I hypothesise that generalist association may be favoured, and that EMF could be shared between co-existing hosts.

By searching for hosts with a team of mycologists and botanists, I have been able to sequence the EMF community associated with 110 individuals belonging to ten host species (the three above mentioned genera, and Myrtaceae, that include putative EMF host) over 8 plots. Two hundred and thirteen OTUs (Operational Taxonomic Units) were detected on 106 host individuals, which confirms the low diversity of EMF in these Neotropical forests. The more abundant OTUs are not shared between hosts (Fig 17A ), and different genera are associated with very contrasted EMF communities and lineages. For example Neea individuals are associated mainly with Russulaceae, while the closely related genus Guapira is associated with Thelephoraceae. Locally, at the plot scale, the sharing of EMF is also extremely low (Fig 17B ), and associations are highly specific and more specialized than a random sampling would predict (estimated by H2, Fernandez et al., in prep). Therefore, the specificity of Neotropical EMF is clear, and is very conservative at a large scale. Indeed, by gathering all data on Coccoloba uvifera, Sene et al. (2018) were able to show how specific was this association, all along its migration routes. In the lesser Antilles, Coccoloba species notably associate with very specific Cantharellus spp. (Buyck et al., 2016). By comparing the EMF community of Pisonia species in Hawaï and Ecuador, [START_REF] Hayward | Phylogenetic trait conservation in the partner choice of a group of ectomycorrhizal trees[END_REF] showed that their association with the genus Tomentella is extremely phylogenetically-conserved. Our first study at the Nouragues station also reveals that Neotropical Myrtaceae can potentially associate with EMF. This result is particularly striking, and contrary to the literature on Myrtaceae, which assumes that only the lineage Eucalyptus is EM [START_REF] Tedersoo | Evolution of ectomycorrhizal symbiosis in plants[END_REF]. A quest for new EM hosts is ongoing in the tropics [START_REF] Tedersoo | Evolution of ectomycorrhizal symbiosis in plants[END_REF] and in herbaceous plants in temperate forests (Hoeksema et al., 2018). For example, Alvarez-Manjarrez et al. ( 2018) tested if dominant Fabaceae were EM in Mexican dry forests and instead, have revealed a new EM host -Achatocarpus (Achatocarpaceae, order Caryophyllales) and showed that Caryophyllales are the main EM hosts in this habitat. Considering the sampling gap for EMF in the Neotropics, we can expect to increase the number of EM hosts. As taxonomists are often going to the field, and describing new EM species in the Neotropics, I have co-organized three field trips to search for and observe EM root tips, twice in Brazil (Rio Negro, Roy et al., 2016; Florianopolis dunes, Roy et al., 2017) and more recently in Argentina (Buenos Aires, Faculty of Agronomy). We have always detected EM structures and interestingly, students and taxonomists have been disappointed with native EM root tips as compared to those of introduced Eucalyptus and Pinus. Indeed, the mantle is often reduced, and the abundance of EM root tips is lower on native trees. [START_REF] Becerra | The ectomycorrhizal symbiosis in south America: morphology, colonization, and diversity[END_REF] have already mentioned a reduced mantle for Neotropical EM root tips, which can make their detection more challenging.

Through repeated field trips to French Guiana, I have had the opportunity to observe in the field and sequence the roots of young trees identified by botanists, and therefore try to detect new EMF hosts. Observations have revealed possible root tips on nine families (Table 2), and sequencing has revealed EMF on 10 families (Table 2). By sequencing 250 bp of the plant barcode rbcL on roots sampled along a phosphorus gradient in French Guiana (axis 1), only a few plants are identified, and only three families are EM. The results are variable between observations and sequencing, and only seven species, belonging to Fabaceae, Malvaceae and Melastomataceae, are always observed associated with EMF. To demonstrate these associations, cuttings of EM roots have been inconclusively attempted. Moreover, among roots collected around EMF fruiting bodies and preserved in 50% alcohol, only 52% have shown a mantle or a Hartig net (188 samples, Master 1 Mike Hélion). Identifications by sequencing were successful only for Apocynaceae, Chrysobalanaceae and Ebenaceae, but not supported by morphological observations (Table2).

Those scattered and non-conclusive observations fit the hypothesis of [START_REF] Singer | Litter decomposition and ectomycorrhiza in Amazonian forests. 1. A comparison of litter decomposing and ectomycorrhizal basidiomycetes in latosol-terra-firme rain forest and white podzol campinarana[END_REF], who suggested that EMF can extend their mycelium and colonize other root trees and then form "contact mycorrhiza" with non-obligate EM hosts in Neotropical forests. [START_REF] Alexander | Ectomycorrhizas ? out of Africa?[END_REF] had already wondered how far EM nutrition might be obligate in the tropics. As an example, together with M.-A. Neves (Santa Catarina, Brazil), we have recently observed EM-like root tips colonized by Trechispora mycelium (Vanegas León et al. submitted). I have also collected fruiting bodies of Trechispora in French Guiana, and their isotopic signature is close to EMF in some sites, but is variable (Fig 18). Indeed, isotopic signatures can help distinguish between EM and saprophytic habits [START_REF] Mayor | Elucidating the nutritional dynamics of fungi using stable isotopes[END_REF]. Those root-associated Trechispora are probably more endophytic than EM, and do not obligatorily form an EM structure. Similarly, Amanitopsis are relatively widespread in the Neotropics, and are closer to saprophytic Amanitaceae [START_REF] Redhead | Saproamanita, a new name for both Lepidella E.-J. Gilbert and Aspidella E.-J. Gilbert (Amaniteae, Amanitaceae)[END_REF].

40 Compared to our delineation of EM symbioses (Rinaldi et al., 2008), Neotropical trees represent a continuum of associations with soil fungi, not obligatory and often superficial, considered as "wrong" observations by [START_REF] Brundrett | Misdiagnosis of mycorrhizas and inappropriate recycling of data can lead to false conclusions[END_REF]. Experiments may be necessary to test if EMF are obligate symbionts and reciprocally how EMF could affect plant fitness. As plants are not water limited in Neotropical forests, and considering the abundance of fungal pathogens in tropical soils, the protective role of EMF [START_REF] Zengpu | Antagonism between Ectomycorrhizal fungi and plant pathogens. Mycorrhizas for Plantation Forestry in Asia[END_REF][START_REF] Mohan | Evaluation of ectomycorrhizal fungi as potential bio-control agents against selected plant pathogenic fungi[END_REF] may be more important than their benefits on plant nutrition. Moreover, if the association with EMF is more advantageous only in some habitats, like the white sands, then a variable association could represent an adaptation to the environmental gradients in the Amazon (e.g. soils and topography). To test this hypothesis, and more generally to test if habitats are drivers of specialization in plant-fungi (and also plant-insect) interactions, I am contributing to an ANR project where 11 lineages of plants are sampled in plateau, slopes and flooded forests, on terrafirme and white sands, in both French Guiana, Peru and Brazil. Within this ongoing and rather ambitious project, we hope to investigate the distribution of fungi (and possibly of EMF) among hosts and habitats, and test if host or habitat are key drivers of fungal specialization.

To summarize, my different projects have revealed and raised questions on different drivers of EMF specialization, for alders and tropical EMF. All these studies are based on field sampling and observations, and would require experimental tests to disentangle all the complex processes shaping EMF communities. The projects presented in the following sections focus on a smaller scale, and intend to target a missing link to understand specialization: the complex interactions of fungi with fungi.

42 from Schwob et al., 2018. Axis 3 : Biotic interactions Projects FUNCHEM, SECIL, RECO-RECO, DROUGHT Articles Kohout et al., 2011;Schwob et al., 2018;Lagarde et al., 2018 ;Roy et al., submitted;Gazal et al., submitted;Donald et al., submitted;Nagati et al., 2018;Nagati et al., submitted Perhaps because NGS data allows for the sequencing of greater numbers of fungi in a community, we are now able to go beyond fungal diversity, and look at fungus-fungus interactions and more generally at ecological networks involving fungi (Vacher et al., 2016b). While ecological networks have been used to study plant-pollinator interactions and food webs for decades, their use to study fungi-plant interactions or fungi-fungi interactions is relatively recent [START_REF] Bahram | Network perspectives of ectomycorrhizal associations[END_REF]. Ecological networks represent interactions within a community, and the tools developed to study them allow for quantifying the interactions and testing hypotheses compared to random distribution of interactions. During my previous projects on EMF communities, I have always wondered if the specialization observed was not a sampling bias, especially in the tropics. In the case of alders, the occurrence of Frankia on roots also raised questions on Frankia-fungi interactions. More generally, the large part of unexplained variability in my previous analysis of EMF communities, and currently published in the literature on fungal communities pushed me to investigate interactions within communities.

a. Interactions within alder roots and populations Interestingly, alders appear as an exception, not only because of their specific EMF, but also for their lack of interactions with other trees. Indeed, [START_REF] Kennedy | Missing checkerboards? An absence of competitive signal in Alnusassociated ectomycorrhizal fungal communities[END_REF] showed that interactions between alder's fungi are not competitive. This result contrasts with the competitive exclusion between other EMF detected in other ecosystems [START_REF] Koide | Evidence of species interactions within an ectomycorrhizal fungal community[END_REF][START_REF] Kennedy | Root tip competition among ectomycorrhizal fungi: are priority effects a rule or an exception?[END_REF][START_REF] Pickles | Spatial analysis of ectomycorrhizal fungi reveals that root tip communities are structured by competitive interactions[END_REF]. Moreover, [START_REF] Huggins | Unlocking environmental keys to host specificity: differential tolerance of acidity and nitrate by Alnus-associated ectomycorrhizal fungi[END_REF] have highlighted the selective role of acidity and nitrate on alder fungi. Indeed, in the presence of Frankia, or under highly acidic conditions, only specific lineages of fungi are able to associate with alders. [START_REF] Kennedy | Interspecific mycorrhizal networks and non-networking hosts: exploring the ecology of the host genus Alnus[END_REF] suggested that reward and sanctions of EMF could also contribute to select few and specialized fungi, dependent on nitrogen fixed by Frankia on alder roots.

There are several Frankia strains on alder roots worldwide and their traits can be variable. [START_REF] Pozzi | In-planta sporulation phenotype: a major life history trait to understand the evolution of A lnus-infective Frankia strains[END_REF] showed that in-planta sporulation phenotype was particularly abundant in montane habitats, or on some species of alders such as A. alnobetula, and can contribute to the resistance of Frankia to cold environments. To better understand how Frankia strains could interact with EMF, and more generally, to investigate how interactions could shape alder specialization, I have collaborated with G. Schwob (during his PhD at Ecologie Microbienne, Lyon) to establish a crossing experiment on young alders (3 alder species, 2 soil provenances with two different Frankia phenotypes, Fig 19A). We hypothesized that in-planta sporulating phenotypes would rapidly invade their host root and reduce possible interactions with EMF.

We also hypothesized that such phenotypes would be more host-specific than others. After 6 months, the colonization by EMF was low, but some specific lineages were already present. The soil provenance explains 15% of the EMF community structure, while the host species explains only 6% (Schwob et al., 2018).

44 Interestingly, the phenotype of Frankia contributes to shape EMF communities, and explains 8% of the EMF community structure as well as 10% in interaction with the habitat. This first experiment should be completed by measures of N-fixation activities to understand if benefits or sanctions can contribute to these interactions on alder roots, as suggested by [START_REF] Kennedy | Interspecific mycorrhizal networks and non-networking hosts: exploring the ecology of the host genus Alnus[END_REF]. These results already show how important habitat and microbial interactions are compared to host effects on alder roots (Fig 19B,C).

The similarity between EMF communities associated with different alder species was particularly puzzling in this experiment, and contrasts with the differences observed in the field (Roy et al., 2013a). Theoretically, closely related species that share a common niche (EMF partners) may compete locally, or avoid growing together. Interestingly, alder species rarely co-exist, except in some locations such as in Corsica. Using ecological networks and the metrics of specialization, I have therefore tested if in case of co-occurrence, EMF could show competitive-exclusion patterns and plants could be more specialized. Such cases are relatively rare and sites in USA, Québec and Europe were analysed by Circé Collongeon during her master 2 internship (Fig 20A). The specialization of alders, reflected by degree and Blüthgen d, is always higher locally than globally (Fig 20B ,C), and at the network level, H2 is higher locally than predicted by null models (Fig 20D, Roy et al., submitted). The resulting networks are highly specialized, while theoretically, 31% of OTUs are potentially shared between alder species. This result fits the idea that closely related species that are associated with similar partners, compete more than species sharing fewer partners or species that are more distant phylogenetically. Moreover, this result confirms the hypothesis of [START_REF] Kennedy | Interspecific mycorrhizal networks and non-networking hosts: exploring the ecology of the host genus Alnus[END_REF], who suggested that alders are avoiding networks, even with co-existing alder species.

Interestingly, a few scattered cases have revealed shared partners between alders and other tree species. In New Zealand, where Alnus and Salix have been co-introduced, alders are able to share fungi with Salix, and partly lose their specificity. In Corsica, where A. cordata often grows in forest dominated by Castanea sativa [START_REF] Gamisans | La végétation de la Corse[END_REF], Fagus sylvatica and Pinus halepensis, very generalist and potentially shared EMF have been detected on A. cordata roots (Pozzi et al., 2018). Growing in mixed forest is not common among alders, and this habit could have favoured novel associations and also lowered their specialization. All these clues lead us to consider interactions with other trees to better understand geographic variations of EMF specialization.

b. Interactions mediated by EMF in the boreal forest

At the ecosystem level, root-associated fungi and microbes have a key role for plant-to-plant interactions (Van der Heijden and [START_REF] Van Der Heijden | Socialism in soil? The importance of mycorrhizal fungal networks for facilitation in natural ecosystems[END_REF][START_REF] Bever | Rooting theories of plant community ecology in microbial interactions[END_REF]. As EMF are often able to associate with multiple hosts and tree individuals, shared EMF can contribute to ecosystem dynamics and succession [START_REF] Dickie | Shared ectomycorrhizal fungi between a herbaceous perennial (Helianthemum bicknellii) and oak (Quercus) seedlings[END_REF][START_REF] Nara | Ectomycorrhizal networks and seedling establishment during early primary succession[END_REF][START_REF] Richard | Facilitated establishment of Quercus ilex in shrub-dominated communities within a Mediterranean ecosystem: do mycorrhizal partners matter?[END_REF]Diédhiou et al., 2010b;[START_REF] Simard | Mycorrhizal networks: mechanisms, ecology and modelling[END_REF]. With climate change, tree migrations are observed, especially in boreal ecotones [START_REF] Midgley | Plant species migration as a key uncertainty in predicting future impacts of climate change on ecosystems: progress and challenges[END_REF][START_REF] Leithead | Northward migrating trees establish in treefall gaps at the northern limit of the temperate-boreal ecotone, Ontario, Canada[END_REF], modifying ecosystem dynamics and tree communities. As dominant trees in boreal ecosystems are EM, changes in distribution may be correlated with below-ground changes in EM communities, and reciprocally.

Figure 21: A, spruce forest with a clear forest gap where aspen can be observed; B, differences of EMF communities on fir saplings depending on dominant forest cover, and correlation with total N in fir needles, and C, possible interactions between EMF communities and fir growth revealed by path analysis (from Nagati et al., 2019).

Figure 22: number of OTUs per 1 cm 2 of leaflet of Astrocaryum sciophilum, showing the high diversity whatever the leaf age in a small surface.

47

Through a collaboration with Université du Québec in Abitibi-Témiscamingue, I co-supervise the PhD of Mélissande Nagati, whose objective is to investigate the role of EMF in boreal ecosystem dynamics at the ecotone between mixed forests and spruce forests. We study an exceptional site, where Abies balsamea -the migrating tree species -grows better under Populus tremuloides than under Picea mariana (Fig 21A). These two species form patches and locally dominate. We have demonstrated that both forest patches host very contrasted fungal communities, both in soil (Nagati et al., 2018) and on young Abies balsamea (Fig 21B). We have also managed to show that Abies needles are richer in N under Populus (Fig 21B, Nagati et al., 2019). The presence of ericaceous shrubs has, on the contrary, a negative effect on the EMF communities (Fig 21C). Finally, we have compared the whole fungal communities with southern patches dominated by Abies, and we have shown that saprophytic fungi are more similar under Abies and Populus than under Picea. This PhD illustrates that Abies dynamics are the result of both positive and negative interactions, partly mediated by soil fungi and involving interactions with other plant.

c. Interactions within endophytic communities

In all my projects on EMF fungi, the host has been central, in the sampling, the questions, and often, the effects. Even if EMF can be generalist, and interactions with bacteria can also shape their diversity, leaving the host is not easy for an ecologist. By studying endophytic communities, I have tried to question the role of the host, and the possible neutral distribution of those above-ground communities. Through the ANR project SECIL, I supervise the post-doc of J. Donald, and we investigate the endophytes community in canopy leaves at the Nouragues station. We have shown that the host tree has an effect, together with the branch identity, and that neighbouring plants do not necessarily host more similar communities (Donald et al., submitted). Conversely, under the canopy, the basket-palm Astrocaryum sp. hosts endophytic communities more similar to its neighbours, probably through the accumulation of leaf litter coming from surrounding trees (Donald et al., in prep). Indeed, in other palm trees which do not accumulate leaf litter, a lower diversity of endophytic fungi is detected. The host effect can result partly from its morphological traits, and indeed, Astrocaryum sp. shares less endophytes with other Astrocaryum individuals than with their neighbouring tree species.

The structuring role of leaf and tree traits is increasingly recognized [START_REF] Saunders | Exploring the evolutionary ecology of fungal endophytes in agricultural systems: using functional traits to reveal mechanisms in community processes[END_REF][START_REF] Sanchez-Azofeifa | Relationships between endophyte diversity and leaf optical properties[END_REF]). It is for example part of the ongoing projects in French Guiana to try to test if drought-resistance traits is correlated with endophytic distribution. The genus Astrocaryum is well known for its slow growth and longevity [START_REF] Chave | Colonization front of the understorey palm Astrocaryum sciophilum in a pristine rain forest of French Guiana[END_REF].

In their review of endophytic diversity in the tropics, [START_REF] Arnold | Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots?[END_REF] suggested that leaf longevity could favour such a diversity. Through the project FUNCHEM, together with chemists interested in communities of slow-growing fungi (which may produce more complex metabolites), I studied endophytic communities of 0.5 to 28 yr-old Astrocaryum leaves in greater details. I hypothesized that the long life-span of Astrocaryum leaves can favour a more diverse endophytic communities. By sequencing the ITS1 barcode on 1-cm 2 leaf samples, I have observed that communities are less diverse and more homogeneous in older leaves than in young ones (Fig 22). Endophyte communities are highly diverse and not distinct between leaf ages. This result contrasts with the dynamics observed on Theobroma cacao leaves [START_REF] Arnold | Canopy cover and leaf age affect colonization by tropical fungal endophytes: ecological pattern and process in Theobroma cacao (Malvaceae)[END_REF], and probably reflects the high variability of communities sampled in the field.

48 The high diversity of fungi and bacteria detected within those leaves also raises questions regarding the interactions between micro-organisms. Interactions between endophytes represent a continuum going from parasitism to mutualism, including commensalism [START_REF] Lindow | Microbiology of the Phyllosphere[END_REF]. Indeed, some competitors have anti-fungal properties, and are now used in agriculture, such as Trichoderma sp. [START_REF] Degenkolb | Trichoderma brevicompactum complex: rich source of novel and recurrent plant-protective polypeptide antibiotics (peptaibiotics)[END_REF]. Even epiphytic lichens can have anti-fungal properties (Lagarde et al., 2018). To progress in our understanding of microbial interactions within endophytic communities, I have collaborated with colleagues interested in interactions and bacterial communications, through the method of Quorum sensing. We have investigated a model plant hosting specialized fungi and diverse bacteria, Posidonia oceanica [START_REF] Panno | Diversity, ecological role and potential biotechnological applications of marine fungi associated to the seagrass Posidonia oceanica[END_REF]Vohnik et al., 2015;2016). Indeed, Lulwoana sp. (a dark-septate fungus) has been revealed only from sea grasses (such as Posidonia) in diverse locations [START_REF] Torta | Lulwoana sp., a dark septate endophyte in roots of Posidonia oceanica (L.) Delile seagrass[END_REF]. We hypothesized that negative interactions between bacteria and fungi could contribute to fungal specialization in P. oceanica leaves. I co-supervised the master 1 of Nina Gazal et al., in prep). Interestingly, one strain of Lulwoana qp.

showed more positive interactions with bacteria than with fungi, but all interactions were mostly positive (Fig 23C, Gazal et al., in prep).

To summarize, through these diverse projects, I have confirmed that specialization is not neutral for alders and I have shown how interactions with other trees and bacteria can modify EMF and fungal specialization. The processes are different for alders and Neotropical trees, and for example dispersal may be more limited for tropical EMF than for the symbionts of alders.

Parameters explaining EMF distribution are different, and specialization is variable for alders while it is mostly explained by host for Neotropical EMF. It is still too early to quantify the importance of each process, and some questions remain unanswered, such as the importance of speciation or extinction in the tropics ( Fig 24). In French Guiana, the distribution of soil fungi has been studied and revealed that 50% of community variations can be explained by neutral models (Sommeria-Klein, 2017). Large-scale analyses of root symbioses by metabarcoding now have the power to evaluate the importance of neutral processes [START_REF] Sommeria-Klein | Inferring neutral biodiversity parameters using environmental DNA data sets[END_REF], and would allow quantifying the importance of distinct processes and factors influencing EMF diversity and specialization.

Building from these results, two subsequent pathways for research were possible, either going deeper in interactions, and searching for mechanisms leading to specialization, or searching for a more integrative level and studying factors shaping EMF communities and specialization. I have decided to investigate the second option, and will now focus on a higher level: the landscape.

50 Landscape ecology is an interdisciplinary field linking geography and ecology. This field was born initially in the first half of the XIX th century, a period during which vegetation and soil maps were produced, but exploded one century later [START_REF] Wiens | Allerton Park 1983: the beginnings of a paradigm for landscape ecology?[END_REF][START_REF] Wu | Key concepts and research topics in landscape ecology revisited: 30 years after the Allerton Park workshop[END_REF]. Studies in landscape ecology have focused on plant, bird, and subsequently insect distributions, only recently including fungi [START_REF] Grilli | Fungal diversity at fragmented landscapes: synthesis and future perspectives[END_REF]. Landscape ecology tries to understand how the landscape, through its heterogeneity, and its elements (patches, corridors) can explain species distributions. One major challenge to delineate patches, and therefore describe a landscape, is to identify the habitat of a species, and the distance at which it may disperse. For fungi, dispersal can occur over long distances [START_REF] Vincenot | Population biology and ecology of ectomycorrhizal fungi[END_REF], and thus patches may be larger than patches for earthworms for example, which disperse vertically and over short distances. As a consequence, several landscapes can be drawn from a single environment, and this explains why in France, we have different corridors for fishes ("trame bleue"), for plants ("trame verte"), and now for bats ("trame noire", Sordello, 2017). However, landscapes are rarely defined for species (except for some endangered ones), but rather for habitats. Therefore, landscapes are often described through the surface of forests, fields, the presence of hedgerows, streams, and the connectivity between all these elements.

The importance of different elements of the landscape may differ among taxa, depending on their dispersal abilities (Fig 25). For fungi, recent studies have shown very contrasted patterns, depending on the community and the scale that are studied [START_REF] Nordén | At which spatial and temporal scales can fungi indicate habitat connectivity?[END_REF] ; Table 3). Wood-associated fungi and birch endophyte communities are distinct at forest edges and are affected by forest fragmentation [START_REF] Helander | Fragmented environment affects birch leaf endophytes[END_REF][START_REF] Saikkonen | Forest structure and fungal endophytes[END_REF][START_REF] Abrego | Response of wood-inhabiting fungal community to fragmentation in a beech forest landscape[END_REF].

In the lava-fragmented landscape of Hawaï, local root-associated fungal diversity increased with forest area, and fungal species composition is correlated with fragment connectivity [START_REF] Vannette | Forest area and connectivity influence root-associated fungal communities in a fragmented landscape[END_REF]. On the contrary, landscape composition has no effect on grapevine foliar endophytic communities (Fort et al., 2016a), while patches of different habitats hosted very contrasted communities (Fort et al., 2016b). [START_REF] Grilli | The composition of arbuscular mycorrhizal fungal communities in the roots of a ruderal forb is not related to the forest fragmentation process[END_REF] have also shown that fragmentation does not shape communities of endomycorrhizal fungi associated with a ruderal forb. Previously, [START_REF] Grilli | Forest fragment size and nutrient availability: complex responses of mycorrhizal fungi in native-exotic hosts[END_REF] had detected a strong relationship with patch size for endomycorrhizal and dark septate endophytes associated with a native host but not for fungi associated with an exotic host. [START_REF] Boeraeve | Effects of host species, environmental filtering and forest age on community assembly of ectomycorrhizal fungi in fragmented forests[END_REF] have also shown that EMF communities associated with three different hosts, Alnus glutinosa, Crataegus monogyna and Corylus avellana, are differently affected by the landscape. The distance between fragments does not explain change in communities, but forest age and host species have more of an effect. Interestingly, [START_REF] Nordén | Specialist species of wood-inhabiting fungi struggle while generalists thrive in fragmented boreal forests[END_REF] have shown that specialist wood-associated fungi are more affected by fragmentation than generalist ones. Overall, [START_REF] Grilli | Fungal diversity at fragmented landscapes: synthesis and future perspectives[END_REF] have concluded that in general, fragmentation negatively affects fungal diversity. Moreover, host, fungal nutritional mode and specialization may modify the tolerance of fungi to habitat disturbance. These recent results have rapidly changed my point of view on alder specialization. Schwob et al., 2017).

(F) but also colonize the grassland (G) and form a mosaic (M) at the edge (A), and differences of soil fungi and EMF communities in this landscape (from

53

Compared to other temperate trees, alders show a rather patchy distribution and extended stands are extremely rare. Alnus alnobetula is a montane shrub growing at the tree line, whose distribution is now extending over abandoned-pasture. In the Vanoise, extended populations can be found, representing one of the oldest alder stands in France (ca. 400 years old, with 80% of A. alnobetula, [START_REF] Anthelme | Environmental and spatial influences of shrub cover (Alnus viridis DC.) on vegetation diversity at the upper treeline in the inner western Alps[END_REF]. With G. Schwob, I have tried to understand how the landscape, through its fragmentation, can shape Alnus-EMF interaction and specialization. We hypothesized that patches with a higher alder density would host more specific symbionts than isolated trees. We did not detect an effect of alder density on EMF diversity, but we detected differences of EMF community structure and revealed a strong difference with grassland soil communities (Fig 26, Schwob et al., 2017). The sequencing of soil cores also revealed contrasting patterns among fungi, and saprophytic fungi distribution is opposed to EMF one. Specific symbionts are poorly distinguished by ITS1 barcodes (250 bp for Miseq) and we did not detect a strong difference between forest and edges. Interestingly, Boeraeve et al. ( 2019) also showed that soil communities are more affected by forest edge than root communities of A. glutinosa. All these examples illustrate the different responses of fungal communities to fragmentation and landscape structure.

Through a collaboration with A. Brin and E. Andrieux (DYNAFOR, Toulouse) on the Cevennes ancient forests, I have begun to get further involved in landscape ecology. The term "Ancient forests" does not refer to forest age or maturity, but rather to the permanence of a forest [START_REF] Cateau | Ancienneté et maturité: deux qualités complémentaires d'un écosystème forestier[END_REF]. Ancient forests are defined in France from maps drawn by Cassini, who reported around 1755 the occurrence of forests in France. Ancient maps are precise enough to constitute a reference of the minimum extent of forests in France. Today, 30% of the French territory is covered by forests, three times more than in 1850. The forest surface was minimal at the beginning of the industrial period, where wood was intensely consumed, and most people were still living in the countryside. Therefore, ancient forests are defined from maps of 1850 [START_REF] Cateau | Ancienneté et maturité: deux qualités complémentaires d'un écosystème forestier[END_REF]. Since then, an ancient forest can have been cut and replanted (Fig 27A ), which explains the difference between ancient forests and mature forests. Interestingly, soils may well reflect the permanency of a forest's cover, and one can expect that soil fungi may be sensitive to such forest history. The literature is rich on forest ages than (e.g. [START_REF] Bonet | The relationship between forest age and aspect on the production of sporocarps of ectomycorrhizal fungi in Pinus sylvestris forests of the central Pyrenees[END_REF][START_REF] Richard | Diversity and specificity of ectomycorrhizal fungi retrieved from an old-growth Mediterranean forest dominated by Quercus ilex[END_REF], notably because forest managers have found many indicators of forest maturity among wood-associated fungi [START_REF] Christensen | Wood-inhabiting fungi as indicators of nature value in European beech forests. Monitoring and Indicators of Forest Biodiversity in Europe-From Ideas to Operationality 229[END_REF]. In the Cevennes National Park, a recent effort made to map ancient forest revealed a scattered distribution, hidden by the continuous forest cover. Today, 80% of the park is forested, but this landscape is apparently recent, as ancient forests represent only 20% of the surface (Fig 27B). As the forest fragmentation is low today, we have hypothesized that fungal communities may rather follow [START_REF] Fahrig | Rethinking patch size and isolation effects: the habitat amount hypothesis[END_REF] hypothesis, which assumes that connectivity may be less important than surface and habitat amount on species distribution. In other words, I have investigated if the fungal diversity can be higher in ancient forest surrounded by a higher quantity of ancient forest, whatever the connectivity of these patches. S. Mennicken worked on this project during her master 2, together with F. Kondratow (PhD supervised by A. Brin and E. Andrieu). Through the use of NGS, EMF, saprobes and pathogenic fungi have been sequenced from soil collected over 50 plots in the National Park (8 root cores per plot). We have shown that different guilds had distinct responses to the amount of habitat, and detected both the effect of soil chemistry and landscape (Mennicken et al., in prep). Interestingly, the surface of the central patch -where samples were collected-has no effect on fungal diversity, which contrasts with the results obtained on isolated stands in other ecosystems [START_REF] Peay | A strong species-area relationship for eukaryotic soil microbes: island size matters for ectomycorrhizal fungi[END_REF].

54 More recently, thanks to an interdisciplinary project with archaeologists and forest historians from Toulouse 2 University, I have sampled soil communities in ancient and recent forests located at the extreme north of the Carpathian Mountains (Romania). There are still pristine patches of forest in Ukraine, in the eastern Carpathians [START_REF] Trotsiuk | Age structure and disturbance dynamics of the relic virgin beech forest Uholka (Ukrainian Carpathians)[END_REF]. In the Maramures (Fig 27C ), forests are extremely tall, show numerous signs of maturity, and are characterized as old-growth forests (OGF). However, OGF have probably been exploited in the past, due to an intense local mining activity. Today, those old-growth beech forests are threatened by logging, even in protected areas [START_REF] Knorn | Continued loss of temperate old-growth forests in the Romanian Carpathians despite an increasing protected area network[END_REF]. Logging can deeply change forest structure and dynamics [START_REF] Durak | Long-term trends in vegetation changes of managed versus unmanaged Eastern Carpathian beech forests[END_REF], and reserve managers are calling for research to monitor the diversity in these OGF. Compared to the Cevennes project, I have instead focused on the difference between ancient and recent forests within old-growth forests, and integrated more habitats and history descriptors. Within this project, I am testing if fungal diversity is shaped not only by forest maturity but also by forest history. For EMF, this might be the case, as [START_REF] Diédhiou | Response of ectomycorrhizal communities to past Roman occupation in an oak forest[END_REF]Diédhiou et al. ( , 2010a) ) have shown that the presence of Roman farms in the forest contributed to shape the distribution and the functions of EMF communities today. In another project, CERES (2018-2020), together with A. Brin, I aim at studying the effect of fragmentation and temporal continuity on diverse communities, including EMF, in the forests of southwestern France. To achieve this, I am studying the soil fungal diversity in both fragmented and extended forests, of either recent or ancient age. In this case, I am testing test if fungal diversity is shaped by forest history and landscape structure and I hope to involve a PhD student in this project soon.

In Amazonian forests, interactions between archaeologists and ecologists have also recently revealed the influence of history -linked with human history-on tree communities. Indeed, sites which have previously been heavily populated host the richest tree communities today [START_REF] Mcmichael | Ancient human disturbances may be skewing our understanding of Amazonian forests[END_REF]. Moreover, archaeologists have revealed clues on past uses for 82 plant families in the Neotropics [START_REF] Levis | Persistent effects of pre-Columbian plant domestication on Amazonian forest composition[END_REF]. The Amazon may be a "jardin sauvage" or a "domesticated forest" [START_REF] Barlow | How pristine are tropical forests? An ecological perspective on the pre-Columbian human footprint in Amazonia and implications for contemporary conservation[END_REF][START_REF] Rostain | Amazonie. Un jardin sauvage ou une forêt domestiquée, Essai d'écologie historique[END_REF]. As Amazonian pre-colombian human populations have been highly connected and have been exchanging products [START_REF] Rostain | Hercule en Amazonie[END_REF], they may have contributed to the dispersal of plants across the Amazon and have definitely modified some landscapes, such as raised fields, shell mounds or terra preta accumulations [START_REF] Rostain | Hercule en Amazonie[END_REF]. In French Guiana, clues of past occupancy are visible nearly everywhere along the streams, or close to inselbergs. In the forest, charcoal fragments and shards can be observed, and ring-ditched hills have recently been detected by LIDAR in socalled "pristine" forests.

Considering the abundance of EMF on slopes and close to inselbergs, I have contributed to a multidisciplinary project involving botanists and archaeologists, to understand the extent of which past forest history can shape EMF distribution in certain habitats in French Guiana. Among the habitats that have been massively occupied in the past, liana forest are particularly interesting, and host EM lianas such as Gnetum spp. and Coccoloba spp. On ring-ditched hills, pedologists suggest that soil has been removed, revealing the laterite crust and increasing the soil drainage when compared to surrounding forests. As a consequence, soil conditions may be similar on inselberg slopes and close to ring-ditched hills. I have therefore tested if EMF could be favoured by past occupancy around ring-ditched hills, during N. Gazal's Master 2 internship. By sequencing soil communities, we have produced comprehensive inventories (Fig 28A ) and detected three EMF and one glomeromycota particularly associated with evidence of past human settlements (Gazal et al., submitted). (Gazal et al., accepted).

57

Fungal diversity is not significantly different on massively occupied sites than on other sites (Fig 28B), nor is EMF diversity, and only sites moderately occupied in the past are more homogeneous (Fig 28C). More generally, EMF are abundant on slopes and in "cambrousses", a fact that confirms the preference of EMF for low-canopy forests. On ring-ditched hills, EMF can be favoured by canopy gaps and the occurrence of EM lianas or small trees. These results illustrate how neotropical EMF can survive in gaps, thanks to numerous and scattered favourable habitats, and eventually, thanks to past human uses.

The question remains if investigating fungal communities in general can be of interest for historical ecology studies. They have already been used but often as indicators. For example, the occurrence of spores of the coprophilous fungi Podospora or Sporormiella can indicate pasture in sediments [START_REF] Orbay-Cerrato | Historic grazing in southern New England, USA, recorded by fungal spores in lake sediments[END_REF]. In the Amazon, there is one puzzling question that may be solved by investigating not only EMF but also pathogenic fungi. Indeed, Neotropical forests are characterized by their tree diversity, and the high and density-dependent mortality, mediated by natural enemies [START_REF] Levi | Tropical forests can maintain hyperdiversity because of enemies[END_REF] including fungi [START_REF] Bagchi | Testing the Janzen-Connell mechanism: pathogens cause overcompensating density dependence in a tropical tree[END_REF][START_REF] Mangan | Negative plant-soil feedback predicts tree-species relative abundance in a tropical forest[END_REF]. Increasing the density of species of cultivated plants in the forest may have been a challenge, and considering the deep soil modifications, one can wonder if the aim of these soil modification by humans could have been to decrease the abundance of saprobes and pathogenic fungi by increasing the soil drainage. Indeed, soils around crowned mountains are very different from terra preta described along the Amazon, where a higher organic matter content favours a rich saprophytic and bacterial community [START_REF] Kim | Bacterial diversity of terra preta and pristine forest soil from the Western Amazon[END_REF][START_REF] Lucheta | Fungal community assembly in the Amazonian Dark Earth[END_REF]2017). Another use of fungi in archaeology can be linked to their dispersal ability. Indeed, evidence of occupancy may reflect local land uses, but the occurrence of indicators, that are habitat-specific and able to disperse, may also reflect changes at the landscape level. Searching for such indicators requires the production of reliable and comprehensive inventories of fungal communities, so that presence or absence records can be considered as reliable. At the EDB lab, efforts have been made to replicate PCRs, include 10% of negative controls, and now positive controls. Our sampling of fungi through NGS over 1 ha tend to show a saturation (Gazal et al., accepted), supporting the idea that soil DNA could be used to produce comprehensive sampling, and therefore to detect possible indicators.

To summarize, there are debates about the definition of landscape and the effect of landscape on fungal communities, but this integrative level of analysis could enlighten our understanding of the distribution pattern of EMF, both in temperate and tropical forests. Based on those recent projects, I am now developping projects focused on soil history and stability in order to understand not only if EMF could be more diverse in ancient forests, but also if mycorrhizal networks could be favoured in these stable habitats, and reciprocally, the extent to which fungi could contribute to forest resilience. An ecosystem's resilience reflects its capacity to recover after a perturbation, and managers are indeed searching to favour forest resilience, for example by increasing tree diversity or functional diversity in general [START_REF] Thompson | Forest Resilience, Biodiversity, and Climate Change[END_REF]. During my short post-doc, I studied with F. Richard at CEFE (Montpellier) the effect of drought on EMF communities. We sampled EMF of Quercus ilex at Puechabon, where a rain exclusion system is settled since 15 years (-30% rain). We revealed only very small changes (Richard et al., 2011) and variations of EMF communities were mainly seasonal. Such observations illustrate the variability, but also the resilience of EMF communities, at least in ecosystems where EMF are abundant and EM trees dominate.

58

59

Using landscape to reconnect students to ecology Projects ACTUAAL Articles Roy et Caillon, submitted Going from community ecology to landscape ecology has brought me closer to geography, not only in my research projects, but also in my teaching. Focusing on landscapes is relatively recent among educators, and becomes increasingly central in my pedagogy. The first classes I modified were botany and mycology, and the first step has been to interest students in learning about landscape through projects on their urban environment. Indeed, students are less and less interested in taxonomy, and rarely enjoy learning Latin names. Thanks to availability of "apps" to identify plants (such as Plantnet, [START_REF] Goëau | Pl@ ntnet mobile app[END_REF], students are autonomous enough to perform inventories of wild plants in their own streets, trying to test if one dispersal mode was dominant over the others. In mycology, I have trained students to identify lichens growing in the city and in the countryside to determine pollution level. In both cases, involving students in participative surveys has really increased their investment in projects, and has brought interesting results. For example, inventories of lichens are often richer in central Toulouse as compared to the periphery. In the streets, long-distance dispersal is rare, and plants are often ant-dispersed. More theoretically, setting community ecology questions in relation to land use probably increases their interest for nature in towns [START_REF] Pellegrini | Streets as new places to bring together both humans and plants: examples from Paris and Montpellier (France)[END_REF] and such teachings now interest geographers as well. More recently and on a research level, I have begun to collaborate with J. Legall and study this increasing interest in urban areas of Buenos Aires and Mexico, where students are particularly disconnected from nature (ACTUALL project).

The second change in my courses, which is intimately linked with landscape ecology, is the use of drawings. This is extremely personal and uncommon in ecology (Roy and Caillon, submitted) while we teach our students how to draw plants in botany. Such drawings are useful for captivating students within a boring powerpoint and for sharing my passions for tropical diversity (Fig 29A). In anthropology and ethnology [START_REF] Brunois | Du dessin au dessein des plantes sauvages[END_REF], the role of drawings has long been dissected and many advantages have been underlined. Reciprocally, in art pedagogy, the ecology and the landscape are key elements for engaging students [START_REF] Inwood | Shades of green: Growing environmentalism through art education[END_REF] and raising their creativity [START_REF] Neperud | Art, ecology and art education: Practices & linkages[END_REF][START_REF] Graham | Art, ecology and art education: Locating art education in a critical place-based pedagogy[END_REF][START_REF] Herzogenrath | Deleuze/Guattari & Ecology[END_REF]. More generally, the development of environmental art and even ecological art illustrates this long-term interest of artists for ecology [START_REF] Brunner | Post-media activism, social ecology and eco-art[END_REF]. Recently, some projects have highlighted the role of sketching in science (http://www.sciencesketches.org), but not particularly in ecology.

The third change in my teaching has then been to integrate both landscape-scale studies and drawings to build a pedagogical project linked with research questions in vineyards (fig 29B). Indeed, Toulouse University is surrounded by an agricultural landscape, especially vineyards. Close to Gaillac, vineyards are concentrated in Mediterranean microclimates and grow on limestones, sandy and clay-rich soils. This diversity of habitats and the occurrence of Mediterranean plants make vineyards particularly interesting for teaching botany in early spring. Rapidly, I have realized that not only students but also vintners are interested in plants and their landscape. With S. Caillon (CEFE, CNRS), I have begun investigating this relationship, through field teaching. The use of art is a real catalyst in this non-funded project, and enables the construction of a network of organic vintners, as a support for teaching and research (Fig 30A). Moreover, students are able to observe a rich plant community, with 133 plants identified over 48 inventories (10 m long transects, Fig 28B,C).

60 Gaillac appellation is not only one of the oldest vineyards in France (recorded from 200 yrs B.C.), but is also the most diverse in terms of grape varieties [START_REF] Plageoles | La saga des cépages gaillacois et tarnais en 2000 ans d'histoire[END_REF]. Over the last century, up to 82 grape varieties have been reported and several are endemic, such as prunelard, ondenc, and loin de l'oeil varieties. Through field-based teaching, we have also observed that vintners are particularly innovative and use their landscape and the grape diversity in various ways to adapt their organic practice to local constraints. Thanks to a "Make our planet great again" project granted to D. Renard (CEFE, Montpellier), I will work with a PhD student (supervised by S. Caillon, 2019-2021) who investigates how practices and grape diversity contribute to vineyard resilience, estimated through the variability of harvests during the past 30 years (other estimators to be defined as well).

This project does not integrate fungi yet, but testing if mycorrhizal fungi can reflect differences in landscape and land use, and therefore contribute to vineyard resilience, would of course be extremely interesting. Vitis sylvestris var. vinifera is a domesticated liana associated with generalist endomycorrhizal fungi [START_REF] Balestrini | Cohorts of arbuscular mycorrhizal fungi (AMF) in Vitis vinifera, a typical Mediterranean fruit crop[END_REF]. Recent investigations of its interaction with surrounding plants have revealed possible carbon and nitrogen transfers from leguminous plants through mycorrhizal fungi [START_REF] Cheng | Arbuscular mycorrhizal fungi-mediated nitrogen transfer from vineyard cover crops to grapevines[END_REF][START_REF] Thompson | The geographic mosaic of coevolution[END_REF]2006). Moreover, projects on mycorrhizae try to detect possible protective effects against other fungal pathogens [START_REF] Pozo | Unraveling mycorrhiza-induced resistance[END_REF]. However, in terms of diversity, the endomycorrhizal community may be of low variability at the scale of Gaillac and between grape varieties [START_REF] Balestrini | Cohorts of arbuscular mycorrhizal fungi (AMF) in Vitis vinifera, a typical Mediterranean fruit crop[END_REF]Schreiner and Mihara, 2017) and the global fungal diversity might be more interesting to study. In the following projects, I have tried to integrate the methods and questions developed through those integrative teachings, to re-orient my research questions on EMF and fungi communities.

How to integrate ecological networks to study ecosystem resilience? Projects CERES, GLOBNET, CHAMPLAIN Article Shefferson et al., 2016 ;2018 ;Nagati et al., submitted Fungi are heterotrophic. They are therefore involved in interactions, often with plants, but also with other soil organisms. The study of specialized interactions has illustrated the effect of bacteria and other soil fungi on EMF interactions and has raised more general questions on multitaxa interactions. The use of ecological networks to describe plant-fungi interactions can indeed be extended to other interactions, through co-occurrence data (Vacher et al., 2016b) and NGS data are beginning to be used to describe such networks [START_REF] Bohan | Next-generation global biomonitoring: large-scale, automated reconstruction of ecological networks[END_REF]. There are still limitations, and for example species delimitation from short sequences (produced by NGS) may bias our description of networks [START_REF] Bohan | Next-generation global biomonitoring: large-scale, automated reconstruction of ecological networks[END_REF]. Trying to describe ecological networks could be particularly interesting for estimating ecosystem resilience capacity, as more connected networks are supposed to increase ecosystem resilience [START_REF] Thébault | Stability of ecological communities and the architecture of mutualistic and trophic networks[END_REF]. Using NGS to characterize below-ground ecological networks involving EMF could allow detecting possible common mycorrhizal network (CMN), comparing ecological with functional common mycorrhizal network, and finally help to draw a more theoretical framework for fungal interactions.

Theories on ecological networks have been developed from the study of plantpollinator interactions (Vasquez et al., 2009) and trophic chains. Interactions between plants and pollinators are highly variable, and mainly shaped by spatial heterogeneity [START_REF] Moreira | Spatial heterogeneity regulates plant-pollinator networks across multiple landscape scales[END_REF] and landscape [START_REF] Ferreira | What do we know about the effects of landscape changes on plantpollinator interaction networks?[END_REF].

62 These mutualist networks are often particularly nested and asymmetric compared to plantherbivore networks [START_REF] Bascompte | The nested assembly of plant-animal mutualistic networks[END_REF][START_REF] Nuismer | Coevolution and the architecture of mutualistic networks[END_REF]. The nestedness of mutualist networks may contribute to network stability and more generally to ecosystem resilience [START_REF] Thébault | Stability of ecological communities and the architecture of mutualistic and trophic networks[END_REF]. Several articles suggest that a higher diversity in soils could also contribute to ecosystem resilience [START_REF] Wagg | Soil biodiversity and soil community composition determine ecosystem multifunctionality[END_REF][START_REF] Bender | An underground revolution: biodiversity and soil ecological engineering for agricultural sustainability[END_REF], especially in agricultural fields, but there are still debates on the complexity-stability relationship (Jacqet et al., 2013). More generally, the review of [START_REF] Simard | Mycorrhizal networks: mechanisms, ecology and modelling[END_REF] highlighted that mycorrhizal networks may have both positive and negative feedbacks and could have different effects on ecosystem dynamics. Their role in ecosystem resilience is often assumed, but may not be obvious. For example, in boreal forests, EMF may promote fir migration to the north and contribute to rapidly changing forest dynamics (axis 3b).

I have been involved in several projects related to ecological networks, but not focused on EMF nor on mycorrhizal networks. In GLOBNET ANR (2016-2020), the aim is to gather soil cores from temperate, boreal, and tropical zones, sequence several taxa, including fungi, and begin designing tools to study interaction networks between taxa based on co-occurrence. This ambitious project definitely allows a better understanding of plant-fungi interactions at a global scale. At a more regional scale, with I. Calderon-Sanou (PhD student of W. Thuiller), I have focused our sampling on a chronosequence of the boreal forest which has been well-described from the standpoint of fire age (Fig 31). This sampling enables the examination of how soil diversity changes along the chronosequence, but data may not be sufficient to test if networks are more connected in older forest patches. In the Amazon, the NEBEDIV ANR (2013-2018) has investigated specialisation of plant natural enemies, including fungi and insects. This project has gathered an immense set of data on variation of specialization and plant-fungi networks.

As the sampling has focused on root interactions, mycorrhiza have been sequenced together with the rhizosphere community, and interactions may be more real than co-occurrence data in soil. However EMF may be rare, as EM hosts had not been targeted. Moreover, based on axis 2, EMF may be relatively rare and specific, and may not be involved in networks.

Back to roots: towards experiments to link ecological and common mycorrhizal networks in a biogeographic context Ecological networks refer to potential interactions, but detecting shared OTUs on different tree species is of course insufficient to detect a possible common mycorrhizal network (CMN). Since the discovery of a possible organic carbon transfer between trees through shared EMF [START_REF] Simard | Net transfer of carbon between ectomycorrhizal tree species in the field[END_REF], some books have spread the idea that CMN are everywhere (such as "The secret life of trees", P. [START_REF] Wohlleben | The hidden life of trees: What they feel, how they communicate-Discoveries from a secret world[END_REF], but this is definitely not the case. Indeed evidence for exchanges through common mycorrhizal networks is relatively scarce (Fig 32, Hoeksema, 2015), perhaps because facilitation can occur without a CMN [START_REF] Bever | Rooting theories of plant community ecology in microbial interactions[END_REF]. For example, shared fungi have been detected in Guinean monodominant forests (Diédhou et al., 2010a), but studies using isotopes have not revealed any transfer between trees. Moreover, Corrales et al. (2016) have not detected a CMN between Oreomunnea individuals in Mexican forests. Experiments are needed to detect functional CMN, for example by excluding shared hyphae with fine nets around trees [START_REF] Booth | Mycorrhizal networks mediate overstorey-understorey competition in a temperate forest[END_REF][START_REF] Booth | Mycorrhizal networks counteract competitive effects of canopy trees on seedling survival[END_REF], or by tracing carbon or nitrogen isotopes between neighboring plants [START_REF] Simard | Net transfer of carbon between ectomycorrhizal tree species in the field[END_REF]. Our knowledge is probably too limited to understand in which environmental conditions such exchanges can occur, and if temperate or boreal ecosystems favor such functioning.

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Setting up more experiments in the field is challenging, but would be crucial to understand the ecological importance of exchanges through common mycorrhizal networks in a biogeographic context.

In the Canadian boreal forest, together with P. Marchand at UQAT, I have recently obtained a project to map interactions between trees and to investigate mycorrhizal and root connections between young trees (Funds from French Consulate in Canada). Indeed, in boreal ecosystems, Populus balsamoides and Pinus banksiana are both able to build root connections with other individual of the same species [START_REF] Tarroux | Frequency of root grafting in naturally and artificially regenerated stands of Pinus banksiana: influence of site characteristics[END_REF][START_REF] Adonsou | Root connections affect radial growth of balsam poplar trees[END_REF] and the question remains if such root grafts can contribute to facilitation between individual trees. Through two co-supervised student projects, we will therefore test if positive spatial interactions between plants are correlated with fungal interactions (shared fungi) or from root connections between individuals of the same species (Fig 33), or if on the contrary spatial aggregation results from a random process of dispersion. We have chosen to study such interactions in an unusual site, an abandoned mine, where up to 10 tree species could be recorded. This site began to be colonized by trees 50 years ago, and represents a simple system to study interactions between trees. Spatial aggregation can be used to target sites where CMN could occur, and this small project can be a base for future experiments on CMN in the field.

To study if mycorrhizal networks, or at least ecological networks between plants and fungi can contribute to ecosystem resilience, other options may be complementary. Indeed these descriptive projects do not include functional measures neither on ecosystem (e.g. decomposition rate) nor on mycorrhizal networks. Measuring functions of fungi may bring more evidence to estimate resilience capacity through a functional redundancy [START_REF] Allison | Resistance, resilience, and redundancy in microbial communities[END_REF][START_REF] Griffiths | Insights into the resistance and resilience of the soil microbial community[END_REF]. This can be approached by reporting functional traits, and perhaps by sequencing more functional genes [START_REF] Hannula | Primer sets developed for functional genes reveal shifts in functionality of fungal community in soils[END_REF]. Moreover, measuring functional consequences of networks may help to link below-ground and above-ground processes.

Through the PhD of M. Nagati, which I co-supervise, we began measuring traits of fir saplings (growth, nutrient status). Path analyses have revealed that the N content in fir needles is more related to EMF community structure than to the mycorrhization rate (Nagati et al., 2019), and that growth is negatively affected by the occurrence of ericaceous shrubs. These analyses suggest that EMF communities can be involved in facilitation of fir under aspen, and can be repeated in other ecosystems to investigate the functional consequences of below-ground networks. Studying plant fitness is central to understanding the functional consequences of CMN, and my studies on mycoheterotrophic orchids have also illustrated that plant survival may be an important parameter to follow (Roy et al., 2013b), especially for perennial species that could also be capable of dormancy (Shefferson et al., 2016 ; Shefferson et al., 2018).

Measuring resilience requires not only data on response traits, such as plant fitness or ecosystem diversity, but also a gradient or a time since perturbation, which is sometimes difficult to date and isolate in the wild. There is an on-going debate on how to measure resilience, and I would prefer to bring clues to measure traits that confer resilience (through functional redundancy, CMN) and how they correlate with EMF diversity, than to measure resilience per se. Such data could later be used by modelers to measure the total resilience of an ecosystem.

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Through the CERES project, with A. Brin, we are studying a gradient of fragmented forests, including ancient undisturbed forests, and focus on the impact of connectivity on below-ground diversity. This framework can also be used to study ecological networks involving fungi, as well as to set up experiments and investigate if young trees interact with surrounding ones through CMN. Moreover, by integrating a spatial and continuity gradient, this project allows testing hypotheses on landscape effect on EMF communities and their resilience. We would expect that the less-fragmented and the more ancient forests would host more functional CMN and connected ecological networks. Such results can be particularly interesting for forest managers or for understanding forest dynamics in a fragmented landscape. For example, in northern Quebec, the results of M. Nagati suggest that CMN could occur between fir and aspen, and may explain why fir regenerate better under aspen than under spruce. This result is also of interest in suggesting the utility of promoting mixed stands instead of monoculture, and thereby contributes to the search for more diverse and resilient forests [START_REF] Thompson | Forest Resilience, Biodiversity, and Climate Change[END_REF].

Another big challenge would be to replicate such experiments in ecosystems where CMN have never been detected and where EMF are relatively abundant. Until now, all experiments on CMN have been done in northern temperate forests, but southern temperate forests may function differently. For example, forest soils are generally richer in Patagonian forests than in boreal forests, and litter decomposition is controlled by nutrients rather than by temperature [START_REF] Vivanco | The importance of macro-and micro-nutrients over climate for leaf litter decomposition and nutrient release in Patagonian temperate forests[END_REF]. Whilst networks have often been detected between distantly related species (for example orchids and trees), Patagonian forests are dominated by one or two Nothofagaceae that are possibly able to share fungi [START_REF] Nouhra | Ectomycorrhizal fungal communities associated to Nothofagus species in Northern Patagonia[END_REF]. As observed for alders, closely-related species may exclude each other, and the question remains whether CMN can occur in Nothofagaceae forests or more generally in southern temperate forests. Beyond the interest of studying CMN in these remote forests, there is a real need to understand and promote forest resilience [START_REF] Thompson | Forest Resilience, Biodiversity, and Climate Change[END_REF], especially in forests where regeneration failure has recently been observed, for example at the ecotone between Araucaria and Nothofagus forests [START_REF] Zamorano-Elgueta | Impacts of cattle on the South American temperate forests: Challenges for the conservation of the endangered monkey puzzle tree (Araucaria araucana) in Chile[END_REF][START_REF] Cóbar-Carranza | Effect of Pinus contorta invasion on forest fuel properties and its potential implications on the fire regime of Araucaria araucana and Nothofagus antarctica forests[END_REF], and more generally in South American forests, which face both climate change and intense deforestation.

Following my previous results on EMF diversity, I would not expect CMN in neotropical forests, but a positive relationship between EMF diversity and functional diversity. In Southern temperate forest, CMN are theoretically possible (due to low specificity, [START_REF] Nouhra | Ectomycorrhizal fungal communities associated to Nothofagus species in Northern Patagonia[END_REF], but on the contrary functional diversity is relatively stable along an elevation gradient [START_REF] Truong | Ectomycorrhizal fungi and soil enzymes exhibit contrasting patterns along elevation gradients in southern Patagonia[END_REF]. I would expect CMN, but not necessarily favored by EMF diversity or functional diversity. Finally, in northern temperate or boreal forests, CMN have been detected, but the relationship with EMF diversity has not been investigated. I would expect a positive effect of temporal continuity (and ancient forests) on both functional diversity and CMN functioning (Fig 34). Testing those hypotheses would require a long-term and large-scale project, but through the CERES project, my collaborations at UQAT and now in Argentina, I am gathering colleagues to answer such questions with the methods developed in my previous projects (Fig [START_REF] Accioly | Hidden fungal diversity from the Neotropics: Geastrum hirsute, G. schweinitzii (Basidiomycota, Geastrales) and their allies[END_REF][START_REF] Vleminckx | Coordinated beta-diversity across five taxonomic groups in Amazonian rainforests[END_REF]. The use of NGS will be essential to estimate EMF diversity, but networks will be described from root sampling, and eventually compared with networks drawn from co-occurrence data. The results of such a project would be a base for a more theoretical framework on mycorrhizal networks, and the links between ecological networks and CMN. Such a framework is clearly missing [START_REF] Bahram | Network perspectives of ectomycorrhizal associations[END_REF] and will be useful even for forest managers and modelers interested in ecosystem resilience [START_REF] Thompson | Forest Resilience, Biodiversity, and Climate Change[END_REF]. Figure 36: An illustration of the dynamic network of colleagues and students interested in EMF in South America, sketched in Florianopolis (Roy et al., 2017) by Mélanie Roy.

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A parallel with mycorrhizal fungi and vineyards history: a project with students?

Resilience can also be measured with a diachronic approach, but for forest, ecosystem age is difficult to estimate, especially in ancient forests. In the vineyards, vintners usually have kept records of plantations, treatments, and especially transition to organic production. Today, a producer must wait three years before being certified as organic, but we have no idea about the time necessary for mycorrhizal fungi to recover from non-organic treatments. Changes are rapidly observed for soil properties, earthworms and bacteria [START_REF] Costantini | Short-term recovery of soil physical, chemical, micro-and mesobiological functions in a new vineyard under organic farming[END_REF] but fungi were not targeted, while mycorrhizal fungi interest vintners more and more. Numerous studies have highlighted that organic vineyards host more plant and even mycorrhizal diversity [START_REF] Bruggisser | Effects of vineyard management on biodiversity at three trophic levels[END_REF][START_REF] Schmid | Functional and structural microbial diversity in organic and conventional viticulture: organic farming benefits natural biocontrol agents[END_REF][START_REF] Nascimbene | Organic farming benefits local plant diversity in vineyard farms located in intensive agricultural landscapes[END_REF]2013). My hypotheses on CMN and ecosystem resilience could also apply to vineyards, and in the future, with students (through my teaching on landscape ecology of vineyards), colleagues interested in landscape and wine (Sophie Caillon and Antoine Brin) and vintners, I will try to develop a project to study mycorrhizal diversity and more generally fungal functional diversity in vineyard soils, along a temporal continuity gradient (time since transition to organic), represented in Gaillac terroirs and integrating plant diversity (wild plants and grapevine varieties) and landscape heterogeneity.

Conclusions

From the diverse projects and experiences I have developed over the last nine years, I have collected different evidence to better understand the ecology, the evolution and the specialization of EMF-plant interactions. Alnus-EMF associations reveal a non-networking strategy, but variations of specialization in isolated populations. The distribution of EMF in the Neotropics confirms their rarity, but reveals favourable environments, notably in low-canopy forests. Their specialization is always extremely high, and probably limits the formation of any mycorrhizal network between trees. In boreal forests, EMF are less specialized, and together with saprophytic fungi, are involved in both positive and negative plant-plant interactions. In temperate forests, integrating the knowledge on ancient forests and soil history contributes to better understand EMF distribution. Finally, working with students in landscape ecology has convinced me to integrate more engaged questions and to collaborate with landscape/forest managers. The future research projects I imagine to build up with colleagues will be intimately linked with ecological networks, and will involve fungi, test the effects of landscape and soil history, include functional traits and field experiments, and finally, will be strongly connected with student projects and landscape managers. Perhaps to better integrate students, and to begin thinking more locally, all those experiences and projects could one day be transposed, not to local EMF, but rather to below-ground networks at a local landscape, the vineyards, where mycorrhizal fungi have only begun to be investigated from an ecological point of view, and could have a key role in the resilience of vineyards faced with faced with climate change.

Teaching and transfer of knowledge Summary Since 2010, I teach at UPS but also in Albi University center. My teaching is closely related to my research on symbioses and has opened my research to biogeography and community ecology. I am responsible at UPS of a master 1 option on tropical ecology and co-responsible for the teaching of botany in Albi. In general, I teach 50% of my time to third-year students, mostly in the field, 40% of my time to master 1 and first year students, and 10% to Master 2 students. I usually do more than the requested amount of hours, and I am trying to reduce these extra hours.

Innovative teachings

Urban ecology through botany courses

In Albi and Toulouse, my third-year students learn botany, through practical courses and field trips. Since 2014, I have organized more local field trips, to vineyards, where they encounter vintners interested in plant diversity and uses, and in streets of Toulouse, Gaillac and Albi. My objective is to favor every-day observation of plants and to make students play with botany, through the use of applications such as PlantNet. Students produce an inventory of plants of their own street, and are evaluated on the basis of this document. They also report their data on participative projects such as sauvage de ma rue. Students are really invested in these inventories and colleagues at UPS have begun to be interested in urban ecology.

Cheese observations through mycology

Teaching microbiology is often restricted to the lab, while we encounter microorganisms every day in our food. In mycology, we give three practical courses on micro-organisms and since 2014, one of them is dedicated to the diversity of micro-organisms on cheese crusts. Introducing food as a topic is also a way to increase student enthusiasm and motivation.

Approaching the field in tropical ecology

In 2016, I became responsible for a course on the biodiversity of tropical ecosystems. However, teaching this topic to students who have never been to the tropics seems surrealistic. Since 2016, we teach three times in Toulouse Natural History museum, where they are greenhouses and tropical plants and collections, and go for one day to Pierre Fabre greenhouse and to the wood museum in Revel. During each visit, we meet colleagues who work in the tropics, such as botanists and forest managers. I always try to invite colleagues to talk to the students in this course, as they are interested in job opportunities in national park or reserves, and contacts could be useful for them later.

Introducing landscape in vineyard ecology

Since 2017, I have taught ecology to third-year students who have chosen a more professional career. I have created a course around the changing ecology of vineyard and teach the students to have a scientific point of view on vineyard adaptation to climate change. I try to give them a broader view on pathogenic fungi and their evolution, and consider the evolutionary ecology of grapevine. Those teachings are unique, as I focus not only on the vine but also the environment. I organize a three-day field trip to encounter vintners, and researchers on wine production and environment from the Institut de la Vigne et du Vin (IFV).

International courses

Abroad, I have been often invited to teach on ectomycorrhizae, especially in the neotropics. These courses are particularly important for training students in taxonomy to observe ectomycorrhizae, as this expertise is rare.

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Supervising experience

Licence At UPS, students are not required to undertake a practical internship, but I have supervised four students, who wanted to discover research before the first year of their master.

Thomas Wesley, came once a week to be trained in molecular biology. He produced sequences of orchids from French Guiana and learned how to produce phylogenies for several genera (Roy et al., 2014). He is now a research engeneer in a private company.

Esther Gomez, attended my lecture in Albi University. Since her first year, she wanted to work with me on orchids or fungi, and she made a first internship during her third year, to work on endophytes of Posidonia oceanica and their phylogeny. She later worked in master 1 with Didier Stien, and her help in sampling was useful for a master 2 student a few years later. A publication is now in process, and she is included among the authors (Gazal et al., in prep). She is now working in a natural reserve in the Pyrénées.

Quentin Fabregal was a former student in Albi, and also applied for a practical internship in the vineyard. He inventoried plant diversity and his internship really improved the pedagogical material for botany teaching. The year after, he got a "service civique" thanks to his knowledge on plants. He is now in master 1 with me and still works on vineyards and mycorrhizae, and we will now try to publish his results.

Morgan Ada spent 6 months working in mycology during a year off (L3). She was motivated by tropical fungi and their diversity, and she spent three months in Toulouse producing sequences of Geastrum, and three months in French Guiana to learn more on these fungi. Her work contributed to collaborations with taxonomists from Brazil (Accioly et al., 2019). She is now in master 1 at UPS. Jocelyn Soulard was my first student in 2011. He was motivated to work on fungi and to conduct some field work. We sampled around Toulouse and tried to detect shared partner between poplars and alders. These data were useful for a project of my colleagues in EDB, but we did not publish these data. He is still working in ecology and did a PhD in New Zealand.

Adeline Lepape was more interested in phylogenies, and did her stage on Ascomycota phylogeny, to confirm if some alder symbionts are specific. Her stage internship confirmed a low specificity, and was useful for the team's work on alders (Roy et al., 2013a).

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Raphaël Gareilh, did a master 1 in 2012, and then 6 months as a technician in 2013. We studied alder symbionts in Georgia [START_REF] Roy | De la scientificité à la une gestion créative multidimensionnelle : échanges de savoirs autours des plantes rencontrées dans le vignoble gaillacois[END_REF] and produced sequences of orchids (Roy et al., 2014). She decided quite quickly to be a technician, and I designed her internship to learn mostly molecular biology and barcoding. She is now a technician in a private lab in Toulouse.

Louis Graf, did a master 1 in 2012 too, and worked on Alnicola phylogeny, to position samples from Alaska. He did a brilliant master 1, and revealed several species that should be described by taxonomists. He moved to Korea the year after, as he got directly a PhD position. He still works on algae phylogeny there.

Mélissande Nagati started to work with me in 2013 as a master 1. She worked on alders in Corsica and collaborated with Adrien Pozzi, PhD student in Lyon (Pozzi et al., 2018). Jan Hackel did his stage also in 2013, and worked on fungi associated with alders in Germany. He produced sequences that are now integrated into a larger database (Roy et al., submitted) and began working on fungi phylogeny. Laura Fernandez was the first student to be trained in next generation sequencing, in 2015. She analysed the sequences isolated from neotropical tree roots in French Guiana, and revealed a high specificity there (Fernandez et al., in prep). The data still have to be published but need to be confirmed first. She is now working in environment at SNCF in France.

Mike Hélion did his master 1 in 2017, and wanted to learn more on tropical ecology. He tested tools to identify tropical mycorrhizae and moved to Montpellier to learn more on tropical ecology. He is now searching for a more applied job. His work supported Laura's observations and they will publish together (Fernandez et al., in prep).

Nina Gazal joined EDB lab in 2016, and began working on fungi in 2017. She did a brilliant Master 1 on interactions between endophytes, and we are now trying to write a paper on her work (Gazal et al., in prep).

Alexandre Ramon was a brilliant student in botany, and began working with me in 2018. He analysed NGS sequences produced from liana roots, and was particularly good at it. He is now in master 2 at EDB and has applied for a PhD position with Antoine Brin and I.

Tristan Lafont-Rapnouil applied for a practical internship in 2019 with Philippe Marchand (UQAT) and me, and has just finished his analyses. He studied how spatial interactions could bring clues for below-ground interactions in the boreal forest. We had the funding to allow him travel and stay in Quebec for two month, and will welcome in Toulouse another master 1 student from UQAT during the next autumn.

Master 2

Thanks to my diverse research projects, I have been able to fund master 2 students nearly every year. I have supervised or co-supervised 7 students, and sometime supervised students both in 98 M1 and M2. In M2, I try to show my students the different steps of research, from the field, even in French Guiana, to the publication or congresses. I have tried to make them more responsible for their data and experimental choices and to test their own hypotheses. Cédric Gonneau, co-supervised with Marc-André Selosse, at CEFE, 2010. He worked on mixotrophic orchids and did field experiments to understand if such orchids could cope with shade by increasing their exchanges with fungi. He wrote an article from his experiments (Gonneau et al., 2014) and did a PhD in Nancy later.

Circé Collongeon, full supervision, M2 BEE, UPS, 2013 During her internship, she studied populations of alders in Quebec and in Alaska to understand their biogeography. She was willing to do research again, after a 7-years break, but finally did not pursue research after this experience. Circé is a very passionate person, and she is now in New Caledonia teaching scuba-diving.

Mélissande Nagati, full supervision, M2 BEE, UPS, 2014 Her master 2 was focused on restricted populations of A. cordata and A. maritima, and she tried to understand the extent to which their specificity was shaped by isolation. She produced sequences, and analyses, and worked later with a PhD student of Lyon (Pozzi et al., 2018). The data she produced contributed to a synthesis on alders (Roy et al., in prep). She had the opportunity to present data to a first congress (French Orchid Society) and I have included her in a paper on orchid phylogeny (Roy et al., 2014). Jan Hackel, full supervison, M2 BEE, UPS, 2014 Jan also wanted to follow in Master 2. During the summer 2013, I involved him in the field in French Guiana, to collect mycorrhizae of neotropical trees around inselbergs. We observed and collected several Russulaceae, and decided to focus his master 2 on Russulaceae biogeography. He did a great job, and we realised we could not finish without collaborations, as Russulaceae represent an extremely diverse and widespread family, even in the neotropics. He is now preparing a paper, including new sequences produced, and has already contributed to a paper with colleagues from Gant herbarium (De Crop et al., 2017). Sophie Mennicken, full supersion, M2 EA, ENSAT, 2017 Sophie was extremely motivated to work in French Guiana, on fungal communities of ancient occupied sites, but she had to face a major strike in French Guiana and could not access the sites. After one month waiting, I decided to change her topic and we began a sampling in landscape ecology with Antoine Brin, in Cevennes National Park. She did the sampling, the sequencing, the analysis, in five months and produced a brilliant manuscript. Her results were very important for A. Brin's PhD student, and we are now working on a common publication (Mennicken et al., in prep). She is now working on orchids in a PhD study, in Czech Republic. Nina Gazal, co-supervision with Antoine Brin (50%), M2 BV, UPS, 2018 The master 1 of Nina was very promising, and we managed to go to French Guiana together. Her Master 2 aimed at testing, if sites occupied in the past were richer in ectomycorrhizal fungi, in the pristine forest of French Guiana. She did the fieldwork, the molecular biology and the analyses, and produced a very solid work. We have already submitted her results (Gazal et al., 99 submitted) and her results are followed by other colleagues in French Guiana. She has recently got a PhD position.

Benjamin Durrington, co-supervision with Marc-André Selosse (25%, MNHN), and Erik Verbruggen (25%, Antwerp University), M2 Erasmus Mundus, 2018 Benjamin is American, studied in England, Belgium, France and Australia, and contacted me to work on tropical mycorrhizae. He studied the specificity of neotropical mycorrhizae along a phosphorus gradient. Erik Verbruggen did the field work and I supervised Benjamin's analyses and molecular biology. We are now working on a paper together (Durrington et al., in prep). Benjamin is now in Miami and would like to get a more practical job in botany.

PhD

Rapidly after my recruitment, and thanks to colleagues in other labs, I had the opportunity to work with PhD students, for example A. Pozzi and G. Schwob in Lyon and A. Sagne in EDB and EcoFoG. For A. Sagne, I was really invested, and worked with her during her stay in Toulouse and my CNRS delegation in French Guiana. The first student I officially co-supervised decided to stop his PhD and return to a job in pharmacy. It was difficult to admit but he had a different professional and personal goal. I have always tried to support him, even after he stopped his PhD. More recently, I co-supervised Mélissande Nagati's PhD. I was perhaps more conscious of the difficulties a student could face during a PhD, and so were my colleagues. Mélissande defended on 27 th of august 2019.

Yannick Eveno, Grant from labex CEBA, 2014-2016, supervised by Didier Stien (Director, CNRS Banyuls, 50%) and I ("co-encadrante", 50%). MNHN.

Bio-and chimiodiversity of endophytic communities

Yannick decided to begin a PhD after his pharmacy studies, he was highly motivated by the field and the lab. His PhD was in between ecology and chemistry, and he intended to relate microorganisms' activity with their interactions, detected from community analyses and NGS. He produced 400 strains of endophytes, and invested most of his time in lab experiments. I helped him mostly for the NGS analyses, and we had regular contacts either by Skype or by meeting for "analyses weeks", as he was mainly based in Gif-sur-Yvette. During the second PhD committee, he announced he wanted to stop his PhD, he had other ambitions, and wanted to go back to pharmacy. We did not at all expect this decision, but indeed, writing was particularly difficult. He stopped his PhD three months later, and was very positive about his decision. He rapidly searched for a more applied job. He is now employed by a private company in pharmacy in Lille. I am now trying with Julian Donald, in post-doc, to publish part of his data, and he will be involved as a co-author (Donald et al., submitted). Mélissande Nagati, Grant MITAC from Quebec Region, "Co-tutelle" between UQAT and UPS, supervised by Yves Bergeron ("Directeur", 25%, UQAT) and Monique Gardes ("Codirectrice", 25%, UPS), Annie DesRochers ("Co-encadrante", 25%, UQAT) and me ("Coencadrante", 25%, UPS). Mélissande is enrolled in UQAT and UPS.

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Canopy and micro-organisms effect on fir establishment in the boreal forest

After her M1 and M2 with me, Mélissande wanted to pursue a PhD on fungal ecology. The year before, with Monique Gardes, we had stimulating discussions with Yves Bergeron, who suspected that fungi were implied in fir regeneration in the boreal forest. He funded a year of salary for Mélissande, so that she could apply for a grant in Québec. During that year, we applied for a MITAC grant and got a 4-year position for Mélissande. She began at the end of 2015 and will finish in August 2019 (28/08/19).

Her PhD focused on the role of fungi in fir regeneration in the boreal forest. She spent the first year in Quebec describing the ecosystem and fungal diversity in the boreal forest, learning NGS analyses in Toulouse, and revealed a huge diversity on her sites (Nagati et al., 2018). The second year, she followed the growth and survival of young firs in the boreal forest, and launched glasshouse experiments on fir germination, on different boreal soils. The third year, she collected the roots of young firs, and showed that tree growth was not related to fungal diversity, but rather to the identity of the dominant tree (Nagati et al., 2019). The fourth year, she collected the samples from her glasshouse experiment, and wrote her PhD (deposited on the 16 th of May, 2019) and a third article on fir germination and soil effect (Nagati et al., in prep).

As a "co-encadrante", I have been really invested in Mélissande's PhD, and searched for funding to allow her to travel and attend congresses and workshops (in Canada, France, Sweden) and achieve her experiments. Mélissande is really autonomous, and enjoyed being abroad, but we managed to keep a regular contact, with stimulating discussions, throughout these four years. We often organized skype meetings with Monique Gardes, and exchanged papers and manuscripts. She has spent 18 months in Toulouse, and I have been to Quebec for the field, and later for discussions. She is now applying for a Post-doctoral contract in Quebec, on fungi, and is still motivated by research.

She is also invested in vulgarization and won a prize for "mon projet nordique" (2017, Institut Nordique de Quebec). Thanks to this prize, she was invited in Iceland, to the Arctic Circle Assembly (October 2017). She also presented her work in a radio program in Quebec ("Chronique Forêt : Réseautage sous la surface du sol", Radio Canada, 14/08/18) and published an article in French (Nagati M. 2017, Les champignons des sols forestiers : des alliés invisibles. Progrès, Forestier N°222).

Post-doctoral contracts

Julian Donald, one year post-doc on SECIL ANR Grant, 2018 Julian applied for a post-doc position with Jérôme Chave and me, on fungal endophytes. He came to learn NGS techniques and analyses, and after one year submitted two papers. He is now in EDB lab for a second post-doc, has kept his interest for endophytes and has presented his results in congresses (British Ecological Society congress, Association for Tropical Biology and Conservation congress). As his PhD was also on tropical ecosystems, I have involved him in my tropical ecology course. He enjoyed teaching, and students really enjoyed his field experience.

Funded research projects

List of projects Following my recruitment in 2010, I immediately began searching for research grants, in France and abroad, with colleagues on plant-fungi interactions and mycology. I managed to receive in total 574,342 E at EDB (141,861 E as a PI). I was PI on my first projects and rapidly joined larger groups of colleagues and became a co-Pi. I am often responsible for tasks in larger projects, or give a hand, for example for the fieldwork in other projects, such as ANR METABAR and GLOBNET. I am now trying to get a CRCT to be able to manage a larger project on network biogeography and resilience, and launch more experimental projects.

ORCHID: Phylogenetic diversity of orchids in French Guiana Société Botanique de France/Société française d'Orchidophilie PI : M. Roy (50%) 2011-2012 3,200 E As orchids rarely produce flowers, botanists have been interested by the use of barcodes to identify orchids. In this project, I sequenced 382 specimens of orchids from French Guiana, including reference specimens. We published the sequences and a synthetic paper (Roy et al., 2014), showing how diverse are orchids in French Guiana, especially Vanilla. I did not submit more projects on orchids as it became a very sensitive project in French Guiana and their sampling was more and more limited.

REFUNG: Fungal diversity in Glacial Refugia EC2CO -Microbien PI: M. Roy (50%) 2012-2015 59,711 E This project aimed at studying alder symbionts (bacteria and fungi) in glacial refugia. I organized the fieldwork, in the Caucasus, the Carpathian mountains, Czech Republic, Germany, Corsica, Poland and Italy, and involved colleagues from all these countries. I supervised the molecular biology and students in master 1 on this topic. This project completed a sampling in France on fungi (Roy et al., 2013a). Thanks to the sampling of bacteria, I worked with a PhD student, A. Pozzi (UCBL, in Lyon) to analyze the patterns for both symbionts (Roy et al., 2017 ; Pozzi et al., 2018). I also collected leaves, and H. Gryta and G. Besnard analyzed the plant diversity in Europe (Gryta et al., 2017). FUNGUY: Diversity of fungi from French Guiana Projet annuel LABEX CEBA PI : M. Roy (30%) and H. Schimann (EcoFoG, Kourou, Guyane Française) 2012 29,650 E 106 This project allowed me to invite 11 experts for two weeks in French Guiana. We gathered more than 1000 specimens, and began describing new species (Henkel et al., 2013 ; Barbosa-Silva et al., 2017; Crous et al., 2017; Gruhn et al., 2017, 2018, Accioly et al., 2019). Most species are still to be described, but specimens are stored in the MNHN herbarium and more taxonomists have been involved. In this project, I organized the fieldwork at Nouragues field station, supervised the sequencing in Toulouse, phylogenetic analyses, and interactions with taxonomists. This project was an essential stepping stone toward following projects in French Guiana on fungal diversity. In this project, we aimed to identify networks between neotropical trees. I organized the fieldwork, the sampling, supervised the molecular biology and sequencing and analyses. In this project, C. Decock identified fungi and D. Frame the host plants. We also collected Russulaceae and material for a master 2 in EDB. We did not detect networks, and needed more observations on Myrtaceae roots. Thanks to recent observations, we can now prepare a publication (Fernandez et al., in prep.). This grant allowed only sequencing, and supporting the sequencing of specimens from French Guiana and ectomycorrhizal roots. It allowed the production of reference barcodes for fungi. I was responsible for the sampling and DNA extraction, and PCR products were then sent to MNHN. I handled this project with S. Manzi, engineer in EDB lab. FUN-CHEM: Functional chemodiversity. Project central LABEX CEBA. PI: Christophe Duplais (EcoFoG, Cayenne, Guyane Française) 2014-2016. 11,900 E to EDB.

In this project, I was responsible for a task on endophyte diversity. I organized the fieldwork in French Guiana, supervised the isolation of strains and their sequencing. This project supported the PhD experiments of Y. Eveno, and was a great base for further projects (SECIL).

ARC: réseau d'étude de la dynamique des aulnaies vertes anciennes. Regional project (Région Rhônes-Alpes). PI : Maria-Fernandez (Ecologie Microbienne, UCBL, Lyon, France) 107

Only expertise in EDB

In this project, I was involved as an expert on ectomycorrhizal fungi of alders. I contributed to discussions, and to the fieldwork. I supervised the molecular analyses and soil sequencing and analyses. We recently published a paper on those old-growth alder stands (Schwob et al., 2017).

NEBEDIV: effect of Natural Enemies on Beta Diversity in tropical forest. ANR Blanc. PI: Christopher Baraloto (EcoFoG and now Florida International University) 2014-2018. 153,900 E to EDB In this Project, I was involved in a task on fungi specialization and diversity. I contributed to the fieldwork in Brazil, and supervised the sequencing of root-associated micro-organisms in EDB. I handled experiments to improve plant identification and supervised students to confirm ectomycorrhizal symbioses. The sampling was longer than expected and the project is not yet finished. Thanks to the fieldwork in Brazil, I published a first paper on white sands (Roy et al., 2016).

DIADEMA: DIssecting Amazonian Diversity by Enhancing a Multiple taxonomic-groups Approach. Project central LABEX CEBA. PI: Christopher Baraloto (EcoFoG and now Florida International University) 2014-2016 72,100 E to EDB In this project, I contributed to the task on biodiversity inventories, and sampled fungi in Mont Itoupé, Saül, Kaw, Laussat and Mitaraka. I was responsible for the identification of fungi and interactions with taxonomists, contributed to fill the database on fungi and supervised students on fungal phylogenies. We have already published our database and some inventories (Roy et al., 2018 ; Schimann et al., 2019) and submitted a synthesis on our analyses.

109

RECO-RECO: Importance des réseaux mycorhiziens et des connexions racinaires dans la revégétalisation des parcs à résidus miniers. Projet Champlain, financé par le Consulat de France au Québec. PI : Mélanie Roy (40%) and Philippe Marchand (UQAT, Canada). 2018-2019. 14,000 E at EDB.

Champlain projects aim at promoting exchanges of students and researchers. In this project, I supervise a master 1 student in France and one in Québec, I organize the fieldwork in northern Québec, and train students in NGS analyses in EDB. My colleagues P. Marchand and N. Fenton will visit Toulouse, and have supervised a master 1 from UPS and trained him in spatial analyses.

ABC Saül : Atlas de la Biodiversité Communale de Saül. AFB PI: Laurent Gode (Parc National Amazonien de Guyane) 2018-2020. Only expertise in EDB In this project, I am responsible for mycological inventories and lead a group of 8 experts, organize field trips to Saül (3) and a mushroom exhibition in French Guiana, supervise a master student and the molecular biology on the collected specimens. We aim at publishing a booklet on fungi from French Guiana for the National Park. Moreover, this project is an excellent way to transfer my knowledge on fungi to the National Park. In CERES, I am involved as an expert on fungi diversity. This project focuses on ecosystem connectivity and the response of bat, invertebrate and fungal communities. I will contribute to the sampling in the Pyrénées, the DNA extraction and sequencing and finally the analyses on fungi. We have also deposited a PhD subject for this project.

ACTUAAL: Accompagner les Transitions de l'Urbain Anthropocène en Amérique latine : l'école comme laboratoire des futurs écosystèmes urbains CNRS -Ecosystèmes Urbains 2019 PI: Julie Legall (CEMCA, Mexico) 2019 25,000 E (only expertise in EDB) Through my teaching on urban diversity, and my projects on landscape ecology, I have begun interacting with colleagues in geography. In this project, I am responsible for plant inventories with two schools of Buenos Aires and Mexico. I will identify plants and teach the pupils how to recognize and observe plants. Julie Legall and her students will then detail how pupils use this 110 knowledge. This project is tightly connected with my botany course and will involve my students at Toulouse in 2020.

MULTIMYCO :

Annual project LABEX CEBA PI : Mélanie Roy (40%) and Francis Brearley (University of Manchester, Great Britain) 2019 14,800 E Ectomycorrhizae are rare in French Guiana but endomycorrhizae are on the contrary extremely diverse. Thanks to this project, we gather expertise on both microorganisms and will study the specialization process on Dicorynia guyanensis roots. In this project, I organize the field, and contribute to analyses. Christina Hazard, in post doc at Ecole Centrale de Lyon, is responsible for the sequencing and Jennifer Rowntree in Manchester University will sequence the plant microsatellite. This project is short, but very stimulating and benefits from the expertise of Francis Brearley and myself in French Guiana.

Field experience and expertise

Through my diverse research projects, I have organized and joined projects in very diverse forests around the world. Fieldwork is essential in my research and expertise, and I have tried to transmit this passion to students, and involve taxonomists -who are often free-lance experts -in my field trips to French Guiana.

Boreal forests

Fieldwork in Québec (2), and Alaska (1) Temperate forests Fieldwork in Cevennes national Park, Vanoise, Corsica Germany (Black forest), Romania (Carpathians), Poland (Tatras), Czech Republic (White Carpathians), Georgia (Colchis), Italy (Sorentino) Tropical forests

French Guiana (14), Brasil (2)

Recently, I have been involved as an expert for Office National des Forêts in French Guiana. This expertise has allowed me to contribute to inventories in Trinité reserve avec fund my projects on fungi around inselbergs.

Around Toulouse, I organize field days for the Natural History Museum of Gaillac, on orchids and urban ecology, and for the Tarn CPIE.

Figure 1 :

 1 Figure 1: Plant-fungi mutualism, from roots to leaves. Images from A. Sagne and M. Roy

10

 10

Figure 2 :

 2 Figure 2: A, distribution of sampling plots of EMF communities(Tedersoo et al. 2012); B, distribution of confirmed EM hosts[START_REF] Soudzilovskaia | Global patterns of mycorrhizal distribution and their environmental drivers[END_REF] and C, location of sampling sites for Alnus-EMF (green) and neotropical EMF (red).

Figure 4 :

 4 Figure 4: Processes shaping fungi (A, from[START_REF] Tedersoo | Global diversity and geography of soil fungi[END_REF] and endophyte community diversity(B, from Vacher et al., 2016a). MAP : Mean annual precipitation

Figure 6 :

 6 Figure 6: A, distribution of EMF species per country since 2010; B, first observation of Cantharellus guyanensis; C, number of EMF collections deposited in herbaria since 1905, Roy et al. 2016.

Figure 8 :Figure 9 :

 89 Figure 8: Map of EMF records in Brazil, based on genus-level identifications (Roy et al., 2016), B, modelling of EMF distribution, Braga-Neto et al. In prep

Figure 10 :

 10 Figure 10: Multigene phylogeny of Lactifluus (A), highlighting species from the Neotropics and French Guiana (violet). Pictures illustrate representative species from French Guiana for Albati (B) and Gymnocarpi (C) sections (DeCrop et al., 2017).

Figure 11 :

 11 Figure 11: A, location of soil cores sampled along a phosphorus gradient in French Guiana, B, sampling scheme of soil cores and C, accumulation curves of EMF (Ecto) OTUs for each site.

Figure 12 :

 12 Figure 12: Observation of mycophagy clues (arrows) on a Pleurotus.

Figure 13 :

 13 Figure 13 : A, number of EMF sequences per family and per host, and B, Shannon indices for EMF diversity on roots of liana roots (L), small trees (< 10 cm DBH), bigger trees (> 10 cm DBH) and bigger trees supporting a liana (> 10L) and on terra-firme soil (red) and white sands (blue).

  10 cm DBH), big trees (> 10 cm DBH), lianas (L) and big trees surrounded by lianas (> 10L = > 10L+lianas), with 5 replicates per category on each site (80 samples in total). I extracted fungal DNA and amplified ITS1 barcode but detected only a few EM sequences (388), confirming that EM hosts are rare even in lowcanopy forests. The distribution of EM families is moreover not homogeneous (Chi-square = 379.56, p-value < 0.0001, Fig 13A) and lianas tend to have even less EM sequences (Fig 13B).

Figure 14 :

 14 Figure 14: A, low similarity of EMF sequences to databases in 2013; B, groups targeted by my projects in French Guiana within the Agaricomycetes tree (Hibbett et al., 2016) and showing the expertise of R. Courtecuisse, P.-A. Moreau, B. Buyck, A.-M. Verbecken, J.L. Cheype and T. Henkel (orange), F. Wartchow and T. Accioly (green), G. Gruhn and H. Voiry (green), C. Decock and S. Welti (blue) ; and C to I, specimen collection from the field to the lab, during the first FUNGUY field trip in 2013 in French Guiana.

Figure 15 :

 15 Figure 15 : A, distribution of EMF OTUs per host species in France, and B, factors shaping EMF community (beta diversity), fromRoy et al. (2013) and C, Distribution of chloroplast haplotypes in Alnus leaves, fromGryta et al. (2017).

Figure 16 :

 16 Figure 16: A, sampling in glacial and Tertiary refugia, B, Metrics reflecting EMF specialization, C, difference of specialization for alders EMF communities, reflected by the mean Blütghen d, between sites in refugia and recently colonized areas, and along a longitudinal gradient (D).

Figure 17 :

 17 Figure 17: A, number of sequences per OTU and per host, and B, sharing of OTUs on each plot between host genera represented by Venn Diagrams(Fernandez et al., in prep).

Figure 18 :

 18 Figure18: δ15 N and δ13 C isotope signature of Trechispora thelephora (green) compared to surrounding fruiting bodies of saprophytic species (red) and EMF (blue). Small letters indicate groups of significance according to Wilcoxon tests. FromVanegas-Léon et al. (submitted in 2019).

Figure 19 :

 19 Figure 19: A, design for crossing experiments (Ag: A. glutinosa, Ai: A. incana, Av: Alnus alnobetula ssp. alnobetula, Sp+: in planta-sporulating phenotype, TR, OR, ORV, LB, FF and XF are soil localities where respectively, Ag, Ai and Av are naturally growing) and NMDS showing the differences between communities colored by their soil origin (B) or by their host identity (C); fromSchwob et al., 2018.

Figure 20 :

 20 Figure 20: A, map of alder populations sampled to calculate network metrics (triangles) and sites where two alder species were sampled (green triangles); comparison of plant degree (B) and Blüthgen d (C) calculated from all interactions (Global) and local interactions (Local) and comparison of H2 (a network level of specialization) between cases of co-occurrence and predictions by null model (D).

Figure 23 :

 23 Figure 23: Interactions between OTUs in Posidonia leaves, for bacteria (A) and fungi (B) and mean coefficient of correlation for a Lulwoana sp.(Gazal et al., in prep).

Figure 24 :

 24 Figure 24: Synthesis of processes shaping EMF communities and specialization on the two model studied, Alnus and Neotropical EM trees.

Figure 25 :

 25 Figure 25: Effect of landscape on fungal communities, based on Grilli et al. 2017 ; watercolor by Mélanie Roy.

Figure 26 :

 26 Figure 26: Recent landscape in the Vanoise, where alder stands are particularly extended(F) but also colonize the grassland (G) and form a mosaic (M) at the edge (A), and differences of soil fungi and EMF communities in this landscape (fromSchwob et al., 2017).

Figure 27 :

 27 Figure 27: A, definition of ancient versus recent forest, from Cateau et al. (2015); B, distribution of ancient forests in Cevennes National Park and C, a mature and ancient beech forest of Maramures in Romania.

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Figure 28 :

 28 Figure 28: A, species accumulation curves produced by sequencing environmental DNA from soil cores on 11 sites at Nouragues station, B, Shannon diversity of fungi on sites massively, moderately or rarely occupied in the past and C, distance to centroid in the NMDS, representing the beta diversity within each group(Gazal et al., accepted).

Figure 29 :

 29 Figure 29: A, example of drawings used in tropical ecology teaching, to speak about plant diversity, size of fruits, and lack of EMF fruiting bodies, and B, example of drawing used in botany teaching with students and wine makers. Watercolors by Mélanie Roy.

Figure 30 :

 30 Figure 30: A, drawing made by Mélanie Roy illustrating the enthusiasm of a wine maker and the integration of plants in his description of the vineyard (Roy et Caillon, submitted), B, inventory of plants in the inter-row and row, and C, species accumulation curves for row and inter-row inventories (over 9 vineyards and 28 transects).

Figure 31 :

 31 Figure 31: A, distribution of last fire events around the Duparquet Lake in Quebec. "Older" plots host conifer forest, more recent host a mixed wood, and the more recent host mainly poplars in the boreal forest.

`

Figure 32 :

 32 Figure 32: How to isolate the effect of CMN, by cutting hyphae directly in soil (left) or enclosing saplings in a 50 micron-wide net, to allow only hyphae to grow, from[START_REF] Hoeksema | Experimentally testing effects of mycorrhizal networks on plant-plant interactions and distinguishing among mechanisms[END_REF]

Figure 33 :

 33 Figure 33: A, recolonization of old mine field in the boreal forest showing young conifers and broad-leaved trees, and B, map of young saplings in a 20*20 m plot.

Figure 34 :

 34 Figure 34: Hypotheses on links between EMF diversity and ecosystem resilience in a biogeographic framework.

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Figure 35 :

 35 Figure 35: Scheme representing the different tasks and experiments to test hypotheses of Fig 34, and on-going and future collaborations with colleagues interested in such questions.

FLAG

  MITAC: Can mixing of tree species improve resilience and productivity of boreal forests? PI: Yves Bergeron (UQAT et UQAM, Canada) projet MITACS (Québec, financement semi-industriel).2015-2019. only expertise in EDBThis project funded Mélissande Nagati's PhD. I was only expert in this project but Mélissande produced very interesting results on microorganisms in the boreal forest.SECIL: Study of leaf endophytic fungi : Exploration and valorization of biosourCed Innovative antibacterial metaboLites. ANR Franco-Suisse. PI: Didier Stien (CNRS, Banyuls, France) and J.-L. Wolfender (University of Geneva)

  CERES : Connectivité des écosystèmes forestiers et rivulaires de l'espace SUDOE. Inter-Reg SUDOE PI: Sébastien Chauvin (FORESPIR, Toulouse, France) 2018-2020. 1 272,214 E euros (only expertise in EDB, collaboration with DYNAFOR)

Table 1 :

 1 Two specialized EMF-host interactions and their characteristics

		Alnus	Neotropical trees :
			Coccoloba, Neea, Guapira, Gnetum
	Host diversity	35 species distributed in the	60	species,		belonging	to
		temperate zone and montane	Achatocarpaceae,	Betulaceae,
		habitats in the Neotropics	Cistaceae,	Dipterocarpaceae,
			Fabaceae, Fagaceae, Gnetaceae*
			Juglandaceae, Nyctaginaceae*
			Pinaceae, Polygonaceae* and
			Salicaceae. In French Guiana only 3
			families are represented (*), and
			occur mainly in low canopy forests
	Specialized	Alnicola, Alpova	No
	genera/lineages
	Specialized	Tomentella, Lactarius, Russula,	Cantharellus, Russula, Tomentella
	species	Cortinarius
	Diversity on host	330 species of EMF worldwide, mean
	individuals	of 8 EMF species per tree and 13
		species per population

Scale/model Processes Axis How could we explain the high specialization of EMF/endophytes?

				Gamma diversity
	Apha diversity =
	community level
			Turnover (beta)
		Selection
		Migration		fungus	interactions
				plant	Mutualism
		Drift			feedbacks
				bacteria
		Speciation/extinction
	Gamma	All	1	What is the pool of EMF in Neotropical forests and why are EMF so rare?
	EMF pool
	Beta	Migration	2a	How far host migrations and isolation could have shaped the low diversity
				and high specialization of alders EMF?
	Host-EMF interactions	Selection by host+migratio	2b	Is specialization an artifact due to host tree isolation and do co-existing host share more EMF in neotropical forests?
		n
	Alpha	Interactions/s	3a	How far selection by Frankia or competition between trees could shape
		election		the low diversity and high specialization of alders EMF?
	Host-EMF-Or bacteria-Bacteria	eedback Interactions/f	3b	How far sharing EMF or not can affect fir growth in boreal forests?
	fungi	Interactions/S	3c	How neutral processes, and host diversity, could shape endophyte fungi
	interactions in	election by		diversity and their interactions within leaves
	leaves	host

Table 2 :

 2 Records of EM observed or EMF sequenced on saplings identified by Tim Paine (in 2013) and later sequenced on ITS1 by Miseq, and on roots collected along a phosphorus gradient inFrench Guiana, and later identified by short sequences of rbcL(Durrington et al., in prep)

	Family	genus	species	Obs 2013	Miseq 2013 Miseq 2018
	Annonaceae	Duguetia	yashinoi	0/5	0
	Apocynaceae	Aspidosperma	sp.	0/1	15	1/2
	Bignoniaceae		sp.	0/1	59
	Burseraceae	Crepidospermum	sp.	0/3	29
		Protium	aracouchini	0/3	3
			opacum	0/3	13
			sagotianum	0/3	39
		Tetragastris	altissima	0/1	37
	Chrysobalanaceae		sp.	0/1	8
		Lycania	alba	0/2	11
		Parinari				1/4
	Clusiaceae	Clusia	sp.	0/2	4
		Clusia	nemorosa	0/3	21
	Dilleniaceae		sp.	0/1	0
	Ebenaceae	Diospyros				1/3
	Euphorbiaceae	Mabea	piriri	0/1	0
	Fabaceae	Bauhinia	guianensis	0/1	0
			sp.	1/1	100
			sp.	1/2	78
		Dicorynia	guyanensis	1/5	8	0/2
		Eperua	falcata	0/1	0
		Inga	sp.	1/1	94
			alba	1/2	282
			rubiginosa	2/2	651
		Parkia	nitida	1/1	229
			sp.	0/1	49
		Swartzia	sp.	0/1	0
	Humiriaceae	Humiria		1/1	25
	Ixonanthaceae	Cyrillopsis	paraensis	0/2	2824
	Lauraceae	Octotea	argyrophylla	0/1	0
	Lecythidaceae	Lecythis	persistens	1/3	2027
	Malvaceae	Eriotheca	cf surinamensis	1/1	153
	Loganiaceae	Quaribea	duckei	1/1	240
	Loganiaceae	Strychnos	erichsonii	1/1	895
	Melastomataceae	Miconia	egerensis	2/2	226
			guyanensis	1/3	223
			suaveolens	0/2	0
	Sapotaceae	Micropholis	melinoniana	1/1	77
	Meliaceae	Trichilia	emetica	0/1	0
	Moraceae	Helicostylis	pedunculata	0/1	0
		Trymatococcus				0/2
	Myrtaceae	Maarvelia	ferruginea	1/1	88
			sp.	10/26	31533
	Olacaceae	Ptychopetalum	olacoides	0/1	229
	Quiinaceae	Touroulia	guianensis	3/4	321
	Rhamnaceae	Ziziphus	cinnamomea	0/1	135
	Sapindaceae	Paullinia	latifolia	0/1	30
	Sapotaceae	Manilkara	bidentata	0/1	0
		Micropholis	sp.	1/1	74
		Pouteria	sp.	0/1	118
		Pradosia	ptychandra	0/1	39
	Simaroubaceae	Simarouba	mama	0/1	11
	Siparunaceae	Siparuna				0/2
	Urticaceae	Pourouma	sp.	0/1	25
	Vochysiaceae	Qualea	rosea	1/2	1407

  Gazal and sequenced fungal and bacterial barcodes (ITS1 and 16S respectively) in 89 samples of P. oceanica. Bacteria and fungi are clearly less abundant than in leaves of tropical trees and show distinct distribution patterns among Posidonia organs (roots, rhizome, leaves). Based on co-occurrence data, interactions between bacteria are more positive, and fungal interactions are rather neutral (Fig 23A, B,

Table 3 :

 3 Contrasted effects of landscape on fungal communities

	Fungi	Landscape element (significant	Publication
		in bold)
	Wood-associated fungi and	Edges, fragmentation	Helander, 2007; Saikkonen,
	birch endophytes		2007; Abrego and Salcedo,
			2014
	root-associated fungal diversity Connectivity, patch area	Vannette et al., 2016
	Grape endophytes	Landscape composition	Fort et al., 2016a
	endomycorrhizal and dark	Patch area	Grilli et al., 2012
	septate endophytes
	EMF of Alnus, Corylus,	Distance, forest age	Boeraeve et al. (2018)
	Crataegus
	specialist wood-associated	fragmentation	Norden et al. (2013)
	fungi
	Generalist wood-associated	fragmentation	Norden et al. (2013)
	fungi

  Ecology at UPS, and met numerous and great students. I have always tried to teach them molecular biology and community ecology, to involve them in research discussions, and to encourage them to cooperate with other students, in master 1 or master 2. More recently, I have trained some to analyse environmental sequences or at least, I made them familiar with those techniques.

	Master 1
	I teach mostly in Master 1

In the Amazon, along the Rio Negro, I gave a one-month field trip on white sands, to students from Peru, Brazil, and USA (Supported by Trebediv project, IRD) with colleagues from INPA (Manaus) and Santa Catarina University (Florianopolis).

Labex TULIP summer School, 13-17/07/2015, in the Pyrénées. Courses on ecological and mycorrhizal networks to international graduate and PhD students.

During the Brazilian Mycology Congress in Florianopolis, I gave a three days course for students of Santa Catarina University. We collected ectomycorrhizae, observed them and discussed with international experts.2019 In Buenos Aires, I have already given two courses, from the field to the lab, to observe and discuss the ecology of ectomycorrhizae, at Faculty of agronomy and Faculty of sciences of Buenos Aires University. Those one-day courses are short, but completely new to students.

Acknowledgments 104

Ceske Budejovice University, collaboration with Jana Jerza, one month (2012) During this stay, I brought my expertise on fungi and we sampled orchid roots in diverse habitats in Czech Republic. I also collected alder-fungi in old growth forests in South Moravia. This stay, together with the visit of Tamara Malinova, allowed us to write three articles (Kohout et al., 2013a ; 2013b ;Tesitelova et al., 2013).

Smithsonian South Field Station, collaboration with Jason D. Hoeksema, two weeks (2016). Teaching in Arizona, with Judith Bronstein, was a revolution for me, and my pedagogy. I was responsible for botany and geology teaching, and discussed coevolution with Judith and the students, through their short projects and articles. With Jason D. Hoeksema, we still collaborate, and we have recently deposited a project for a summer school in 2020, in Brazil (Campinas), funded by the New Phytologist.

111

Five selected articles I have focused my research on three models, alder-EMF symbiosis, neotropical EMF and more recently boreal ecosystems. I have chosen 5 articles, to reflect these three topics, and show the results of collaboration with other PhD students (A. Pozzi) and present Mélissande Nagati's first article.

87

Research activities : publication list and strategy

I still have not published as a last author, but I have submitted manuscripts as a last author twice this year (Gazal et al. and Schimann et al.). Even when I was PI of the grant that gave rise to the publication, I have let the last position to taxonomists, who trained me in mycology. There were a few conflicts about the last position, but I have always let that place, being the youngest on most projects. Beginning a few years ago, I let the first position to students, as they are more and more willing to write, and I keep the second position. The last position in that case remains for colleagues who co-supervised the students with me.

As I am convinced we have to work with taxonomists to know and preserve biodiversity, I have helped a lot of colleagues describe their specimens and publish articles in society journals. I recognize I should write more "big" papers on my data on French Guiana, and this is one of my objectives. However, "big" papers in taxonomy rely on species description, which are more likely to be accepted by specialized journals.

Finally, I continue to write for, and give conferences to a broad audience, in French. These publications are rarely recognized, but are useful locally, even for my students, who realize how interesting their research topic can be.

Peer-reviewed journals 103

Her work allowed the description of a new species of Tylopilus (Barbosa-Silva et al., 2017), and she worked with Jan Hackel during his M2.

Claudèle Ghotsamekontchou, UQAT, PhD supervised by Yves Bergeron, 1 month (2018).

Claudèle came for one month to learn NGS techniques, and study ectomycorrhizal fungi diversity on aspen roots in the boreal forest. He rapidly became autonomous and is now using NGS for his analyses. Mélissande Nagati is working with him at UQAT and we hope the synthesis will produce a final article for both of them.

Supun Madhumadhawa Pawuluwage, UQAT, Master 1, supervised by Philippe Marchand, 3 months (2019).

Supun will come in autumn 2019. He is now working with Tristan Lafont Rapnouil and will test if positive spatial interactions could be explained by shared mycorrhizal fungi. He will learn NGS analyses and molecular biology in EDB lab. His stay is funded by the French Consulat in Québec.

Visiting scientists

During two years (2011-2013), I was co-responsible of external seminars in the lab and I invited mainly colleagues from Montpellier, but also taxonomists, such as Cony Decock (Mycothèque de Louvain) and Terry Henkel (Humboldt State University, California, USA). I am still really invested in international exchanges and regularly invite and welcome colleagues from France and abroad.

Thanks to the Labex TULIP, I managed to get grants and invite two colleagues to discuss future projects, exchange with colleagues at EDB, and teach in M2 BEE. Jason D. Hoeksema, University of Mississippi, USA, three weeks (2016). Jason is an expert on plant-fungi coevolution and he invited me in spring 2016 for a two-weeks course on coevoluton. We used his stay at EDB to work on alder-fungi coevolution and submitted a first paper on this topic (Roy et al. submitted). We also handled experiments together in Poland, and published a paper on the unusual ectomycorrhizae of a forest-dwelling herb, Pulsatilla patens (Hoeksema et al., 2018). Diego Vasquez, CONICET, Mendoza, Argentina, two weeks (2019). During my stay in Argentina, I met Diego to discuss and compare mycorrhizal networks with his background on ecological networks. We decided to apply for a visiting scientist grant, and we plan several meetings, in Argentina and France, to think about this comparison and develop a project in Argentina.

Invited visits

Reciprocally, I have been invited for several invited conferences in labs (see section invited conferences) but also for stays abroad. From the UPS, I received a mobility grant to sample in Alaska (2011, 2500 E ) and in Canada (2016, 2500 E ).

108 2015-2019. 79,040 E to EDB.

In this project, I was responsible for a task on endophytes communities. I contributed to the field in French Guiana, supervised master students and involved Julian Donald as a Post-Doc. I supervised the metabarcoding at EDB, and acquired impressive datasets on endophytes communities and strains. I also helped my colleagues in chemistry identifying their strains with phylogenies. We are currently writing papers on this project (Donald et al., submitted ; Donald et al., in prep ; Gazal et al., in prep), and my colleagues in chemistry isolated very promising strains.

LONGTIME: Long Term Impact of ancient Amerindian settlements on Guianese Forests. Project central LABEX CEBA. PI: Jean-François Molino (AMAP, Montpellier, France) and G. Odonne (LEESIA, Guyane) 2016-2018. 15,000 E at EDB In this project, I was responsible for a task on soil biodiversity, and organized the fieldwork for 8 researchers and students in French Guiana. I supervised the soil sequencing and biodiversity analyses for fungi, bacteria and earthworms and the master 2 of Nina Gazal. We have already submitted a book chapter about our methods (Gazal et al., submitted) and a master 2 (Isis Poinas), supervised by Maxime Rejou-Méchain (AMAP, Montpellier), is now gathering our data with archaeological data.

DROUGHT: Functional diversity and response to drought in tropical forests. Project central LABEX CEBA. PI: Damien Bonal (EEF, Nancy, France) 2016-2018. [START_REF] Roy | Alder and the Golden Fleece: high diversity of Frankia and ectomycorrhizal fungi revealed from Alnus glutinosa subsp. barbata roots close to a Tertiary and glacial refugium[END_REF],000 E at EDB. In this project, I was co-responsible for a task on micro-organisms associated with trees and their interaction with drought stress. I focused on mycorrhizae and gathered mycorrhizae along a phosphorus and rainfall gradient in French Guiana, that was analysed by B. Durrington during his master 2 (Durrington et al., in prep). The project also focused on endophytes of leaves and branches and the sequencing was finally handled in C. Vacher's lab, through another master 2.

DIAMOND: Dissecting and monitoring Amazonian diversity. Project central LABEX CEBA. PI: Jérôme Murienne (EDB), Jérôme Orivel (EcoFoG, Kourou, Guyane Française) 2016-2018. 137,541 E at EDB In this project, I contribute to improve databases on fungal barcodes and fungal phylogenies. The ABC Saül is tightly linked with this project, as fungi identified by experts are useful to analyze metabarcoding short sequences.