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Title: Fungal ecological strategies reflected in gene transcription - a case study of two litter decomposers

Abstract

Microbial communities interplay with their environment through their functional traits that can be a response or an effect on the environment. Here, we explore how a functional trait-the decomposition of organic matter, can be addressed based on genetic markers and how the expression of these markers reflect ecological strategies of two fungal litter decomposer Gymnopus androsaceus and Chalara longipes. We sequenced the genomes of these two fungi, as well as their transcriptomes at different steps of Pinus sylvestris needles decomposition in microcosms. Our results highlighted that if the gene content of the two species could indicate similar potential decomposition abilities, the expression levels of specific gene families belonging to the glycoside hydrolase category reflected contrasting ecological strategies. Actually, C. longipes, the weaker decomposer in this experiment, turned out to have a high content of genes involved in cell wall polysaccharides decomposition but low expression levels, reflecting a versatile ecology compare to the more competitive G. androsaceus with high expression levels of keystone functional genes. Finally, we established that sequential expression of genes coding for different components of the decomposer machinery indicated adaptation to chemical changes in the substrate as decomposition progressed.

Authors:
ORCiD logo [1];  [2];  [3];  [1];  [3];  [2];  [1];  [3];  [3];  [3];  [2];  [4];  [5];  [6];  [7]
  1. Swedish Univ. of Agricultural Sciences, Uppsala (Sweden)
  2. Univ. de Lorraine, Champenoux (France)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
  5. Aix‐Marseille Univ., Marseille (France); INRA, Marseille (France); King Abdulaziz Univ., Jeddah (Saudi Arabia)
  6. Department of Soil and EnvironmentSwedish University of Agricultural Sciences Box 7014, SE‐750 07 Uppsala Sweden
  7. Univ. de Lorraine, Champenoux (France); Beijing Forestry Univ. (China)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); Swedish Research Council (SRC)
OSTI Identifier:
1619166
Alternate Identifier(s):
OSTI ID: 1577420
Grant/Contract Number:  
AC02-05CH11231; 2011-1747; ANR-11-LABX-0002_ARBRE
Resource Type:
Accepted Manuscript
Journal Name:
Environmental Microbiology
Additional Journal Information:
Journal Volume: 22; Journal Issue: 3; Journal ID: ISSN 1462-2912
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Barbi, Florian, Kohler, Annegret, Barry, Kerrie, Baskaran, Preetisri, Daum, Chris, Fauchery, Laure, Ihrmark, Katarina, Kuo, Alan, LaButti, Kurt, Lipzen, Anna, Morin, Emmanuelle, Grigoriev, Igor V., Henrissat, Bernard, Lindahl, Björn D., and Martin, Francis. Fungal ecological strategies reflected in gene transcription - a case study of two litter decomposers. United States: N. p., 2019. Web. https://doi.org/10.1111/1462-2920.14873.
Barbi, Florian, Kohler, Annegret, Barry, Kerrie, Baskaran, Preetisri, Daum, Chris, Fauchery, Laure, Ihrmark, Katarina, Kuo, Alan, LaButti, Kurt, Lipzen, Anna, Morin, Emmanuelle, Grigoriev, Igor V., Henrissat, Bernard, Lindahl, Björn D., & Martin, Francis. Fungal ecological strategies reflected in gene transcription - a case study of two litter decomposers. United States. https://doi.org/10.1111/1462-2920.14873
Barbi, Florian, Kohler, Annegret, Barry, Kerrie, Baskaran, Preetisri, Daum, Chris, Fauchery, Laure, Ihrmark, Katarina, Kuo, Alan, LaButti, Kurt, Lipzen, Anna, Morin, Emmanuelle, Grigoriev, Igor V., Henrissat, Bernard, Lindahl, Björn D., and Martin, Francis. Sun . "Fungal ecological strategies reflected in gene transcription - a case study of two litter decomposers". United States. https://doi.org/10.1111/1462-2920.14873. https://www.osti.gov/servlets/purl/1619166.
@article{osti_1619166,
title = {Fungal ecological strategies reflected in gene transcription - a case study of two litter decomposers},
author = {Barbi, Florian and Kohler, Annegret and Barry, Kerrie and Baskaran, Preetisri and Daum, Chris and Fauchery, Laure and Ihrmark, Katarina and Kuo, Alan and LaButti, Kurt and Lipzen, Anna and Morin, Emmanuelle and Grigoriev, Igor V. and Henrissat, Bernard and Lindahl, Björn D. and Martin, Francis},
abstractNote = {Microbial communities interplay with their environment through their functional traits that can be a response or an effect on the environment. Here, we explore how a functional trait-the decomposition of organic matter, can be addressed based on genetic markers and how the expression of these markers reflect ecological strategies of two fungal litter decomposer Gymnopus androsaceus and Chalara longipes. We sequenced the genomes of these two fungi, as well as their transcriptomes at different steps of Pinus sylvestris needles decomposition in microcosms. Our results highlighted that if the gene content of the two species could indicate similar potential decomposition abilities, the expression levels of specific gene families belonging to the glycoside hydrolase category reflected contrasting ecological strategies. Actually, C. longipes, the weaker decomposer in this experiment, turned out to have a high content of genes involved in cell wall polysaccharides decomposition but low expression levels, reflecting a versatile ecology compare to the more competitive G. androsaceus with high expression levels of keystone functional genes. Finally, we established that sequential expression of genes coding for different components of the decomposer machinery indicated adaptation to chemical changes in the substrate as decomposition progressed.},
doi = {10.1111/1462-2920.14873},
journal = {Environmental Microbiology},
number = 3,
volume = 22,
place = {United States},
year = {2019},
month = {11}
}

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