Recherches Avancées sur la Biologie de l'Arbre et les Ecosystèmes Forestiers

Summary Almost all land plants form symbiotic associations with mycorrhizal fungi. These below‐ground fungi play a key role in terrestrial ecosystems as they regulate nutrient and carbon cycles, and influence soil structure and ecosystem multifunctionality. Up to 80% of plant N and P is provided by mycorrhizal fungi and many plant species depend on these symbionts for growth and survival. Estimates suggest that there are c . 50 000 fungal species that form mycorrhizal associations with c . 250 000 plant species. The development of high‐throughput molecular tools has helped us to better understand the biology, evolution, and biodiversity of mycorrhizal associations. Nuclear genome assemblies and gene annotations of 33 mycorrhizal fungal species are now available providing fascinating opportunities to deepen our understanding of the mycorrhizal lifestyle, the metabolic capabilities of these plant symbionts, the molecular dialogue between symbionts, and evolutionary adaptations across a range of mycorrhizal associations. Large‐scale molecular surveys have provided novel insights into the diversity, spatial and temporal dynamics of mycorrhizal fungal communities. At the ecological level, network theory makes it possible to analyze interactions between plant–fungal partners as complex underground multi‐species networks. Our analysis suggests that nestedness, modularity and specificity of mycorrhizal networks vary and depend on mycorrhizal type. Mechanistic models explaining partner choice, resource exchange, and coevolution in mycorrhizal associations have been developed and are being tested. This review ends with major frontiers for further research. Contents Summary 1406 I. Introduction 1407 II. Biodiversity of mycorrhizal associations 1408 III. Carbon and nutrient cycling and ecosystem multifunctionality 1410 IV. Mycorrhizal networks 1411 V. Evolution and partner selection 1413 VI. Mycorrhizal genomics and symbiotic molecular crosstalk 1416 VII. Conclusions and future research 1418 Acknowledgements 1418 References 1419

The diversity of fungi along environmental gradients has been little explored in contrast to plants and animals. Consequently, environmental factors influencing the composition of fungal assemblages are poorly understood. The aim of this study was to determine whether the diversity and composition of leaf and root-associated fungal assemblages vary with elevation and to investigate potential explanatory variables. High-throughput sequencing of the Internal Transcribed Spacer 1 region was used to explore fungal assemblages along three elevation gradients, located in French mountainous regions. Beech forest was selected as a study system to minimise the host effect. The variation in species richness and specific composition was investigated for ascomycetes and basidiomycetes assemblages with a particular focus on root-associated ectomycorrhizal fungi. The richness of fungal communities associated with leaves or roots did not significantly relate to any of the tested environmental drivers, i.e. elevation, mean temperature, precipitation or edaphic variables such as soil pH or the ratio carbon∶nitrogen. Nevertheless, the ascomycete species richness peaked at mid-temperature, illustrating a mid-domain effect model. We found that leaf and root-associated fungal assemblages did not follow similar patterns of composition with elevation. While the composition of the leaf-associated fungal assemblage correlated primarily with the mean annual temperature, the composition of root-associated fungal assemblage was explained equally by soil pH and by temperature. The ectomycorrhizal composition was also related to these variables. Our results therefore suggest that above and below-ground fungal assemblages are not controlled by the same main environmental variables. This may be due to the larger amplitude of climatic variables in the tree foliage compared to the soil environment.

BACKGROUND: Saprophytic filamentous fungi are ubiquitous micro-organisms that play an essential role in photosynthetic carbon recycling. The wood-decayer Pycnoporus cinnabarinus is a model fungus for the study of plant cell wall decomposition and is used for a number of applications in green and white biotechnology. RESULTS: The 33.6 megabase genome of P. cinnabarinus was sequenced and assembled, and the 10,442 predicted genes were functionally annotated using a phylogenomic procedure. In-depth analyses were carried out for the numerous enzyme families involved in lignocellulosic biomass breakdown, for protein secretion and glycosylation pathways, and for mating type. The P. cinnabarinus genome sequence revealed a consistent repertoire of genes shared with wood-decaying basidiomycetes. P. cinnabarinus is thus fully equipped with the classical families involved in cellulose and hemicellulose degradation, whereas its pectinolytic repertoire appears relatively limited. In addition, P. cinnabarinus possesses a complete versatile enzymatic arsenal for lignin breakdown. We identified several genes encoding members of the three ligninolytic peroxidase types, namely lignin peroxidase, manganese peroxidase and versatile peroxidase. Comparative genome analyses were performed in fungi displaying different nutritional strategies (white-rot and brown-rot modes of decay). P. cinnabarinus presents a typical distribution of all the specific families found in the white-rot life style. Growth profiling of P. cinnabarinus was performed on 35 carbon sources including simple and complex substrates to study substrate utilization and preferences. P. cinnabarinus grew faster on crude plant substrates than on pure, mono- or polysaccharide substrates. Finally, proteomic analyses were conducted from liquid and solid-state fermentation to analyze the composition of the secretomes corresponding to growth on different substrates. The distribution of lignocellulolytic enzymes in the secretomes was strongly dependent on growth conditions, especially for lytic polysaccharide mono-oxygenases. CONCLUSIONS: With its available genome sequence, P. cinnabarinus is now an outstanding model system for the study of the enzyme machinery involved in the degradation or transformation of lignocellulosic biomass.

The genetic structure of ectomycorrhizal (ECM) fungal populations results from both vegetative and sexual propagation. In this study, we have analysed the spatial genetic structure of Tuber melanosporum populations, a heterothallic ascomycete that produces edible fruit bodies. Ectomycorrhizas from oaks and hazels from two orchards were mapped and genotyped using simple sequence repeat markers and the mating type locus. The distribution of the two T. melanosporum mating types was also monitored in the soil. In one orchard, the genetic profiles of the ascocarps were compared with those of the underlying mycorrhizas. A pronounced spatial genetic structure was found. The maximum genet sizes were 2.35 and 4.70 m in the two orchards, with most manifesting a size < 1 m. Few genets persisted throughout two seasons. A nonrandom distribution pattern of the T. melanosporum was observed, resulting in field patches colonized by genets that shared the same mating types. Our findings suggest that competition occurs between genets and provide basic information on T. melanosporum propagation patterns that are relevant for the management of productive truffle orchards.

N(6)-threonylcarbamoyladenosine (t(6)A) is a universal tRNA modification essential for normal cell growth and accurate translation. In Archaea and Eukarya, the universal protein Sua5 and the conserved KEOPS/EKC complex together catalyze t(6)A biosynthesis. The KEOPS/EKC complex is composed of Kae1, a universal metalloprotein belonging to the ASHKA superfamily of ATPases; Bud32, an atypical protein kinase and two small proteins, Cgi121 and Pcc1. In this study, we investigated the requirement and functional role of KEOPS/EKC subunits for biosynthesis of t(6)A. We demonstrated that Pcc1, Kae1 and Bud32 form a minimal functional unit, whereas Cgi121 acts as an allosteric regulator. We confirmed that Pcc1 promotes dimerization of the KEOPS/EKC complex and uncovered that together with Kae1, it forms the tRNA binding core of the complex. Kae1 binds l-threonyl-carbamoyl-AMP intermediate in a metal-dependent fashion and transfers the l-threonyl-carbamoyl moiety to substrate tRNA. Surprisingly, we found that Bud32 is regulated by Kae1 and does not function as a protein kinase but as a P-loop ATPase possibly involved in tRNA dissociation. Overall, our data support a mechanistic model in which the final step in the biosynthesis of t(6)A relies on a strictly catalytic component, Kae1, and three partner proteins necessary for dimerization, tRNA binding and regulation.

Due to climate change, many lakes in Europe will be subject to higher variability of hydrological characteristics in their littoral zones. These different hydrological regimes might affect the use of allochthonous and autochthonous carbon sources. We used sandy sediment microcosms to examine the effects of different hydrological regimes (wet, desiccating, and wet-desiccation cycles) on carbon turnover. (13)C-labelled particulate organic carbon was used to trace and estimate carbon uptake into bacterial biomass (via phospholipid fatty acids) and respiration. Microbial community changes were monitored by combining DNA- and RNA-based real-time PCR quantification and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA. The shifting hydrological regimes in the sediment primarily caused two linked microbial effects: changes in the use of available organic carbon and community composition changes. Drying sediments yielded the highest CO2 emission rates, whereas hydrological shifts increased the uptake of allochthonous organic carbon for respiration. T-RFLP patterns demonstrated that only the most extreme hydrological changes induced a significant shift in the active and total bacterial communities. As current scenarios of climate change predict an increase of drought events, frequent variations of the hydrological regimes of many lake littoral zones in central Europe are anticipated. Based on the results of our study, this phenomenon may increase the intensity and amplitude in rates of allochthonous organic carbon uptake and CO2 emissions.

Fungi provide relevant ecosystem services contributing to primary productivity and the cycling of nutrients in forests. These fungal inputs can be decisive for the resilience of Mediterranean forests under global change scenarios, making necessary an in-deep knowledge about how fungal communities operate in these ecosystems. By using high-throughput sequencing and enzymatic approaches, we studied the fungal communities associated with three genotypic variants of Pinus pinaster trees, in 45-year-old common garden plantations. We aimed to determine the impact of biotic (i.e., tree genotype) and abiotic (i.e., season, site) factors on the fungal community structure, and to explore whether structural shifts triggered functional responses affecting relevant ecosystem processes. Tree genotype and spatial-temporal factors were pivotal structuring fungal communities, mainly by influencing their assemblage and selecting certain fungi. Diversity variations of total fungal community and of that of specific fungal guilds, together with edaphic properties and tree's productivity, explained relevant ecosystem services such as processes involved in carbon turnover and phosphorous mobilization. A mechanistic model integrating relations of these variables and ecosystem functional outcomes is provided. Our results highlight the importance of structural shifts in fungal communities because they may have functional consequences for key ecosystem processes in Mediterranean forests.

The phytohormones jasmonate, gibberellin, salicylate, and ethylene regulate an interconnected reprogramming network integrating root development with plant responses against microbes. The establishment of mutualistic ectomycorrhizal symbiosis requires the suppression of plant defense responses against fungi as well as the modification of root architecture and cortical cell wall properties. Here, we investigated the contribution of phytohormones and their crosstalk to the ontogenesis of ectomycorrhizae (ECM) between grey poplar (Populus tremula x alba) roots and the fungus Laccaria bicolor. To obtain the hormonal blueprint of developing ECM, we quantified the concentrations of jasmonates, gibberellins, and salicylate via liquid chromatography-tandem mass spectrometry. Subsequently, we assessed root architecture, mycorrhizal morphology, and gene expression levels (RNA sequencing) in phytohormone-treated poplar lateral roots in the presence or absence of L. bicolor. Salicylic acid accumulated in mid-stage ECM. Exogenous phytohormone treatment affected the fungal colonization rate and/or frequency of Hartig net formation. Colonized lateral roots displayed diminished responsiveness to jasmonate but regulated some genes, implicated in defense and cell wall remodelling, that were specifically differentially expressed after jasmonate treatment. Responses to salicylate, gibberellin, and ethylene were enhanced in ECM. The dynamics of phytohormone accumulation and response suggest that jasmonate, gibberellin, salicylate, and ethylene signalling play multifaceted roles in poplar L. bicolor ectomycorrhizal development.

Almost all land plant species form a symbiosis with mycorrhizal fungi. These soil fungi provide nutrients and other services to plants in return for plant carbohydrates. The recent application of microbial metagenomics, metatranscriptomics, and metabolomics to plants and their immediate surroundings confirms the key role of mycorrhizal fungi, rhizosphere bacteria and fungi, and suggests a world of hitherto undiscovered interactions (van der Heijden et al., this issue, pp. 1406–1423). This novel knowledge is leading to a paradigm-shifting view: plants cannot be considered as isolated individuals any more, but as metaorganisms, or holobionts (Hacquard & Schadt, this issue, pp. 1424– 1430) encompassing an active microbial community re-programming host physiology (see Pozo et al., this issue, pp. 1431–1436). This bears tremendous implications for plant ecophysiology and evolution, plant breeding, crop management and sustainable ecosystem management.

Threonylcarbamoyladenosine (t(6)A) is a universal modification located in the anticodon stem-loop of tRNAs. In yeast, both cytoplasmic and mitochondrial tRNAs are modified. The cytoplasmic t(6)A synthesis pathway was elucidated and requires Sua5p, Kae1p, and four other KEOPS complex proteins. Recent in vitro work suggested that the mitochondrial t(6)A machinery of Saccharomyces cerevisiae is composed of only two proteins, Sua5p and Qri7p, a member of the Kae1p/TsaD family (L. C. K. Wan et al., Nucleic Acids Res. 41:6332-6346, 2013, http://dx.doi.org/10.1093/nar/gkt322). Sua5p catalyzes the first step leading to the threonyl-carbamoyl-AMP intermediate (TC-AMP), while Qri7 transfers the threonyl-carbamoyl moiety from TC-AMP to tRNA to form t(6)A. Qri7p localizes to the mitochondria, but Sua5p was reported to be cytoplasmic. We show that Sua5p is targeted to both the cytoplasm and the mitochondria through the use of alternative start sites. The import of Sua5p into the mitochondria is required for this organelle to be functional, since the TC-AMP intermediate produced by Sua5p in the cytoplasm is not transported into the mitochondria in sufficient amounts. This minimal t(6)A pathway was characterized in vitro and, for the first time, in vivo by heterologous complementation studies in Escherichia coli. The data revealed a potential for TC-AMP channeling in the t(6)A pathway, as the coexpression of Qri7p and Sua5p is required to complement the essentiality of the E. coli tsaD mutant. Our results firmly established that Qri7p and Sua5p constitute the mitochondrial pathway for the biosynthesis of t(6)A and bring additional advancement in our understanding of the reaction mechanism.

Fire is a major disturbance linked to the evolutionary history and climate of Mediterranean ecosystems, where the vegetation has evolved fire-adaptive traits (e.g., serotiny in pines). In Mediterranean forests, mutualistic feedbacks between trees and ectomycorrhizal (ECM) fungi, essential for ecosystem dynamics, might be shaped by recurrent fires. We tested how the structure and function of ECM fungal communities of Pinus pinaster and Pinus halepensis vary among populations subjected to high and low fire recurrence in Mediterranean ecosystems, and analysed the relative contribution of environmental (climate, soil properties) and tree-mediated (serotiny) factors. For both pines, local and regional ECM fungal diversity were lower in areas of high than low fire recurrence, although certain fungal species were favoured in the former. A general decline of ECM root-tip enzymatic activity for P. pinaster was associated with high fire recurrence, but not for P. halepensis. Fire recurrence and fire-related factors such as climate, soil properties or tree phenotype explained these results. In addition to the main influence of climate, the tree fire-adaptive trait serotiny recovered a great portion of the variation in structure and function of ECM fungal communities associated with fire recurrence. Edaphic conditions (especially pH, tightly linked to bedrock type) were an important driver shaping ECM fungal communities, but mainly at the local scale and probably independently of the fire recurrence. Our results show that ECM fungal community shifts are associated with fire recurrence in fire-prone dry Mediterranean forests, and reveal complex feedbacks among trees, mutualistic fungi and the surrounding environment in these ecosystems.

Microbial communities interplay with their environment through their functional traits that can be a response or an effect on the environment. Here, we explore how a functional trait-the decomposition of organic matter, can be addressed based on genetic markers and how the expression of these markers reflect ecological strategies of two fungal litter decomposer Gymnopus androsaceus and Chalara longipes. We sequenced the genomes of these two fungi, as well as their transcriptomes at different steps of Pinus sylvestris needles decomposition in microcosms. Our results highlighted that if the gene content of the two species could indicate similar potential decomposition abilities, the expression levels of specific gene families belonging to the glycoside hydrolase category reflected contrasting ecological strategies. Actually, C. longipes, the weaker decomposer in this experiment, turned out to have a high content of genes involved in cell wall polysaccharides decomposition but low expression levels, reflecting a versatile ecology compare to the more competitive G. androsaceus with high expression levels of keystone functional genes. Thus, we established that sequential expression of genes coding for different components of the decomposer machinery indicated adaptation to chemical changes in the substrate as decomposition progressed.

Abstract Palaeontology relies on the description of fossil morphologies to understand the evolutionary history of life on Earth. Yet much remains unknown about the impact of fossilization processes, even though these may introduce biases into palaeobiological interpretations. Here, we report the characterization of fossilized remains of the earliest known woody plant Armoricaphyton chateaupannense preserved either in 2D (as flat carbonaceous films) or in 3D (as organo‐mineral structures) in early Devonian shales ( c . 407 Ma) of the Armorican Massif on the northern margin of Gondwana. To document the fine‐scale structure and the chemistry of the tracheids of this ancient plant, we used propagation phase contrast synchrotron radiation X‐ray microcomputed tomography ( PPC ‐ SR μ CT ), transmission electron microscopy ( TEM ) and synchrotron‐based scanning transmission X‐ray microscopy ( STXM ) coupled with X‐ray absorption near edge structure ( XANES ) spectroscopy. PPC ‐ SR μ CT enables digital visualization of cell walls in unprecedented detail for the specimens preserved in 3D revealing structures similar to those observed in extant lignified cells, thereby strongly suggesting that the earliest woody plant A. chateaupannense originally contained lignin compounds. STXM ‐based XANES and TEM data show that, whatever the preservation modes (3D vs 2D), the remaining organic matter has a chemical composition rather typical of pyrobitumen compounds, raising the possibility of an original source other than lignin. The pyrobitumen compounds also contains automorphic Ti‐nanominerals interpreted as a diagenetic feature. Altogether, the present study illustrates that anatomical and chemical preservations may not always be correlated.

International audience

We entered the Anthropocene with the industrial revolution. This geological era is defined by the unprecedented impact of human activities on the planet's geochemical cycles, making us the main driving force of Earth environmental changes (Crutzen, 2002; Steffen et al., 2011). Since the middle of the twentieth century the human population has tripled, reaching seven billion today and probably 10 billion by 2050 (United Nations, 2015). This dramatic increase, associated with the improvement in the welfare of the population, has led to the overexploitation of natural resources. Intensive agriculture and industrialization has resulted in global warming, modification of nutrient cycles, pollution and reduction of wilderness; and endangering the preservation of eco- and agro-systems (Tilman et al., 2002; Steffen et al., 2011; Ehrlich & Harte, 2015). Today, the challenge is not only to intensify agro-productions to feed, fuel and shelter the growing population; but to do so in spite of the consequences of climate change while lessening our impact on the supporting ecosystems (Godfray et al., 2010; Ehrlich & Harte, 2015; Byrne et al., 2018). Plant sciences can play an important part in mitigating both the causes and consequences of the pressure population growth imposes on the environment. As the primary producer of eco- and agro-systems, plants are essential to assess and understand human-driven environmental changes (Loreau et al., 2001; Lin et al., 2008). They are also central tools to develop sustainable production methods (Godfray et al., 2010; Ehrlich & Harte, 2015; Byrne et al., 2018). In this context, the 41st New Phytologist Symposium ‘Plant sciences for the future’ was set as an experimental interdisciplinary platform. Bringing together early career and leader scientists from different fields of plant sciences, it aimed to promote the development of transdisciplinary research projects to build a better understanding of the multiple aspects of the upcoming environmental challenges; and to produce robust solutions for society. A special debate chaired by Marc-André Selosse (Natural History Museum of Paris, France) and Richard Norby (Oak Ridge National Laboratory, TN, USA) highlighted the critical topics and knowledge gaps the scientific community needs to fill in order to harness plant sciences to solve these societal issues. This event, held in Nancy, France on 11–13 April 2018, hosted researchers from 70 universities, research institutes and companies representing 29 countries in the fields of Developmental biology, Evolutionary biology, Ecology, Plant–microorganism interactions, Physiology and Genetic engineering (Fig. 1). In this article we outline how all plant science fields contribute to understand the effects of global change and to developing innovative solutions to maintain agro-productions, promote sustainability and counteract climate change. Human activities have altered global biogeochemical cycles. Colin Brownlee (Marine Biological Association, Plymouth, UK) illustrated the role of marine phytoplankton in the carbon (C) cycle, reminding that coccolithophores are responsible for much of the calcium carbonate formation on Earth. The increasing input of CO2 into the atmosphere since the industrial revolution, which is responsible for ocean warming and acidification, is compromising the ability of coccolithophores to form calcium carbonate and therefore affecting the completion of the global C cycle (Orr et al., 2005). Brownlee demonstrated the role of proton channels in the calcification process of calcite coccoliths. Elucidating the cellular mechanisms involved in biomineralization is essential to minimize human impact on these critical species. Forests represents a major C sink (Pan et al., 2011). Björn Lindahl (Swedish University of Agricultural Sciences, Uppsala, Sweden) highlighted the importance of plant–fungi interactions in nutrient cycling and soil fertility in boreal forests. Using high-throughput sequencing to elucidate boreal forest mycobiome and combining it with climatic, edaphic and forest productivity parameters, Lindahl's group showed that the composition of the fungal community is the principal driver of organic matter storage in those environments. Lindahl proposed that intensification of forest practices by changing soil fungal communities could improve the soil C stock in boreal forest but presents long-term soil fertility risks. From the boreal forest to the steppe, Amy Austin (University of Buenos Aires, Argentina) demonstrated that photodegradation is a dominant force controlling C losses in semi-arid ecosystems (Austin & Vivanco, 2006). Recent findings of her team suggests that photodegradation of the leaf litter promotes its subsequent biotic degradation by increasing accessibility of labile C compounds to microbes (Austin et al., 2016). Land-use or climate change altering vegetation cover could largely influence the effect of sunlight on C cycling in these ecosystems. Croplands are an anthropogenic biome that we could manage to increase potential C sequestration. Carbon dioxide reaction with minerals naturally moderates atmospheric CO2 and this effect has been enhanced since the emergence of land plants (Berner, 1997). David Beerling (University of Sheffield, UK) proposed to exploit this natural phenomenon by adding fast-reacting silicate rocks on croplands to trap CO2. Eventually, weathering products could run-off in to oceans and enhance alkalinity, counteracting acidification, and sustaining the growth of marine phytoplankton that we presented as crucial for the completion of C cycle earlier in this paragraph. Together, these results highlight the importance of expanding our knowledge about C and nutrient turnover on Earth to predict and actively minimize our impact on climate. Global warming has increased the intensity and frequency of extreme climactic events. High amplitude of temperature variation is the major cause of important plant losses in eco- and agro-systems (Eiche, 1966; Boyer, 1982; Hatfield & Prueger, 2015). Plant pre-adaptation to climate variations could limit losses (Wikberg & Ögren, 2007; Yordanov et al., 2000). Drought acclimation of trees involves structural changes in wood formation and abscisic acid (ABA) is a key plant regulator of this acclimation (Gupta et al., 2017). Andrea Polle (University of Göttingen, Germany) showed the importance of ABA signal perception and response in wood formation of drought-stressed trees. Cecilia Brunetti (CNR, Sesto Fiorentino, Italy) demonstrated how trees limit xylem conduits embolism by modulating their carbohydrate metabolism and how ABA is involved in restoring xylem transport ability. Limiting water loss by modulating stomatal aperture is another plant survival response to drought. Predicting plant responses to different levels of drought is still difficult. Belinda Medlyn (University of Western Sydney, Australia) reviewed recent advances in ‘optimal stomatal theory’ and presented a new in silico model to understand and predict stomatal responses to drought and heat. Environmental stresses such as changes in temperature can affect plant metabolism and growth (Sampaio et al., 2016). Shuhua Yang (China Agricultural University, Beijing, China) showed that stomatal conductance and, in consequence, leaf photosynthesis and respiration are affected by cold stress via the regulation of the CBF-dependent cold signalling pathway in Arabidopsis (Zhou et al., 2011). Owen Atkin (Australian National University, Canberra, Australia) suggested that, by boosting plant respiratory metabolism, global warming could increase CO2 release and influence the future atmospheric CO2 concentrations. Understanding plant physiological and metabolic adaptive responses to climate change are key factors for the production of efficient prediction models. These models are necessary to improve or develop novel management methods of eco- and agro-systems that could limit plant losses in the future. In our demographic context, maintaining population welfare depends on our ability to intensify agro-production. Environmental changes are threats to the maintenance of crop yields in both agricultural and forests agro-systems. They have direct impacts on plant mortality and biomass (Lobell & Field, 2007; Schlenker & Roberts, 2009), and indirectly affect plant productivity by altering population dynamics of plant pests, symbiotic microorganisms and competitive species (Gregory et al., 2009; Lindner et al., 2010). Biotechnological or agronomic solutions are necessary to lessen the consequences of global change on plant production. In this frame, understanding the genetic basis of wood production in different tree lineages may help to mitigate the repercussions of abiotic stress on forest productivity through adapted management plans. Andrew T. Groover (US Forest Service and University of California, Davis, CA, USA) reviewed the genetic basis of evolution of woody plants and highlighted species-specific or conserved gene modules regulating the development of dicot and monocot cambium (Zinkgraf et al., 2017). Environmental changes are modifying development and distribution of plant pests, threatening crop and forest productivity (Porter et al., 1991; Logan et al., 2003). Plant diseases are now responsible for c. 25% of crop losses (Martinelli et al., 2015). Controlling their outbreak is crucial to maintain plant productivity. A strategy to contrast future pest spread is to engineer crops resistant to a wide variety of pathogens. Ralph Panstruga's team (University of Aachen, Germany) explores the role of the MILDEW RESISTANCE LOCUS O genes (Jørgensen, 1992) – encoding members of a family of membrane integral proteins conserved in plants – in conferring multiple resistances. They showed that mutations in MLO genes improved Arabidopsis thaliana resistance to several leaf epidermal cell penetrating pathogens, but increased susceptibility to microbes with different invasion strategies (Acevedo-Garcia et al., 2017). Stella Cesari (INRA, France), 2017 Tansley Medal winner, proposed to exploit the complex mechanistic and structural variability of nucleotide-binding domain and leucine-rich repeat-containing proteins (NLRs) to increase sensitivity or extend specificity of pathogen effector recognition (Cesari, 2017). Plants are increasingly exposed to new environmental stresses such as habitat degradation, climate change and the expanding range of invasive species and pests (Anderson et al., 2011). To predict the consequences of global change on ecosystems, it is necessary to understand the different levels of plant adaptation (phenotypic plasticity, dispersion capacity and evolution) to new threats. Plants can modulate the phenotypic plasticity of their neighbours by emission of volatile organic compounds (VOCs). André Kessler (Cornell University, Ithaca, NY, USA) showed that VOCs emitted by Solidago altissima upon herbivore attack alter herbivore dispersal and feeding behaviour through the modification of the metabolism of non-attacked plants. This indicates spreading the risk of herbivory to neighbours as a fitness-optimizing strategy. The high variability of VOC types and levels in the field suggests the possibility of herbivore-driven natural selection on chemical communication (Morrell & Kessler, 2017). This might modulate crop adaptability to newly introduced pests. Linda F. Delph (Indiana University, Bloomington, IN, USA) reminded the audience that the phenotype is the direct interface between the organism and its environment and therefore at the centre of evolution. She showed that genetic selection on key fitness traits such as flower number and height was strongly influenced by the environmental conditions in Silene latifolia. In-depth investigation of environmental factors influencing plant evolution may help predict phenotypic traits and fitness of plants in changing ecosystems. Flower development is one of the most intricate and finely tuned processes influencing plant reproductive success. The floral organ must acquire specialized structures, bloom at the right time of the year and bear coevolving traits with its pollinators. By taking advantage of the -omics technologies, several groups found that specific transcription factors (TFs) evolved to allow the formation of elaborate and diverse floral petals. Elena Kramer (Harvard University, Cambridge, MA, USA) presented the role of the AqJAGGED gene, a TF involved in multiple key aspects in Aquilegia flower morphogenesis (Min & Kramer, 2017), while Hongzhi Kong (Institute of Botany, Beijing, China) showed that NpLMI1 and NpYAB5-1 are involved in the control of Nigella petal shape. Since the first observations of pollination systems by Darwin (1862), researchers have been seeking for evidence of pollinator-promoted selection for diverse floral shapes. Babu Ram Paudel (Yunnan University, China) showed how two alpine gingers (Roscoea purpurea and R. tumjensis) occur sympatrically and have similar morphology, but are reproductively isolated through a combination of phenological displacement of flowers and different attracted pollinators. Global change might reshape these evolutionary boundaries and modify population or speciation dynamics. Human impacts on the environment will influence plant traits and drive their evolution by modulating plant fitness (resistance to pathogens, pollination, population dynamics). However, plant plasticity might provide a key for plant adaptability on the short term. Understanding the genetic and molecular basis of phenotypes is key to groundbreaking biotechnological applications; hence the importance of tight coordination and synergy between basic and applied sciences. The Symposium hosted researchers interested in fundamental biological mechanisms, scientists involved in both basic and applied research and developers employed in biotechnology companies, aiming to bridge their complementary mindsets. Understanding the molecular aspects of nutrient uptake and storage by plants is crucial to improving the yield or nutritional properties of crops. By investigating the developmental biology of rooting systems in early land plants, Liam Dolan (University of Oxford, UK) showed that the development of rooting structures in land plants is tightly controlled by some conserved TF networks (Breuninger et al., 2016; Proust et al., 2016). Such highly conserved key regulators can be used to enhance crops ability to access nutrients (Dolan et al., 2011; US Patent Application no. 12/451,574). The fine-tuning of lateral root emergence is another central aspect of root systems development. Keith Lindsey (Durham University, UK) showed how the 36-aa peptide POLARIS, orchestrating the auxin–ethylene crosstalk, modulates lateral root emergence (Chilley et al., 2006). These signalling mechanisms affect plants’ access to water and nutrients and mediate plant plasticity in a changing environment. The regulation of the level of reserves is also fundamental to plant nutrition. Alison M. Smith (John Innes Centre, Norwich, UK) highlighted the importance of clock genes, which modulate starch production and degradation for efficient plant sustainment (Graf et al., 2010; Scialdone et al., 2013). Arabidopsis leaves modulate the rate of starch degradation according to the duration of the night, in order not to starve before dawn (Fernandez et al., 2017). A better understanding of the dynamics of plant nutrient reserves may help engineering stress-resistant or nutrient-rich crops. Examples of basic sciences translated into innovative plant technologies were given at the symposium. As presented earlier, David Beerling is exploiting silica weathering to counter accumulation of excess atmospheric CO2. These results involved integrative studies spanning through geology, chemistry, economy and plant sciences, demonstrating once more the inestimable power of transdisciplinary research. Anne Osbourn (John Innes Centre) showed that through coexpression, evolutionary co-occurrence and epigenomic coregulation genomes can be mined for biosynthetic gene clusters involved in production of secondary metabolites (Medema & Osbourn, 2016). Their genetic manipulation allows the production of specific chemicals at a lower cost than conventional synthetic chemistry (Owen et al., 2017). Technical platforms and start-ups are being born in the exciting field of plant chemistry (Reed et al., 2017). In conclusion, the symposium highlighted the need of integrative research to (1) understand, model, predict the consequences of global change on ecosystems and plant physiology, productivity, epidemiology; (2) create innovative solutions to future challenges in the fields of food security, sustainable crop management and efficient production; (3) diffuse knowledge and know-how among specialists and the general public. To this purpose, the symposium was closed by a public talk on plant–microorganism interactions, given by Marc-André Selosse with the beautiful background of the Hôtel de Ville of Nancy. The authors thank the New Phytologist Trust and the Lab of Excellence ARBRE for organizing this symposium. The authors are grateful to all attendees who contributed to the stimulating atmosphere of this conference. A special acknowledgement to M-A. Selosse and R. Norby for leading the debate on the role of plant sciences in solving societal issues. The authors thank A. Austin, A. Polle, B. Medlyn, L. Wingate and A. Kessler for their time and advice during the mentoring session on Gender equality in plant sciences. The authors are grateful to F. Martin and the New Phytologist Trust for their support and helpful comments on the report. This work was supported by the LabEx ARBRE (ANR-11-LABX-0002-01), the Région Grand-Est, the University of Lorraine, the Genomic Science Programme of the US Department of Energy as part of the Plant–Microbe Interfaces Scientific Focus Area and, the ANPCyT (PICT 2015-1231, PICT 2016-1780), the University of Buenos Aires (UBACyT) and the CONICET of Argentina.

The ecology of fungi, and the sub-field of community ecology of ectomycorrhizal (ECM) fungi, has changed significantly since the introduction of PCR and its application to fungal species identification. This chapter discusses recent progress and pitfalls in molecular technologies, and new highlights and future research domains in the ecology of ECM communities, derived from quantitative PCR, Second-Generation Sequencing (SGS), and 'meta-omics' approaches. The recent application of SGS and associated molecular studies has largely increased our understanding of ECM fungal ecology, including studies of factors that influence diversity, community structure, and the distribution and abundance of ECM fungal species at different spatial scales. The chapter presents analyses that were accomplished using bulk soil, but it is also possible to use molecular ecology to unravel which micro-organisms, mainly bacteria, are directly associated with ECM fungi. It highlights how the use of molecular high-throughput techniques improves our knowledge of truffle ecology and the quality of inoculated seedlings.

This paper aims to study a numerical model of an adsorption chiller driven with solar energy that is confronted to experimental measurements. This article deals with numerical study of refrigeration systems using a pair of silica gel and water with simulink. The results include the temperature of desorber, the temperature of chilled, cooling and hot water, temperature of two adsorption/desorption beds, condenser and evaporator, the refrigerant saturation pressures in the two compartments and the time variation of water uptake in two adsorbent beds.

Energy cogeneration is a way to improve global efficiency of energy production systems since it consumes a unique resource in order to supply heat and electrical power through optimal use of heat fluxes associated to power production. Energy trigeneration enlarges the concept to the production of cold also. It consumes a unique resource to produce electricity, heat and cold. Nevertheless, we could go more ahead by substituting a part of the primary fuel resource by renewable energy as solar energy in order to reduce the carbon impact. This is conducted through the use of adsorption refrigeration which needs hot water to produce cold water. However, even if energy utilities are provided with the best efficient way, the final use of energy could make all the efforts fall. Cooling ceilings present one of the best solutions to be coupled to solar cooling since it needs a medium range cold temperature of the fluid in order to avoid condensation if the wall ceiling temperature drops below the ambient air dew point temperature. All these constraints need to be checked experimentally and confronted to numerical simulation. For this purpose, an experimental platform has been developed combining an internal combustion gas engine (cogenerator), a refrigerating adsorption machine, thermal solar collectors and wooden construction split in two compartment, a cold one conditioned by cooling ceilings and a hot one conditioned by heating floors. The platform is completely instrumented. In this paper we focus only on the refrigeration machine for which we developed a simulation model that is confronted to experimental measurements.

Fusarium species, recognised as global priority pathogens, frequently induce severe diseases in crops; however, certain species exhibit alternative symbiotic lifestyles and are either non-pathogenic or endophytic. In this study, we characterised the mutualistic relationship between the eFp isolate of F. pseudograminearum and five poplar species, resulting in formation root structures reminiscent of ectomycorrhizal (ECM) symbiosis. This functional symbiosis is evidenced by enhanced plant growth, reciprocal nutrient exchange, improved nitrogen and phosphorus uptake and upregulation of root sugar transporter gene expression ( PtSweet1 ). Comparative and population genomics confirmed that eFp maintains a structurally similar genome, but exhibits significant divergence from ten conspecific pathogenic isolates. Notably, eFp enhanced the growth of diverse plant lineages ( Oryza , Arabidopsis , Pinus and non-vascular liverworts), indicating a near-complete loss of virulence. Although this specialised symbiosis has only been established in vitro , it holds significant value in elucidating the evolutionary track from endophytic to mycorrhizal associations.

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