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Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex

The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR) with potential applications in biocontrol and biofertilization. So far the phy...

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Autores principales: Garrido-Sanz, Daniel, Meier-Kolthoff, Jan P., Göker, Markus, Martín, Marta, Rivilla, Rafael, Redondo-Nieto, Miguel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4767706/
https://www.ncbi.nlm.nih.gov/pubmed/26915094
http://dx.doi.org/10.1371/journal.pone.0150183
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author Garrido-Sanz, Daniel
Meier-Kolthoff, Jan P.
Göker, Markus
Martín, Marta
Rivilla, Rafael
Redondo-Nieto, Miguel
author_facet Garrido-Sanz, Daniel
Meier-Kolthoff, Jan P.
Göker, Markus
Martín, Marta
Rivilla, Rafael
Redondo-Nieto, Miguel
author_sort Garrido-Sanz, Daniel
collection PubMed
description The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR) with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH) identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI) approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as PGPR.
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spelling pubmed-47677062016-03-09 Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex Garrido-Sanz, Daniel Meier-Kolthoff, Jan P. Göker, Markus Martín, Marta Rivilla, Rafael Redondo-Nieto, Miguel PLoS One Research Article The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR) with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH) identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI) approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as PGPR. Public Library of Science 2016-02-25 /pmc/articles/PMC4767706/ /pubmed/26915094 http://dx.doi.org/10.1371/journal.pone.0150183 Text en © 2016 Garrido-Sanz et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Garrido-Sanz, Daniel
Meier-Kolthoff, Jan P.
Göker, Markus
Martín, Marta
Rivilla, Rafael
Redondo-Nieto, Miguel
Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex
title Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex
title_full Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex
title_fullStr Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex
title_full_unstemmed Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex
title_short Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex
title_sort genomic and genetic diversity within the pseudomonas fluorescens complex
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4767706/
https://www.ncbi.nlm.nih.gov/pubmed/26915094
http://dx.doi.org/10.1371/journal.pone.0150183
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