Article: Nature Ecology & Evolution

Megaphylogeny resolves global patterns of mushroom evolution T Varga, K Krizsán, C Földi, B Dima, M Sánchez-García, … Nature Ecology & Evolution, 1


Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with the spread of (sub)tropical coniferous forests and a warming climate. A possible mass extinction, several clade-specific adaptive radiations and morphological diversification of fruiting bodies followed during the Cretaceous and the Paleogene, convergently giving rise to the classic toadstool morphology, with a cap, stalk and gills (pileate-stipitate morphology). This morphology is associated with increased rates of lineage diversification, suggesting it represents a key innovation in the evolution of mushroom-forming fungi. The increase in mushroom diversity started during the Mesozoic-Cenozoic radiation event, an era of humid climate when terrestrial communities dominated by gymnosperms and reptiles were also expanding.

article: Environmental Microbiology

Broad‐specificity GH131 β‐glucanases are a hallmark of Fungi and Oomycetes that colonise plants GE Anasontzis, MH Lebrun, M Haon, C Champion, A Kohler, N Lenfant, … Environmental Microbiology


Plant‐tissue‐colonising fungi fine‐tune the deconstruction of plant‐cell walls (PCW) using different sets of enzymes according to their lifestyle. However, some of these enzymes are conserved among fungi with dissimilar lifestyles. We identified genes from Glycoside Hydrolase family GH131 as commonly expressed during plant‐tissue colonisation by saprobic, pathogenic, and symbiotic fungi. By searching all the publicly available genomes, we found that GH131‐coding genes were widely distributed in the Dikarya subkingdom, except in Taphrinomycotina and Saccharomycotina, and in phytopathogenic Oomycetes, but no other eukaryotes nor prokaryotes. The presence of GH131 in a species was correlated with its association with plants as symbiont, pathogen, or saprobe. We propose that GH131‐family expansions and horizontal‐gene transfers contributed to this adaptation. We analysed the biochemical activities of GH131 enzymes whose genes were up‐regulated during plant‐tissue colonisation in a saprobe (Pycnoporus sanguineus), a plant symbiont (Laccaria bicolor), and three hemibiotrophic‐plant pathogens (Colletotrichum higginsianum, C. graminicola, Zymoseptoria tritici). These enzymes were all active on substrates with β‐1,4, β‐1,3, and mixed β‐1,4/1,3 glucosidic linkages. Combined with a cellobiohydrolase, GH131 enzymes enhanced cellulose degradation. We propose that secreted GH131 enzymes unlock the PCW barrier and allow further deconstruction by other enzymes during plant tissue colonisation by symbionts, pathogens and saprobes.

Article: Journal of Plant Pathology

Comparison and validation of Oomycetes metabarcoding primers for Phytophthora high throughput sequencing J Legeay, C Husson, T Cordier, C Vacher, B Marcais, M Buée Journal of Plant Pathology, 1-6


Oomycetes are eukaryotic plant pathogens that require health monitoring. High-throughput sequencing (HTS) methods replace progressively cultivation-based approaches in soil surveys of Oomycetes, but very little control has been done from synthetic communities. Indeed, several potential biases do exist and need to be assessed for Oomycetes communities. We created a mock community by mixing DNA from 24 Phytophthora species. We amplified two barcode regions with Oomycete-specific primers before HTS. With this aim, we used three primer sets in nested PCR amplification, targeting the ITS-1 region or the RAS gene region. The three nested PCR strategies proved to be a reliable qualitative approach, identifying approximately 95% of the species after Illumina Miseq sequencing and bioinformatic analysis. However, quantitative proportions of each species showed distortions compared to the original mixture of the mock. In addition, we compared the two ITS primer sets on soil environmental DNA sampled from temperate forests. The ‘oom18S-ITS7/18ph2f-5.8S-1R’ primer set, more specific to Phytophthora, was able to detect seven Phytophthora species, confirming what was expected for temperate forests. Using the ‘DC6-ITS7/oom18S-ITS7’ primer set that covers the broader Peronosporaceans, we detected only one Phytophthora species among the dominance of Pythium and Phytopythium species. We concluded that ‘oom18S-ITS7/18ph2f-5.8S-1R’ primer set is a reliable tool for the qualitative description of environmental Phytophthoracommunities.

Article: Frontiers in Microbiology

Identification of Populus small RNAs responsive to mutualistic interactions with mycorrhizal fungi, Laccaria bicolor and Rhizophagus irregularis R Mewalal, H Yin, R Hu, SS Jawdy, P Vion, GA Tuskan, F Le Tacon, … Frontiers in Microbiology 10, 515


Ecto- and endo-mycorrhizal colonization of Populus roots have a positive impact on the overall tree health and growth. A complete molecular understanding of these interactions will have important implications for increasing agricultural or forestry sustainability using plant:microbe-based strategies. These beneficial associations entail extensive morphological changes orchestrated by the genetic reprogramming in both organisms. In this study, we performed a comparative analysis of two Populus species (Populus deltoides and P. trichocarpa) that were colonized by either an arbuscular mycorrhizal fungus (AmF), Rhizophagus irregularis or an ectomycorrhizal fungus (EmF), Laccaria bicolor, to describe the small RNA (sRNA) landscape including small open reading frames (sORFs) and micro RNAs (miRNAs) involved in these mutualistic interactions. We identified differential expression of sRNAs that were, to a large extent, 1) within the genomic regions lacking annotated genes in the Populus genome and 2) distinct for each fungal interaction. These sRNAs may be a source of novel sORFs within a genome, and in this regard, we identified potential sORFs encoded by the sRNAs. We predicted a higher number of differentially-expressed miRNAs in P. trichocarpa (4 times more) than in P. deltoides (conserved and novel). In addition, 44 miRNAs were common in P. trichocarpa between the EmF and AmF treatments, and only 4 miRNAs were common in P. deltoides between the treatments. Root colonization by either fungus was more effective in P. trichocarpa than in P. deltoides, thus the relatively few differentially-expressed miRNAs predicted in P. deltoides might reflect the extent of the symbiosis. Finally, we predicted several genes targets for the plant miRNAs identified here, including potential fungal gene targets. Our findings shed light on additional molecular tiers with a role in Populus-fungal mutualistic associations and provides a set of potential molecular targets for future enhancement.

Article: New Phytologist

A two genes-for-one gene interaction between Leptosphaeria maculans Brassica napus. Y Petit-Houdenot, A Degrave, M Meyer, F Blaise, B Ollivier, CL Marais, … The New phytologist


Interactions between Leptosphaeria maculans, causal agent of stem canker of oilseed rape, and its Brassica hosts are models of choice to explore the multiplicity of “gene‐for‐gene” complementarities and how they diversified to increased complexity in the course of plant‐pathogen co‐evolution. Here, we comfort this postulate by investigating the AvrLm10 avirulence that induces a resistance response when recognized by the Brassica nigra resistance gene Rlm10.

Using genome‐assisted map‐based cloning, we identified and cloned two AvrLm10 candidates as two genes in opposite transcriptional orientation located in a subtelomeric repeat‐rich region of the genome. The AvrLm10genes encode small secreted proteins and show expression profiles in plantasimilar to those of all L. maculans avirulence genes identified so far.

Complementation and silencing assays indicated that both genes are necessary to trigger Rlm10 resistance. Three assays for protein‐protein interactions showed that the two AvrLm10 proteins physically interact in vitroand in planta.

Some avirulence genes are recognized by two distinct resistance genes and some avirulence genes hide the recognition specificities of another. Our L. maculans model illustrates an additional case where two genes located in opposite transcriptional orientation are necessary to induce resistance. Interestingly, orthologues exist for both L. maculans genes in other phytopathogenic species, with a similar genome organization, which may point to an important conserved effector function linked to heterodimerization of the two proteins.

Article: Soil Biology and Biochemistry

Soil microbial functions are affected by organic matter removal in temperate deciduous forest F Maillard, V Leduc, C Bach, A Reichard, L Fauchery, L Saint-André, … Soil Biology and Biochemistry


A growing demand for renewable carbon (C) has led to intensified forest management resulting in the use of forest residues (e.g. canopy, bark or litter layer) as energy sources with potential modifications of soil properties and tree productivity. Because microbes mediate the recycling of C and nutrients sequestered in organic matter, we investigated the effects of organic matter (OM) removal on soil properties, root surfaces, microbial functions and abundance using a new observational forest network. We compared leaf litter and logging residue removal plots to reference plots in six beech forests located in the northern half of France. After three consecutive years of OM removal, C and nitrogen (N) pools were not affected, but OM exportation decreased the cation exchange capacity and available phosphorus (P) pool by respectively 12% and 30% in the topsoil (0–5 cm depth). Fine root surface area significantly increased by 21% in the subsoil (5–10 cm depth) in response to OM removal. Enzymatic activities involved in N and P mobilisation decreased from 12 to 38% with the manipulation of OM. Community-level profiling (CLPP) based on BIOLOG approach revealed that the metabolic potential of the microbial community strongly decreased in response to OM removal. Our results indicated that intensive forestry could affect microbial functions implicated in nutrients mobilisation. We demonstrated that soil organic matter (SOM) content is a predictor of microbial functions resistance to forest residue removal. We recommend that intensive forestry should be reduced or limited in beech forests characterised by low soil OM contents.

Article: Journal of experimental botany

The iron-sulfur protein NFU2 plays a predominant role in branched-chain amino acid synthesis in Arabidopsis roots B Touraine, F Vignols, J Przybyla-Toscano, T Ischebeck, T Dhalleine, … Journal of experimental botany


Numerous proteins require a metallic cofactor for their function. In plastids, the maturation of iron-sulfur (Fe-S) proteins necessitates a complex assembly machinery. We focused on Arabidopsis thaliana NFU1, NFU2 and NFU3, which participate in the late maturation steps. According to the strong photosynthesis defects observed in high chlorophyll fluorescence 101 (hcf101), nfu2and nfu3 plants, we determined that NFU2 and NFU3, but not NFU1, act immediately upstream from HCF101 for the maturation of [Fe4S4]-containing photosystem I subunits. An additional function of NFU2 in the maturation of the [Fe2S2] cluster of a dihydroxyacid dehydratase was obvious from the accumulation of precursors of the branched-chain amino acid synthesis pathway in nfu2 roots and the rescue of the primary root growth defect by supplying branched-chain amino acids. The absence of NFU3 in roots precluded any compensation. Overall, unlike their eukaryotic and prokaryotic counterparts, which are specific of [Fe4S4] proteins, NFU2 and NFU3 contribute to the maturation of both [Fe2S2] and [Fe4S4] proteins either as a relay in conjunction with other proteins such as HCF101 or by directly delivering Fe-S clusters to client proteins. Considering the low number of Fe-S cluster transfer proteins relative to final acceptors, additional targets probably await identification.

Article: Molecular Plante-Microbe Interactions

Fungal endophytes of Populus trichocarpa alter host phenotype, gene expression and rhizobiome composition HL Liao, gregory bonito, JA Rojas, K Hameed, S Wu, CW Schadt, … Molecular Plant-Microbe Interactions


Mortierella and Ilyonectria include common species of soil fungi which are frequently detected as root endophytes in many plants including Populus spp. However, the ecological roles of these and other endophytic fungi with respect to plant growth and function are still not well understood. The functional ecology of two key taxa from the Populus rhizobiome, Mortierella elongata PMI93 and Ilyonectria europaea PMI82, was studied by coupling forest soil bioassays with environmental metatranscriptomics. Using soil bioassay experiments amended with fungal inoculants, M. elongata was observed to promote the growth of Populus. This response was cultivar independent. In contrast, I. europaea had no visible effect on Populus growth. Metatranscriptomic studies reveal that these fungi impact rhizophytic and endophytic activities in Populus and induce shifts in soil and root microbial communities. Differential expression of core genes in P. trichocarpa roots was observed in response to both fungal species. Expression of Populus genes for lipid signaling and nutrient uptake were up-regulated and expression of genes associated with gibberellin signaling were altered in plants inoculated with M elongata, but not I. europaea. Up-regulation of genes for growth promotion, down-regulation of genes for several LRR-receptors/kinases, and alteration of expression of genes associated with plant defense responses (e.g., JA/ET/SA pathways) also suggest that M. elongata manipulates plant defenses while promoting plant growth

Article: Scientific reports

Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect P Plassart, NC Prévost-Bouré, S Uroz, S Dequiedt, D Stone, R Creamer, … Scientific Reports 9 (1), 605


To better understand the relationship between soil bacterial communities, soil physicochemical properties, land use and geographical distance, we considered for the first time ever a European transect running from Sweden down to Portugal and from France to Slovenia. We investigated 71 sites based on their range of variation in soil properties (pH, texture and organic matter), climatic conditions (Atlantic, alpine, boreal, continental, Mediterranean) and land uses (arable, forest and grassland). 16S rRNA gene amplicon pyrosequencing revealed that bacterial communities highly varied in diversity, richness, and structure according to environmental factors. At the European scale, taxa area relationship (TAR) was significant, supporting spatial structuration of bacterial communities. Spatial variations in community diversity and structure were mainly driven by soil physicochemical parameters. Within soil clusters (k-means approach) corresponding to similar edaphic and climatic properties, but to multiple land uses, land use was a major driver of the bacterial communities. Our analyses identified specific indicators of land use (arable, forest, grasslands) or soil conditions (pH, organic C, texture). These findings provide unprecedented information on soil bacterial communities at the European scale and on the drivers involved; possible applications for sustainable soil management are discussed.

Article : New Phytologist

Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina E Morin, S Miyauchi, H San Clemente, ECH Chen, A Pelin, … New Phytologist


Glomeromycotina is a lineage of early diverging Fungi establishing arbuscular mycorrhizal (AM) symbiosis with land plants. Despite their major ecological role, genetic bases of their obligate mutualism are largely unknown, hindering our understanding of their evolution and biology. • We compared the genomes of Glomerales (Rhizophagus irregularis, Rhizophagus diaphanus, Rhizophagus cerebriforme) and Diversisporales (Gigaspora rosea) species, together with those of saprotrophic Mucoromycota, to identify gene families and processes associated with these lineages and to understand the molecular underpinning of their symbiotic lifestyle. • Genomic features in Glomeromycotina appear to be very similar with a very high content in transposons and protein-coding genes, extensive duplications of protein kinase genes, and loss of genes coding for lignocellulose degradation, thiamin biosynthesis and cytosolic fatty acid synthase. Most symbiosis-related genes in R. irregularis and G. rosea are specific to Glomeromycotina. We also confirmed that the present species have a homokaryotic genome organization. • The high interspecific diversity of Glomeromycotina gene repertoires, affecting all known protein domains, as well as symbiosis-related orphan genes, may explain the known adaptation of Glomeromycotina to a wide range of environmental settings. Our findings contribute to an increasingly detailed portrait of genomic features defining the biology of AM fungi.