Functional soil mycobiome across ecosystems

Fungi support a wide range of ecosystem processes such as decomposition of organic matter and plant-soil relationships. Yet, our understanding of the factors driving the metaproteome of fungal communities is still scarce. Here, we conducted a field survey including data on fungal biomass (by phospho...

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Autores: Lima Parente Fernandes, Maysa, Bastida, F., Jehmlich, Nico, Martinovič, Tijana, Větrovský, Tomáš, Baldrian, Petr, Delgado-Baquerizo, Manuel, Starke, Robert
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2021
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/271617
Acceso en línea:http://hdl.handle.net/10261/271617
Access Level:acceso abierto
Palabra clave:Soil
Fungi
Metabarcoding
Metaproteomics
PLFA
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spelling Functional soil mycobiome across ecosystemsLima Parente Fernandes, MaysaBastida, F.Jehmlich, NicoMartinovič, TijanaVětrovský, TomášBaldrian, PetrDelgado-Baquerizo, ManuelStarke, RobertSoilFungiMetabarcodingMetaproteomicsPLFAFungi support a wide range of ecosystem processes such as decomposition of organic matter and plant-soil relationships. Yet, our understanding of the factors driving the metaproteome of fungal communities is still scarce. Here, we conducted a field survey including data on fungal biomass (by phospholipid fatty acids, PLFA), community composition (by metabarcoding of the 18S rRNA gene from extracted DNA) and functional profile (by metaproteomics) to investigate soil fungi and their relation to edaphic and environmental variables across three ecosystems (forests, grasslands, and shrublands) distributed across the globe. We found that protein richness of soil fungi was significantly higher in forests than in shrublands. Among a wide suite of edaphic and environmental variables, we found that soil carbon content and plant cover shaped evenness and diversity of fungal soil proteins while protein richness correlated to mean annual temperature and pH. Functions shifted from metabolism in forests to information processing and storage in shrublands. The differences between the biomes highlight the utility of metaproteomics to investigate functional microbiomes in soil. Significance: Understanding the structure and the function of fungal communities and the driving factors is crucial to determine the contribution to ecosystem services of fungi and what effect future climate has. While there is considerable knowledge on the ecosystem processes provided by fungi such as decomposition of organic matter and plant-soil relationships, our understanding of the driving factors of the fungal metaproteome is scarce. Here we present the first estimates of fungal topsoil protein diversity in a wide range of soils across global biomes. We report taxonomic differences for genes delivered by amplicon sequencing of the 18S rRNA gene and differences of the functional microbiome based on metaproteomics. Both methods gave a complementary view on the fungal topsoil communities, unveiling both taxonomic and functional changes with changing environments. Such a comprehensive multi-omic analysis of fungal topsoil communities has never been performed before, to our knowledge.Authors thank the i-LINK+ 2018 (LINKA20069) grant from CSIC. Grant PID2020-114942RB-I00 funded by MCIN/AEI/ 10.13039/501100011033 and by “ERDF A way of making Europe”. We would like to thank the researchers involved in the CLIMIFUN project for the help with soil sampling. This project has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 702057. M.D-B. is supported by a Ramón y Cajal grant from the Spanish Government (agreement no. RYC2018-025483-I). RS was supported by the Czech Science Foundation (20-02022Y)Elsevier BVConsejo Superior de Investigaciones Científicas (España)Ministerio de Ciencia, Innovación y Universidades (España)Agencia Estatal de Investigación (España)European CommissionCzech Science FoundationConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2022202220212022info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/271617reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-114942RB-I00info:eu-repo/grantAgreement//Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RYC2018-025483-Ihttp://dx.doi.org/10.1016/j.jprot.2021.104428Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2716172026-05-22T06:33:51Z
dc.title.none.fl_str_mv Functional soil mycobiome across ecosystems
title Functional soil mycobiome across ecosystems
spellingShingle Functional soil mycobiome across ecosystems
Lima Parente Fernandes, Maysa
Soil
Fungi
Metabarcoding
Metaproteomics
PLFA
title_short Functional soil mycobiome across ecosystems
title_full Functional soil mycobiome across ecosystems
title_fullStr Functional soil mycobiome across ecosystems
title_full_unstemmed Functional soil mycobiome across ecosystems
title_sort Functional soil mycobiome across ecosystems
dc.creator.none.fl_str_mv Lima Parente Fernandes, Maysa
Bastida, F.
Jehmlich, Nico
Martinovič, Tijana
Větrovský, Tomáš
Baldrian, Petr
Delgado-Baquerizo, Manuel
Starke, Robert
author Lima Parente Fernandes, Maysa
author_facet Lima Parente Fernandes, Maysa
Bastida, F.
Jehmlich, Nico
Martinovič, Tijana
Větrovský, Tomáš
Baldrian, Petr
Delgado-Baquerizo, Manuel
Starke, Robert
author_role author
author2 Bastida, F.
Jehmlich, Nico
Martinovič, Tijana
Větrovský, Tomáš
Baldrian, Petr
Delgado-Baquerizo, Manuel
Starke, Robert
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Consejo Superior de Investigaciones Científicas (España)
Ministerio de Ciencia, Innovación y Universidades (España)
Agencia Estatal de Investigación (España)
European Commission
Czech Science Foundation
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Soil
Fungi
Metabarcoding
Metaproteomics
PLFA
topic Soil
Fungi
Metabarcoding
Metaproteomics
PLFA
description Fungi support a wide range of ecosystem processes such as decomposition of organic matter and plant-soil relationships. Yet, our understanding of the factors driving the metaproteome of fungal communities is still scarce. Here, we conducted a field survey including data on fungal biomass (by phospholipid fatty acids, PLFA), community composition (by metabarcoding of the 18S rRNA gene from extracted DNA) and functional profile (by metaproteomics) to investigate soil fungi and their relation to edaphic and environmental variables across three ecosystems (forests, grasslands, and shrublands) distributed across the globe. We found that protein richness of soil fungi was significantly higher in forests than in shrublands. Among a wide suite of edaphic and environmental variables, we found that soil carbon content and plant cover shaped evenness and diversity of fungal soil proteins while protein richness correlated to mean annual temperature and pH. Functions shifted from metabolism in forests to information processing and storage in shrublands. The differences between the biomes highlight the utility of metaproteomics to investigate functional microbiomes in soil. Significance: Understanding the structure and the function of fungal communities and the driving factors is crucial to determine the contribution to ecosystem services of fungi and what effect future climate has. While there is considerable knowledge on the ecosystem processes provided by fungi such as decomposition of organic matter and plant-soil relationships, our understanding of the driving factors of the fungal metaproteome is scarce. Here we present the first estimates of fungal topsoil protein diversity in a wide range of soils across global biomes. We report taxonomic differences for genes delivered by amplicon sequencing of the 18S rRNA gene and differences of the functional microbiome based on metaproteomics. Both methods gave a complementary view on the fungal topsoil communities, unveiling both taxonomic and functional changes with changing environments. Such a comprehensive multi-omic analysis of fungal topsoil communities has never been performed before, to our knowledge.
publishDate 2021
dc.date.none.fl_str_mv 2021
2022
2022
2022
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/271617
url http://hdl.handle.net/10261/271617
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-114942RB-I00
info:eu-repo/grantAgreement//Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RYC2018-025483-I
http://dx.doi.org/10.1016/j.jprot.2021.104428
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Elsevier BV
publisher.none.fl_str_mv Elsevier BV
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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