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Molecular identification of Azospirillum spp.: limitations of 16S rRNA and qualities of rpoD as genetic markers
Resumen
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
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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.
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Fuente
Microbiological research 195 : 1-10. (January 2017)
Fecha
2017
ISSN
0944-5013
Formato
pdf
Tipo de documento
artículo
Palabras Claves
Derechos de acceso
Abierto
Excepto donde se diga explicitamente, este item se publica bajo la siguiente descripción: Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Unported (CC BY-NC-SA 2.5)