Article: Fungal Biology Reviews

Antifungal activities of wood extractives N Valette, T Perrot, R Sormani, E Gelhaye, M Morel-Rouhier. Fungal Biology Reviews


Extractives are non-structural wood molecules that represent a minor fraction in wood. However, they are source of diverse molecules putatively bioactive. Inhibition of fungal growth is one of the most interesting properties of wood extractives in a context of wood preservation, crop protection or medical treatments. The antifungal effect of molecules isolated from wood extractives has been mainly attributed to various mechanisms such as metal and free radical scavenging activity, direct interaction with enzymes, disruption of membrane integrity and perturbation of ionic homeostasis. Lignolytic fungi, which are microorganisms adapted to wood substrates, have developed various strategies to protect themselves against this toxicity. A better knowledge of these strategies could help both developing new systems for extractive removal in biomass valorization processes and using these molecules as antifungal agents

Article: BMC genomics

The transcriptional landscape of basidiosporogenesis in mature Pisolithus microcarpus basidiocarp M de Freitas Pereira, AN da Rocha Campos, TC Anastacio, E Morin, …BMC genomics 18 (1), 157


Background: Pisolithus microcarpus (Cooke & Massee) G. Cunn is a gasteromycete that produces closed basidiocarps in symbiosis with eucalypts and acacias. The fungus produces a complex basidiocarp composed of peridioles at different developmental stages and an upper layer of basidiospores free of the hyphae and ready for wind dispersal upon the rupture of the basidiocarp pellis. During basidiosporogenesis, a process that takes place inside the basidiocarp peridioles, a conspicuous reserve of fatty acids is present throughout development. While several previous studies have described basidiosporogenesis inside peridioles, very little is known about gene expression changes that may occur during this part of the fungal life cycle. The objective of this work was to analyze gene transcription during peridiole and basidiospore development, while focusing specifically on cell cycle progression and lipid metabolism.

Results: Throughout different developmental stages of the peridioles we analyzed, 737 genes were regulated between adjacent compartments (>5 fold, FDR-corrected p-value < 0.05) corresponding to 3.49% of the genes present in the P. microcarpus genome. We identified three clusters among the regulated genes which showed differential expression between the peridiole developmental stages and the basidiospores. During peridiole development, transcripts for proteins involved in cellular processes, signaling, and information storage were detected, notably those for coding transcription factors, DNA polymerase subunits, DNA repair proteins, and genes involved in chromatin structure. For both internal embedded basidiospores (hereto referred to as “Internal spores”, IS) and external free basidiospores (hereto referred to as “Free spores”, FS), upregulated transcripts were found to involve primary metabolism, particularly fatty acid metabolism (FA). High expression of transcripts related to β-oxidation and the glyoxylate shunt indicated that fatty acids served as a major carbon source for basidiosporogenesis.

Conclusion: Our results show that basidiocarp formation in P. microcarpus involves a complex array of genes that are regulated throughout peridiole development. We identified waves of transcripts with coordinated regulation and identified transcription factors which may play a role in this regulation. This is the first work to describe gene expression patterns during basidiocarp formation in an ectomycorrhizal gasteromycete fungus and sheds light on genes that may play important roles in the developmental process.

Keywords: Gene expression, Peridiole development, Spores, Cell cycle, Fatty acid metabolism

Article: MBio

The Identification of Phytohormone Receptor Homologs in Early Diverging Fungi Suggests a Role for Plant Sensing in Land Colonization by Fungi A Hérivaux, TD de Bernonville, C Roux, M Clastre, V Courdavault, … mBio 8 (1), e01739-16


Histidine kinases (HKs) are among the most prominent sensing proteins studied in the kingdom Fungi. Their distribution and biological functions in early diverging fungi (EDF), however, remain elusive. We have taken advantage of recent genomic resources to elucidate whether relationships between the occurrence of specific HKs in some EDF and their respective habitat/lifestyle could be established. This led to the unexpected discovery of fungal HKs that share a high degree of similarity with receptors for plant hormones (ethylene and cytokinin). Importantly, these phytohormone receptor homologs are found not only in EDF that behave as plant root symbionts or endophytes but also in EDF species that colonize decaying plant material. We hypothesize that these particular sensing proteins promoted the interaction of EDF with plants, leading to the conquest of land by these ancestral fungi.

Article: Geobiology

Identification, distribution, and quantification of biominerals in a deciduous forest C Krieger, C Calvaruso, C Morlot, S Uroz, L Salsi, MP Turpault Geobiology


Biomineralization is a common process in most vascular plants, but poorly investigated for trees. Although the presence of calcium oxalate and silica accumulation has been reported for some tree species, the chemical composition, abundance, and quantification of biominerals remain poorly documented. However, biominerals may play important physiological and structural roles in trees, especially in forest ecosystems, which are characterized by nutrient-poor soils. In this context, our study aimed at investigating the morphology, distribution, and relative abundance of biominerals in the different vegetative compartments (foliage, branch, trunk, and root) of Fagus sylvatica L. and Acer pseudoplatanus L. using a combination of scanning electron microscopy and tomography analyses. Biomineral crystallochemistry was assessed by X-ray diffraction and energy-dispersive X-ray analyses, while calcium, silicon, and oxalic acid were quantified in the compartments and at the forest scale. Our analyses revealed that biominerals occurred as crystals or coating layers mostly in bark and leaves and were identified as opal, whewellite, and complex biominerals. In both tree species, opal was mostly found in the external tissues of trunk, branch, and leaves, but also in the roots of beech. In the stand, opal represents around 170 kg/ha. Whewellite was found to suit to conductive tissues (i.e., axial phloem parenchyma, vascular bundles, vessel element) in all investigated compartments of the two tree species. The shape of whewellite was prismatic and druses in beech, and almost all described shapes were seen in sycamore maple. Notably, the amount of whewellite was strongly correlated with the total calcium in all investigated compartments whatever the tree species is, suggesting a biologic control of whewellite precipitation. The amount of whewellite in the aboveground biomass of Montiers forest was more important than that of opal and was around 1170 kg/ha. Therefore, biominerals contribute in a substantial way to the biogeochemical cycles of silicon and calcium.

Article: Plos one

New Insights into the Complex Relationship between Weight and Maturity of Burgundy Truffles (Tuber aestivum) U Büntgen, I Bagi, O Fekete, V Molinier, M Peter, R Splivallo, … PLOS ONE 12 (1), e0170375


Despite an increasing demand for Burgundy truffles (Tuber aestivum), gaps remain in our understanding of the fungus’ overall lifecycle and ecology. Here, we compile evidence from three independent surveys in Hungary and Switzerland. First, we measured the weight and maturity of 2,656 Taestivum fruit bodies from a three-day harvest in August 2014 in a highly productive orchard in Hungary. All specimens ranging between 2 and 755 g were almost evenly distributed through five maturation classes. Then, we measured the weight and maturity of another 4,795 Taestivum fruit bodies harvested on four occasions between June and October 2015 in the same truffière. Again, different maturation stages occurred at varying fruit body size and during the entire fruiting season. Finally, the predominantly unrelated weight and maturity of 81 Taestivum fruit bodies from four fruiting seasons between 2010 and 2013 in Switzerland confirmed the Hungarian results. The spatiotemporal coexistence of 7,532 small-ripe and large-unripe Taestivum, which accumulate to ~182 kg, differs from species-specific associations between the size and ripeness that have been reported for other mushrooms. Although size-independent truffle maturation stages may possibly relate to the perpetual belowground environment, the role of mycelial connectivity, soil property, microclimatology, as well as other abiotic factors and a combination thereof, is still unclear. Despite its massive sample size and proof of concept, this study, together with existing literature, suggests consideration of a wider ecological and biogeographical range, as well as the complex symbiotic fungus-host interaction, to further illuminate the hidden development of belowground truffle fruit bodies.

Article: Mycorrhiza

Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes. F Rineau, H Lmalem, D Ahren, F Shah, T Johansson, L Coninx, J Ruytinx, … Mycorrhiza, 1-14


Hydrophobins are small secreted proteins that are present as several gene copies in most fungal genomes. Their properties are now well understood: they are amphiphilic and assemble at hydrophilic/hydrophobic interfaces. However, their physiological functions remain largely unexplored, especially within mycorrhizal fungi. In this study, we identified hydrophobin genes and analysed their distribution in eight mycorrhizal genomes. We then measured their expression levels in three different biological conditions (mycorrhizal tissue vs. free-living mycelium, organic vs. mineral growth medium and aerial vs. submerged growth). Results confirmed that the size of the hydrophobin repertoire increased in the terminal orders of the fungal evolutionary tree. Reconciliation analysis predicted that in 41% of the cases, hydrophobins evolved from duplication events. Whatever the treatment and the fungal species, the pattern of expression of hydrophobins followed a reciprocal function, with one gene much more expressed than others from the same repertoire. These most-expressed hydrophobin genes were also among the most expressed of the whole genome, which suggests that they play a role as structural proteins. The fine-tuning of the expression of hydrophobin genes in each condition appeared complex because it differed considerably between species, in a way that could not be explained by simple ecological traits. Hydrophobin gene regulation in mycorrhizal tissue as compared with free-living mycelium, however, was significantly associated with a calculated high exposure of hydrophilic residues.

Article: Phytopathology

Can oak powdery mildew severity be explained by indirect effects of climate on the composition of the Erysiphe pathogenic complex? B Marçais, D Piou, D Dezette, ML Desprez-Loustau Phytopathology


Coinfection by several pathogens is increasingly recognized as an important feature in the epidemiology and evolution of plant fungal pathogens. Oak mildew is induced by 2 closely related Erysiphe invasive species E. alphitoides and E. quercicola, which differ in their mode of overwintering. We investigated how climate influences the co-occurrence of the 2 species in oak young stands and whether this is important for the disease epidemiology We studied the frequency of flag-shoots (i.e. shoots developing from infected buds, usually associated with E. quercicola) in 95 oak regenerations over a 6 year period.. Additionally, in 2012 and 2013, the oak mildew severity and the 2 Erysiphe species relative frequencies were determined both in spring and in autumn in 51 regenerations and 43 one-year-old plantations of oaks. Both the frequency of flag-shoots and the proportion of Erysiphe lesions with E. quercicola presence were related to climate. We showed that survival of E. quercicola was improved after mild winters, with increase of both the flag-shoot frequency and the proportion of Erysiphe lesions with E. quercicola presence in spring. However, disease severity was not related to any complementarity effect between the two Erysiphe species causing oak powdery mildew. By contrast, increased E. alphitoides prevalence in spring was associated with higher oak mildew severity in autumn. Our results point out the critical role of between season transmission and primary inoculum to explain disease dynamics which could be significant in a climate warming context.

Article: Fungal Biology

Photoreceptors in the dark: a functional white collar-like complex and other putative light-sensing components encoded by the genome of the subterranean fungus Tuber melanosporumR Gerace, B Montanini, M Proietto, E Levati, C De Luca, A Brenna, … Fungal Biology


Light is perceived and transduced by fungi, where it modulates processes as diverse as growth and morphogenesis, sexual development and secondary metabolism. A special case in point is that of fungi with a subterranean, light-shielded habitat such as Tuber spp. Using as reference the genome sequence of the black truffle Tuber melanosporum, we employed sequence prediction tools and expression data to gain insight on the photoreceptor systems expressed by this hypogeous ectomycorryzal fungus. These include a chromophore-less opsin preferentially expressed in fruiting bodies, a putative red light-sensing phytochrome that is not expressed at detectable levels in any of the examined developmental conditions, and a nearly canonical two-component (WC-1/WC-2) photoreceptor system similar to the Neurospora white collar complex. The latter is expressed at relatively high levels throughout the different developmental stages of T. melanosporum, except for sexual stage fruiting bodies where it is down-regulated. Various evidences, including the growth arrest phenotype elicited by blue light and the ability of a chimeric Tuber/Neurospora WC-1 protein to complement a N. crassa wc-1koblind strain suggest that the Tuber white collar complex is likely functional and capable of responding to blue-light. The other putative photoreceptor components we have identified in the T. melanosporum genome, especially the chromophore-less opsin and the likely non-functional phytochrome, may represent the signatures of adaptation to a hypogeous (light-shielded) lifestyle.

Article: Current Biology

Regulation of Differentiation of Nitrogen-Fixing Bacteria by Microsymbiont Targeting of Plant Thioredoxin s1 CW Ribeiro, F Baldacci-Cresp, O Pierre, M Larousse, S Benyamina, … Current Biology


  • The plant thioredoxin Trx s1 is targeted to nitrogen-fixing bacteroids
  • Trx s1 is necessary for bacteroid differentiation
  • Trx s1 controls the redox state of nodule-specific cysteine-rich peptides (NCRs)
  • Trx s1 regulates the cytotoxic activity of NCR335 in Sinorhizobium meliloti


Legumes associate with rhizobia to form nitrogen (N2)-fixing nodules, which is important for plant fitness [ 1, 2 ]. Medicago truncatula controls the terminal differentiation of Sinorhizobium melilotiinto N2-fixing bacteroids by producing defensin-like nodule-specific cysteine-rich peptides (NCRs) [ 3, 4 ]. The redox state of NCRs influences some biological activities in free-living bacteria, but the relevance of redox regulation of NCRs in planta is unknown [ 5, 6 ], although redox regulation plays a crucial role in symbiotic nitrogen fixation [ 7, 8 ]. Two thioredoxins (Trx), Trx s1 and s2, define a new type of Trx and are expressed principally in nodules [ 9 ]. Here, we show that there are four Trx s genes, two of which, Trx s1 and s3, are induced in the nodule infection zone where bacterial differentiation occurs. Trx s1 is targeted to the symbiosomes, the N2-fixing organelles. Trx s1 interacted with NCR247 and NCR335 and increased the cytotoxic effect of NCR335 in S. meliloti. We show that Trx s silencing impairs bacteroid growth and endoreduplication, two features of terminal bacteroid differentiation, and that the ectopic expression of Trx s1 in S. meliloti partially complements the silencing phenotype. Thus, our findings show that Trx s1 is targeted to the bacterial endosymbiont, where it controls NCR activity and bacteroid terminal differentiation. Similarly, Trxs are critical for the activation of defensins produced against infectious microbes in mammalian hosts. Therefore, our results suggest the Trx-mediated regulation of host peptides as a conserved mechanism among symbiotic and pathogenic interactions.

Article: Applied and Environmental Microbiology

Mineral type and tree species determine the functional and taxonomic structure of forest soil bacterial communities Y Colin, O Nicolitch, MP Turpault, S Uroz Applied and Environmental Microbiology, AEM. 02684-16


Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with varying chemistries (i.e., obsidian, apatite and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards and Corsican pine) for 2.5 years to determine the relative impact of mineralogy and mineral weatherability on the taxonomic and functional diversity of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that, after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.

IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil mineralogy influences the diversity, structure and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivation-dependent and -independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.