Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems

Auer, Lucas; Buée, Marc; Fauchery, Laure; Lombard, Vincent; Barry, Kerry W.; Clum, Alicia; Copeland, Alex; Daum, Chris; Foster, Brian; LaButti, Kurt; Singan, Vasanth; Yoshinaga, Yuko; Martineau, Christine; Alfaro, Manuel; Castillo, Federico J.; Imbert, J. Bosco; Ramírez, Lucia; Castanera, Raúl; Pisabarro, Antonio G.; Finlay, Roger; Lindahl, Björn; Olson, Ake; Séguin, Armand; Kohler, Annegret; Henrissat, Bernard; Grigoriev, Igor V.; Martin, Francis M.

doi:10.1111/nph.19471

Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems

Journal Article · Mon Dec 25 23:00:00 EST 2023 · New Phytologist

DOI:https://doi.org/10.1111/nph.19471· OSTI ID:2473667

Auer, Lucas ^[1]; ^[1]; Fauchery, Laure ^[1]; Lombard, Vincent ^[2]; Barry, Kerry W. ^[3]; Clum, Alicia ^[3]; Copeland, Alex ^[3]; Daum, Chris ^[3]; Foster, Brian ^[3]; LaButti, Kurt ^[3]; Singan, Vasanth ^[3]; Yoshinaga, Yuko ^[3]; Martineau, Christine ^[4]; Alfaro, Manuel ^[5]; Castillo, Federico J. ^[5]; Imbert, J. Bosco ^[5]; Ramírez, Lucia ^[5]; Castanera, Raúl ^[5]; Pisabarro, Antonio G. ^[5]; ^[6] more »

Universite de Lorraine, Nancy (France); French National Research Institute for Agriculture, Food and Environment (INRAE), Nancy (France)
Centre National de la Recherche Scientifique (CNRS), Marseille (France); Aix-Marseille Univ., Marseille (France); French National Research Institute for Agriculture, Food and Environment (INRAE), Marseille (France)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Natural Resources Canada, Quebec, QC (Canada). Canadian Forest Service
Public University of Navarra (UPNA), Pamplona (Spain)
Swedish Univ. of Agricultural Sciences, Uppsala (Sweden)
Technical Univ. of Denmark, Copenhagen (Denmark); King Abdulaziz Univ., Jeddah (Saudi Arabia)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); University of California, Berkeley, CA (United States)

Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. Here, we showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science (BSS); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); Spanish National Research Agency (CICYT)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2473667

Journal Information:: New Phytologist, Journal Name: New Phytologist Journal Issue: 4 Vol. 242; ISSN 0028-646X

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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Leaf and Root-Associated Fungal Assemblages Do Not Follow Similar Elevational Diversity Patterns Coince, Aurore; Cordier, Tristan; Lengellé, Juliette PLoS ONE, Vol. 9, Issue 6 https://doi.org/10.1371/journal.pone.0100668	journal	June 2014
Welcome to the Tidyverse Wickham, Hadley; Averick, Mara; Bryan, Jennifer Journal of Open Source Software, Vol. 4, Issue 43 https://doi.org/10.21105/joss.01686	journal	November 2019
Bacterial and Fungal Contributions to Carbon Sequestration in Agroecosystems Six, J.; Frey, S. D.; Thiet, R. K. Soil Science Society of America Journal, Vol. 70, Issue 2 https://doi.org/10.2136/sssaj2004.0347	journal	January 2006
Nitrogen Mineralization Following Fertilization of Douglas‐fir Forests with Urea in Western Washington Fox, Thomas R. Soil Science Society of America Journal, Vol. 68, Issue 5 https://doi.org/10.2136/sssaj2004.1720	journal	September 2004
The Niche Exploitation Pattern of the Blue-Gray Gnatcatcher Root, Richard B. Ecological Monographs, Vol. 37, Issue 4 https://doi.org/10.2307/1942327	journal	February 1967
Strong primer bias for Tulasnellaceae fungi in metabarcoding: Specific primers improve the characterization of the mycorrhizal communities of epiphytic orchids Rammitsu, Kento; Kajita, Tadashi; Imai, Ryosuke Mycoscience, Vol. 62, Issue 6 https://doi.org/10.47371/mycosci.2021.06.005	journal	November 2021

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59 BASIC BIOLOGICAL SCIENCES
forest soil
functional traits
fungal guilds
metatranscriptomics
organic matter degradation

Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems

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