DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Journal Article · · Environmental Microbiology
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)

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.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC); Swedish Research Council (SRC)
Grant/Contract Number:
AC02-05CH11231; 2011-1747; ANR-11-LABX-0002_ARBRE
OSTI ID:
1619166
Alternate ID(s):
OSTI ID: 1577420
Journal Information:
Environmental Microbiology, Vol. 22, Issue 3; ISSN 1462-2912
Publisher:
WileyCopyright Statement
Country of Publication:
United States
Language:
English

References (47)

Vegetation classification by reference to strategies journal July 1974
Manganese availability is negatively associated with carbon storage in northern coniferous forest humus layers journal November 2017
Fungal community on decomposing leaf litter undergoes rapid successional changes journal October 2012
Fungal Cellulases journal January 2015
A Theoretical Model of Litter Decay and Microbial Interaction journal May 2006
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes journal June 2012
Widespread Occurrence of Expressed Fungal Secretory Peroxidases in Forest Soils journal April 2014
Nitrogen dynamics of decomposing Scots pine needle litter depends on colonizing fungal species journal April 2019
Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists journal February 2015
Stimulation of Lignocellulosic Biomass Hydrolysis by Proteins of Glycoside Hydrolase Family 61 Structure and Function of a Large, Enigmatic Family journal April 2010
Covalent Cross-Links in the Cell Wall journal February 1994
Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists journal January 2018
The carbohydrate-active enzymes database (CAZy) in 2013 journal November 2013
Coupling Secretomics with Enzyme Activities To Compare the Temporal Processes of Wood Metabolism among White and Brown Rot Fungi journal June 2018
Untangling the fungal niche: the trait-based approach journal October 2014
Below-ground organic matter accumulation along a boreal forest fertility gradient relates to guild interaction within fungal communities journal October 2017
Carbon-13 nuclear magnetic resonance of polymers spinning at the magic angle journal February 1976
Multi-omic Analyses of Extensively Decayed Pinus contorta Reveal Expression of a Diverse Array of Lignocellulose-Degrading Enzymes journal August 2018
The structure and synthesis of the fungal cell wall journal January 2006
New species of Chalara occupying coniferous needles journal April 2011
Substrate factors that influence the synergistic interaction of AA9 and cellulases during the enzymatic hydrolysis of biomass journal January 2014
Prospects and challenges for fungal metatranscriptomics of complex communities journal April 2015
Plant cell walls throughout evolution: towards a molecular understanding of their design principles journal August 2009
Decomposing capacity of fungi commonly detected in Pinus sylvestris needle litter journal February 2011
Effects of Cellulose Crystallinity, Hemicellulose, and Lignin on the Enzymatic Hydrolysis of Miscanthus sinensis to Monosaccharides journal March 2008
Litter chemistry influences decomposition through activity of specific microbial functional guilds journal May 2018
Functional guild classification predicts the enzymatic role of fungi in litter and soil biogeochemistry journal September 2015
Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus journal December 2015
Determining place and process: functional traits of ectomycorrhizal fungi that affect both community structure and ecosystem function journal October 2013
Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion journal February 2009
Transformation of Quercus petraea litter: successive changes in litter chemistry are reflected in differential enzyme activity and changes in the microbial community composition: Transformation of Quercus petraea litter journal November 2010
Changes in fungal communities along a boreal forest soil fertility gradient journal May 2015
Microbial genomics, transcriptomics and proteomics: new discoveries in decomposition research using complementary methods journal January 2014
Fungal Traits That Drive Ecosystem Dynamics on Land journal May 2015
The Plant Cell Wall-Decomposing Machinery Underlies the Functional Diversity of Forest Fungi journal July 2011
PeroxiBase: a database for large-scale evolutionary analysis of peroxidases journal November 2012
New and classic families of secreted fungal heme peroxidases journal May 2010
Quantification and monosaccharide composition of hemicelluloses from different plant functional types journal January 2010
MycoCosm portal: gearing up for 1000 fungal genomes journal December 2013
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi journal June 2014
Reviews and syntheses: Carbon use efficiency from organisms to ecosystems – definitions, theories, and empirical evidence journal January 2018
PCR Primers to Study the Diversity of Expressed Fungal Genes Encoding Lignocellulolytic Enzymes in Soils Using High-Throughput Sequencing journal December 2014
Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes journal January 2013
Comparative mitochondrial genome analysis reveals intron dynamics and gene rearrangements in two Trametes species journal January 2021
Fungal cellulases journal February 1992
Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha text January 2021
Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus collection January 2015