Genetics and Functional Genomics of the Pseudomonas fluorescens Group

Seaton, Sarah C.; Silby, Mark W.

doi:10.1007/978-3-642-55378-3_5

Cited by 5 publications

(14 citation statements)

References 114 publications

(144 reference statements)

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“…fluorescens group [ 22 , 23 ] have led into a difficult assessment of its phylogeny that does not fully encompass the taxonomy, and, the proposal that a species complex is shaping the P . fluorescens group phylogeny [ 23 , 24 ]. Another difficulty within this group is the frequent description of novel species, such as P .…”

Section: Introductionmentioning

confidence: 99%

Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex

et al. 2016

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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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Section: Introductionmentioning

confidence: 99%

Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex

et al. 2016

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“…The P. fluorescens species group (including P. protegens , P. chlororaphis and other sub‐species) displays very extensive genomic diversity, with a core genome of around 2800 genes supplemented by an accessory genome of 2500–3500 genes (Silby et al ., ; Loper et al ., ; Redondo‐Nieto et al ., ; Seaton and Silby, ). This genomic diversity manifests in a similarly extensive range of different phenotypes (Loper et al ., ), and in turn into marked differences in plant colonization efficiency and biocontrol ability (Naseby et al ., ).…”

Section: Discussionmentioning

confidence: 97%

“…In agreement with previous soil/rhizosphere metagenomic studies, amplicon sequencing of the Great Harpenden 2 field reveals a highly complex and diverse microbial community (Mendes et al ., ; Bulgarelli et al ., ). Subsequent genomic analysis indicated that this diversity extends not only to the level of species/genus, but also to variability within the P. fluorescens species group, with genetic diversity in our single experimental field site only slightly lower than that recorded for all P. fluorescens strains annotated to date (Loper et al ., ; Seaton and Silby, ).…”

Section: Discussionmentioning

confidence: 97%

“…Genetic variation was observed both at the single nucleotide level for core housekeeping genes, and in terms of the variability present in the accessory genome. The pangenome for the 19 sequenced strains in our experiment contains 9907 predicted protein‐coding open reading frames, compared with previously published values of 13 872 (Loper et al ., ) and 13 914 (Seaton and Silby, ) for all annotated Pseudomonas strains. This pangenome encodes an extensive array of phenotypic outputs and secondary metabolite operons, including a substantial proportion of the Pseudomonas output pathways characterized to date.…”

Section: Discussionmentioning

confidence: 99%

“…A major reason for this is an incomplete understanding of the phenotypic characteristics relevant for biocontrol and colonization in different plant environments. The issue is further complicated by the extensive genetic diversity found within the Pseudomonas species group, with the core genome representing as little as 45% of an individual bacterial genome (Silby et al ., ; Loper et al ., ; Redondo‐Nieto et al ., ; Seaton and Silby, ).…”

Section: Introductionmentioning

confidence: 97%

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An analysis of Pseudomonas genomic diversity in take‐all infected wheat fields reveals the lasting impact of wheat cultivars on the soil microbiota

Mauchline

Chedom-Fotso

Chandra

et al. 2015

Environmental Microbiology

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SummaryManipulation of the soil microbiota associated with crop plants has huge promise for the control of crop pathogens. However, to fully realize this potential we need a better understanding of the relationship between the soil environment and the genes and phenotypes that enable microbes to colonize plants and contribute to biocontrol. A recent 2 years of investigation into the effect of wheat variety on second year crop yield in the context of take‐all fungal infection presented the opportunity to examine soil microbiomes under closely defined field conditions. Amplicon sequencing of second year soil samples showed that P seudomonas spp. were particularly affected by the wheat cultivar grown in year one. Consequently, 318 rhizosphere‐associated P seudomonas fluorescens strains were isolated and characterized across a variety of genetic and phenotypic traits. Again, the wheat variety grown in the first year of the study was shown to exert considerable selective pressure on both the extent and nature of P seudomonas genomic diversity. Furthermore, multiple significant correlations were identified within the phenotypic/genetic structure of the Pseudomonas population, and between individual genotypes and the external wheat field environment. The approach outlined here has considerable future potential for our understanding of plant–microbe interactions, and for the broader analysis of complex microbial communities.

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Phylogenomics of 2,4-Diacetylphloroglucinol-Producing Pseudomonas and Novel Antiglycation Endophytes from Piper auritum

et al. 2017

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2,4-Diacetylphloroglucinol (DAPG) (1) is a phenolic polyketide produced by some plant-associated Pseudomonas species, with many biological activities and ecological functions. Here, we aimed at reconstructing the natural history of DAPG using phylogenomics focused at its biosynthetic gene cluster or phl genes. In addition to around 1500 publically available genomes, we obtained and analyzed the sequences of nine novel Pseudomonas endophytes isolated from the antidiabetic medicinal plant Piper auritum. We found that 29 organisms belonging to six Pseudomonas species contain the phl genes at different frequencies depending on the species. The evolution of the phl genes was then reconstructed, leading to at least two clades postulated to correlate with the known chemical diversity surrounding DAPG biosynthesis. Moreover, two of the newly obtained Pseudomonas endophytes with high antiglycation activity were shown to exert their inhibitory activity against the formation of advanced glycation end-products via DAPG and related congeners. Its isomer, 5-hydroxyferulic acid (2), detected during bioactivity-guided fractionation, together with other DAPG congeners, were found to enhance the detected inhibitory activity. This report provides evidence of a link between the evolution and chemical diversity of DAPG and congeners.

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Genetics and Functional Genomics of the Pseudomonas fluorescens Group

Cited by 5 publications

References 114 publications

Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex

Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex

An analysis of Pseudomonas genomic diversity in take‐all infected wheat fields reveals the lasting impact of wheat cultivars on the soil microbiota

Phylogenomics of 2,4-Diacetylphloroglucinol-Producing Pseudomonas and Novel Antiglycation Endophytes from Piper auritum

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