Population Structure and Biodiversity of Pectobacterium parmentieri Isolated from Potato Fields in Temperate Climate

Abstract

Pectobacterium parmentieri (formerly Pectobacterium wasabiae) is a newly established species of pectinolytic plant-pathogenic bacteria responsible for the symptoms of soft rot and blackleg on potato. In this work, we describe biodiversity and the population structure of P. parmentieri strains isolated during two consecutive growing seasons from the seed potato fields in Poland. About 450 samples of diseased potato tubers, potato plants, or accompanying weeds were collected throughout the country and tested for the presence of P. parmentieri by molecular identification methods. We found that P. parmentieri strains commonly occur in almost all regions of Poland. Furthermore, these isolates constituted significant fraction of pectinolytic bacteria from seed potato fields because 16% (2013) and 13% (2014) of the analyzed plant samples were infected with P. parmentieri. Subsequently, a detailed characterization of the obtained strains was conducted basing on repetitive sequences profiling, recA-gene-based phylogeny, and phenotypic features. By applying repetitive extragenic palindromic sequence-based polymerase chain reaction (REP-PCR), we revealed the presence of five distinct genomic profiles among P. parmentieri strains, with profile I being the most abundant (approximately 44%). The performed recA gene-based phylogenetic analysis divided P. parmentieri isolates into two distinct clades, although the strains originating from different years did not group separately. Evaluation of the phenotypic traits playing crucial roles for the virulence of pectinolytic bacteria (namely, pectinase, cellulase and protease activities, and siderophore production, in addition to potato tissue maceration, swimming, and swarming motility) indicated some differences among the characterized strains. To the best of our knowledge, this is the first study that describes biodiversity and the population structure of P. parmentieri isolated in two growing seasons under temperate climate conditions and, hence, illustrates high heterogeneity within this species.

High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes

“…The here-described P. parmentieri intraspecies variation is in agreement with several previous studies, in which P. parmentieri isolates differed in the plant maceration efficacy and PCWDE activities [ 20 , 21 , 23 , 24 , 28 ].…”

“…P. parmentieri strains used in this study are presented in Table 1 . Ten of these strains originating from Poland have been partially described previously regarding their phenotypic features [ 21 ]. The additional two strains have been isolated in Belgium by Johan van Vaerenbergh (ILVO, Belgium) and are included in this type of analysis for the first time.…”

“…The maceration ability of the selected P. parmentieri strains was evaluated by performing the potato slice assay as previously described [ 21 ]. Briefly, potatoes (cv.…”

“…The activity of pectinases, cellulases, proteases, siderophores as well as swarming motility was performed as described before [ 21 ]. To obtain consistent results and prevent undirected bacterial movement, swimming motility was evaluated on NB medium supplemented with 0.3% agar and also 0.4% PGA (Sigma-Aldrich, USA) [ 66 ].…”

Metabolic modeling of Pectobacterium parmentieri SCC3193 provides insights into metabolic pathways of plant pathogenic bacteria

“…These Gram(-), rod-shaped bacteria are necrotrophs, that are able to destroy plant tissue components through the activity of PCWDE such as pectinases, cellulases, and proteases, further secreted via Type I or II secretion system 8,9 . Nonetheless, bacteria belonging to this species can exhibit a different level of activities of above-mentioned enzymes 10 . Pectinolytic bacteria, and among them P. parmentieri , require favorable environmental conditions to cause disease symptoms; however, they can reside inside plant tissues as endophytes for a long time 11 .…”