Impact des arbres génétiquement modifiés sur les communautés fongiques du sol

La constante augmentation des surfaces cultivées avec des plantes génétiquement modifiées (PGM) pose la question du risque environnemental qu'elles représentent. Afin de documenter cette problématique, nous avons dans un premier temps fait la synthèse de 20 années de recherche sur l'impact potentiel des cultures et des arbres génétiquement modifiés sur les champignons. L'analyse des publications scientifiques sur ce sujet montre que les conséquences des plantes transgéniques tolérantes aux herbicides et aux insectes ravageurs sur les champignons sont sous-étudiées alors qu'elles représentent la majorité des PGM cultivées dans le monde. Des changements significatifs affectant les champignons ont été relevés dans 18 études, dans lesquelles les PGM étudiées n'exprimaient pas de caractères transgéniques laissant présager un effet sur les champignons. En dépit du fait qu'elles sont commercialisées depuis 1996, le risque que les PGM représentent à l'heure actuelle pour les communautés fongiques ne peut être clairement défini à partir des données disponibles. L'impact potentiel de peupliers exprimant une résistance à la kanamycine a été évalué sur la communauté des ectomycorhizes (EM), après 8 années de déploiement au champ. Les mesures qualitatives et quantitatives de la diversité des EM n'ont pas mises en évidence de différence significative entre la structure de la communauté des EM provenant des peupliers témoins et celle provenant des peupliers transgéniques. Par contre, la communauté des EM identifée par l'analyse des extrémités racinaires était significativement différente de celle obtenue par le clonage de l'ADN fongique du sol. Ces deux stratégies d'échantillonnage, en les combinant, se sont révélées complémentaires pour une définition plus fine de la diversité des EM. Des travaux effectués en serre sur les conséquences de la surexpression de l'endochitinase dans les racines et les exsudats racinaires d'épinettes blanches transformées avec le gène ech42 n'ont pas détecté d'effet délétère sur la symbiose ectendomycorhizienne et la biomasse fongique du sol. De plus, les effets potentiels de ces épinettes transgéniques sur deux communautés fongiques provenant de sols forestiers ont été suivis pendant 8 mois. Les analyses ont montré que l'insertion dans le génome des épinettes blanches du gène ech42 et son expression n'affectaient pas de manière significative la biomasse, la diversité et la structure des communautés fongiques des deux sols analysés. Cette thèse a permis de faire le point sur l'impact des PGM sur les champignons et d'évaluer le risque que peuvent représenter différents types d'arbres génétiquement modifiés sur les champignons du sol

RocTest: A standardized method to assess the performance of root organ cultures in the propagation of arbuscular mycorrhizal fungi

Over the past three decades, root organ cultures (ROCs) have been the gold standard method for studying arbuscular mycorrhizal fungi (AMF) under in vitro conditions, and ROCs derived from various plant species have been used as hosts for AM monoxenic cultures. While there is compelling evidence that host identity can significantly modify AMF fitness, there is currently no standardized methodology to assess the performance of ROCs in the propagation of their fungal symbionts. We describe RocTest, a robust methodological approach that models the propagation of AMF in symbiosis with ROCs. The development of extraradical fungal structures and the pattern of sporulation are modeled using cumulative link mixed models and linear mixed models. We demonstrate functionality of RocTest by evaluating the performance of three species of ROCs (Daucus carota, Medicago truncatula, Nicotiana benthamiana) in the propagation of three species of AMF (Rhizophagus clarus, Rhizophagus irregularis, Glomus sp.). RocTest produces a simple graphical output to assess the performance of ROCs and shows that fungal propagation depends on the three-way interaction between ROC, AMF, and time. RocTest makes it possible to identify the best combination of host/AMF for fungal development and spore production, making it an important asset for germplasm collections and AMF research

The Impact of Reconstructed Soils Following Oil Sands Exploitation on Aspen and Its Associated Belowground Microbiome

Oil sands surface mining in the Athabasca region of northern Alberta (Canada) is a significant anthropogenic disturbance that resets boreal forest development and succession to early stages. During surface mining, the vegetation is cleared, the topsoil is salvaged, and the overburden (the layer of sand and clay in between the topsoil and the oil sands) is piled (see Fig. 2 in Audet et al.1 for an explanation of the land-reclamation procedure). After mining is finished, the landforms (composed of overburden and tailings sand) are capped with organic matter-rich soil covers made of either upland-derived forest floor-mineral mix (FFMM) or a lowland-derived peat-mineral mix (PMM)2. Alberta’s oil sands deposits represent an economically viable proven reserve of about 166 billion barrels of crude bitumen covering 142,200 km2 of land in the boreal forest3. Among the three oil sands deposits in Alberta (Peace River, Cold Lake and Athabasca areas), surface mining is only possible in the Athabasca region. The surface mineable area represents a total of 4,750 km2, with 895 km2 of land already disturbed. Ecosystems affected by oil sands surface mining lose their ecological functions due to the disappearance of above- and below- ground species. It is, therefore, crucial to reclaim these areas using strategies that provide the best conditions for site recolonization in order to quickly reestablish a self-sustaining and functioning ecosystem. Reclamation is the process of recovering ecosystem services through revegetation but not necessarily with the original species

Impact of Endochitinase-Transformed White Spruce on Soil Fungal Biomass and Ectendomycorrhizal Symbiosis▿

The impact of transgenic white spruce [Picea glauca (Moench) Voss] containing the endochitinase gene (ech42) on soil fungal biomass and on the ectendomycorrhizal fungi Wilcoxina spp. was tested using a greenhouse trial. The measured level of endochitinase in roots of transgenic white spruce was up to 10 times higher than that in roots of nontransformed white spruce. The level of endochitinase in root exudates of three of four ech42-transformed lines was significantly greater than that in controls. Analysis soil ergosterol showed that the amount of fungal biomass in soil samples from control white spruce was slightly larger than that in soil samples from ech42-transformed white spruce. Nevertheless, the difference was not statistically significant. The rates of mycorrhizal colonization of transformed lines and controls were similar. Sequencing the internal transcribed spacer rRNA region revealed that the root tips were colonized by the ectendomycorrhizal fungi Wilcoxina spp. and the dark septate endophyte Phialocephala fortinii. Colonization of root tips by Wilcoxina spp. was monitored by real-time PCR to quantify the fungus present during the development of ectendomycorrhizal symbiosis in ech42-transformed and control lines. The numbers of Wilcoxina molecules in the transformed lines and the controls were not significantly different (P > 0.05, as determined by analysis of covariance), indicating that in spite of higher levels of endochitinase expression, mycorrhization was not inhibited. Our results indicate that the higher levels of chitinolytic activity in root exudates and root tissues from ech42-transformed lines did not alter the soil fungal biomass or the development of ectendomycorrhizal symbiosis involving Wilcoxina spp

Taxonomic assignment of arbuscular mycorrhizal fungi in an 18S metagenomic dataset: a case study with saltcedar (Tamarix aphylla)

International audienceMany studies describing communities of arbuscular mycorrhizal fungi (AMF, Glomeromycota) based on high-throughput sequencing target the V4 variable region of the 18S ribosomal gene. However, an accurate taxonomic assignment of these short 18S sequences is challenging. Here we describe a simple approach based on a phylogenetic analysis using a backbone of reference sequences with taxonomic names updated in MycoBank to improve the taxonomic assignment of amplicon sequence variants (ASVs). As a case study, paired-end sequencing (2 × 250 bp) was carried out to describe the community of AMF associated with Tamarix aphylla from Algerian steppe ecosystems. AMF from root and soil samples were targeted with a nested PCR, using the AMF-discriminating primers pair AML1/AML2 for the first amplification and a new primer pair for the second. The proportion of the sequences assigned to Glomeromycota was 85.9%, representing a total of 87 ASVs. Seven well-defined genera (Claroideoglomus, Dominikia, Funneliformis, Innospora, Microkamienskia, Rhizophagus, Septoglomus) and seven phylogenetic divergent clades of Glomus (27% of the ASVs) were identified with the proposed approach. This taxonomic assignment was in sharp contrast with querying the MaarjAM or GenBank databases. Out-of-date taxonomy led the MaarjAM database to attribute 85% of the ASVs to the genus Glomus and the GenBank database to assign 18% of the ASVs to unclassified taxa. We recommend using the simple workflow presented in this study so that up-to-date taxonomic information is accurately assigned to AMF communities analyzed by high-throughput sequencing