Third french-german meeting on plant-microbe interactions

Membres du comité d'organisation scientifique JFM6

Glomeromycotina: what is a species and why should we care?

International audience; A workshop at the recent International Conference on Mycorrhiza was focused on species recognition in Glomeromycotina and parts of their basic biology that define species. The workshop was motivated by the paradigm-shifting evidence derived from genomic data for sex and for the lack of heterokaryosis, and by published exchanges in Science that were based on different species concepts and have led to differing views of dispersal and endemism in these fungi. Although a lively discussion ensued, there was general agreement that species recognition in the group is in need of more attention, and that many basic assumptions about the biology of these important fungi includ…

Les Champignons sous la loupe des méthodes criminalistiques. Festival des Spores 2019

National audience

Evaluation of the performance of MALDI-TOF-MS biotyping to identify Gigasporaceae

Développement d’une méthode d’identification des champignons mycorhiziens à arbuscules par spectrométrie de masse. (MALDI- TOF-MS)

International audience

Mitochondrial genotyping of isolates of the arbuscular mycorrhizal fungus "Glomus intraradices" from the isolate collection of the International Bank of Glomeromycota

International audience; The culture collection of the International Bank of Glomeromycota (BEG) provides an important service to scientific community and industry by acting as a repository for well-defined AMF isolates which are made available to the public. The most widely-used species has been referred to as "Glomus intraradices", and was recently renamed Rhizophagus irregularis. This species has emerged as a model organism for experimental research and is the subject of the first AMF genome to be sequenced. The only genetic marker that can currently be used to distinguish strains of R. irregularis in field settings is the mitochondrial large subunit (mtLSU). In addition, genetically dist…

Changements à court terme de la composition des communautés de champignons mycorhiziens à arbuscules et des populations de Rhizophagus irregularis en fonction des pratiques culturales

La mycorhize à arbuscule a un important potentiel d’amélioration de la nutrition minérale des plantes, fort utile dans le contexte agricole. Cependant, certaines pratiques culturales sont connues pour avoir un effet néfaste sur la diversité des champignons mycorhiziens à arbuscules (Glomeromycètes). Il est donc nécessaire de mieux comprendre les dynamiques de leurs communautés et populations pour pouvoir préserver et gérer le potentiel symbiotique. Dans cette étude, nous avons étudié les effets séparés et conjoints du retournement du sol et des fertilisations phosphatée et azotée du sol sur la structure des communautés des Glomeromycètes et sur les populations de l’espèce Rhizophagus irregu…

Diversity of arbuscular mycorrhizal fungi (Glomeromycota) in european soils analysed by pyrosequencing

Arbuscular mycorrhiza provides essential ecosystem functions in natural and humandominated ecosystems. Generally human activities like agriculture seem to have a negative effect on diversity of arbuscular mycorrhizal fungi (AMF), and thus on ecosystem functioning. New sequencing technologies now allow to assess AMF diversity on a much larger scale than previously. In the context of the European project EcoFINDERS, five Long-Term Observatories across Europe with different soil management have been studied. The diversity of AMF in these soils is analyzed by pyrosequencing, using the ITS (rDNA Internal Transcribed Spacers) as marker, which were recently determined as the standard barcoding gen…

Is this fungus everywhere? Elucidating the genetic structure of populations of the arbuscular mycorrhizal fungus Glomus intraradices

Arbuscular mycorrhizal fungi (Glomeromycota) are ubiquitous mutualistic associates of plants. Only relatively recently it has become possible to study the population biology of some species of these fungi. The model organism Glomus intraradices has been found across an extremely wide range of habitats and succession stages on different continents using molecular identification approaches. We used regions of the mitochondrially-encoded rDNA as novel molecular markers to resolve the intraspecies structure of G. intraradices and found a high diversity of mitochondrial haplotypes among isolates from all over the world. These markers for the first time also offer to genotype G. intraradices dire…

RPB1 as a marker gene to analyze communities of arbuscular mycorrhizal fungi (Glomeromycota)

The influence of agricultural practice on the diversity of Arbuscular mycorrhizal fungi (AMF, Glomeromycota) continues to be an important research question as these mutualistic symbionts are known to improve plant growth and soil quality. To this day, studies of community diversity in AMF have exclusively been based on nuclear ribosomal gene regions, such as the small and large subunits and the ITS region. In the Glomeromycota, these regions show high intra-organism polymorphism, which can seriously complicate interpretation of diversity data. We chose the rpb1 gene as an alternative marker as this putative single-copy gene has been shown to be monomorphic within fungal isolates but shows a…

Molecular studies of diversity of populations of arbuscular mycorrhizal fungi

National audience; Arbuscular mycorrhiza fungi (AMF) which form a mutualistic symbiosis with most terrestrial plants are not only important for natural ecosystems, but also for agricultural production. The aim of this study is to characterize fungal populations at different geographic scales in order to better understand the processes influencing AMF taxonomic and functional diversity and to determine the environmental factors affecting AMF populations, especially in the context of agricultural management. The mitochondrial large subunit gene of ribosomal RNA will be used as molecular marker to resolve population structure of Rhizophagus irregularis (formerly known as Glomus intraradices). …

Regional-scale analysis of arbuscular mycorrhizal fungi: the case of Burgundy vineyards

SPE IPM INRA UB; Aim : To improve knowledge of arbuscular fungal communities for a sustainable management in vineyards. Methods and results : In 16 plots across Burgundy under contrasted soil properties and agricultural practices, we assessed arbuscular mycorrhizal fungal (AMF) diversity in vine roots, using pyrosequencing of ribosomal Internal Transcribed Spacers (ITS). AMF sequences could be retrieved from all plots across Burgundy, both in organic and in conventional vineyards with high chemical inputs. Sequences from the survey were almost exclusively affiliated to molecular taxa in the Glomerales, including six “core species” found in all plots, corresponding to 77% of all sequences, s…

Microbial metacommunity: a METABAR coding approach

Microbial metacommunity: a METABAR coding approach. 2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens)

Ecological network analysis reveals the inter-connection between soil biodiversity and ecosystem function as affected by land use across Europe

Soil organisms are considered drivers of soil ecosystem services (primary productivity, nutrient cycling, carbon cycling, water regulation) associated with sustainable agricultural production. Soil biodiversity was highlighted in the soil thematic strategy as a key component of soil quality. The lack of quantitative standardised data at a large scale has resulted in poor understanding of how soil biodiversity could be incorporated into legislation for the protection of soil quality. In 2011, the EcoFINDERS (FP7) project sampled 76 sites across 11 European countries, covering five biogeographical zones (Alpine, Atlantic, Boreal, Continental and Mediterranean) and three land-uses (arable, gra…

Effects of mowing on fungal endophytes and arbuscular mycorrhizal fungi in subalpine grasslands

International audience; In French subalpine grasslands, cessation of mowing promotes dominance of Festuca paniculata, which alters plant diversity and ecosystem functioning. One of the mechanisms underpinning such effects may be linked to simultaneous changes in the abundance of fungal symbionts such as endophytes and arbuscular mycorrhizal fungi. In field conditions, mowing reduced the abundance of the endophyte Neotyphodium sp. in leaves of F. paniculata by a factor of 6, and increased mycorrhizal densities by a factor of 15 in the soil. In greenhouse experiments, the mycorrhizal colonization of Trifolium pratense and Allium porrum increased 3- fold and 3.8- fold respectively in mown vs u…

Tracing of the inoculated arbuscular mycorrhizal fungal strain Glomus intraradices BEG140 in a field experiment over 3 years

Single-Spore Extraction for Genetic Analyses of Arbuscular Mycorrhizal Fungi

International audience; Biomass of arbuscular mycorrhizal fungi (AMF, Glomeromycota) is often only available in small quantities as these fungi are obligate biotrophs and many species are difficult to cultivate under controlled conditions. Here, I describe a simple, efficient approach to produce crude extracts from single or a small number of spores that can be used for genotyping AMF.

Discontinuities in morphospace vs. reproductive isolation: species descriptions in the Glomeromycota

Elucidating the population structure of the ubiquitous arbuscular mycorrhizal fungal species Rhizophagus irregularis: implications for fungal community assembly

Exploring the Genome of glomeromycotan fungi

Chapitre 1; International audience; All fungi forming a mutualistic symbiosis with plant roots called arbuscular mycorrhiza were formerly grouped together in one order, the Glomales, placed in the Zygomycota (Morton 1993). Based on molecular analyses suggestingthat arbuscular mycorrhizal fungi should be separated from other fungal taxa, they were transferred a decade ago to the Glomeromy-cota , a new phylum created specifically for them (Schu¨ ssler et al. 2001). Whilst members of this monophyletic group originated from the same common ancestor as the Ascomycota and Basidiomycota, they have no obvious affinity to other major extant phylogenetic groups in the kingdom Fungi (James et al. 2006) …

Un code-barre pour les champignons - La détermination d'un gène type pour tous les champignons va faciliter les analyses de biodiversité à large échelle

Le 17 avril 2012 est paru dans la revue internationale "Proceedings of the Academy of the Sciences of the USA" (PNAS) un article avec le titre "Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi". Ce travail dirigé par le Dr. Conrad Schoch du National Center for Biotechnology Information (USA) est le fruit du travail d'un consortium de chercheurs mycologistes, le "Fungal Barcoding Consortium" de près de 160 scientifiques de 74 laboratoires (25 pays) différents dont deux laboratoires français : le Muséum National d’Histoire Naturelle à Paris et l'UMR 1347 Agroécologie (INRA/AgroSup/Université de Bourgogne) de Dijon. Ce travail a permis de d…

Divisio/Phylum Glomeromycota

SPE IPM Chapitre 11

Etude de la structure génétique des populations du champignon mycorhizogène à arbuscules Glomus intraradices. S’agit-il d’un champignon ubiquiste?

The Largest Subunit of RNA Polymerase II as a New Marker Gene to Study Assemblages of Arbuscular Mycorrhizal Fungi in the Field

Due to the potential of arbuscular mycorrhizal fungi (AMF, Glomeromycota) to improve plant growth and soil quality, the influence of agricultural practice on their diversity continues to be an important research question. Up to now studies of community diversity in AMF have exclusively been based on nuclear ribosomal gene regions, which in AMF show high intra-organism polymorphism, seriously complicating interpretation of these data. We designed specific PCR primers for 454 sequencing of a region of the largest subunit of RNA polymerase II gene, and established a new reference dataset comprising all major AMF lineages. This gene is known to be monomorphic within fungal isolates but shows an…

Persistence and effectiveness of Rhizophagus irregularis isolate IR27 on the fruit production of jujube trees in a semi-arid field condition

International audience

Mycorhization en viticulture : état des lieux et étude de l’intérêt au vignoble

SPEIPMUBINRA; Mycorhization en viticulture : état des lieux et étude de l’intérêt au vignoble. 13. Journée Technique du CIVB (Conseil Interprofessionnel du Vin de Bordeaux)

A multigene phylogenetic study of Tuber aestivum/uncinatum

International audience; Tuber aestivum and Tuber uncinatum share a complicated common history from a taxonomic point of view. Indeed, different previous studies have shown contradictory conclusions. For some authors, Tuber aestivum and Tuber uncinatum are one species and for others, they are two different species. In those studies, few phylogenetic markers have been used, mainly the ITS marker. However, it has become the standard in phylogenetic studies to combine several genes to obtain a more robust phylogenetic representation. In our study, we used 9 molecular markers and sampled fruiting bodies from different European populations including 14 Tuber “aestivum” types and 14 “uncinatum” ty…

Importance of dispersal and thermal environment for mycorrhizal communities: lessons from Yellowstone National Park

International audience; The relative importance of dispersal and niche restrictions remains a controversial topic in community ecology, especially for microorganisms that are often assumed to be ubiquitous. We investigated the impact of these factors for the community assembly of the root-symbiont arbuscular mycorrhizal fungi (AMF) by sampling roots from geothermal and nonthermal grasslands in Yellowstone National Park (YNP), followed by sequencing and RFLP of AMF ribosomal DNA. With the exception of an apparent generalist RFLP type closely related to Glomus intraradices, a distance-based redundancy analysis indicated that the AMF community composition correlated with soil pH or pH-driven c…

Emerging mutualisms: fungal endophytes and their relationships with mycorrhizal fungi

National audience; De nombreuses maladies émergentes apparaissent qui sont dues à des champignons, aussi bien chez les plantes, les animaux que chez l’homme. Il est donc important de comprendre les mécanismes à l’origine de ces maladies, et la biologie évolutive fournit un cadre théorique indispensable, en particulier pour comprendre l’adaptation des pathogènes aux nouveaux environnements ou aux nouveaux hôtes.

Appendix B. Plant species observed within the three nonthermal grasslands.

Plant species observed within the three nonthermal grasslands.

Appendix J. Phylogenetic tree of Paraglomus based on ITS 1, 5.85 rDNA, and ITS 2.

Phylogenetic tree of Paraglomus based on ITS 1, 5.85 rDNA, and ITS 2.

Appendix D. Presence of RFLP types in the five geothermal and three nonthermal grasslands sampled.

Presence of RFLP types in the five geothermal and three nonthermal grasslands sampled.

Appendix F. Phylogenetic tree of Glomus group A based on ITS 1, 5.85 rDNA, and ITS 2.

Phylogenetic tree of Glomus group A based on ITS 1, 5.85 rDNA, and ITS 2.

Appendix E. RFLP species accumulation curves for the geothermal and non-thermal grasslands.

RFLP species accumulation curves for the geothermal and non-thermal grasslands.

Appendix G. Phylogenetic tree of Scutellospora based on 18S.

Phylogenetic tree of Scutellospora based on 18S.

Appendix C. Ribotype name, their closest BLASTN match, fragment sizes with Mbo1 and Hinf1 digestion, and accession numbers.

Ribotype name, their closest BLASTN match, fragment sizes with Mbo1 and Hinf1 digestion, and accession numbers.

Appendix I. Phylogenetic tree of Archaeospora based on ITS 1, 5.85 rDNA, and ITS 2.

Phylogenetic tree of Archaeospora based on ITS 1, 5.85 rDNA, and ITS 2.

Appendix H. Phylogenetic tree of Acaulospora based on ITS 1, 5.85 rDNA, and ITS 2.

Phylogenetic tree of Acaulospora based on ITS 1, 5.85 rDNA, and ITS 2.

Appendix A. GPS coordinates, harvest dates, soil temperature measured, and PCR (polymerase chain reaction) success of the five geothermal and three nonthermal sites.

GPS coordinates, harvest dates, soil temperature measured, and PCR (polymerase chain reaction) success of the five geothermal and three nonthermal sites.