Molecular identification of Azospirillum spp.: limitations of 16S rRNA and qualities of rpoD as genetic markers

Autores
Maroniche, Guillermo Andrés; Garcia, Julia Elena; Salcedo, Florencia; Creus, Cecilia Mónica
Año de publicación
2017
Idioma
inglés
Tipo de recurso
artículo
Estado
versión aceptada
Descripción
Since their discovery, plant-growth promoting rhizobacteria from the genus Azospirillum have been sub-jected to intensive research due to their biotechnological potential as crop inoculants. Phylogeneticanalysis of Azospirillum spp. is carried out by 16S rRNA sequencing almost exclusively, but inconsis-tencies and low confidence often arise when working with close species. In this work, it was observedthat these difficulties might be explained by a high number of rRNA operons with considerable inter-genic variability within Azospirillum genomes. To search for alternative genetic markers from a list ofhousekeeping genes, the correlation between pairwise gene and whole-genome similarities was exam-ined. Due to its good performance, rpoD was selected for further analyses. Genus-specific primers for thePCR-amplification and sequencing of rpoD from Azospirillum spp. were designed and tested on 16 typestrains of different species. The sequences obtained were used for inferring a phylogenetic tree of thegenus, which was in turn used as a reference to successfully identify a collection of 31 azospirilla iso-lated from many different locations of Argentine. In addition, several strains that might represent novelspecies were detected. The results indicate that the sequencing of rpoD is a suitable alternative methodfor a confident molecular identification in Azospirillum spp.
Inst. de Microbiología y Zoología Agrícola IMyZA
Fil: Maroniche, Guillermo Andrés. Unidad Integrada Balcarce-Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias-Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Garcia, Julia Elena. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Microbiología y Zoología Agrícola; Argentina
Fil: Salcedo, Florencia. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Creus, Cecilia Mónica. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina
Fuente
Microbiological research 195 : 1-10. (January 2017)
Materia
Azospirillum
Marcadores Genéticos
Rizobacterias
Genotipos
Genetic Markers
Rhizobacteria
Genotypes
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
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spelling Molecular identification of Azospirillum spp.: limitations of 16S rRNA and qualities of rpoD as genetic markersMaroniche, Guillermo AndrésGarcia, Julia ElenaSalcedo, FlorenciaCreus, Cecilia MónicaAzospirillumMarcadores GenéticosRizobacteriasGenotiposGenetic MarkersRhizobacteriaGenotypesSince their discovery, plant-growth promoting rhizobacteria from the genus Azospirillum have been sub-jected to intensive research due to their biotechnological potential as crop inoculants. Phylogeneticanalysis of Azospirillum spp. is carried out by 16S rRNA sequencing almost exclusively, but inconsis-tencies and low confidence often arise when working with close species. In this work, it was observedthat these difficulties might be explained by a high number of rRNA operons with considerable inter-genic variability within Azospirillum genomes. To search for alternative genetic markers from a list ofhousekeeping genes, the correlation between pairwise gene and whole-genome similarities was exam-ined. Due to its good performance, rpoD was selected for further analyses. Genus-specific primers for thePCR-amplification and sequencing of rpoD from Azospirillum spp. were designed and tested on 16 typestrains of different species. The sequences obtained were used for inferring a phylogenetic tree of thegenus, which was in turn used as a reference to successfully identify a collection of 31 azospirilla iso-lated from many different locations of Argentine. In addition, several strains that might represent novelspecies were detected. The results indicate that the sequencing of rpoD is a suitable alternative methodfor a confident molecular identification in Azospirillum spp.Inst. de Microbiología y Zoología Agrícola IMyZAFil: Maroniche, Guillermo Andrés. Unidad Integrada Balcarce-Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias-Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Garcia, Julia Elena. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Microbiología y Zoología Agrícola; ArgentinaFil: Salcedo, Florencia. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Creus, Cecilia Mónica. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina2017-08-24T13:50:00Z2017-08-24T13:50:00Z2017info:eu-repo/semantics/articleinfo:eu-repo/semantics/acceptedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/1032http://www.sciencedirect.com/science/article/pii/S0944501316307327?via%3Dihub0944-5013https://doi.org/10.1016/j.micres.2016.11.009Microbiological research 195 : 1-10. (January 2017)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-10-16T09:28:59Zoai:localhost:20.500.12123/1032instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-10-16 09:28:59.525INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Molecular identification of Azospirillum spp.: limitations of 16S rRNA and qualities of rpoD as genetic markers
title Molecular identification of Azospirillum spp.: limitations of 16S rRNA and qualities of rpoD as genetic markers
spellingShingle Molecular identification of Azospirillum spp.: limitations of 16S rRNA and qualities of rpoD as genetic markers
Maroniche, Guillermo Andrés
Azospirillum
Marcadores Genéticos
Rizobacterias
Genotipos
Genetic Markers
Rhizobacteria
Genotypes
title_short Molecular identification of Azospirillum spp.: limitations of 16S rRNA and qualities of rpoD as genetic markers
title_full Molecular identification of Azospirillum spp.: limitations of 16S rRNA and qualities of rpoD as genetic markers
title_fullStr Molecular identification of Azospirillum spp.: limitations of 16S rRNA and qualities of rpoD as genetic markers
title_full_unstemmed Molecular identification of Azospirillum spp.: limitations of 16S rRNA and qualities of rpoD as genetic markers
title_sort Molecular identification of Azospirillum spp.: limitations of 16S rRNA and qualities of rpoD as genetic markers
dc.creator.none.fl_str_mv Maroniche, Guillermo Andrés
Garcia, Julia Elena
Salcedo, Florencia
Creus, Cecilia Mónica
author Maroniche, Guillermo Andrés
author_facet Maroniche, Guillermo Andrés
Garcia, Julia Elena
Salcedo, Florencia
Creus, Cecilia Mónica
author_role author
author2 Garcia, Julia Elena
Salcedo, Florencia
Creus, Cecilia Mónica
author2_role author
author
author
dc.subject.none.fl_str_mv Azospirillum
Marcadores Genéticos
Rizobacterias
Genotipos
Genetic Markers
Rhizobacteria
Genotypes
topic Azospirillum
Marcadores Genéticos
Rizobacterias
Genotipos
Genetic Markers
Rhizobacteria
Genotypes
dc.description.none.fl_txt_mv Since their discovery, plant-growth promoting rhizobacteria from the genus Azospirillum have been sub-jected to intensive research due to their biotechnological potential as crop inoculants. Phylogeneticanalysis of Azospirillum spp. is carried out by 16S rRNA sequencing almost exclusively, but inconsis-tencies and low confidence often arise when working with close species. In this work, it was observedthat these difficulties might be explained by a high number of rRNA operons with considerable inter-genic variability within Azospirillum genomes. To search for alternative genetic markers from a list ofhousekeeping genes, the correlation between pairwise gene and whole-genome similarities was exam-ined. Due to its good performance, rpoD was selected for further analyses. Genus-specific primers for thePCR-amplification and sequencing of rpoD from Azospirillum spp. were designed and tested on 16 typestrains of different species. The sequences obtained were used for inferring a phylogenetic tree of thegenus, which was in turn used as a reference to successfully identify a collection of 31 azospirilla iso-lated from many different locations of Argentine. In addition, several strains that might represent novelspecies were detected. The results indicate that the sequencing of rpoD is a suitable alternative methodfor a confident molecular identification in Azospirillum spp.
Inst. de Microbiología y Zoología Agrícola IMyZA
Fil: Maroniche, Guillermo Andrés. Unidad Integrada Balcarce-Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias-Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Garcia, Julia Elena. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Microbiología y Zoología Agrícola; Argentina
Fil: Salcedo, Florencia. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Creus, Cecilia Mónica. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina
description Since their discovery, plant-growth promoting rhizobacteria from the genus Azospirillum have been sub-jected to intensive research due to their biotechnological potential as crop inoculants. Phylogeneticanalysis of Azospirillum spp. is carried out by 16S rRNA sequencing almost exclusively, but inconsis-tencies and low confidence often arise when working with close species. In this work, it was observedthat these difficulties might be explained by a high number of rRNA operons with considerable inter-genic variability within Azospirillum genomes. To search for alternative genetic markers from a list ofhousekeeping genes, the correlation between pairwise gene and whole-genome similarities was exam-ined. Due to its good performance, rpoD was selected for further analyses. Genus-specific primers for thePCR-amplification and sequencing of rpoD from Azospirillum spp. were designed and tested on 16 typestrains of different species. The sequences obtained were used for inferring a phylogenetic tree of thegenus, which was in turn used as a reference to successfully identify a collection of 31 azospirilla iso-lated from many different locations of Argentine. In addition, several strains that might represent novelspecies were detected. The results indicate that the sequencing of rpoD is a suitable alternative methodfor a confident molecular identification in Azospirillum spp.
publishDate 2017
dc.date.none.fl_str_mv 2017-08-24T13:50:00Z
2017-08-24T13:50:00Z
2017
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/acceptedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/1032
http://www.sciencedirect.com/science/article/pii/S0944501316307327?via%3Dihub
0944-5013
https://doi.org/10.1016/j.micres.2016.11.009
url http://hdl.handle.net/20.500.12123/1032
http://www.sciencedirect.com/science/article/pii/S0944501316307327?via%3Dihub
https://doi.org/10.1016/j.micres.2016.11.009
identifier_str_mv 0944-5013
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv Microbiological research 195 : 1-10. (January 2017)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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