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3. Modulation of Plant and Fungal Gene Expression Upon Cd Exposure and Symbiosis in Ericoid Mycorrhizal Vaccinium myrtillus.

Author

Casarrubia, Salvatore, Martino, Elena, Daghino, Stefania, Kohler, Annegret, Morin, Emmanuelle, Khouja, Hassine-Radhouane, Murat, Claude, Barry, Kerrie, Lindquist, Erika, Martin, Francis, and Perotto, Silvia

Subjects
Cd tolerance, Oidiodendron maius, Vaccinium myrtillus, ericoid mycorrhiza, transcriptomics
Abstract

The success of Ericaceae in stressful habitats enriched in heavy metals has been ascribed to the distinctive abilities of their mycorrhizal fungal partners to withstand heavy metal stress and to enhance metal tolerance in the host plant. Whereas heavy metal tolerance has been extensively investigated in some ericoid mycorrhizal (ERM) fungi, the molecular and cellular mechanisms that extend tolerance to the host plant are currently unknown. Here, we show a reduced Cd content in Cd-exposed mycorrhizal roots of Vaccinium myrtillus colonized by a metal tolerant isolate of the fungus Oidiodendron maius as compared to non-mycorrhizal roots. To better understand this phenotype, we applied Next Generation Sequencing technologies to analyze gene expression in V. myrtillus and O. maius Zn grown under normal and Cd-stressed conditions, in the free living and in the mycorrhizal status. The results clearly showed that Cd had a stronger impact on plant gene expression than symbiosis, whereas fungal gene expression was mainly regulated by symbiosis. The higher abundance of transcripts coding for stress related proteins in non-mycorrhizal roots may be related to the higher Cd content. Regulated plant metal transporters have been identified that may play a role in reducing Cd content in mycorrhizal roots exposed to this metal.

Published
2020

5. Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists

Author

Martino, Elena, Morin, Emmanuelle, Grelet, Gwen‐Aëlle, Kuo, Alan, Kohler, Annegret, Daghino, Stefania, Barry, Kerrie W, Cichocki, Nicolas, Clum, Alicia, Dockter, Rhyan B, Hainaut, Matthieu, Kuo, Rita C, LaButti, Kurt, Lindahl, Björn D, Lindquist, Erika A, Lipzen, Anna, Khouja, Hassine‐Radhouane, Magnuson, Jon, Murat, Claude, Ohm, Robin A, Singer, Steven W, Spatafora, Joseph W, Wang, Mei, Veneault‐Fourrey, Claire, Henrissat, Bernard, Grigoriev, Igor V, Martin, Francis M, and Perotto, Silvia

Subjects
Microbiology, Biological Sciences, Ecology, Biotechnology, Genetics, Responsible Consumption and Production, Conserved Sequence, Fungi, Gene Expression Regulation, Fungal, Genes, Fungal, Genomics, Mycorrhizae, Phylogeny, Plants, Secondary Metabolism, Substrate Specificity, Symbiosis, Transcriptome, Up-Regulation, comparative genomics, Ericaceae, ericoid mycorrhizal fungi, Leotiomycetes, transcriptomics, Agricultural and Veterinary Sciences, Plant Biology & Botany, Plant biology, Climate change impacts and adaptation, Ecological applications
Abstract

Some soil fungi in the Leotiomycetes form ericoid mycorrhizal (ERM) symbioses with Ericaceae. In the harsh habitats in which they occur, ERM plant survival relies on nutrient mobilization from soil organic matter (SOM) by their fungal partners. The characterization of the fungal genetic machinery underpinning both the symbiotic lifestyle and SOM degradation is needed to understand ERM symbiosis functioning and evolution, and its impact on soil carbon (C) turnover. We sequenced the genomes of the ERM fungi Meliniomyces bicolor, M. variabilis, Oidiodendron maius and Rhizoscyphus ericae, and compared their gene repertoires with those of fungi with different lifestyles (ecto- and orchid mycorrhiza, endophytes, saprotrophs, pathogens). We also identified fungal transcripts induced in symbiosis. The ERM fungal gene contents for polysaccharide-degrading enzymes, lipases, proteases and enzymes involved in secondary metabolism are closer to those of saprotrophs and pathogens than to those of ectomycorrhizal symbionts. The fungal genes most highly upregulated in symbiosis are those coding for fungal and plant cell wall-degrading enzymes (CWDEs), lipases, proteases, transporters and mycorrhiza-induced small secreted proteins (MiSSPs). The ERM fungal gene repertoire reveals a capacity for a dual saprotrophic and biotrophic lifestyle. This may reflect an incomplete transition from saprotrophy to the mycorrhizal habit, or a versatile life strategy similar to fungal endophytes.

Published
2018

6. Three new clades of putative viral RNA-dependent RNA polymerases with rare or unique catalytic triads discovered in libraries of ORFans from powdery mildews and the yeast of oenological interest Starmerella bacillaris

Author

European Commission, Forgia, Marco [0000-0003-0101-1046], Daghino, Stefania [0000-0001-5722-1558], Crucitti, D [0000-0003-1860-5983], Turina, Massimo [0000-0002-9659-9470], Pacifico, Davide [0000-0003-3620-9829], Forgia, Marco, Chiapello, M., Daghino, Stefania, Pacifico, Davide, Crucitti, D, Oliva, Daniele, Ayllón, María A., Turina, Massimo, European Commission, Forgia, Marco [0000-0003-0101-1046], Daghino, Stefania [0000-0001-5722-1558], Crucitti, D [0000-0003-1860-5983], Turina, Massimo [0000-0002-9659-9470], Pacifico, Davide [0000-0003-3620-9829], Forgia, Marco, Chiapello, M., Daghino, Stefania, Pacifico, Davide, Crucitti, D, Oliva, Daniele, Ayllón, María A., and Turina, Massimo

Abstract

High throughput sequencing allowed the discovery of many new viruses and viral organizations increasing our comprehension of virus origin and evolution. Most RNA viruses are currently characterized through similarity searches of annotated virus databases. This approach limits the possibility to detect completely new virus-encoded proteins with no detectable similarities to existing ones, i.e. ORFan proteins. A strong indication of the ORFan viral origin in a metatranscriptome is the lack of DNA corresponding to an assembled RNA sequence in the biological sample. Furthermore, sequence homology among ORFans and evidence of co-occurrence of these ORFans in specific host individuals provides further indication of a viral origin. Here, we use this theoretical framework to report the finding of three conserved clades of protein-coding RNA segments without a corresponding DNA in fungi. Protein sequence and structural alignment suggest these proteins are distantly related to viral RNA-dependent RNA polymerases (RdRP). In these new putative viral RdRP clades, no GDD catalytic triad is present, but the most common putative catalytic triad is NDD and a clade with GDQ, a triad previously unreported at that site. SDD, HDD, and ADD are also represented. For most members of these three clades, we were able to associate a second genomic segment, coding for a protein of unknown function. We provisionally named this new group of viruses ormycovirus. Interestingly, all the members of one of these sub-clades (gammaormycovirus) accumulate more minus sense RNA than plus sense RNA during infection.

Published
2022

12. Extant hybrids of RNA viruses and viroid-like elements

Author

Forgia, Marco, primary, Navarro, Beatriz, additional, Daghino, Stefania, additional, Cervera, Amelia, additional, Gisel, Andreas, additional, Perotto, Silvia, additional, Aghayeva, Dilzara N., additional, Akinyuwa, Mary Funmilayo, additional, Gobbi, Emanuela, additional, Zheludev, Ivan N., additional, Edgar, Robert C., additional, Chikhi, Rayan, additional, Turina, Massimo, additional, Babaian, Artem, additional, Serio, Francesco Di, additional, and de la Peña, Marcos, additional

Published
2022
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17. Modulation of Plant and Fungal Gene Expression Upon Cd Exposure and Symbiosis in Ericoid Mycorrhizal Vaccinium myrtillus

Author

Casarrubia, Salvatore, primary, Martino, Elena, additional, Daghino, Stefania, additional, Kohler, Annegret, additional, Morin, Emmanuelle, additional, Khouja, Hassine-Radhouane, additional, Murat, Claude, additional, Barry, Kerrie W., additional, Lindquist, Erika A., additional, Martin, Francis M., additional, and Perotto, Silvia, additional

Published
2020
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18. Polyketide synthases in the ericoid endomycorrhizal fungus Oidiodendron maius

Author

Belmondo, Simone, Daghino, Stefania, Miyauchi, Shingo, Wu, Gang, Meloni, Domitilla, Aiello, Carola, Collin, Sabrina, Kohler, Annegret, Perotto, Silvia, Martino, Elena, Jacob, Christophe, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Life Sciences and Systems Biology [University of Turin], University of Turin, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), and Jacob, Christophe

Subjects
[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

19. Genomic and phenotypic divergence among heavy metal tolerant and sensitive isolates of the ericoid fungus Oidiodendron maius

Author

Daghino, Stefania, Murat, Claude, De Mita, Stéphane, Martino, Elena, Martin, Francis, Perotto, Silvia, Department of Life Sciences and Systems Biology [University of Turin], University of Turin, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Dipartimento di Scienze della Vita e Biologia dei Sistemi, and Università degli studi di Torino (UNITO)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

20. Characterization of polyketide synthases in an ericoid endomycorrhizal fungus using a molecular approach

Author

Belmondo, Simone, Daghino, Stefania, Miyauchi, Shingo, Wu, Gang, Meloni, Domitilla, Aiello, Carola, Collin, Sabrina, Kohler, Annegret, Perotto, Silvia, Martino, Elena, Jacob, Christophe, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Scienze della Vita e Biologia dei Sistemi, Université de Turin, and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

22. Transcriptomic analysis of plant and fungal Cd-regulated genes in the ericoid mycorrhizal symbiosis

Author

Casarrubia, Salvatore, Martino, Elena, Daghino, Stefania, Kohler, Annegret, Morin, Emmanuelle, Barry, Kerrie W, Lindquist, Erika A., Martin, Francis M., Perotto, Silvia, University of Turin, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli studi di Torino (UNITO), Department of Life Sciences and Systems Biology [University of Turin], Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), United States Department of Energy, Joint Genome Institute (JGI), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Martino, Elena

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

23. Polyketide synthases in the ericoid endomycorrhizal fungus Oidiodendron maius

Author

Martino, Elena, Daghino, Stefania, Belmondo, Simone, Meloni, Domitilla, Miyauchi, Shingo, Collin, Sabrina, Kohler, Annegret, Jacob, Christophe, Perotto, Silvia, Jacob, Christophe, Department of Life Sciences and Systems Biology [University of Turin], University of Turin, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), and Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019
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24. OmSSP1, a hydrophobin-like small secreted protein, is a putative effector in ericoid mycorrhiza

Author

Daghino, Stefania, Casarrubia, Salvatore, Kohler, Annegret, Morin, Emmanuelle, Daguerre, Yohann, Veneault-Fourrey, Claire, Martin, Francis M., Perotto, Silvia, Martino, Elena, Martino, Elena, Department of Life Sciences and Systems Biology [University of Turin], University of Turin, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Dipartimento di Scienze della Vita e Biologia dei Sistemi, and Università degli studi di Torino (UNITO)

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

25. Cd-regulated plant and fungal genes in the ericoid mycorrhizal symbiosis

Author

Casarrubia, Salvatore, Martino, Elena, Daghino, Stefania, Kohler, Annegret, Morin, Emmanuelle, Martin, Francis, Perotto, Silvia, University of Turin, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli studi di Torino (UNITO), Department of Life Sciences and Systems Biology [University of Turin], Interactions Arbres-Microorganismes (IAM), and Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

29. Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists

Author

Sub Molecular Microbiology, Molecular Microbiology, Martino, Elena, Morin, Emmanuelle, Grelet, Gwen-Aëlle, Kuo, Alan, Kohler, Annegret, Daghino, Stefania, Barry, Kerrie W., Cichocki, Nicolas, Clum, Alicia, Dockter, Rhyan B, Hainaut, Matthieu, Kuo, Rita C, LaButti, Kurt M, Lindahl, Björn D, Lindquist, Erika A, Lipzen, Anna, Khouja, Hassine-Radhouane, Magnuson, Jon, Murat, Claude, Ohm, Robin A, Singer, Steven W, Spatafora, Joseph W, Wang, Mei, Veneault-Fourrey, Claire, Henrissat, Bernard, Grigoriev, Igor V, Martin, Francis M., Perotto, Silvia, Sub Molecular Microbiology, Molecular Microbiology, Martino, Elena, Morin, Emmanuelle, Grelet, Gwen-Aëlle, Kuo, Alan, Kohler, Annegret, Daghino, Stefania, Barry, Kerrie W., Cichocki, Nicolas, Clum, Alicia, Dockter, Rhyan B, Hainaut, Matthieu, Kuo, Rita C, LaButti, Kurt M, Lindahl, Björn D, Lindquist, Erika A, Lipzen, Anna, Khouja, Hassine-Radhouane, Magnuson, Jon, Murat, Claude, Ohm, Robin A, Singer, Steven W, Spatafora, Joseph W, Wang, Mei, Veneault-Fourrey, Claire, Henrissat, Bernard, Grigoriev, Igor V, Martin, Francis M., and Perotto, Silvia

Published
2018

30. Homeostasis of trace elements in mycorrhizal fungi

Author

Ruytinx, Joske, Martino, Elena, Rozpądek, Piotr, Daghino, Stefania, Turnau, Katarzyna, Colpaert, Jan V, Perotto, Silvia, Hasselt University (UHasselt), INRAE Université de Lorraine, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Dipartimento di Scienze della Vita e Biologia dei Sistemi, Université de Turin, Institute of Environmental Sciences, Jagiellonian University, The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków, Poland, Department of Life Sciences and Systems Biology [University of Turin], University of Turin, Malopolska Centre of Biotechnology [Krakow] (MCB), and Uniwersytet Jagielloński w Krakowie = Jagiellonian University (UJ)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2016

31. Fungi with different ecological strategies affect Arabidopsis development in vitro: contribution of some soluble and volatile compounds

Author

Casarrubia, Salvatore, Sapienza, Sara, Fritz, Héma, Daghino, Stefania, Rosenkranz, Maaria, Schnitzler, Jörg-Peter, Martin, Francis, Perotto, Silvia, Martino, Elena, University of Turin, Department of Life Sciences and Systems Biology [University of Turin], Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), German Research Center for Environmental Health, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Dipartimento di Scienze della Vita e Biologia dei Sistemi, and Università degli studi di Torino (UNITO)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2016

32. Phenotypic and genomic adaptation of the ericoid fungus Oidiodendron maius to heavy metals

Author

Daghino, Stefania, Murat, Claude, de Mita, Stéphane, Martino, Elena, Martin, Francis, Perotto, Silvia, Department of Life Sciences and Systems Biology [University of Turin], University of Turin, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli studi di Torino (UNITO), and Martino, Elena

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2016

33. New insights from genome and transcriptome analyses of four ericoid mycorrhizal fungi

Author

Martino, Elena, Grelet, Gwen-Aëlle, Morin, Emmanuelle, Kohler, Annegret, Daghino, Stefania, Henrissat, Bernard, Kuo, Alan, Grigoriev, Igor, Martin, Francis M., Perotto, Silvia, Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli studi di Torino = University of Turin (UNITO), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Manaaki Whenua – Landcare Research [Lincoln], Department of Life Sciences and Systems Biology [University of Turin], Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Joint Genome Institute (JGI), US Department of Energy Joint Genome Institute, University of California (UC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Università degli studi di Torino (UNITO), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Turin, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), and University of California

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2016

40. Asbestos hazard in Western Alps: the use of soil fungi in bioremediation of asbestos fibres dispersed in the environment; a chemical-molecular integrated analysis

Author

Daghino, Stefania and Daghino, Stefania

Subjects
[SDV.OT] Life Sciences [q-bio]/Other [q-bio.OT], siderophores, ADN, radicaux libres, free radicals, DNA, champignons, asbestos, fer, iron, superoxide-dismutase, bioremediation, amiante, fungi
Abstract

The interaction of soil fungi with rocks and minerals is called geomycology. Serpentine rocks belong to the ophiolites family and can contain chrysotile (serpentine asbestos). Asbestos fibres reactivity is related to their surface chemical composition, i.g. the presence of iron, catalysing free radicals release, which is harmful for cells and tissues. Asbestos represents an environmental issue, related not only to serpentine rocks naturally exposed and weathered, but also (and mainly) to asbestos mines and wastes. Soil fungi are good candidates for the bioremediation of asbestos rich soils.The main goal of this thesis is the isolation of soil fungi from asbestos rich soils and the selection of the more suitable to interact and modify asbestos fibres in vitro. The metabolic responses of fungi are also investigated.Verticillium leptobactrum is the most abundant specie in all the serpentinic soils considered. This and interesting result, since this specie has bees previously seldom isolated.V. leptobactrum and other fungal species are able to extract iron and magnesium from chrysotile and crocidolite fibres, modifying their surface chemical composition and reactivity, and their génotoxicity (in acellular experiments). The fungi express anti-oxydant enzymes., L'étude de l'impact des champignons sur les processus géologiques qui altèrent les mineraux s'appelle la “géo-mycologie”. Les serpentinites sont des roches de la famille des ophiolites et peuvent contenir du chrysotile (amiante serpentine).La réactivité des fibres d'amiante est due à la composition chimique de surface et principalement à la présence d'ions métalliques qui peuvent catalyser des réactions chimiques dangereuses. L'amiante est un problème ambiantale à cause de la présence de roches contenant ce minéral mais aussi à cause des anciennes mines d'amiante. La revalorisation (remediation) de ces sites naturellement contaminés passe par la modification de la toxicité des fibres. Les champignons sont des bons candidats pour la bioremediation de l'amiante.L'objectif de cette thèse est l'isolement de souches fongiques à partir de sols serpentiniques afin de savoir quelles sont les espèces fongiques les plus abondantes dans ces sols et de sélectionner les souches les plus efficaces pour leur interaction avec les fibres d'amiantes. Les modifications des fibres et l'altération du métabolisme fongique ont été considérés.Verticillium leptobactrum semble être l'espèce fongique dominante dans tous les sols serpentiniques examinés : cette espèce n'avait jusque là été que rarement isolée, ce qui rend ces résultats intéressants. Trois espèces fongique peuvent extraire Fe et Mg des fibres de amiante (chrysotile et crocidolite), en modifiant la composition et la réactivité chimique de la surface de fibres et la génotoxicité mesuré dans un système acellulaire.Les champignons expriment, en présence des fibres, des enzymes liés à la réponse aux stress oxydants.

Published
2005

42. Pyrosequencing analysis of fungal assemblages from geographically distant, disparate soils reveals spatial patterning and a core mycobiome

Author

Orgiazzi, Alberto, Bianciotto, Valeria, Bonfante, Paola, Daghino, Stefania, Ghignone, Stefano, Lazzari, Alexandra, Lumini, Erica, Mello, Antonietta, Napoli, Chiara, Perotto, Silvia, Vizzini, Alfredo, Bagella, Simonetta, Murat, Claude, and Girlanda, Mariangela

Subjects
BIO/03 Botanica ambientale e applicata
Abstract

Identifying a soil core microbiome is crucial to appreciate the established microbial consortium, which is not usually subjected to change and, hence, possibly resistant/resilient to disturbances and a varying soil context. Fungi are a major part of soil biodiversity, yet the mechanisms driving their large-scale ecological ranges and distribution are poorly understood. The degree of fungal community overlap among 16 soil samples from distinct ecosystems and distant geographic localities (truffle grounds, a Mediterranean agro-silvo-pastoral system, serpentine substrates and a contaminated industrial area) was assessed by examining the distribution of fungal ITS1 and ITS2 sequences in a dataset of 454 libraries. ITS1 and ITS2 sequences were assigned to 1,660 and 1,393 Operational Taxonomic Units (OTUs; as defined by 97% sequence similarity), respectively. Fungal beta-diversity was found to be spatially autocorrelated. At the level of individual OTUs, eight ITS1 and seven ITS2 OTUs were found in all soil sample groups. These ubiquitous taxa comprised generalist fungi with oligotrophic and chitinolytic abilities, suggesting that a stable core of fungi across the complex soil fungal assemblages is either endowed with the capacity of sustained development in the nutrient-poor soil conditions or with the ability to exploit organic resources (such as chitin) universally distributed in soils.

Published
2013

44. Genomic suppression subtractive hybridization as a tool to identify differences in mycorrhizal fungal genomes

Author

Murat, Claude, Zampieri, Elisa, Vallino, Marta, Daghino, Stefania, Perotto, Silvia, Bonfante, Paola, Universita di Torino, University of Turin, Fondazione Sanpaolo, and Regione Piemonte

Subjects
genomic suppressive subtractive hybridization, Tuber, IDENTIFICATION, [SDV]Life Sciences [q-bio], fungi, DIVERSITY, GENUS TUBER, POLYMORPHISM, MECHANISMS, mycorrhizal fungi, TUBER-INDICUM, genomic suppressive subtractive hybridizationmycorrhizal fungigenomic variationTuberOidiodendron maius, TOLERANCE, genomic variation, GLUTATHIONE SYNTHETASE, Oidiodendron maius, MYCOPLASMA-AGALACTIAE, ACCUMULATION
Abstract

Characterization of genomic variation among different microbial species, or different strains of the same species, is a field of significant interest with a wide range of potential applications. We have investigated the genomic variation in mycorrhizal fungal genomes through genomic suppressive subtractive hybridization. The comparison was between phylogenetically distant and close truffle species (Tuber spp.), and between isolates of the ericoid mycorrhizal fungus Oidiodendron maius featuring different degrees of metal tolerance. In the interspecies experiment, almost all the sequences that were identified in the Tuber melanosporum genome and absent in Tuber borchii and Tuber indicum corresponded to transposable elements. In the intraspecies comparison, some specific sequences corresponded to regions coding for enzymes, among them a glutathione synthetase known to be involved in metal tolerance. This approach is a quick and rather inexpensive tool to develop molecular markers for mycorrhizal fungi tracking and barcoding, to identify functional genes and to investigate the genome plasticity, adaptation and evolution.

Published
2011
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