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

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

doi:10.1111/nph.14974

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

Journal Article · Sun Jan 07 04:00:00 EST 2018 · New Phytologist

DOI:https://doi.org/10.1111/nph.14974· OSTI ID:1619093

^[1]; Morin, Emmanuelle ^[2]; Grelet, Gwen‐Aëlle ^[3]; Kuo, Alan ^[4]; Kohler, Annegret ^[5]; Daghino, Stefania ^[6]; Barry, Kerrie W. ^[4]; Cichocki, Nicolas ^[2]; Clum, Alicia ^[4]; Dockter, Rhyan B. ^[4]; Hainaut, Matthieu ^[7]; Kuo, Rita C. ^[4]; LaButti, Kurt ^[4]; Lindahl, Björn D. ^[8]; Lindquist, Erika A. ^[4]; Lipzen, Anna ^[4]; Khouja, Hassine‐Radhouane ^[6]; Magnuson, Jon ^[9]; Murat, Claude ^[2]; Ohm, Robin A. ^[10] more »

University of Turin (Italy); INRA Centre de Nancy-Lorraine, Champenoux (France)
INRA Centre de Nancy-Lorraine, Champenoux (France)
Manaaki Whenua – Landcare Research, Lincoln (New Zealand)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
NRA Centre de Nancy-Lorraine, Champenoux (France)
University of Turin (Italy)
Aix-Marseille University, Marseille (France); INRA, USC 1408 AFMB, Marseille (France)
Swedish University of Agricultural Sciences, Uppsala (Sweden)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Utrecht University (Netherlands)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Oregon State University, Corvallis, OR (United States)
INRA Centre de Nancy-Lorraine, Champenoux (France); University of Lorraine (France)
Aix-Marseille University, Marseille (France); INRA, USC 1408 AFMB, Marseille (France); King Abdulaziz University, Jeddah (Saudi Arabia)

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). Here 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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); Laboratory of Excellence ARBRE; Lorraine Region Council; University of Turin; Landcare Research – SSIF

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1619093

Alternate ID(s):: OSTI ID: 1416386
OSTI ID: 1543995

Journal Information:: New Phytologist, Journal Name: New Phytologist Journal Issue: 3 Vol. 217; ISSN 0028-646X

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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Challenges and Approaches in Microbiome Research: From Fundamental to Applied Sergaki, Chrysi; Lagunas, Beatriz; Lidbury, Ian Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.01205	journal	August 2018
Fungal and Bacterial Communities Exhibit Consistent Responses to Reversal of Soil Acidification and Phosphorus Limitation over Time R. Carrino-Kyker, Sarah; P. Coyle, Kaitlin; A. Kluber, Laurel Microorganisms, Vol. 8, Issue 1 https://doi.org/10.3390/microorganisms8010001	journal	December 2019
Extensive sampling and high-throughput sequencing reveal Posidoniomyces atricolor gen. et sp. nov. (Aigialaceae, Pleosporales) as the dominant root mycobiont of the dominant Mediterranean seagrass Posidonia oceanica Vohník, Martin; Borovec, Ondřej; Kolaříková, Zuzana MycoKeys, Vol. 55 https://doi.org/10.3897/mycokeys.55.35682	journal	June 2019
Additional file 1 of Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis Rosling, Anna; Eshghi Sahraei, Shadi; Kalsoom Khan, Faheema figshare https://doi.org/10.6084/m9.figshare.25929209	dataset	January 2024
Structural plasticity in root-fungal symbioses: diverse interactions lead to improved plant fitness Kariman, Khalil; Barker, Susan Jane; Tibbett, Mark PeerJ, Vol. 6 https://doi.org/10.7717/peerj.6030	journal	December 2018

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59 BASIC BIOLOGICAL SCIENCES
Ericaceae
Leotiomycetes
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ericoid mycorrhizal fungi
transcriptomics.

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

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