Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems
Lucas Auer
(1)
,
Marc Buée
(2, 3)
,
Laure Fauchery
(4)
,
Vincent Lombard
(5, 6)
,
Kerry Barry
,
Alicia Clum
(7)
,
Alex Copeland
(8)
,
Chris Daum
(4)
,
Brian Foster
(9)
,
Kurt Labutti
(4)
,
Vasanth Singan
(10)
,
Yuko Yoshinaga
(11)
,
Christine Martineau
(12)
,
Manuel Alfaro
,
Federico Castillo
(13)
,
J. Bosco Imbert
,
Lucia Ramírez
(14)
,
Raúl Castanera
(15)
,
Antonio Pisabarro
(16)
,
Roger Finlay
,
Björn Lindahl
(17)
,
Ake Olson
(17)
,
Armand Séguin
,
Annegret Kohler
,
Bernard Henrissat
,
Igor Grigoriev
,
Francis Martin
1
IAM -
Interactions Arbres-Microorganismes
2 INRAE - Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement
3 UL - Université de Lorraine
4 State Herbarium of South Australia
5 CNRS - Centre National de la Recherche Scientifique
6 AMU - Aix Marseille Université
7 DOE - Department of Energy / Joint Genome Institute
8 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
9 The Ohio State University Press
10 Lawrence Berkeley Natl Lab, Phys Biosci Div
11 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
12 Laurentian Forestry Centre
13 UC Davis - University of California [Davis]
14 UPNA - Universidad Pública de Navarra [Espagne] = Public University of Navarra
15 Structure and evolution of plant genomes
16 Genetics and Microbiology Research Group
17 SLU - Swedish University of Agricultural Sciences = Sveriges lantbruksuniversitet
2 INRAE - Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement
3 UL - Université de Lorraine
4 State Herbarium of South Australia
5 CNRS - Centre National de la Recherche Scientifique
6 AMU - Aix Marseille Université
7 DOE - Department of Energy / Joint Genome Institute
8 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
9 The Ohio State University Press
10 Lawrence Berkeley Natl Lab, Phys Biosci Div
11 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
12 Laurentian Forestry Centre
13 UC Davis - University of California [Davis]
14 UPNA - Universidad Pública de Navarra [Espagne] = Public University of Navarra
15 Structure and evolution of plant genomes
16 Genetics and Microbiology Research Group
17 SLU - Swedish University of Agricultural Sciences = Sveriges lantbruksuniversitet
Marc Buée
- Function : Author
- PersonId : 748217
- IdHAL : marc-buee
- ORCID : 0000-0001-8614-3886
- IdRef : 063239108
Vincent Lombard
- Function : Author
- PersonId : 751357
- IdHAL : vincent-lombard
- ORCID : 0000-0002-9684-7067
Kerry Barry
- Function : Author
Manuel Alfaro
- Function : Author
J. Bosco Imbert
- Function : Author
Roger Finlay
- Function : Author
- PersonId : 1389572
- ORCID : 0000-0002-3652-2930
Armand Séguin
- Function : Author
Annegret Kohler
- Function : Author
Bernard Henrissat
- Function : Author
Igor Grigoriev
- Function : Author
- PersonId : 791663
- ORCID : 0000-0002-3136-8903
- IdRef : 229928536
Francis Martin
- Function : Author
- PersonId : 802015
- ORCID : 0000-0002-4737-3715
Abstract
Summary 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. 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.