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

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.

European Population of Pectobacterium punjabense: Genomic Diversity, Tuber Maceration Capacity and a Detection Tool for This Rarely Occurring Potato Pathogen

“…In recent surveys of water from French rivers, no P. punjabense have been isolated [ 63 ], while P. versatile [ 10 ] or P. aquaticum [ 17 ] were recovered. P. punjabense was also not found within the French Collection for Plant-associated Bacteria (CIRM-CFBP), which includes over 265 Pectobacterium strains isolated from 1944 to 2020 and which represent isolates from a high diversity of plants [ 28 ]. Furthermore, the low incidence of P. punjabense strains sampled from blackleg-diseased plants in comparison to other species of Pectobacterium, such as P. brasiliense , P. parmentieri or P. atrosepticum , indicates that the potato plant is probably not the preferred host for this species.…”

“…wasabiae and Erwinia chrysanthemi [ 21 , 22 , 23 ]. On the basis of the current taxonomy, P. atrosepticum , P. brasiliense, P. parmentieri, P. versatile , P. polaris and P. carotovorum are the most prevalent Pectobacterium species responsible for soft rot and/or blackleg diseases [ 24 , 25 , 26 , 27 , 28 , 29 , 30 ]. It should be noted, however, that the ability of pectinolytic bacteria to grow as well as develop blackleg and soft rot symptoms depends on many environmental factors such as temperature and humidity, in a species-dependent way [ 31 ].…”

Pectobacterium brasiliense: Genomics, Host Range and Disease Management

“…Infection of cucumber was reported in China [ 6 ] and South Africa [ 90 ], and was characterized by the appearance of gummosis on the surface of leaves, stems, petioles, and fruits, dark brown coloration of the basal stems, as well as yellow spots could sometimes emerge at the edge of infected leaves [ 6 ]. The infection of zucchini were reported in Poland [ 69 ], Serbia [ 65 ], Austria [ 91 ], Brazil [ 92 ], and Italy [ 88 ], and was characterized by water-soaked lesions and fruits macerating. Infection of squash and watermelon were reported in Northern Serbia [ 65 ] with disease appearing in squash as light brown, slightly sunken, soft, and macerated tissue with the presence of a water-soaked lesions.…”

“…This study isolated the pathogens from different cultivars of banana ( Musa sp.) in India and the French overseas territory Martinique [ 64 , 88 ], in which the pathogen causing rhizome rot was characterized by disagreeable foul-smelling and internal decay of the pseudostem [ 64 ].…”

“…Moreover, Pbr has been isolated from non-host environment, including water in Spain and the rhizosphere of S. dulcamara in France [ 34 , 88 ]. Pbr is considered a major threat for horticulture crops in these regions, as can be easily transmitted to other fields through irrigation water systems or by its persistence in the soil.…”