Two species with a peculiar evolution within the genus Pectobacterium suggest adaptation to a new environmental niche

Abstract

Historically, research on Soft Rot Pectobacteriacea (SRP) has focused on economically important crops and ornamentals and knowledge of these bacteria outside the plant context remains poorly investigated. Recently, two closely related species Pectobacterium aquaticum and Pectobacterium quasiaquaticum were isolated from water and have not been isolated from any plant yet. To identify the distinctive characteristics of these two species, we performed a comparative genomic analysis of 80 genomes representing 19 Pectobacterium species and performed an evolutionary reconstruction. Both water species underwent a reduction in genome size associated with a high pseudogene content. A high gene loss was predicted at the emergence of both species. Among the 199 gene families missing from both P. aquaticum and P. quasiaquaticum genomes but present in at least 80% of other Pectobacterium genomes, COG analysis identified many genes involved in nutrient transport systems. In addition, many type II secreted proteins were also missing in both species. Phenotypic analysis revealed that both species had reduced pectinolytic activity, a biofilm formation defect, were highly motile and had reduced virulence on several plants. These genomic and phenotypic data suggest that the ecological niche of P. aquaticum and P. quasiaquaticum may differ from that of other Pectobacterium species.

Bacterial pathogens dynamic during multi-species infections

“…After inoculation with P. aquaticum , bacterial multiplication within the tubers was much lower than with other single inoculated single species, confirming P. aquaticum poor ability to rot potato tuber (Fig. 2B) as already described (Ben Moussa et al, 2023). The addition of either P. versatile or P. aquaticum to the inoculation mix did not affect the severity of the symptoms observed compared to the other single species inoculation but P. aquaticum (Fig.…”

“…We noticed here the poor capacity of the P. aquaticum strains to rot potato tuber and to multiply within symptoms (Fig. 2), a phenotypic trait that was already described previously (Ben Moussa et al 2023). We observed nevertheless, that P. aquaticum when co-inoculated with another species, could be maintained and even become dominant in several synthetic communities tested (Fig.…”

“…2). This is a previously described phenotypic trait that could be linked to a reduced production of PCWDEs (Ben Moussa et al 2023). We observed nevertheless, that P. aquaticum when co-inoculated with another species, could be maintained and even become dominant in several synthetic communities tested (Fig.…”

“…(Royer et al 2022; Smoktunowicz et al 2022; Ben Moussa et al 2022; Portier et al 2020) but this species is currently considered as a minor pathogen not responsible for severe outbreaks but frequent companion species during disease or on symptomless plants (Curland et al 2021; Ma et al 2022; Smoktunowicz et al 2022). Some newly described species like Pectobacterium aquaticum or Pectobacterium quasiaquaticum have been isolated solely from river water and their potential host plants (if any) are currently unknown raising the possibility that these species act are merely saprophytes on plant debris or evolved toward hosts alternative to plant, for example as gut species of plant feeding insect or water microfauna (Pédron et al 2019; Ben Moussa et al 2022, 2023). Species belonging to the Dickeya genus are well known to infect ornamentals of high economical value but several species could also be observed on major crops such as maize ( Dickeya zeae ) rice ( Dickeya oryzae ) or potato ( Dickeya dianthicola or D. solani ) where they have been responsible of severe outbreaks (Hugouvieux-Cotte-Pattat et al 2023).…”

Bacterial pathogens dynamic during multi-species infections

“…2). This is a previously described phenotypic trait that could be linked to a reduced production of PCWDEs (Ben Moussa et al, 2023). We observed nevertheless, that P. aquaticum when co-inoculated with another species, could be maintained and even become dominant in several synthetic communities tested (Fig.…”