Updated Taxonomy of Pectobacterium Genus in the CIRM-CFBP Bacterial Collection: When Newly Described Species Reveal "Old" Endemic Population.

Perrine Portier,Cécile Dutrieux,Géraldine Taghouti,Marie-Anne Barny,Jacques Pédron

doi:10.3390/microorganisms8091441

Abstract

Bacterial collections are invaluable tools for microbiologists. However, their practical use is compromised by imprecise taxonomical assignation of bacterial strains. This is particularly true for soft rotting plant pathogens of the Pectobacterium genus. We analysed the taxonomic status of 265 Pectobacterium strains deposited at CIRM-CFBP collection from 1944 to 2020. This collection gathered Pectobacterium strains isolated in 27 countries from 32 plant species representing 17 botanical families or from nonhost environments. The MLSA approach completed by genomic analysis of 15 strains was performed to update the taxonomic status of these 265 strains. The results showed that the CIRM-CFBP Pectobacterium collection harboured at least one strain of each species, with the exception of P. polonicum. Yet, seven strains could not be assigned to any of the described species and may represent at least two new species. Surprisingly, P. versatile, recently described in 2019, is the most prevalent species among CIRM-CFBP strains. An analysis of P. versatile strains revealed that this species is pandemic and isolated from various host plants and environments. At the opposite, other species gathered strains isolated from only one botanical family or exclusively from a freshwater environment. Our work also revealed new host plants for several Pectobacterium spp.

Highlights

Bacterial collections are invaluable tools for microbiologists, as they host many strains isolated at different times on different hosts or environments and on different countries and continents
Concerning the host plants or environments from which these 265 strains were isolated, a large majority of 136 strains were isolated from potato tubers or potato plants, accounting for the threat provoked by Pectobacterium spp. on this economically important crop plant (Figure 1B) [4]
The studied collection gathered 100 strains isolated from 31 host plants covering 17 botanical families, accounting for the broad host range of Pectobacterium spp. [3], as well as 29 strains isolated from freshwater, soil or rhizosphere

Summary

Introduction

Bacterial collections are invaluable tools for microbiologists, as they host many strains isolated at different times on different hosts or environments and on different countries and continents As such, they summarise the collective sampling and research efforts performed by bacteriologists from all over the world on many different bacterial species. They summarise the collective sampling and research efforts performed by bacteriologists from all over the world on many different bacterial species This collective treasure is often underexploited for several reasons, the main one being the poor taxonomical assignation of many deposited strains to current taxonomical standard. Currently, collections harbour many strains with old names no longer reflecting their actual taxonomical status Such ancient strains are important to understand the epidemiology of a given species, when and where a particular species was first isolated in the world and what is its historical prevalence all over the world

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Conclusion