Taxonomic and functional diversity of a quercus pyrenaica willd. Rhizospheric microbiome in the mediterranean mountains

[EN] Altitude significantly affects vegetation growth and distribution, including the developmental stages of a forest. We used shotgun Illumina sequencing to analyze microbial community composition and functional potential in melojo-oak (Quercus pyrenaica Willd.) rhizospheric soil for three differe...

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Detalles Bibliográficos
Autores: Cobo Díaz, José Francisco, Fernández González, Antonio J., Villadas, Pablo J., Toro, Nicolás, Tringe, Susannah G., Fernández López, Manuel
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2017
País:España
Institución:Universidad de León
Repositorio:BULERIA. Repositorio Institucional de la Universidad de León
OAI Identifier:oai:buleria.unileon.es:10612/23809
Acceso en línea:https://www.mdpi.com/1999-4907/8/10/390
https://hdl.handle.net/10612/23809
Access Level:acceso abierto
Palabra clave:Botánica
Metagenomics
Mediterranean forests
Melojo-oak
Microbial functional diversity
Biogeochemical cycles
Rhizosphere metabolism
2417 Biología Vegetal (Botánica)
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spelling Taxonomic and functional diversity of a quercus pyrenaica willd. Rhizospheric microbiome in the mediterranean mountainsCobo Díaz, José FranciscoFernández González, Antonio J.Villadas, Pablo J.Toro, NicolásTringe, Susannah G.Fernández López, ManuelBotánicaMetagenomicsMediterranean forestsMelojo-oakMicrobial functional diversityBiogeochemical cyclesRhizosphere metabolism2417 Biología Vegetal (Botánica)[EN] Altitude significantly affects vegetation growth and distribution, including the developmental stages of a forest. We used shotgun Illumina sequencing to analyze microbial community composition and functional potential in melojo-oak (Quercus pyrenaica Willd.) rhizospheric soil for three different development stages along an altitudinal gradient: (a) a low altitude, non-optimal site for forest maintenance; (b) an intermediate altitude, optimal site for a forest; and (c) a high altitude, expansion site with isolated trees but without a real forest canopy. We observed that, at each altitude, the same microbial taxa appear both in the taxonomic analysis of the whole metagenome and in the functional analysis of the methane, sulfur and nitrogen metabolisms. Although there were no major differences at the functional level, there were significant differences in the abundance of each taxon at the phylogenetic level between the rhizospheres of the forest (low and intermediate altitudes) and the expansion site. Proteobacteria and Actinobacteria were the most differentially abundant phyla in forest soils compared to the expansion site rhizosphere. Moreover, Verrucomicrobia, Bacteroidetes and Nitrospirae phyla were more highly represented in the non-forest rhizosphere. Our study suggests that rhizospheric microbial communities of the same tree species may be affected by development stage and forest canopy cover via changes in soil pH and the C/N ratio.SIThis work was supported by research grants including ERDF (European Regional Development Funds): P08-CVI-03549 from Consejería de Innovación, Ciencia y Empresa from Junta de Andalucía, OAPN 021/2007 from Organismo Autónomo Parques Nacionales (Spanish Ministry of Environment) and 20134R069-RECUPERA 2020 from the Spanish Ministerio de Economía y Competitividad and CSIC. We would like to thank the authorities of the Sierra Nevada National Park for the access, facilities and soil sampling, and also Edward Kirton (JGI, California) for technical assistance with bioinformatics. JFCD was awarded a postdoctoral contract from Junta de Andalucía, and AJFG was awarded a postdoctoral contract from RECUPERA 2020. The work of the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.MDPIMicrobiologiaFacultad de Veterinaria2017info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://www.mdpi.com/1999-4907/8/10/390https://hdl.handle.net/10612/23809reponame:BULERIA. Repositorio Institucional de la Universidad de Leóninstname:Universidad de LeónInglésinfo:eu-repo/grantAgreement/Junta de Andalucía/ Programa Nacional de Investigación Fundamental / P08-CVI-03549http://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessoai:buleria.unileon.es:10612/238092026-06-24T12:43:27Z
dc.title.none.fl_str_mv Taxonomic and functional diversity of a quercus pyrenaica willd. Rhizospheric microbiome in the mediterranean mountains
title Taxonomic and functional diversity of a quercus pyrenaica willd. Rhizospheric microbiome in the mediterranean mountains
spellingShingle Taxonomic and functional diversity of a quercus pyrenaica willd. Rhizospheric microbiome in the mediterranean mountains
Cobo Díaz, José Francisco
Botánica
Metagenomics
Mediterranean forests
Melojo-oak
Microbial functional diversity
Biogeochemical cycles
Rhizosphere metabolism
2417 Biología Vegetal (Botánica)
title_short Taxonomic and functional diversity of a quercus pyrenaica willd. Rhizospheric microbiome in the mediterranean mountains
title_full Taxonomic and functional diversity of a quercus pyrenaica willd. Rhizospheric microbiome in the mediterranean mountains
title_fullStr Taxonomic and functional diversity of a quercus pyrenaica willd. Rhizospheric microbiome in the mediterranean mountains
title_full_unstemmed Taxonomic and functional diversity of a quercus pyrenaica willd. Rhizospheric microbiome in the mediterranean mountains
title_sort Taxonomic and functional diversity of a quercus pyrenaica willd. Rhizospheric microbiome in the mediterranean mountains
dc.creator.none.fl_str_mv Cobo Díaz, José Francisco
Fernández González, Antonio J.
Villadas, Pablo J.
Toro, Nicolás
Tringe, Susannah G.
Fernández López, Manuel
author Cobo Díaz, José Francisco
author_facet Cobo Díaz, José Francisco
Fernández González, Antonio J.
Villadas, Pablo J.
Toro, Nicolás
Tringe, Susannah G.
Fernández López, Manuel
author_role author
author2 Fernández González, Antonio J.
Villadas, Pablo J.
Toro, Nicolás
Tringe, Susannah G.
Fernández López, Manuel
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv Microbiologia
Facultad de Veterinaria
dc.subject.none.fl_str_mv Botánica
Metagenomics
Mediterranean forests
Melojo-oak
Microbial functional diversity
Biogeochemical cycles
Rhizosphere metabolism
2417 Biología Vegetal (Botánica)
topic Botánica
Metagenomics
Mediterranean forests
Melojo-oak
Microbial functional diversity
Biogeochemical cycles
Rhizosphere metabolism
2417 Biología Vegetal (Botánica)
description [EN] Altitude significantly affects vegetation growth and distribution, including the developmental stages of a forest. We used shotgun Illumina sequencing to analyze microbial community composition and functional potential in melojo-oak (Quercus pyrenaica Willd.) rhizospheric soil for three different development stages along an altitudinal gradient: (a) a low altitude, non-optimal site for forest maintenance; (b) an intermediate altitude, optimal site for a forest; and (c) a high altitude, expansion site with isolated trees but without a real forest canopy. We observed that, at each altitude, the same microbial taxa appear both in the taxonomic analysis of the whole metagenome and in the functional analysis of the methane, sulfur and nitrogen metabolisms. Although there were no major differences at the functional level, there were significant differences in the abundance of each taxon at the phylogenetic level between the rhizospheres of the forest (low and intermediate altitudes) and the expansion site. Proteobacteria and Actinobacteria were the most differentially abundant phyla in forest soils compared to the expansion site rhizosphere. Moreover, Verrucomicrobia, Bacteroidetes and Nitrospirae phyla were more highly represented in the non-forest rhizosphere. Our study suggests that rhizospheric microbial communities of the same tree species may be affected by development stage and forest canopy cover via changes in soil pH and the C/N ratio.
publishDate 2017
dc.date.none.fl_str_mv 2017
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://www.mdpi.com/1999-4907/8/10/390
https://hdl.handle.net/10612/23809
url https://www.mdpi.com/1999-4907/8/10/390
https://hdl.handle.net/10612/23809
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv info:eu-repo/grantAgreement/Junta de Andalucía/ Programa Nacional de Investigación Fundamental / P08-CVI-03549
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0/
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv reponame:BULERIA. Repositorio Institucional de la Universidad de León
instname:Universidad de León
instname_str Universidad de León
reponame_str BULERIA. Repositorio Institucional de la Universidad de León
collection BULERIA. Repositorio Institucional de la Universidad de León
repository.name.fl_str_mv
repository.mail.fl_str_mv
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