Mediation of plant–mycorrhizal interaction by a lectin receptor-like kinase J Labbé, W Muchero, O Czarnecki, J Wang, X Wang, AC Bryan, K Zheng, … Nature plants 5 (7), 676-680

Abstract

The molecular mechanisms underlying mycorrhizal symbioses, the most ubiquitous and impactful mutualistic plant–microbial interaction in nature, are largely unknown. Through genetic mapping, resequencing and molecular validation, we demonstrate that a G-type lectin receptor-like kinase (lecRLK) mediates the symbiotic interaction between Populus and the ectomycorrhizal fungus Laccaria bicolor. This finding uncovers an important molecular step in the establishment of symbiotic plant–fungal associations and provides a molecular target for engineering beneficial mycorrhizal relationships.

SlZRT2 encodes a ZIP family Zn transporter with dual localization in the ectomycorrhizal fungus Suillus luteusL Coninx, N Smisdom, A Kohler, N Arnauts, M Ameloot, F Rineau, … Frontiers in microbiology 10

Ectomycorrhizal (ECM) fungi are important root symbionts of trees, as they can have significant effects on the nutrient status of plants. In polluted environments, particular ECM fungi can protect their host tree from Zn toxicity by restricting the transfer of Zn while securing supply of essential nutrients. However, mechanisms and regulation of cellular Zn homeostasis in ECM fungi are largely unknown, and it remains unclear how ECM fungi affect the Zn status of their host plants. This study focuses on the characterization of a ZIP (Zrt/IrtT-like protein) transporter, SlZRT2, in the ECM fungus Suillus luteus, a common root symbiont of young pine trees. SlZRT2 is predicted to encode a plasma membrane-located Zn importer. Heterologous expression of SlZRT2 in yeast mutants with impaired Zn uptake resulted in a minor impact on cellular Zn accumulation and growth. The SlZRT2 gene product showed a dual localization and was detected at the plasma membrane and perinuclear region. S. luteus ZIP-family Zn uptake transporters did not show the potential to induce trehalase activity in yeast and to function as Zn sensors. In response to excess environmental Zn, gene expression analysis demonstrated a rapid but minor and transient decrease in SlZRT2 transcript level. In ECM root tips, the gene is upregulated. Whether this regulation is due to limited Zn availability at the fungal–plant interface or to developmental processes is unclear. Altogether, our results suggest a function for SlZRT2 in cellular Zn redistribution from the ER next to a putative role in Zn uptake in S. luteus.

Plant Glutathione Transferases: Diverse, Multi-Tasking Enzymes with Yet-to-Be Discovered Functions J Csiszár, A Hecker, NE Labrou, P Schröder, DE Riechers Frontiers in plant science 10, 1304

Comparative transcriptomics of Gymnosporangium spp. teliospores reveals a conserved genetic program at this specific stage of the rust fungal life cycle SQ Tao, B Cao, E Morin, YM Liang, S Duplessis BMC genomics 20 (1), 723

Abstract

Background

Gymnosporangium spp. are fungal plant pathogens causing rust disease and most of them are known to infect two different host plants (heteroecious) with four spore stages (demicyclic). In the present study, we sequenced the transcriptome of G. japonicum teliospores on its host plant Juniperus chinensis and we performed comparison to the transcriptomes of G. yamadae and G. asiaticum at the same life stage, that happens in the same host but on different organs.

Results

Functional annotation for the three Gymnosporangium species showed the expression of a conserved genetic program with the top abundant cellular categories corresponding to energy, translation and signal transduction processes, indicating that this life stage is particularly active. Moreover, the survey of predicted secretomes in the three Gymnosporangiumtranscriptomes revealed shared and specific genes encoding carbohydrate active enzymes and secreted proteins of unknown function that could represent candidate pathogenesis effectors. A transcript encoding a hemicellulase of the glycoside hydrolase 26 family, previously identified in other rust fungi, was particularly highly expressed suggesting a general role in rust fungi. The comparison between the transcriptomes of the three Gymnosporangium spp. and selected Pucciniales species in different taxonomical families allowed to identify lineage-specific protein families that may relate to the biology of teliospores in rust fungi. Among clustered gene families, 205, 200 and 152 proteins were specifically identified in G. japonicum, G. yamadaeand G. asiaticum, respectively, including candidate effectors expressed in teliospores.

Conclusions

This comprehensive comparative transcriptomics study of three Gymnosporangium spp. identified gene functions and metabolic pathways particularly expressed in teliospores, a stage of the life cycle that is mostly overlooked in rust fungi. Secreted protein encoding transcripts expressed in teliospores may reveal new candidate effectors related to pathogenesis. Although this spore stage is not involved in host plant infection but in the production of basidiospores infecting plants in the Amygdaloideae, we speculate that candidate effectors may be expressed as early as the teliospore stage for preparing further infection by basidiospores.

At the nexus of three kingdoms: the genome of the mycorrhizal fungus Gigaspora margaritaprovides insights into plant, endobacterial and fungal interactions F Venice, S Ghignone, A Salvioli di Fossalunga, J Amselem, M Novero, … Environmental Microbiology

Summary

As members of the plant microbiota, arbuscular mycorrhizal fungi (AMF, Glomeromycotina) symbiotically colonize plant roots. AMF also possess their own microbiota, hosting some uncultivable endobacteria. Ongoing research has revealed the genetics underlying plant responses to colonization by AMF, but the fungal side of the relationship remains in the dark. Here, we sequenced the genome of Gigaspora margarita, a member of the Gigasporaceae in an early diverging group of the Glomeromycotina. In contrast to other AMF, G. margarita may host distinct endobacterial populations and possesses the largest fungal genome so far annotated (773.104 Mbp), with more than 64% transposable elements. Other unique traits of the G. margaritagenome include the expansion of genes for inorganic phosphate metabolism, the presence of genes for production of secondary metabolites and a considerable number of potential horizontal gene transfer events. The sequencing of G. margarita genome reveals the importance of its immune system, shedding light on the evolutionary pathways that allowed early diverging fungi to interact with both plants and bacteria.

Soil temperature and hydric potential influences the monthly variations of soil Tuber aestivum DNA in a highly productive orchard F Todesco, S Belmondo, Y Guignet, L Laurent, S Fizzala, F Le Tacon, … Scientific Reports 9 (1), 1-10

Abstract

Tuber aestivum, also known as the summer or Burgundy truffle, is an ectomycorrhizal Ascomycete associated with numerous trees and shrubs. Its life cycle occurs in the soil, and thus soil parameters such as temperature and water availability could influence it. T. aestivumcultivation has started in several countries, but ecological and agronomic requirements for the establishment and management of orchards are largely unknown. The aims of this work were: 1) to design a specific qPCR protocol using genomic data to trace and quantify T. aestivum DNA in the soil; and 2) to assess the monthly soil DNA dynamic according to soil parameters (i.e. soil hydric potential and temperature) in this orchard. The study was conducted in a highly productive T. aestivum orchard (hazels, oaks, pines, lime and hornbeam). The production started five years after the plantation and then increased exponentially to reach a maximum of 320 kg/ha in 2017. The soil hydric potential and temperature partially explained the monthly T. aestivum soil DNA variability. The data presented here offer new insights into T. aestivum ecology and cultivation.

le 27 septembre, l’unité de mycologie accueillera Guillaume Bilodeau, un collègue scientifique du Canadian Food Inspection Agency qui travaille principalement sur l’identification et la caractérisation des champignons phytopathogènes (https://www.researchgate.net/profile/Guillaume_Bilodeau).

Guillaume proposera un séminaire : “Détection / identification d’agents phytopathogènes réglementés utilisant des données de génomes et métagénomique ”

Le séminaire aura lieu en nos locaux de Pixérécourt, Malzéville, le 27 à 14h00.

The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata D Armaleo, O Müller, F Lutzoni, ÓS Andrésson, G Blanc, HB Bode, … BMC genomics 20 (1), 60

Abstract

Background

Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first parallel genomic analysis of the mycobiont Cladonia grayi and of its green algal photobiont Asterochloris glomerata. We focus on genes/predicted proteins of potential symbiotic significance, sought by surveying proteins differentially activated during early stages of mycobiont and photobiont interaction in coculture, expanded or contracted protein families, and proteins with differential rates of evolution.

Results

A) In coculture, the fungus upregulated small secreted proteins, membrane transport proteins, signal transduction components, extracellular hydrolases and, notably, a ribitol transporter and an ammonium transporter, and the alga activated DNA metabolism, signal transduction, and expression of flagellar components. B) Expanded fungal protein families include heterokaryon incompatibility proteins, polyketide synthases, and a unique set of G-protein α subunit paralogs. Expanded algal protein families include carbohydrate active enzymes and a specific subclass of cytoplasmic carbonic anhydrases. The alga also appears to have acquired by horizontal gene transfer from prokaryotes novel archaeal ATPases and Desiccation-Related Proteins. Expanded in both symbionts are signal transduction components, ankyrin domain proteins and transcription factors involved in chromatin remodeling and stress responses. The fungal transportome is contracted, as are algal nitrate assimilation genes. C) In the mycobiont, slow-evolving proteins were enriched for components involved in protein translation, translocation and sorting.

Conclusions

The surveyed genes affect stress resistance, signaling, genome reprogramming, nutritional and structural interactions. The alga carries many genes likely transferred horizontally through viruses, yet we found no evidence of inter-symbiont gene transfer. The presence in the photobiont of meiosis-specific genes supports the notion that sexual reproduction occurs in Asterochloriswhile they are free-living, a phenomenon with implications for the adaptability of lichens and the persistent autonomy of the symbionts. The diversity of the genes affecting the symbiosis suggests that lichens evolved by accretion of many scattered regulatory and structural changes rather than through introduction of a few key innovations. This predicts that paths to lichenization were variable in different phyla, which is consistent with the emerging consensus that ascolichens could have had a few independent origins.

Ascoma genotyping and mating type analyses of mycorrhizas and soil mycelia of Tuber borchii in a truffle orchard established by mycelial inoculated plants P Leonardi, C Murat, F Puliga, M Iotti, A Zambonelli Environmental Microbiology

Summary

Tuber borchii (the Bianchetto truffle) is a heterothallic Ascomycete living in symbiotic association with trees and shrubs. Maternal and paternal genotype dynamics have already been studied for the black truffles Tuber melanosporumand Tuber aestivum but not yet for T. borchii. In this study, we analysed maternal and paternal genotypes in the first truffle orchard realized with plants inoculated with five different T. borchii mycelia. Our aims were to test the persistence of the inoculated mycelia, if maternal and/or paternal genotypes correspond to inoculated mycelia and to assess the hermaphroditism of T. borchii. The mating type of each isolate as well as those of mycorrhizas, ascomata and extraradical soil mycelia was determined. Moreover, simple sequence repeat (SSR) profiles of maternal and paternal genotypes were assessed in 18 fruiting bodies to investigate the sexual behaviour of this truffle. The maternal genotypes of the fruiting bodies corresponded to those of the inoculated mycelia with only two exceptions. This confirmed that the inoculated mycelia persisted 9 years after plantation. As regards paternal partner, only two had the same genotype as those of the inoculated mycelia, suggesting hermaphroditism. Most of the new paternal genotypes originated from a recombination of those of inoculated mycelia.

Multi‐omic analyses of exogenous nutrient bag decomposition by the black morel Morchella importuna reveal sustained carbon acquisition and transferring H Tan, A Kohler, R Miao, T Liu, Q Zhang, B Zhang, L Jiang, Y Wang, L Xie, … Environmental microbiology

Summary

The black morel (Morchella importuna Kuo, O’Donnell and Volk) was once an uncultivable wild mushroom, until the development of exogenous nutrient bag (ENB), making its agricultural production quite feasible and stable. To date, how the nutritional acquisition of the morel mycelium is fulfilled to trigger its fruiting remains unknown. To investigate the mechanisms involved in ENB decomposition, the genome of a cultivable morel strain (M. importunaSCYDJ1‐A1) was sequenced and the genes coding for the decay apparatus were identified. Expression of the encoded carbohydrate‐active enzymes (CAZymes) was then analyzed by metatranscriptomics and metaproteomics in combination with biochemical assays. The results show that a diverse set of hydrolytic and redox CAZymes secreted by the morel mycelium is the main force driving the substrate decomposition. Plant polysaccharides such as starch and cellulose present in ENB substrate (wheat grains plus rice husks) were rapidly degraded, whereas triglycerides were accumulated initially and consumed later. ENB decomposition led to a rapid increase in the organic carbon content in the surface soil of the mushroom bed, which was thereafter consumed during morel fruiting. In contrast to the high carbon consumption, no significant acquisition of nitrogen was observed. Our findings contribute to an increasingly detailed portrait of molecular features triggering morel fruiting.

New insights into black truffle biology: discovery of the potential connecting structure between a Tuber aestivum ascocarp and its host root A Deveau, P Clowez, F Petit, JP Maurice, F Todesco, C Murat, M Harroué, … Mycorrhiza 29 (3), 219-226

Abstract

According to isotopic labeling experiments, most of the carbon used by truffle (Tuber sp.) fruiting bodies to develop underground is provided by host trees, suggesting that trees and truffles are physically connected. However, such physical link between trees and truffle fruiting bodies has never been observed. We discovered fruiting bodies of Tuber aestivum adhering to the walls of a belowground quarry and we took advantage of this unique situation to analyze the physical structure that supported these fruiting bodies in the open air. Observation of transversal sections of the attachment structure indicated that it was organized in ducts made of gleba-like tissue and connected to a network of hyphae traveling across soil particles. Only one mating type was detected by PCR in the gleba and in the attachment structure, suggesting that these two organs are from maternal origin, leaving open the question of the location of the opposite paternal mating type.

Are bacteria responsible for aroma deterioration upon storage of the black truffle Tuber aestivum: A microbiome and volatilome study M Vahdatzadeh, A Deveau, R Splivallo Food Microbiology, 103251

Abstract

Truffle fungi, luxurious food items with captivating aromas, are highly valued in the culinary world. However, truffles are perishable and their aroma undergoes deep changes upon storage. Additionally, truffle aroma might be partially derived from microbes. Hence, we investigated here the influence of storage on two factors, namely the volatile profile and bacterial community composition in the black truffle Tuber aestivum. The possible linkage among those factors was further explored.

Our results demonstrate important changes in the volatile profiles of truffles over nine days of storage at room temperature. In the same time frame, dominant bacterial classes characteristic of fresh truffles (α-Proteobacteria, β-Proteobacteria, and Sphingobacteria classes) were gradually replaced by food spoilage bacteria (γ-Proteobacteria and Bacilli classes). Freshness and spoilage volatile markers (i.e. dimethyl sulfide (DMS), butan-2-one, 2- and, 2- and 3-methylbutan-1-ol, and 2-phenylethan-1-ol) were identified. Lastly, network analysis showed correlations between those markers and specific bacterial classes typical of fresh and spoiled truffles.

Overall, our results demonstrate the profound effect of storage on the aroma and bacterial community composition of truffles and highlight how the gradual replacement of the commensal microbiome by spoilage microbes mirrors shifts in aroma profile and the possible loss of fresh truffle flavor.

Increasing access to microfluidics for studying fungi and other branched biological structures LJ Millet, J Aufrecht, J Labbé, J Uehling, R Vilgalys, ML Estes, … Fungal Biology and Biotechnology 6 (1), 1

Background

Microfluidic systems are well-suited for studying mixed biological communities for improving industrial processes of fermentation, biofuel production, and pharmaceutical production. The results of which have the potential to resolve the underlying mechanisms of growth and transport in these complex branched living systems. Microfluidics provide controlled environments and improved optical access for real-time and high-resolution imaging studies that allow high-content and quantitative analyses. Studying growing branched structures and the dynamics of cellular interactions with both biotic and abiotic cues provides context for molecule production and genetic manipulations. To make progress in this arena, technical and logistical barriers must be overcome to more effectively deploy microfluidics in biological disciplines. A principle technical barrier is the process of assembling, sterilizing, and hydrating the microfluidic system; the lack of the necessary equipment for the preparatory process is a contributing factor to this barrier. To improve access to microfluidic systems, we present the development, characterization, and implementation of a microfluidics assembly and packaging process that builds on self-priming point-of-care principles to achieve “ready-to-use microfluidics.”

Results

We present results from domestic and international collaborations using novel microfluidic architectures prepared with a unique packaging protocol. We implement this approach by focusing primarily on filamentous fungi; we also demonstrate the utility of this approach for collaborations on plants and neurons. In this work we (1) determine the shelf-life of ready-to-use microfluidics, (2) demonstrate biofilm-like colonization on fungi, (3) describe bacterial motility on fungal hyphae (fungal highway), (4) report material-dependent bacterial-fungal colonization, (5) demonstrate germination of vacuum-sealed Arabidopsis seeds in microfluidics stored for up to 2 weeks, and (6) observe bidirectional cytoplasmic streaming in fungi.

Conclusions

This pre-packaging approach provides a simple, one step process to initiate microfluidics in any setting for fungal studies, bacteria-fungal interactions, and other biological inquiries. This process improves access to microfluidics for controlling biological microenvironments, and further enabling visual and quantitative analysis of fungal cultures.

Jean Legeay soutiendra sa thèse intitulée:

“Ecologie des Oomycètes et champignons phytopathogènes dans les sols des forêts de Guyane Française : éclairages sur les relations spécifiques entre les communautés de Phytophthora et d’arbres”

dans la salle de conférence du bâtiment des SDAR le vendredi 21 juin à 9h00.

Résumé:

Les mécanismes expliquant le maintien de la diversité végétale dans les forêts tropicales sont mal connus. Une hypothèse particulièrement étudiée est l’hypothèse Janzen-Connell qui postule que ces mécanismes sont essentiellement causés par les interactions entre les plantes et leurs ennemis naturels, en particulier les organismes pathogènes. Dans cette thèse, nous nous sommes donc intéressés aux agents pathogènes présents dans les sols d’une forêt néotropicale guyanaise et à leur lien de spécificité avec les plantes. Dans le cas où l’hypothèse Janzen-Connell serait vérifiée, on peut s’attendre à ce que les plantes structurent les communautés de micro-organismes pathogènes. Nos travaux se sont focalisés sur les Oomycètes et en particulier les Phytophthora, pathogènes des arbres très importants, mais nous nous sommes aussi intéressés aux champignons pathogènes.
Ainsi, nous avons développé et comparé des jeux d’amorces PCR spécifiques des Phytophthora et des Péronosporomycètes afin d’étudier ces organismes par metabarcoding. Ces amorces ont ensuite servi à étudier la diversité des communautés de Phytophthora dans des échantillons de sols de deux sites forestiers de Guyane Française prélevés au pied d’arbres appartenant à 10 familles végétales. Une faible diversité a été retrouvée, avec seulement 8 espèces ou taxons en tout, et la très large dominance d’un complexe d’espèces Phytophthora heveae. La structuration par la plante-hôte de ces communautés est plutôt faible. Dans une étude complémentaire, nous avons analysé la diversité des Oomycètes (dont le genre Phytophthora) et des champignons pathogènes dans les sols et les litières de six plantations monospécifiques et au sein d’une forêt naturelle de Guyane Française. La structuration par l’hôte s’est avérée nulle pour les Oomycètes et faible, bien que significative, pour les champignons pathogènes. Enfin, nous n’avons pas réussi à déclencher expérimentalement des mortalités ou dépérissements par des Oomycètes sur le wacapou, une espèce d’arbre guyanaise, via des inoculations de sols de forêt.
Au final, les résultats de cette thèse ne supportent pas l’hypothèse selon laquelle les Oomycètes seraient d’importants acteurs du maintien de la diversité végétale dans les forêts tropicales. Par ailleurs, ils nous interrogent sur la faible diversité de ce groupe de microorganismes dans les sols et litières dans un hotspot de diversité végétale.