Environmental metabarcoding reveals contrasting belowground and aboveground fungal communities from poplar at a Hg phytomanagement site

Characterization of microbial communities in stressful conditions at a field level is rather scarce, especially when considering fungal communities from aboveground habitats. We aimed at characterizing fungal communities from different poplar habitats at a Hg-contaminated phytomanagement site by using Illumina-based sequencing, network analysis approach, and direct isolation of Hg-resistant fungal strains. The highest diversity estimated by the Shannon index was found for soil communities, which was negatively affected by soil Hg concentration. Among the significant correlations between soil operational taxonomic units (OTUs) in the co-occurrence network, 80% were negatively correlated revealing dominance of a pattern of mutual exclusion. The fungal communities associated with Populus roots mostly consisted of OTUs from the symbiotic guild, such as members of the Thelephoraceae, thus explaining the lowest diversity found for root communities. Additionally, root communities showed the highest network connectivity index, while rarely detected OTUs from the Glomeromycetes may have a central role in the root network. Unexpectedly high richness and diversity were found for aboveground habitats, compared to the root habitat. The aboveground habitats were dominated by yeasts from the Lalaria, Davidiella, and Bensingtonia genera, not detected in belowground habitats. Leaf and stem habitats were characterized by few dominant OTUs such as those from the Dothideomycete class producing mutual exclusion with other OTUs. Aureobasidium pullulans, one of the dominating OTUs, was further isolated from the leaf habitat, in addition to Nakazawaea populi species, which were found to be Hg resistant. Altogether, these findings will provide an improved point of reference for microbial research on inoculation-based programs of tailings dumps

Plasma membrane in arbuscular mycorrhiza

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Association antibiotique – extraits d’huiles essentielles : effets antagonistes chez Pseudomonas aeruginosa

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Proteomic analysis of Medicago truncatula root plastids

International audienceDespite the recognized importance of non-photosynthetic plastids in a wide array of plant processes, the root plastid proteome of soil-grown plants still remains to be explored. In this study, we used a protocol allowing the isolation of Medicago truncatula root plastids with sufficient protein recovery and purity for their subsequent in-depth analysis by nanoscale capillary LC-MS/MS. Besides providing the first picture of a root plastid proteome, the results obtained highlighted the identification of 266 protein candidates whose functional distribution mainly resembled that of wheat endosperm amyloplasts and tobacco proplastids together with displaying major differences to those reported for chloroplasts. Most of the identified proteins have a role in nucleic acid-related processes (16%), carbohydrate (15%) and nitrogen/sulphur (12%) metabolisms together with stress response mechanisms (10%). It is noteworthy that BLAST searches performed against the proteins reported in different plastidomes allowed detecting 30 putative root plastid proteins for which homologues were previously unsuspected as plastid-located, most of them displaying a common putative role in participating in the plant cell responses against abiotic and/or biotic stresses. Taken together, the data obtained provide new insights into the functioning of root plastids and reinforce the emerging idea for an important role of these organelles in sustaining plant defence reactions

Intra-patient evolution of a pulmonary strain of Pseudomonas aeruginosa from primo-colonisation to lung transplant

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Contribution of proteomics to arbuscular mycorrhiza in Medicago truncatula

International audienceBecause proteins are key effectors of plant responses to environmental cues including recognition, signalling, transport and defence reactions, main interest has been paid to characterize those involved in the establishment and functioning of arbuscular mycorrhizal (AM) symbiosis. In our group, the setting up of high throughput proteomic techniques on the model species, Medicago truncatula, is providing step-by-step a large-scale analysis of AM symbiosis-related proteins. Depending on the symbiotic stage targeted and on the abundance of mycorrhizal material, different proteomic strategies that can be combined with other large-scale approaches (transcriptomic and metabolomic) will be presented. Modification of the M. truncatula root proteome during the early stage of AM symbiosis has been investigated by comparing the protein patterns obtained from non-inoculated roots and roots synchronized for appressorium formation in wild-type (J5), penetration-defective (TRV25, dmi3) and autoregulation-defective (TR122, sunn) genotypes. In mature mycorrhiza, sub-cellular proteomic approaches have been developed in M. truncatula to target symbiosis-related membrane proteins eligible as involved in nutrient transport and signalling between symbionts upon arbuscule formation. In addition, with the aim of determining overlaps in response to the two most commonly employed AM fungal isolates we recently launched a high throughput comparative proteomic analysis. The future release of the genome sequencing programs launched for M. truncatula and Glomus intraradices is likely to provide additional knowledge about AM symbiosis-related proteins

Contribution of proteomics to arbuscular mycorrhiza in Medicago truncatula

International audienceBecause proteins are key effectors of plant responses to environmental cues including recognition, signalling, transport and defence reactions, main interest has been paid to characterize those involved in the establishment and functioning of arbuscular mycorrhizal (AM) symbiosis. In our group, the setting up of high throughput proteomic techniques on the model species, Medicago truncatula, is providing step-by-step a large-scale analysis of AM symbiosis-related proteins. Depending on the symbiotic stage targeted and on the abundance of mycorrhizal material, different proteomic strategies that can be combined with other large-scale approaches (transcriptomic and metabolomic) will be presented. Modification of the M. truncatula root proteome during the early stage of AM symbiosis has been investigated by comparing the protein patterns obtained from non-inoculated roots and roots synchronized for appressorium formation in wild-type (J5), penetration-defective (TRV25, dmi3) and autoregulation-defective (TR122, sunn) genotypes. In mature mycorrhiza, sub-cellular proteomic approaches have been developed in M. truncatula to target symbiosis-related membrane proteins eligible as involved in nutrient transport and signalling between symbionts upon arbuscule formation. In addition, with the aim of determining overlaps in response to the two most commonly employed AM fungal isolates we recently launched a high throughput comparative proteomic analysis. The future release of the genome sequencing programs launched for M. truncatula and Glomus intraradices is likely to provide additional knowledge about AM symbiosis-related proteins

Functional Genomic of Arbuscular Mycorrhizal Symbiosis: Why and How Using Proteomics

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Identification of in planta-expressed arbuscular mycorrhizal fungal proteins upon comparison of the root proteomes of Medicago truncatula colonised with two Glomus species

International audienceIn the absence of sequenced genomes for arbuscular mycorrhizal (AM) fungi, their obligatory biotrophy makes their intra-radical biology especially recalcitrant to functional analyses. Because tandem mass spectrometry-based proteomics enables fungal gene product identifications in phyla lacking genomic information, we have compared as a way to enlarge the coverage of in planta expressed-mycorrhiza-related proteins, the root proteome responses of Medicago truncatula upon colonisation with two AM fungi, Glomus mosseae and G. intraradices, using two-dimensional electrophoresis. In contrast to phosphate fertilization, mycorrhization led to specific changes in the abundance of 99 spots, including 42 overlapping modifications between G. mosseae- and G. intraradices-colonised roots. The 32 confident identifications that could be retrieved following tandem mass spectrometry encompassed 21 fungal proteins whose homology-inferred functions were found to complement the working models so far proposed for the intra-radical functioning of AM fungi with regard to carbon utilization, energy generation, redox homeostasis and protein turnover-related processes

Genome Analysis of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus ST398 Strains Isolated from Patients with Invasive Infection

Background: Using genomic data, we determined the origin of MRSA ST398 isolates responsible for invasive infection in patients with no known livestock contact. Methods: We sequenced the genome of seven MSSA and four MRSA ST398 isolates from patients with invasive infections between 2013 and 2017, using the Illumina technique. Prophage-associated virulence genes and resistance genes were identified. To determine the origin of the isolates, their genome sequences were included in phylogenetic analysis also encompassing the ST398 genomes available on NCBI. Results: All isolates carried the φSa3 prophage, but with variations in the immune evasion cluster: type C in MRSA isolates, and type B in MSSA isolates. All MSSA belonged to the spa type t1451. MRSA strains had the same SCCmec type IVa (2B) cassette and belonged to spa types t899, t4132, t1939 and t2922. All MRSA harbored the tetracycline resistance gene, tet(M). Phylogenetic analysis revealed that MSSA isolates belonged to a cluster of human-associated isolates, while MRSA isolates belonged to a cluster containing livestock-associated MRSA. Conclusion: We showed that the clinical isolates MRSA and MSSA ST398 have different origins. An acquisition of virulence genes by livestock-associated MRSA isolates allows them to induce an invasive infection in human