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Genome Sequence and Antifungal Activity of Two Niche-Sharing Pseudomonas protegens Related Strains Isolated from Hydroponics

  • Cesare Polano
  • Marta Martini
  • Francesco Savian
  • Serena Moruzzi
  • Paolo Ermacora
  • Giuseppe Firrao
Genes and Genomes

Abstract

This work reports the comparison of the genome sequence and the ability to inhibit fungal growth of two Pseudomonas protegens related strains that were isolated from the same hydroponic culture of lamb’s lettuce. The two strains were very similar in their core genome but one strain, Pf4, contained three gene clusters for the production of secondary metabolites, i.e., pyoluteorin (plt), pyrrolnitrin (prn), and rhizoxin (rzx), that were missing in the other strain, Pf11. The difference between the two strains was not due to simple insertion events, but to a relatively complex differentiation focused on the accessory genomes. In dual culture assays, both strains inhibited nearly all tested fungal strains, yet Pf4 exerted a significantly stronger fungal growth inhibition than Pf11. In addition to the differences in the secondary metabolite production associated genes abundance, the genome of Pf4 was more stable, smaller in size and with a lower number of transposons. The preservation of a dynamic equilibrium within natural populations of different strains comprised in the same species but differing in their secondary metabolite repertoire and in their genome stability may be functional to the adaptation to environmental changes.

Keywords

Biocontrol Floating system Population dynamic Pseudomonads Genome draft 

Notes

Acknowledgments

This research was supported by a grant (L. R. 26) from Friuli Venezia Giulia Region Administration (Italy) and by “Ager – Agroalimentare e Ricerca” Foundation, project “Novel strategies meeting the needs of the fresh-cut vegetable sector – STAYFRESH,” no. 2370.

Supplementary material

248_2018_1238_MOESM1_ESM.pdf (160 kb)
ESM 1 (PDF 160 kb)
248_2018_1238_MOESM2_ESM.csv (22 kb)
Table S1 Genes exclusive to Pf4 as determined by the stand-alone OMA program.450 (CSV 21 kb)
248_2018_1238_MOESM3_ESM.csv (37 kb)
Table S2 –Genes exclusive to Pf11 as determined by the stand-alone OMA program. (CSV 37 kb)
248_2018_1238_MOESM4_ESM.doc (238 kb)
Table S3 Sequence analysis of gene clusters for the synthesis of antibiotics, exoenzyme, cyclic lipopeptide, siderophores, and toxin, and of Gac/Rsm homologs in P. protegens Pf11 and Pf-4455 and similarities to those in P. protegens strains (Pf-5, PH1b) and other closely related Pseudomonassp.(CMAA1215, NFPP17, Os17). Gene clusters present only in Pf-4 are: pyoluteorin (plt), pyrrolnitrin (prn), rhizoxin (rzx). Gene clusters present in both are: hydrogen cyanide (hcn), 2,4-diacetylphloroglucinol (phl), AprX protease (apr), gac/rsmhomologues, small regulatory RNAs, pyoverdine (pvd), enantio-pyochelin 460 (pch), hemophore biosynthesis (has), ferric-enterobactin receptor (pfe), orfamide A (ofa), and FitD toxin (fit). (DOC 237 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Agricultural, Food, Environmental and Animal Sciences (DI4A)University of UdineUdineItaly
  2. 2.National Institute of Biostructures and BiosystemsRomeItaly

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