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Title: Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists

Authors:
ORCiD logo [1];  [2];  [3];  [4];  [2];  [5];  [4];  [2];  [4];  [4];  [6];  [4];  [4];  [7];  [4];  [4];  [5];  [8];  [2];  [9] more »;  [10];  [11];  [4];  [12];  [13];  [4]; ORCiD logo [2];  [5] « less
  1. Department of Life Sciences and Systems Biology, University of Turin, Turin 10125 Italy, INRA, UMR 1136 INRA-Université de Lorraine ‘Interactions Arbres/Microorganismes’, Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280 Champenoux France
  2. INRA, UMR 1136 INRA-Université de Lorraine ‘Interactions Arbres/Microorganismes’, Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280 Champenoux France
  3. Manaaki Whenua - Landcare Research, Ecosystems and Global Change Team, Gerald Street PO Box 69040 Lincoln 7640 New Zealand
  4. US Department of Energy Joint Genome Institute, Walnut Creek CA 94598 USA
  5. Department of Life Sciences and Systems Biology, University of Turin, Turin 10125 Italy
  6. Architecture et Fonction des Macromolécules Biologiques, UMR7257 Centre National de la Recherche Scientifique - Aix-Marseille Université, Case 932, 163 Avenue de Luminy Marseille 13288 France, INRA, USC 1408 AFMB, Marseille 13288 France
  7. Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala 75007 Sweden
  8. Pacific Northwest National Laboratory, Chemical and Biological Process Development Group, Richland WA 99354 USA
  9. US Department of Energy Joint Genome Institute, Walnut Creek CA 94598 USA, Microbiology, Department of Biology, Utrecht University, 3508 TB Utrecht the Netherlands
  10. Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720 USA
  11. Department of Botany and Plant Pathology, Oregon State University, Corvallis OR 97331 USA
  12. INRA, UMR 1136 INRA-Université de Lorraine ‘Interactions Arbres/Microorganismes’, Laboratoire d'Excellence ARBRE, Centre INRA-Lorraine, 54280 Champenoux France, Laboratoire d'Excellence ARBRE, Faculté des Sciences et Technologies, UMR 1136 INRA-Université de Lorraine ‘Interactions Arbres/Microorganismes’, Université de Lorraine, Campus Aiguillettes, BP 70239 Vandoeuvre les Nancy cedex 54506 France
  13. Architecture et Fonction des Macromolécules Biologiques, UMR7257 Centre National de la Recherche Scientifique - Aix-Marseille Université, Case 932, 163 Avenue de Luminy Marseille 13288 France, INRA, USC 1408 AFMB, Marseille 13288 France, Department of Biological Sciences, King Abdulaziz University - KSA, Jeddah 21589 Saudi Arabia
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1416386
Grant/Contract Number:
AC02-05CH11231; ANR-11-LABX-0002-01
Resource Type:
Journal Article: Publisher's Accepted Manuscript
Journal Name:
New Phytologist
Additional Journal Information:
Journal Volume: 217; Journal Issue: 3; Related Information: CHORUS Timestamp: 2018-01-16 07:41:16; Journal ID: ISSN 0028-646X
Publisher:
Wiley-Blackwell
Country of Publication:
United Kingdom
Language:
English

Citation Formats

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. Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists. United Kingdom: N. p., 2018. Web. doi:10.1111/nph.14974.
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., & Perotto, Silvia. Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists. United Kingdom. doi:10.1111/nph.14974.
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. 2018. "Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists". United Kingdom. doi:10.1111/nph.14974.
@article{osti_1416386,
title = {Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists},
author = {Martino, Elena and Morin, Emmanuelle and Grelet, Gwen-Aëlle and Kuo, Alan and Kohler, Annegret and Daghino, Stefania and Barry, Kerrie W. and Cichocki, Nicolas and Clum, Alicia and Dockter, Rhyan B. and Hainaut, Matthieu and Kuo, Rita C. and LaButti, Kurt and Lindahl, Björn D. and Lindquist, Erika A. and Lipzen, Anna and Khouja, Hassine-Radhouane and Magnuson, Jon and Murat, Claude and Ohm, Robin A. and Singer, Steven W. and Spatafora, Joseph W. and Wang, Mei and Veneault-Fourrey, Claire and Henrissat, Bernard and Grigoriev, Igor V. and Martin, Francis M. and Perotto, Silvia},
abstractNote = {},
doi = {10.1111/nph.14974},
journal = {New Phytologist},
number = 3,
volume = 217,
place = {United Kingdom},
year = 2018,
month = 1
}

Journal Article:
Free Publicly Available Full Text
This content will become publicly available on January 7, 2019
Publisher's Accepted Manuscript

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  • To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergentmore » evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.« less
  • Of all effects of elevated atmospheric CO{sub 2} on plants and ecosystems, the least is known about plant rhizosphere responses. Rhizosphere fungi are fed primarily by root-derived substrates, and fulfill functions such as immobilization, decomposition, pathogeneity, and improvement of plant nutrition. This study describes the effect of elevated CO{sub 2} on the interaction between the pathogen Fusarium solani and the AM fungus Glomus intraradices in the rhizosphere of Artemisia tridentata. We measured intraradical infection and extraradical growth by the two fungi under elevated and ambient CO{sub 2} concentrations. We found a strong interaction between the two fungi. Root infection bymore » and extraradical hyphal length of solani did not differ significantly between CO{sub 2} treatments in the presence of G. intraradices. In the absence of G. intraradices, however, infection by F. solani and its extraradical hyphal length increased under elevated CO{sub 2}. Our results indicate that pathogenic fungi do respond to elevated CO{sub 2} by increased hyphal growth and root infection (potential response), but also show that mycorrhizal fungi can profit more from the new conditions and serve to suppress the pathogen.« less
  • The origins and composition of soil organic matter (SOM) are still largely uncertain. Arbuscular mycorrhizal fungi (AMF) are recognized as indirect contributors through their influence on soil aggregation, plant physiology, and plant community composition. Here we present evidence that AMF can also make large, direct contributions to SOM. Glomalin, a recently discovered glycoprotein produced by AMF hyphae, was detected in tropical soils in concentrations of over 60 mg cm-3. Along a chronosequence of soils spanning ages from 300 to 4.1 Mio years, a pattern of glomalin concentrations is consistent with the hypothesis that this protein accumulates in soil. Carbon datingmore » of glomalin indicated turnover at time scales of several years to decades, much longer than the turnover of AMF hyphae (which is assumed to be on the order of days to weeks). This suggests that contributions of mycorrhizae to soil carbon storage based on hyphal biomass in soil and roots may be an underestimate. The amount of C and N in glomalin represented a sizeable amount (ca. 4-5 percent) of total soil C and N in the oldest soils. Our results thus indicate that microbial (fungal) carbon that is not derived from above- or below-ground litter can make a significant contribution to soil carbon and nitrogen pools and can far exceed the contributions of soil microbial biomass (ranging from 0.08 to 0.2 percent of total C for the oldest soils).« less
  • The interactions between two plant growth promoting rhizobacteria (PGPR), Pseudomonas fluorescens SBW25 and Paenibacillus brasilensis PB177, two arbuscular mycorrhizal (AM) fungi (Glomus mosseae and G. intraradices) and one pathogenic fungus (Microdochium nivale) were investigated on winter wheat (Triticum aestivum cultivar Tarso) in a greenhouse trial. PB177, but not SBW25, had strong inhibitory effects on M. nivale in dual culture plate assays. The results from the greenhouse experiment show very specific interactions; e.g. the two AM fungi react differently when interacting with the same bacteria on plants. G. intraradices (single inoculation or together with SBW25) increased plant dry weight on M.more » nivale infested plants, suggesting that the pathogenic fungus is counteracted by G. intraradices, but PB177 inhibited this positive effect. This is an example of two completely different reactions between the same AM fungus and two species of bacteria, previously known to enhance plant growth and inhibit pathogens. When searching for plant growth promoting microorganisms it is therefore important to test for the most suitable combination of plant, bacteria and fungi in order to get satisfactory plant growth benefits.« less
  • Arbuscular mycorrhizal (AM) and dark-septate endophytic (DSE) fungi were quantified in plant roots from high-elevation sites in the Cordillera Vilcanota of the Andes (Per ) and the Front Range of the Colorado Rocky Mountains (U.S.A.). At the highest sites in the Andes (5391 m) AM fungi were absent in the two species of plants sampled (both Compositae) but roots of both were heavily colonized by DSE fungi. At slightly lower elevations (5240 5250 m) AM fungi were present in roots while DSE fungi were rare in plants outside of the composite family. At the highest sites sampled in Colorado (4300more » m) AM fungi were present, but at very low levels and all plants sampled contained DSE fungi. Hyphae of coarse AM fungi decreased significantly in plant roots at higher altitude in Colorado, but no other structures showed significant decreases with altitude. These new findings indicate that the altitudinal distribution of mycorrhizal fungi observed for European mountains do not necessarily apply to higher and drier mountains that cover much of the Earth (e.g. the Himalaya, Hindu Kush, Andes, and Rockies) where plant growth is more limited by nutrients and water than in European mountains. This paper describes the highest altitudinal records for both AM and DSE fungi, surpassing previous reported altitudinal maxima by about 1500 meters.« less