Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina

Autores
Vega Avila, Angela Daniela; Gumiere, T.; Andrade, P. A. M.; Lima Perim, J. E.; Durrer, A.; Baigori, Mario Domingo; Vazquez, Fabio; Andreote, F. D.
Año de publicación
2015
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Plants interact with a myriad of microbial cells in the rhizosphere, an environment that is considered to be important for plant development. However, the differential structuring of rhizosphere microbial communities due to plant cultivation under differential agricultural practices remains to be described for most plant species. Here we describe the rhizosphere microbiome of grapevine cultivated under conventional and organic practices, using a combination of cultivation-independent approaches. The quantification of bacterial 16S rRNA and nifH genes, by quantitative PCR (qPCR), revealed similar amounts of these genes in the rhizosphere in both vineyards. PCR-DGGE was used to detect differences in the structure of bacterial communities, including both the complete whole communities and specific fractions, such as Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and those harboring the nitrogen-fixing related gene nifH. When analyzed by a multivariate approach (redundancy analysis), the shifts observed in the bacterial communities were poorly explained by variations in the physical and chemical characteristics of the rhizosphere. These approaches were complemented by high-throughput sequencing (67,830 sequences) based on the V6 region of the 16S rRNA gene, identifying the major bacterial groups present in the rhizosphere of grapevines: Proteobacteria, Actinobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Cloroflexi, Verrucomicrobia and Planctomycetes, which occur in distinct proportions in the rhizosphere from each vineyard. The differences might be related to the selection of plant metabolism upon distinct reservoirs of microbial cells found in each vineyard. The results fill a gap in the knowledge of the rhizosphere of grapevines and also show distinctions in these bacterial communities due to agricultural practices.
Fil: Vega Avila, Angela Daniela. Universidad Nacional de San Juan. Facultad de Ingeniería. Instituto de Biotecnología; Argentina. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; Brasil. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Gumiere, T.. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; Brasil
Fil: Andrade, P. A. M.. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; Brasil
Fil: Lima Perim, J. E.. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; Brasil
Fil: Durrer, A.. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; Brasil
Fil: Baigori, Mario Domingo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Planta Piloto de Procesos Industriales Microbiologicos; Argentina
Fil: Vazquez, Fabio. Universidad Nacional de San Juan. Facultad de Ingeniería. Instituto de Biotecnología; Argentina
Fil: Andreote, F. D.. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; Brasil
Materia
Bacterial Communities
Cultivation
Cultivationindependent
Plant?Microbe Interactions
Rhizosphere Microbiome
Organic Management
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/29569
Acceder
id CONICETDig_0d1dec5f06738f27e659591c0f4738d9
oai_identifier_str oai:ri.conicet.gov.ar:11336/29569
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in ArgentinaVega Avila, Angela DanielaGumiere, T.Andrade, P. A. M.Lima Perim, J. E.Durrer, A.Baigori, Mario DomingoVazquez, FabioAndreote, F. D.Bacterial CommunitiesCultivationCultivationindependentPlant?Microbe InteractionsRhizosphere MicrobiomeOrganic Managementhttps://purl.org/becyt/ford/1.5https://purl.org/becyt/ford/1Plants interact with a myriad of microbial cells in the rhizosphere, an environment that is considered to be important for plant development. However, the differential structuring of rhizosphere microbial communities due to plant cultivation under differential agricultural practices remains to be described for most plant species. Here we describe the rhizosphere microbiome of grapevine cultivated under conventional and organic practices, using a combination of cultivation-independent approaches. The quantification of bacterial 16S rRNA and nifH genes, by quantitative PCR (qPCR), revealed similar amounts of these genes in the rhizosphere in both vineyards. PCR-DGGE was used to detect differences in the structure of bacterial communities, including both the complete whole communities and specific fractions, such as Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and those harboring the nitrogen-fixing related gene nifH. When analyzed by a multivariate approach (redundancy analysis), the shifts observed in the bacterial communities were poorly explained by variations in the physical and chemical characteristics of the rhizosphere. These approaches were complemented by high-throughput sequencing (67,830 sequences) based on the V6 region of the 16S rRNA gene, identifying the major bacterial groups present in the rhizosphere of grapevines: Proteobacteria, Actinobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Cloroflexi, Verrucomicrobia and Planctomycetes, which occur in distinct proportions in the rhizosphere from each vineyard. The differences might be related to the selection of plant metabolism upon distinct reservoirs of microbial cells found in each vineyard. The results fill a gap in the knowledge of the rhizosphere of grapevines and also show distinctions in these bacterial communities due to agricultural practices.Fil: Vega Avila, Angela Daniela. Universidad Nacional de San Juan. Facultad de Ingeniería. Instituto de Biotecnología; Argentina. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; Brasil. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gumiere, T.. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; BrasilFil: Andrade, P. A. M.. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; BrasilFil: Lima Perim, J. E.. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; BrasilFil: Durrer, A.. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; BrasilFil: Baigori, Mario Domingo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Planta Piloto de Procesos Industriales Microbiologicos; ArgentinaFil: Vazquez, Fabio. Universidad Nacional de San Juan. Facultad de Ingeniería. Instituto de Biotecnología; ArgentinaFil: Andreote, F. D.. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; BrasilSpringer2015-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/29569Vega Avila, Angela Daniela; Gumiere, T.; Andrade, P. A. M.; Lima Perim, J. E.; Durrer, A.; et al.; Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina; Springer; Antonie van Leeuwenhoek; 107; 2; 2-2015; 575-5880003-6072CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1007/s10482-014-0353-7info:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007%2Fs10482-014-0353-7info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T15:09:13Zoai:ri.conicet.gov.ar:11336/29569instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-15 15:09:14.072CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina
title Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina
spellingShingle Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina
Vega Avila, Angela Daniela
Bacterial Communities
Cultivation
Cultivationindependent
Plant?Microbe Interactions
Rhizosphere Microbiome
Organic Management
title_short Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina
title_full Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina
title_fullStr Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina
title_full_unstemmed Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina
title_sort Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina
dc.creator.none.fl_str_mv Vega Avila, Angela Daniela
Gumiere, T.
Andrade, P. A. M.
Lima Perim, J. E.
Durrer, A.
Baigori, Mario Domingo
Vazquez, Fabio
Andreote, F. D.
author Vega Avila, Angela Daniela
author_facet Vega Avila, Angela Daniela
Gumiere, T.
Andrade, P. A. M.
Lima Perim, J. E.
Durrer, A.
Baigori, Mario Domingo
Vazquez, Fabio
Andreote, F. D.
author_role author
author2 Gumiere, T.
Andrade, P. A. M.
Lima Perim, J. E.
Durrer, A.
Baigori, Mario Domingo
Vazquez, Fabio
Andreote, F. D.
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Bacterial Communities
Cultivation
Cultivationindependent
Plant?Microbe Interactions
Rhizosphere Microbiome
Organic Management
topic Bacterial Communities
Cultivation
Cultivationindependent
Plant?Microbe Interactions
Rhizosphere Microbiome
Organic Management
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.5
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Plants interact with a myriad of microbial cells in the rhizosphere, an environment that is considered to be important for plant development. However, the differential structuring of rhizosphere microbial communities due to plant cultivation under differential agricultural practices remains to be described for most plant species. Here we describe the rhizosphere microbiome of grapevine cultivated under conventional and organic practices, using a combination of cultivation-independent approaches. The quantification of bacterial 16S rRNA and nifH genes, by quantitative PCR (qPCR), revealed similar amounts of these genes in the rhizosphere in both vineyards. PCR-DGGE was used to detect differences in the structure of bacterial communities, including both the complete whole communities and specific fractions, such as Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and those harboring the nitrogen-fixing related gene nifH. When analyzed by a multivariate approach (redundancy analysis), the shifts observed in the bacterial communities were poorly explained by variations in the physical and chemical characteristics of the rhizosphere. These approaches were complemented by high-throughput sequencing (67,830 sequences) based on the V6 region of the 16S rRNA gene, identifying the major bacterial groups present in the rhizosphere of grapevines: Proteobacteria, Actinobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Cloroflexi, Verrucomicrobia and Planctomycetes, which occur in distinct proportions in the rhizosphere from each vineyard. The differences might be related to the selection of plant metabolism upon distinct reservoirs of microbial cells found in each vineyard. The results fill a gap in the knowledge of the rhizosphere of grapevines and also show distinctions in these bacterial communities due to agricultural practices.
Fil: Vega Avila, Angela Daniela. Universidad Nacional de San Juan. Facultad de Ingeniería. Instituto de Biotecnología; Argentina. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; Brasil. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Gumiere, T.. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; Brasil
Fil: Andrade, P. A. M.. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; Brasil
Fil: Lima Perim, J. E.. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; Brasil
Fil: Durrer, A.. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; Brasil
Fil: Baigori, Mario Domingo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Planta Piloto de Procesos Industriales Microbiologicos; Argentina
Fil: Vazquez, Fabio. Universidad Nacional de San Juan. Facultad de Ingeniería. Instituto de Biotecnología; Argentina
Fil: Andreote, F. D.. Universidade Do Sao Paulo. Escola Superior de Agricultura Luiz de Queiroz Esalq; Brasil
description Plants interact with a myriad of microbial cells in the rhizosphere, an environment that is considered to be important for plant development. However, the differential structuring of rhizosphere microbial communities due to plant cultivation under differential agricultural practices remains to be described for most plant species. Here we describe the rhizosphere microbiome of grapevine cultivated under conventional and organic practices, using a combination of cultivation-independent approaches. The quantification of bacterial 16S rRNA and nifH genes, by quantitative PCR (qPCR), revealed similar amounts of these genes in the rhizosphere in both vineyards. PCR-DGGE was used to detect differences in the structure of bacterial communities, including both the complete whole communities and specific fractions, such as Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and those harboring the nitrogen-fixing related gene nifH. When analyzed by a multivariate approach (redundancy analysis), the shifts observed in the bacterial communities were poorly explained by variations in the physical and chemical characteristics of the rhizosphere. These approaches were complemented by high-throughput sequencing (67,830 sequences) based on the V6 region of the 16S rRNA gene, identifying the major bacterial groups present in the rhizosphere of grapevines: Proteobacteria, Actinobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Cloroflexi, Verrucomicrobia and Planctomycetes, which occur in distinct proportions in the rhizosphere from each vineyard. The differences might be related to the selection of plant metabolism upon distinct reservoirs of microbial cells found in each vineyard. The results fill a gap in the knowledge of the rhizosphere of grapevines and also show distinctions in these bacterial communities due to agricultural practices.
publishDate 2015
dc.date.none.fl_str_mv 2015-02
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/29569
Vega Avila, Angela Daniela; Gumiere, T.; Andrade, P. A. M.; Lima Perim, J. E.; Durrer, A.; et al.; Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina; Springer; Antonie van Leeuwenhoek; 107; 2; 2-2015; 575-588
0003-6072
CONICET Digital
CONICET
url http://hdl.handle.net/11336/29569
identifier_str_mv Vega Avila, Angela Daniela; Gumiere, T.; Andrade, P. A. M.; Lima Perim, J. E.; Durrer, A.; et al.; Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina; Springer; Antonie van Leeuwenhoek; 107; 2; 2-2015; 575-588
0003-6072
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1007/s10482-014-0353-7
info:eu-repo/semantics/altIdentifier/url/https://link.springer.com/article/10.1007%2Fs10482-014-0353-7
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1846083239744110592
score 13.221938

Publicaciones similares