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Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex
Daniel Garrido-Sanz1, Jan P Meier-Kolthoff2, Markus Göker2
1Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin, 2, Madrid, 28049, Spain.
Plos One
|February 26, 2016
Summary
The Pseudomonas fluorescens complex was divided into eight phylogenomic groups using whole-genome analysis, revealing significant genetic diversity and potential for biocontrol and biofertilization applications. This study clarifies taxonomy and highlights the complex
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- The Pseudomonas fluorescens complex comprises over 50 species, many identified as plant growth-promoting rhizobacteria (PGPR).
- Previous phylogenetic analyses relied on phenotypic traits, 16S rDNA, and MLSA, with limited whole-genome data hindering taxonomic accuracy.
- Genomic heterogeneity within the complex necessitates updated phylogenomic approaches for accurate classification.
Purpose of the Study:
- To establish a robust phylogenomic framework for the Pseudomonas fluorescens complex.
- To correlate genomic data with existing taxonomic classifications.
- To explore the genomic diversity and identify traits relevant to PGPR and biocontrol applications.
Main Methods:
- Phylogenomic analysis of 93 sequenced strains using Multi-Locus Sequence Analysis (MLSA).
- Whole-genome sequence-based analyses, including digital DNA-DNA hybridization (dDDH) and Average Nucleotide Identity (ANI).
- Identification and analysis of group-specific genomic content and distinctive traits.
Main Results:
- The P. fluorescens complex was resolved into eight distinct phylogenomic groups, consistent with MLSA and dDDH clustering.
- Digital DDH identified 69 species and 75 subspecies within the analyzed genomes.
- Average Nucleotide Identity (ANI) showed inconsistencies in species and group assignments.
- A small core genome (1,334 CDSs) and a large pan-genome (30,848 CDSs) highlight extensive genetic diversity.
- Group-specific genomic analyses revealed phylogenomic distribution of traits relevant to PGPR and bioremediation.
Conclusions:
- The study provides a refined phylogenomic classification of the P. fluorescens complex into eight groups.
- Genomic data confirms significant genetic and functional diversity within the complex.
- Identified traits offer insights into the ecological roles and biotechnological potential of P. fluorescens strains, particularly as PGPR and in bioremediation.
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