The International Trade of Ware Vegetables and Orna-Mental Plants—An Underestimated Risk of Accelerated Spreading of Phytopathogenic Bacteria in the Era of Globalisation and Ongoing Climatic Changes
by
, ,
Magdalena Smoktunowicz
1, 
Joanna Jonca
2,
Aneta Stachowska
2,
Michal May
2,
Michal Mateusz Waleron
2,
Malgorzata Waleron
2,* and
Krzysztof Waleron
1,* 1
Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdansk, 80-416 Gdansk, Poland
2
Laboratory of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, 80-307 Gdansk, Poland
*
Authors to whom correspondence should be addressed.
Pathogens 2022, 11(7), 728; https://doi.org/10.3390/pathogens11070728
Submission received: 25 April 2022
/
Revised: 18 June 2022
/
Accepted: 22 June 2022
/
Published: 26 June 2022
(This article belongs to the Special Issue Plant Pathogenic Bacteria in Crops)
Abstract
:Bacteria of the genus Pectobacterium are globally occurring pathogens that infect a broad spectrum of plants. The plant cell wall degrading enzymes allow them to cause diseases like soft rot and blackleg. Worldwide trade and exchange of plant material together with the accompanying microorganisms contributed to the rapid spread and consequently the acquisition of new traits by bacteria. The 161 pectinolytic strains were isolated from symptomless vegetables and ornamental plants acquired from Polish and foreign local food markets. All strains except four Dickeya isolates were identified as belonging to the Pectobacterium genus by PCR with species-specific primers and recA gene sequencing. The newly isolated bacteria were assigned to eight species, P. versatile (50 strains), P. carotovorum (33), P. brasiliense (27), P. atrosepticum (19), P. parmentieri (12), P. polaris (11), P. parvum (3) and P. odoriferum (2). ERIC PCR and phenotypic characteristics revealed high heterogeneity among P. carotovorum, P. brasiliense and P. versatile isolates. Moreover, a subset of the newly isolated strains was characterised by high tolerance to changing environmental conditions such as salinity, pH and water availability. These bacteria can effectively macerate the tissues of various plants, including potato, chicory and orchid. Our results indicate that Pectobacterium strains isolated from internationally traded, symptomless vegetables and ornamental plants have high potential for adaptation to adverse environmental conditions and to infect various host plants. These features may contribute to the success of the genus Pectobacterium in spreading between different climatic zones and facilitate the colonisation of different ecological niches.
1. Introduction
Bacteria of the genus Pectobacterium are widespread and cause many diseases on a wide range of economically important plants worldwide. Those bacteria have a broad host range, and most do not demonstrate specificity for host plants. Although the genus Pectobacterium is known mainly as plant pathogens, they may also be saprophytes [1]. Nevertheless, the infections with these pathogens lead to severe economic losses of horticultural and ornamental plants in the fields and during their storage. Thus, the genus is recognised as one of the ten most important bacterial plant pathogens and is the subject of research by numerous groups of scientists [2].
The taxonomy of the genus Pectobacterium is being constantly rearranged. Currently, twenty different Pectobacterium species, P. actinidiae, P. aquaticum, P. aroidearum, P. atrosepticum, P. betavasculorum, P. brasiliense, P. cacticidum, P. carotovorum, P. fontis, P. odoriferum, P. peruviense, P. polaris, P. polonicum, P. parmentieri, P. parvum, P. punjabense, P. quasiaquaticum, P. versatile, P. wasabiae and P. zantedeschiae have been described [3].
Most Pectobacterium species can inhabit and infect different plant species; however, P. aroidearum and P. zantedeschiae have been mainly isolated from monocotyledonous [4,5]. Strains of P. wasabiae are isolated from horseradish in Japan [6], P. actinidiae from kiwi [7], and P. betavasculorum derived from sugar beets, potato, artichoke, and sunflower [8]. Apart from this, P. cacticidum occurs only in desert regions where bacteria inhabit different cacti [9], while the species P. atrosepticum is much more common in cooler climates, and it is isolated from potatoes most often [10]. It is likewise for recently described species P. polaris [11], P. parvum [12], P. parmentieri [13], P. peruviense [14], and P. punjabense [15,16].
However, the species P. carotovorum, P. brasiliense, P. odoriferum and P. versatile have been isolated from various plants and different climatic zones [3,17,18]. Moreover, P. versatile [19], P. odoriferum [20] and P. brasiliense [21] have been isolated from invertebrates. In contrast, P. fontis [22], P. aquaticum [23], P. polonicum [24] and P. quasiaquaticum [25] have been isolated from water.
It can be noted that the cardinal temperatures for individual Pectobacterium species [26] correlate with climatic regions in which the common occurrence of particular species is recorded. For example, the growth temperature for the Pectobacterium genus ranges from 20 °C to 34 °C and 43 °C for P. cacticidum [9,26].
In addition to the differences in the optimal growth temperature, species within the genus Pectobacterium are biochemically diverse. They differ in the use of nutrients and the production of plant cell wall degrading enzymes (PCWDEs) like pectin lyases, cellulases, proteases or amylases [27]. However, the analysis of physiological and biochemical properties of Pectobacterium strains does not provide sufficient information to classify newly isolated strains to a particular species [28]. Detailed identification of Pectobacterium strains is possible by PCR that uses primers specific for a given species, e.g., P. atrosepticum [29], P. brasiliense [30] or P. wasabiae and P. parmentieri [31]. Unfortunately, the primers developed so far allow for effective detection of P. atrosepticum only. The primers proposed by Darrasse et al. [32] enable the detection of bacteria from the genus Pectobacterium, except for the species P. betavasculorum. Likewise, primers proposed for detecting P. parmentieri [31] and P. brasiliense [30] do not seem to be sufficiently universal. Currently, the accurate identification of Pectobacterium species relies on gene sequencing methods. The Multi Locus Sequence Analysis (MLSA) is the most effective method to identify Pectobacterium species [14,19,33]. While analysing the genetic diversity of bacteria of the genus Pectobacterium, the rep-PCR reaction with ERIC primers [34] has been successfully applied [5,14].
The aim of this study was to check whether the ware vegetables or ornamental plants that can be purchased in the market can transmit bacteria from the genus Pectobacterium. The sequencing of the recA gene was applied to identify newly isolated Pectobacterium strains. The comprehensive characteristics of phenotypic features, such as biochemical properties, ability to macerate different plant species and tolerance to different pH, temperatures, salinity, or water availability, were performed. This phenotypic biology allows us to determine whether the isolated strains have the potential for adaptation to adverse environmental conditions and successful spreading between different climatic regions.
2. Results
2.1. Species Identification and Diversity Analysis
We collected 241 samples of asymptomatic ware vegetable and ornamental plant samples (110 of which were potato), among which 149 (62%) were carrying pectinolytic bacteria (65 of which were potato, 43 vegetables and 41 ornamental and herbaceous). The number of pectinolytic bacteria detected in the tested samples differed. The highest number of pectinolytic bacteria, 104 of bacterial cells on surface equal to 1 cm2 of the sample was observed for unwashed vegetables stuck with soil. For most of the samples from which we isolated pectinolytic bacteria, their estimated numbers ranged from 102 to 103 per 1 cm2 of plant sample.
The initial species identification was carried out by PCR, using primers specific for Pectobacterium and Dickeya genera [32,35]. Among 161 pectinolytic strains, 157 could be classified into the Pectobacterium and four into the Dickeya genus (Table 1).
Apart from the 161 isolates mentioned above, another five isolates, which did not belong to the genus Pectobacterium or Dickeya were isolated. They were identified by recA gene sequencing as belonging to Serratia spp. (strains DPMP88, DPMP93 and DPMP337), Klebsiella oxytoca (DPMP79), and Rahnella aquatilis (DPMP382). These strains of Serratia, Klebsiella and Rahnella were not included in further analyses.
Furthermore, among 157 strains identified as Pectobacterium, nineteen strains were classified as P. atrosepticum, twelve strains isolated from symptomless potatoes as P. parmentieri, and ten strains were identified as P. brasiliense, based on species-specific PCR reactions [29,30,31]. Unfortunately, 115 out of 157 newly isolated strains could not be classified to the species level with applied species-specific primers (Table 1).
The genetic diversity of 161 new Pectobacterium and Dickeya isolates originating from symptomless plants and 31 reference strains isolated from symptomatic plants was assessed by the ERIC-PCR method. In total, 23 different ERIC profiles were discriminated (Table 1).
In the next step, based on obtained results, 75 strains with different ERIC fingerprints and different geographical origins or isolated from distinct plant materials were selected for the recA gene sequencing. Finally, the obtained sequences of newly isolated strains were compared with the recA gene sequences available in the Genbank and the phylogenetic analysis was conducted.
The topology of the maximum likelihood tree based on the recA gene sequences clearly shows the phylogenetic position of newly isolated Pectobacterium and Dickeya strains. The recA gene sequences of 73 Pectobacterium and 1 Dickeya strains that have been isolated from asymptomatic plants were grouped together with 26 strains originated from symptomatic plants, as well as with Pectobacterium spp. and Dickeya dadantii type and reference strains (Figure 1).
Out of the 160 pectinolytic strains, 157 isolates (98%) were identified as Pectobacterium and classified into the following species: P. versatile (50 isolates), P. carotovorum (33 isolates), P. brasiliense (27 isolates), P. atrosepticum (19 isolates), P. parmentieri (12 isolates), P. polaris (11 isolates), P. parvum (3 isolates), and P. odoriferum (2 isolates) (Figure 2, Table 1).
The most abundant species were P. versatile (30%), P. carotovorum (20%), P. brasiliense (16%), and P. atrosepticum (11%) that have been isolated from different plant species (vegetables and ornamental plants as well), originating from different countries. Only from Potatoes have we isolated all detected Pectobacterium species (Table 1).
It should be noted that different Pectobacterium species can occur on the same asymptomatic plant sample. For example, the presence of two species, P. brasiliense and P. polaris, has been detected on Sugar beet sample 111 (DPMP394 and DPMP403), Bittersweet sample 112 (DPMP396 and DPMP397) and Moroccan potato tuber sample 13 (DPMP55 and DPMP730). On the other hand, from the same potato tuber samples, the other combinations of Pectobacterium species have been isolated. P. atrosepticum and P. versatile were detected in Potato stem sample 98 from Poland (DPMP344 and DPMP133) and Potato tuber from Belgium (DPMP133 and DPMP134). P. atrosepticum DPMP278 was co-isolated with P. polaris DPMP280 from Potato tuber sample 73 from Norway. Meanwhile, in Poland, the P. versatile DPMP352 strain was co-isolated with the P. parmentieri DPMP353 strain from the same sample of potato tuber 99.1. Another two Pectobacterium species combinations, P. parmentieri DPMP370 and P. carotovorum DPMP369 and P. parvum DPMP20 and P. versatile MKW18 were extracted from Cyprus potato tuber samples number 100 and mkw18, respectively. Furthermore, three different species: P. brasilense (strain DPMP152), P. carotovorum (strain DPMP146), and P. versatile (strain DPMP155) were observed on the same potato tuber sample number 44 from Morocco. Meanwhile, from Potato tuber sample number 155 from Kazakhstan, P. atrosepticum DPMP634, P. carotovorum DPMP331 and P. versatile DPMP632 and DPMP633 were detected (Table 2).
2.2. Phenotypic Characteristics
2.2.1. Plant Tissue Maceration
The ability to macerate plant tissue was investigated for randomly selected strains representing each of the isolated eight Pectobacterium and one Dickeya species. The number of strains selected for adaptation tests reflects the percentage of strains classified into each Pectobacterium species detected on asymptomatic plants. The pathogenicity of 47 strains was assessed by maceration of potato tuber, while, for 44 strains, the assay was performed on chicory and iris leaves. None of the selected strains caused disease on Iris leaves (data not shown). All the tested strains were capable to macerate potato tuber tissues; among them, 41 strains caused soft rot of potato tubers and chicory leaves also. However, five strains: P. atrosepticum DPMP634, P. brasiliense IFB5258, P. parmentieri DPMP353 and SCC3193, as well as P. versatile DPMP633 macerated efficiently potato tubers but exhibited weak pathogenicity on chicory. Other four strains, P. atrosepticum ICMP1526T, P. carotovorum LMG2404T, P. parmentieri IFB5322, and D. dadantii DPMP625, caused maceration of potato tuber tissue and did not cause significant damage to chicory leaves (Figure 3 and Figure 4, Tables S1 and S2).
Of 47 strains for which the potato tuber maceration capacity was tested, 27 were isolated in this study from asymptomatic plant samples, and the remaining 20 (marked with asterisks in Table S1 and Figure 3 and Figure 4) were the reference strains or originated from plants with disease symptoms. Both groups of strains were characterised by the ability to macerate both potato tubers and chicory leaves.
Strains isolated from symptomless plants have nearly similar ability to macerate plant tissues as strains retrieved from plants with disease symptoms (Figure 3 and Figure 4, Figures S1 and S2, Tables S1 and S2). However, for the strains originated from symptomatic plants, a slightly smaller rot area was observed than for asymptomatic strains (Figure 5, Table S2). The p-value was 0.02 according to the ANOVA with Welch corrections for nonhomogeneous variances criterion followed by a post-hoc Games–Howell analysis (Figure 5).
2.2.2. Adaptation for Various Environmental Conditions
Adaptation tests for different environmental conditions: variable pH, salinity levels and water availability were performed for 35 Pectobacterium strains (Table 3, Table 4 and Table 5). Strains representing each of identified Pectobacterium species were randomly selected.
pH Influence on Bacterial Growth
All tested strains showed the ability to grow in a Tryptic Soy Broth (TSB) medium with a pH of 5 to 10 but their growth efficiency declined with the more alkaline pH. Only five strains, one strain P. brasiliense DPMP55, isolated from a Moroccan potato, and two strains of P. carotovorum DPMP199 and DPMP200, also isolated from potatoes originating in Egypt, as well as P. polaris DPMP286 and P. versatile DPMP198 were able to tolerate low pH (pH= 4). On the contrary, the highest pH value = 11 was tolerated by all strains except two P. brasiliense strains, DPMP68 from symptomatic potato and DPMP396 from Bittersweet, and one P. polaris DPMP403 from Sugar beet grown in Poland. All tested strains showed their optimum growth at a slightly acidic pH of 5 or 6, except that P. brasiliense strain DPMP396 and P. parvum DPMP20, which showed their optimal at a neutral pH = 7. Only three strains, P. brasiliense DPMP55, P. polaris DPMP286, and P. versatile DPMP198 were able to grow and were metabolically active in all tested pH ranges, from 4 up to 11 (Table 3).
The Salinity Impact on Bacterial Growth
Most of the tested strains (31 out of 35) showed their optimum growth at very low salinity up to 1% of NaCl in the medium. Only two strains, P. brasiliense DPMP396, and P. carotovorum DPMP199 grew best in medium containing 4 and 3% NaCl, respectively. Three P. parmentieri strains DPMP390, IFB5322, and SCC3193 were the most salinity-sensitive and only grew in a medium containing less than 4% NaCl. A vast spectrum of salinity from 0 to 8% NaCl in the medium was tolerated by the strain P. brasiliense DPMP55. In salinity equal to 11%, none of the tested isolates maintained an active metabolism, as evidenced by the resazurin test. However, ten strains, P. carotovorum DPMP199 and DPMP399, P. brasiliense DPMP55, DPMP224, DPMP372, DPMP396, and DPMP374, P. atrosepticum DPMP275, P. versatile DPMP402 and DPMP452 can survive in medium containing 11% of NaCl and were viable in a spot test performed on an MH medium without NaCl (Table 4).
The Impact of Variable Water Availability on Bacterial Growth
All tested strains achieved the highest optical density value in medium without the addition of PEG. Out of 35 tested isolates, 13 were viable at PEG concentration above 200 g L−1. Four Pectobacterium strains were viable in the TSB medium containing 300–400 g L−1 PEG, and two P. versatile strains DPMP198 and DPMP202 were isolated from cactus and P. carotovorum strains DPMP199 and DPMP200 that were isolated from potato that was grown in Egypt. The most resistant was one P. carotovorum strain DPMP202 isolated from cactus, which remained viable and active metabolically at a concentration of PEG equal to 500 g L−1 (Table 5).
2.2.3. Antibiotic Susceptibility Test and Growth on Chromogenic Media for Antibiotic Resistance Detection
Due to the lack of EUCAST guidelines for Pectobacterium spp. strains, it was assumed that the zone of growth inhibition in the range of 0–6 mm means antibiotic-resistant strains, growth inhibition zone in the range of 7–13 mm means moderately sensitive strains for a given antibiotic, and a zone of growth inhibition >13 mm means strains sensitive to a given antibiotic.
Among 34 tested isolates, 13 strains, were resistant to ampicillin, 9 strains to erythromycin, 2 to gentamicin, 6 strains to kanamycin, and 5 to streptomycin and tetracycline (Table 6).
The most susceptible to tested antibiotics were P. atrosepticum, P. brasiliense and P. polaris strains. The latter one revealed sensitivity to all of tested antibiotics. In contrast, P. versatile strains were most resistant among tested Pectobacterium species. Seven out of 9 P. versatile strains were resistant to ampicillin, 5 to the erythromycin, 4 to kanamycin and tetracycline, 3 to streptomycin, and 2 were growing in the presence of gentamicin.
We additionally observed that some strains of P. brasiliense, P. carotovorum and P versatile were able to grow on ESBL, while 3 P. versatile, 1 P. odoriferum and 1 P. parmentieri strains grew on CARBA chromagar plates (Table 6).
Two P. versatile strains DPMP198 and DPMP202, which were isolated from cactus and strain DPMP633 from Kazakhstan, were resistant to all tested antibiotics and revealed an ESBL type of resistance. Three other P. versatile strains DPMP108 and DPMP112 isolated from Iris and DPMP181 from zucchini in Poland exhibited resistance to carbapenems.
3. Discussion
In the period of 1999–2018, we collected 241 samples of asymptomatic ware vegetable, ornamental, and herbaceous plant samples. From 149 (62%) of symptomless plants that came from twenty-two countries from Africa, America, Asia, and Europe samples, we have isolated 161 pectinolytic bacteria.
Genetic identification revealed that 98% of isolates belonged to eight Pectobacterium spp., and only 2% of isolates were classified as Dickeya. However, it should be noted that bacteria were isolated at temperature 28 °C, which is not optimal for Dickeya growth.
Among Pectobacterium species, P. versatile was most frequently isolated from symptomless plants. Likewise, it was the most abundant Pectobacterium species deposited in CIRM-CFBP—a French collection of plant pathogenic bacteria [36]. Furthermore, this observation agrees with our earlier studies from 2001 and 2002 [37,38]. Analysis of the recA PCR-RFLP profiles for strains present in Polish and international collections of Erwinia carotovora indicated that only seven profiles: 3, 4, 5, 6, 7, 13 and 18 were common for both groups. Four profiles: 3, 4, 5, 6 were predominant in Polish and worldwide collection, and, in both populations, about 44% of the collected strains belonged to profile number 4. Currently, profiles 4 and 5 gather P. versatile strains, while profiles 3 and 6 are characteristic for P. parmentieri and P. polaris species, respectively. The sequencing of the recA gene for strains that have been used for RFLP analysis of an amplified fragment of recA gene confirmed that the most frequently observed RFLP profiles 4 and 5 are typical for P. versatile species.
Furthermore, P. versatile was also most frequently isolated from water [39]. Thus, it is possible to conclude that, for the last twenty years, P. versatile continues to be the most frequently isolated taxon among the Pectobacterium species.
Strains belonging into P. versatile together with P. brasiliense, P. carotovorum, and P. polaris are the most divergent among Pectobacterium species. For each species, four different fingerprinting profiles were observed. In the case of P. atrosepticum and P. parmentieri, three and two ERIC profiles were determined, respectively. The above observations are in line with numerous reports on genetic diversity within the species belonging to the genus Pectobacterium. It should be noted that strains isolated from symptomatic plants do not differ genetically from those isolated from asymptomatic plants. Both groups of strains are assigned to the same fingerprinting profiles and recA gene sequences.
It should be emphasised that, in this study, we have detected the presence of the same Pectobacterium and Dickeya species on asymptomatic vegetables and ornamental plants as those which occurred on plants with disease symptoms in the same countries from which we have analysed samples (Brasil, Egypt, Morocco, UK, USA, Israel, Finland, Norway, the Netherlands and Poland) [3,12,17,18,21,40,41,42,43,44,45,46,47,48,49,50,51]. In addition, the presence of virulent strains of the same species of Pectobacterium and Dickeya has been described in the rivers of Finland [45] and France [39].
We also observed that different Pectobacterium species can occur on the same asymptomatic plant sample. So far, the co-occurrence of various Pectobacterium species on the same plant samples have been noted on the symptomatic plants only [3]. Based on the obtained results, we can conclude that in the same sample of the plant we did not observe the coexistence of P. brasiliense with P. atrosepticum or P. parmentieri. It can be assumed that the strains belonging to the above-mentioned species may be antagonistic towards each other. It has been experimentally shown that P. brasiliense PBR1692T produces bacteriocins against P. atrosepticum SCRI1043 and P. carotovorum WPP14 [52]. Indeed, in our observations, we did not observe strains of P. brasilense co-existing on the same plant sample with P. atrosepticum or P. parmentieri strains. Besides bacteriocins, some strains of Pectobacterium, Dickeya and Serratia (all these species were detected by us on asymptomatic plants) produce β-lactam and carbapenem antibiotics that play a role in bacterial competition and might give them better fitness in the ecological niche [53].
Furthermore, some of the tested Pectobacterium strains showed resistance to antibiotics. Under natural conditions, this feature is acquired as a means of protection against bacteriocins secreted by other bacteria with which the genus Pectobacterium competes for ecological niche (e.g., the genus Pseudomonas). Plants also produce bactericidal compounds, e.g., isothiocyanates. Genetic determinants of the enzymes responsible for their degradation have been found in the chromosomes of many Pectobacterium species [20]. Conjugation plasmids are a possible way of acquiring resistance to antibiotics or other bactericidal compounds. In addition, plasmids carry, for example, genes coding heavy metal removal pump systems that allow the survival in the presence of many plant protection compounds. Such plasmids carrying enzymes enabling antibiotic degradation have been described in P. versatile SCC1 and P. zantedeschiae 9MT strains [5,54]. The ability to take in plasmids and acquire new traits provides an advantage for bacteria in adapting to new environmental conditions. We also decided to check if Pectobacterium isolates are susceptible to specific antibiotics. This may pose a serious economic problem in the future. Strains with the Extended Spectrum Betalactamases positive (ESBL+) phenotype are resistant to many β-lactam antibiotics and other chemical compounds, which makes it easier for them to undergo positive selection and persist in flora, and finally spread in the environment. The ESBL coding genes are located on plasmids, which usually also contain genes conditioning resistance to e.g., aminoglycosides, co-trimoxazole, tetracyclines or chloramphenicol [55]. This is currently the most important topic in the field of antimicrobial drug resistance. Build-up of multiresistance carbapenemase-producing microbes provokes questions about the future of treatment of clinical and environmental infections [56,57]. Some of the isolates tested showed resistance or low sensitivity to ampicillin.
In our recent studies, we have shown that bacteria from the genus Pectobacterium produce extracellular membrane vesicles (MVs) harbouring various enzymes, among them β-lactamases. Furthermore, we have shown that MVs produced by ampicillin resistant P. versatile strain DPMP190 enable the growth of sensitive E. coli strain in the presence of 300 µg mL−1 of ampicillin in the medium [58]. The mechanism of secretion of enzymes degrading antibiotics outside the cell via MVs has the key importance of the effective colonisation of an ecological niche and competence with other microorganisms present in it. Thus, the presence on the same plant samples strains of P. versatile that are resistant to antibiotics and produce MVs with active β-lactamases and carbapenemases and might allow for the growth of strains that are susceptible to bacteriocins produced by strains co-existing in the same niche. Furthermore, β-lactamases which can cut the lactam ring are able to degrade the homoserine lactones. Therefore, they can play a significant role in disrupting the cell signalling of other bacteria competing for the same niche, for example, hindering their biofilm formation or reducing virulence. In our observations, P. versatile occurred on the same plant sample together with P. carotovorum, P. brasiliense, P. atrosepticum or with P. parvum. This co-existence could be due to secretion via MVs of enzymes degrading antimicrobial compounds produced by other microorganisms present on the same plant.
Recently, numerous P. versatile strains and limited number of P. brasiliense and P. polaris strains harbouring genetic determinates of beta-lactamases have been described [59]. The large variety of environments from which P. versatile strains carrying β-lactamases have been isolated indicates the extraordinary ability of these bacteria to colonise various environments.
Based on the results of pathogenicity tests, we have demonstrated that strains isolated from asymptomatic plants could macerate plant tissues in laboratory conditions. Furthermore, strains isolated from symptomless plants have a similar ability to macerate plant tissues as strains retrieved from plants with disease symptoms. Except for four strains, all of them were able to macerate plant species other than those from which they have been isolated. Similar observations are widely described in the literature in the case of strains isolated from symptomatic plants or water [3].
However, for the strains from symptomatic plants a slightly smaller rot area was observed than for asymptomatic strains (Figure 5). The observed difference between mean rotting area of strains isolated from symptomatic and asymptomatic plants is statistically significant; however, the ranges exhibited by both groups of strains are very similar and overlapping. This difference may be due to the fact that the reference strains and Polish strains derived from plants with disease symptoms were isolated much earlier and have been stored in laboratories at least for 25 years; therefore, it cannot be excluded that they have partially lost their virulence. However, to definitively ascertain whether the strains from symptomatic and asymptomatic plants exhibit a statistically significant difference in virulence, additional tests should be carried out on a larger group of strains. Primarily because in the range of each of the tested species, the strains show a very diverse ability to macerate plant tissues.
Undoubtedly, Pectobacterium strains are sensitive to the lack of water in the environment in which they occur. However, they possess the ability to survive in conditions of limited water availability. Some of the strains tested after 48 h of incubation in the condition of limited water availability by adding PEG to the medium were able to resume their growth. This may explain why Pectobacterium is able to survive on the vegetables or ornamental plants in warm climates or during transport and storage. We also checked the survivability of tested bacteria in different pH. The most optimal range of pH for growth of Pectobacterium spp. was between 5 and 6, which is comparable to pH usually occurring in plant tissues [60,61]. They were also able to cope well at pH 7 and 8. After 48 h of incubation, the strains were also able to adjust to pH 10 and 11 and resumed their growth. Most of the strains could not survive in the environment with pH = 4. Bacteria of the genus Pectobacterium grew well in the medium with salinity in the range from 0 to 4%. Above that value, bacteria grew poorly. However, the spot tests indicated that the bacteria remained viable in such extreme conditions. It can be concluded that they were able to arrest their metabolism and survive while awaiting favourable growth conditions. The most resistant to the changes in the pH and salinity conditions was the Moroccan strain P. brasiliense DPMP55 isolated from potato. It is worth underlining that ware potatoes from Mediterranean regions are sold frequently and are readily available in European stores during the winter period. Other stress-resistant strains were two isolates of P. carotovorum DPMP199 and DPMP200 from Egyptian potatoes and two P. versatile isolates from cactus DPMP198 DPMP202. These strains are extremely resistant to the reduced water content in the environment, and thus they have a much greater possibility of surviving long-term transport and storage.
Undoubtedly, the results of adaptation tests and antibiotic resistance indicate that, among the detected Pectobacterium species, strains classified as P. versatile are the most resistant to antibiotics and are characterised by the ability to secrete β-lactamases and carbapenemases. In addition, of all the strains tested, two strains of P. versatile DPMP198 and DPMP202 from the cactus can grow in the most extensive pH range and the lowest water availability, while the P. versatile DPMP402 strain is viable in a medium containing from 0–11% NaCl. Thus, the species P. versatile, characterised by high genetic and phenotypic variability and high adaptation abilities, has the greatest potential to spread and effectively colonise new environments. It is confirmed by the number of strains isolated from various environments, from plants to water, soil, or insects. This taxon is the most numerous among the strains collected in the collections and among species detected on asymptomatic plants, which was shown in this study.
4. Materials and Methods
4.1. Bacterial Strains and Growth Conditions
Pectobacterium strains used in this study are listed in Table 1. The one hundred and sixty-one bacteria strains were isolated from 149 different symptomless plant samples collected from 1999 up to 2018. They were 108 samples of ware vegetables (Broccoli, Cabbage, Cactus, Carrot, Celery, Fennel, Garlic, Ginger, Leek, Onion, Parsley, Peppers, Potato, Prickly Pear, Rhubarb, Rutabaga, Sugar Beet, Sweet Potato, Tomato, and Zucchini). Of these, 65 were potatoes. In addition, we have tested 41 samples of ornamental and herbaceous plant species (Alpine violet, Bean, Beetroot, Bittersweet, Black nightshade, Cactus, Dieffenbachia, Iris, Kalonchoe, Opuntia, Rose, Pigweed).
Plants were originated from 25 countries (Armenia, Belgium, Brasil, Cyprus, Egypt, Finland, France, Germany, Georgia, Israel, Italy, Japan, Kazakhstan, Morocco, Poland, Portugal, the Netherlands, New Zealand, Norway, Serbia, Spain, Tenerife, Tunisia, UK, USA).
Additionally, 26 strains isolated from symptomatic plants were used as a reference for comparison purposes.
To isolate new bacterial strains, about 15 cm2 of plant area were suspended in 15 mL of 0.96% NaCl and were homogenised by grinding in a mortar and pestle. After 2 h of preincubation with shaking at 28 °C, the samples were serially diluted. Next, 100 μL aliquots of serial dilutions of homogenate (10−2, 10−3, 10−4 and 10−5) were plated on a Crystal Violet Pectate (CVP) medium [62] and incubated for 48 h at 28 °C. Colonies that formed cavities were restreaked on CVP medium and incubated as previously. For long time storage, all isolates were kept as frozen stocks at −80 °C To prepare frozen stocks, single bacterial colonies were transferred to 7 mL of TSB medium and then grown for 48 h at 28 °C with shaking. Next, 500 µL of bacterial culture was mixed with 500 µL sterile 80% glycerol.
4.2. Phenotypic Characteristics of Newly Isolated Strains
4.2.1. Plant Tissue Maceration Assays
The ability to macerate plant tissue was determined for 26 pectinolytic strains newly isolated from asymptomatic plants and 21 strains originating from plants with disease symptoms. For the pathogenicity assays, bacteria of various origins were chosen (Table S1).
Leaves of Irises and Chicory were washed with distilled water. An overnight bacterial culture in the TSB medium was diluted with physiological saline solution to an optical density of 0.5 McF. A one-centimeter cut was made on the surface of the leaf across the conductive bundle, and 25 μL of the bacterial suspension was then dripped into the cut. Inoculated leaves (in three replicates per strain) were placed in plastic sampling bags with sealing strips lined with paper towels soaked in sterile distilled water. Such prepared samples were incubated at 28 °C for 48 h. After 24 and 48 h of inoculation, the average area of rotten tissue was calculated. As a negative control, leaves were inoculated with 25 μL of sterile water.
Potato tubers were thoroughly washed, and their surface was disinfected in a 1% hypochlorite solution bath. The overnight bacterial culture in TSB medium was diluted with Ringer solution to an optical density of 0.5 McF. The tubers were punctured with pipette tips containing 50 μL of the suspension. The tips were left in the tubers. A total of three punctures were made on each tuber. Each strain was tested on 3 tubers in triplicates. Inoculated tubers were placed in plastic boxes. In addition, 500 mL of distilled water was poured into the bottom of the boxes to achieve relative humidity above 90%. After 72 h of incubation at 28 °C, the diameter of the macerated tissue was measured. As a negative control, pipette tips inserted into tubers contained sterile water rather than a bacterial suspension.
4.2.2. Adaptation to Various Environmental Conditions
The ability to grow in various environmental conditions such as different pH, salinity and water availability was determined for 22 pectinolytic strains newly isolated from asymptomatic plants and 13 strains originating from plants with disease symptoms. (Table 3, Table 4 and Table 5).
The pH effect on bacterial growth was studied in TSB medium under pH values of 4, 5, 6, 7, 8, 9, 10 and 11, respectively.
The ability to grow in various salinity conditions was conducted in TSB medium supplemented with 0 g L−1, 10 g L−1, 20 g L−1, 30 g L−1, 40 g L−1, 50 g L−1, 60 g L−1, 70 g L−1 NaCl and 80 g L−1.
The tolerance for limited water availability was estimated in TSB medium supplemented with 0.0 g L−1, 50.0 g L−1, 75.0 g L−1, 100.0 g L−1, 200.0 g L−1, 300.0 g L−1, 400.0 g L−1 and 500.0 g L−1 of polyethylene glycol (PEG).
The assays were performed in 96-well titration plates. The 200 μL of TSB medium with various pH, salinity and PEG concentration was inoculated with 5 μL of bacterial suspension with an optical density of 0.5 McF. The plates were incubated with shaking at 28 °C. The absorbance readings at 600 nm were made after 0, 6, 24 and 48 h of incubation, using the Infinite M200 Pro (Tecan). The experiments with two replicates were performed twice.
To assess the viability of bacteria under different pH conditions, salinity and water availability after 48 h of incubation, spot tests were performed on TSA medium. Furthermore, 5 μL of bacterial culture was withdrawn from each well and dropped onto a plate, which was then incubated for 48 h at 28 °C. Additionally, after performing the spot test, 20 μL of 0.02% resazurin solution was added to each well, and the plate was incubated for 24 h at 28 °C. The result was read colorimetrically. During bacterial metabolism, purple resazurin is transformed to pink resorufin (pH = 6.5). Under acidic conditions, resorufin takes on a yellow colour (pH = 3.8). This allows for a colorimetric reading of the presence of acid metabolism products in the medium.
4.2.3. Antibiotic Susceptibility Assay
The antibiotic susceptibility of 34 selected Pectobacterium strains (31 isolated from asymptomatic plants and 3 from symptomatic) was tested by a standard disc diffusion method. In addition, 100 μL of a bacterial suspension with an optical density of 0.5 McF was spread on a Mueller–Hinton (MH) medium. Antibiotic discs containing ampicillin 10 μg, erythromycin 15 μg, gentamicin 250 μg, kanamycin 30 μg, streptomycin 10 μg, tetracycline 15 μg were then applied (Emapol). The plates were incubated for 24 h at 28 °C. Next, the zone of bacterial growth inhibition around the antibiotic disc was assessed.
Moreover, for strains that showed resistance to at least one antibiotic in the disc diffusion test, the production of beta-lactamases and carbapenemases was determined with application of two chromogenic media, ESBL (extended-spectrum beta-lactamases) chromagar and KPC (Klebsiella pneumoniae carbapenemase) plates (GRASSO). The control Escherichia coli NCTC 13351 and Klebsiella pneumoniae BAA-1705, which grow on the above-mentioned media and have ESBL and KPC resistance mechanisms, have been used.
4.2.4. Statistical Analysis
The analysis of differences between the groups was performed using the ANOVA with Welch corrections for nonhomogeneous variances criterion followed by a post-hoc Games–Howell analysis in R [63].
4.3. Molecular Identification of Newly Isolated Strains
4.3.1. DNA Isolation
For DNA isolation, bacterial strains were grown overnight in 7 mL of Tryptic Soy Broth (TSB) at 28 °C with shaking. Cells were harvested by centrifugation and resuspended in 500 µl TE buffer (50 mM Tris/HCl, 40 mM EDTA, pH 8.0). Afterwards, the cell lysis and nucleic acids extraction were carried out according to the protocol proposed by a Joint Genome Institute for bacterial DNA isolation using CTAB [64] followed by the RNA digestion using Turbo RNase (Ambion). DNA quantity and quality were assessed first using a NanoDrop Spectrophotometer and later with agarose gel electrophoresis.
4.3.2. PCR Amplification Sequencing and Phylogenetic Analysis
DNA amplification was performed in 25 µL reaction volumes using PCR Master Mix (Thermo Scientific; K0171) according to the manufacturer’s instruction. Amplification was performed using a T100 Bio-Rad thermocycler. The amplified products were separated in 1.5% (w/v) agarose gel at 100 V for 40 min in 0.5xTAE buffer and visualised with UV light after staining in ethidium bromide (0.5 g mL−1).
Species specific PCR reactions were performed according to the previously described protocols [29,30,31,32,35]. The genetic diversity of Pectobacterium and Dickeya strains was analysed with a fingerprinting method, Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR), according to the procedure described by Versalovic et al. [34]. For amplification and sequencing of the recA gene fragment, primers previously described were used [38]. Sequencing was carried out using an ABI PRISM DNA Sequencer (PerkinElmer) according to the manufacturer’s manual. Both strands were sequenced using the forward and reverse PCR primers.
Furthermore, the obtained sequences were subjected to BLAST sequence similarity search analysis to identify the nearest taxa. The obtained sequences of the recA gene and sequences of the closest representative taxa that belong to Pectobacterium and Dickeya were aligned using an MAFFT algorithm in Geneious v9.1.8. [65]. The phylogenetic analysis was performed with the MEGA v. X software, (www.megasoftware.net, accessed on 20 May 2022), and trees were constructed using the Maximum Likelihood algorithm and Hasegawa–Kishino–Yano models selected on the model test module implemented in MEGA. Bootstrap analysis with 1000 replications was performed to assess the robustness of the clusters.
5. Conclusions
Our research proved that bacteria of the genus Pectobacterium isolated from asymptomatic ware vegetables and ornamental plants can cause maceration of plant tissues of more than one plant species. These strains were also able to adapt to extreme environmental conditions, such as low water accessibility, acidic and alkaline pH, and high salinity. The antibiograms’ results showed that some of these bacteria had resistance to betalactams, macrolides, aminoglicosides and tetracyclines; in addition, they might possess beta-lactamases of extended spectrum or carbapenemases.
Undoubtedly, we have demonstrated that Pectobacterium strains isolated from symptomless vegetables and ornamental plants traded internationally show a high potential for adaptation to adverse environmental conditions and ability to change the host plant. As a result, they may contribute to the success of the genus Pectobacterium and accelerate its spreading between different climatic zones and facilitate the colonisation of different ecological niches.
The most important claim we want to make, which has not been previously described, is that internationally traded ware vegetables, ornamental plants and herbs which do not undergo strict phytosanitary control serve as a significant transmission medium responsible for global distribution of widely observed species such as P. versatile, which remains the most frequently isolated pathogenic taxon from Pectobacterium genus. Thus, we would like to bring the attention of the scientific community to this underexplored area, and look beyond pathogen presence in seed material, towards mass market wares and organic waste which become more and more important in the age of sustainable agriculture and a zero waste lifestyle.
Supplementary Materials
The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/pathogens11070728/s1, Table S1: Results of pathogenicity tests. Table S2: Calculations of statistical significance; Figure S1 Comparison of the potato tissue maceration ability; Figure S2: Comparison of the chicory tissue maceration ability.
Author Contributions
Conceptualization, M.W. and K.W.; methodology, J.J., M.W. and K.W.; validation, M.W. and K.W.; formal analysis, M.S., M.M., A.S., J.J., M.W., K.W.; investigation, M.S., M.M., A.S., J.J., M.M.W.; resources, M.W. and K.W.; data curation, M.M.W.; writing—original draft preparation, M.S., M.W., K.W.; writing—review and editing, M.W., K.W., M.M.W., J.J.; visualisation, M.W., K.W., M.M.W., M.S., J.J.; supervision, M.W. and K.W.; project administration, M.W. and K.W.; funding acquisition, M.W. and K.W. All authors have read and agreed to the published version of the manuscript.
Funding
This research was funded by the National Science Centre, project OPUS9 2015/17/B/NZ9/01730.
Institutional Review Board Statement
Not applicable.
Informed Consent Statement
Not applicable.
Data Availability Statement
The data that support the findings of this study are available from the corresponding authors (K.W., M.W.), upon request. The nucleotide sequence data reported in this paper are available in the Genbank under the following accession numbers: ON381409-ON381476, MK024783, MK024784, KU510130, KU510135, KU510136, KU510109-KU510113, KU510119.
Conflicts of Interest
The authors declare no conflict of interest.
References
- Lelliott, R.A.; Dickey, R.S. Genus VII. Erwinia. In Bergey’s Manual of Systematic Bacteriology Williams & Wilkins, Baltimore; Krieg, N.R., Holt, J.G., Eds.; Williams & Wilkins: Philadelphia, PA, USA, 1984; pp. 469–476. [Google Scholar]
- Mansfield, J.; Genin, S.; Magori, S.; Citovsky, V.; Sriariyanum, M.; Ronald, P.; Dow, M.; Verdier, V.; Beer, S.V.; Machado, M.A.; et al. Top 10 Plant Pathogenic Bacteria in Molecular Plant Pathology. Mol. Plant Pathol. 2012, 13, 614–629. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Toth, I.K.; Barny, M.; Brurberg, M.B.; Condemine, G.; Czajkowski, R.; Elphinstone, J.G.; Helias, V.; Johnson, S.B.; Moleleki, L.N.; Pirhonen, M.; et al. Pectobacterium and Dickeya: Environment to Disease Development. In Plant Diseases Caused by Dickeya and Pectobacterium Species; Van Gijsegem, F., van der Wolf, J.M., Toth, I.K., Eds.; Springer International Publishing: Cham, Switzerland, 2021; pp. 39–84. ISBN 978-3-030-61458-4. [Google Scholar]
- Nabhan, S.; De Boer, S.H.; Maiss, E.; Wydra, K. Pectobacterium Aroidearum sp. nov., a Soft Rot Pathogen with Preference for Monocotyledonous Plants. Int. J. Syst. Evol. Microbiol. 2013, 63, 2520–2525. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Waleron, M.; Misztak, A.; Waleron, M.; Franczuk, M.; Jońca, J.; Wielgomas, B.; Mikiciński, A.; Popović, T.; Waleron, K. Pectobacterium zantedeschiae sp. nov. a New Species of a Soft Rot Pathogen Isolated from Calla Lily (Zantedeschia spp.). Syst. Appl. Microbiol. 2019, 42, 275–283. [Google Scholar] [CrossRef] [PubMed]
- Goto, M.; Matsumoto, K. Erwinia carotovora subsp. Wasabiae subsp. nov. Isolated from Diseased Rhizomes and Fibrous Roots of Japanese Horseradish (Eutrema Wasabi Maxim.). Int. J. Syst. Bacteriol. 1987, 37, 130–135. [Google Scholar] [CrossRef] [Green Version]
- Koh, Y.; Kim, G.; Lee, Y.; Sohn, S.; Koh, H.; Kwon, S.; Heu, S.; Jung, J. Pectobacterium carotovorum subsp. Actinidiae subsp. nov., a New Bacterial Pathogen Causing Canker-like Symptoms in Yellow Kiwifruit, Actinidia Chinensis. N. Z. J. Crop Hortic. Sci. 2012, 40, 269–279. [Google Scholar] [CrossRef] [Green Version]
- Gardan, L.; Gouy, C.; Christen, R.; Samson, R. Elevation of Three Subspecies of Pectobacterium Carotovorum to Species Level: Pectobacterium atrosepticum sp. nov., Pectobacterium betavasculorum sp. nov. and Pectobacterium wasabiae sp. nov. Int. J. Syst. Evol. Microbiol. 2003, 53, 381–391. [Google Scholar] [CrossRef]
- Alcorn, S.M.; Orum, T.V.; Steigerwalt, A.G.; Foster, J.L.M.; Fogleman, J.C.; Brenner, D.J. Taxonomy and Pathogenicity of Erwinia cacticida sp. nov. Int. J. Syst. Bacteriol. 1991, 41, 197–212. [Google Scholar] [CrossRef] [Green Version]
- Pérombelon, M.C.M. Potato Diseases Caused by Soft Rot Erwinias: An Overview of Pathogenesis. Plant Pathol. 2002, 51, 1–12. [Google Scholar] [CrossRef]
- Dees, M.W.; Lysøe, E.; Rossmann, S.; Perminow, J.; Brurberg, M.B. Pectobacterium polaris sp. nov., Isolated from Potato (Solanum tuberosum). Int. J. Syst. Evol. Microbiol. 2017, 67, 5222–5229. [Google Scholar] [CrossRef]
- Pasanen, M.; Waleron, M.; Schott, T.; Cleenwerck, I.; Misztak, A.; Waleron, K.; Pritchard, L.; Bakr, R.; Degefu, Y.; van der Wolf, J.; et al. Pectobacterium parvum sp. nov., Having a Salmonella SPI-1-like Type III Secretion System and Low Virulence. Int. J. Syst. Evol. Microbiol. 2020, 70, 2440–2448. [Google Scholar] [CrossRef]
- Khayi, S.; Cigna, J.; Chong, T.M.; Quêtu-Laurent, A.; Chan, K.-G.; Hélias, V.; Faure, D. Transfer of the Potato Plant Isolates of Pectobacterium Wasabiae to Pectobacterium parmentieri sp. nov. Int. J. Syst. Evol. Microbiol. 2016, 66, 5379–5383. [Google Scholar] [CrossRef] [PubMed]
- Waleron, M.; Misztak, A.; Waleron, M.; Franczuk, M.; Wielgomas, B.; Waleron, K. Transfer of Pectobacterium carotovorum subsp. Carotovorum Strains Isolated from Potatoes Grown at High Altitudes to Pectobacterium peruviense sp. nov. Syst. Appl. Microbiol. 2018, 41, 85–93. [Google Scholar] [CrossRef] [PubMed]
- Sarfraz, S.; Riaz, K.; Oulghazi, S.; Cigna, J.; Sahi, S.T.; Khan, S.H.; Faure, D. Pectobacterium punjabense sp. nov., Isolated from Blackleg Symptoms of Potato Plants in Pakistan. Int. J. Syst. Evol. Microbiol. 2018, 68, 3551–3556. [Google Scholar] [CrossRef] [PubMed]
- Cigna, J.; Laurent, A.; Waleron, M.; Waleron, K.; Dewaegeneire, P.; van der Wolf, J.; Andrivon, D.; Faure, D.; Hélias, V. European Population of Pectobacterium punjabense: Genomic Diversity, Tuber Maceration Capacity and a Detection Tool for This Rarely Occurring Potato Pathogen. Microorganisms 2021, 9, 781. [Google Scholar] [CrossRef]
- Waleron, M.; Waleron, K.; Lojkowska, E. Characterization of Pectobacterium carotovorum subsp. Odoriferum Causing Soft Rot of Stored Vegetables. Eur. J. Plant Pathol. 2014, 139, 457–469. [Google Scholar] [CrossRef] [Green Version]
- Oulghazi, S.; Sarfraz, S.; Zaczek-Moczydłowska, M.A.; Khayi, S.; Ed-Dra, A.; Lekbach, Y.; Campbell, K.; Novungayo Moleleki, L.; O’Hanlon, R.; Faure, D. Pectobacterium Brasiliense: Genomics, Host Range and Disease Management. Microorganisms 2021, 9, 106. [Google Scholar] [CrossRef]
- Portier, P.; Pédron, J.; Taghouti, G.; Fischer-Le Saux, M.; Caullireau, E.; Bertrand, C.; Laurent, A.; Chawki, K.; Oulgazi, S.; Moumni, M.; et al. Elevation of Pectobacterium carotovorum subsp. Odoriferum to Species Level as Pectobacterium odoriferum sp. nov., Proposal of Pectobacterium brasiliense sp. nov. and Pectobacterium actinidiae sp. nov., Emended Description of Pectobacterium Carotovorum and Description of Pectobacterium versatile sp. nov., Isolated from Streams and Symptoms on Diverse Plants. Int. J. Syst. Evol. Microbiol. 2019, 69, 3207–3216. [Google Scholar] [CrossRef]
- Welte, C.U.; de Graaf, R.M.; van den Bosch, T.J.M.; Op den Camp, H.J.M.; van Dam, N.M.; Jetten, M.S.M. Plasmids from the Gut Microbiome of Cabbage Root Fly Larvae Encode SaxA That Catalyses the Conversion of the Plant Toxin 2-Phenylethyl Isothiocyanate. Environ. Microbiol. 2016, 18, 1379–1390. [Google Scholar] [CrossRef]
- Jonkheer, E.M.; Brankovics, B.; Houwers, I.M.; van der Wolf, J.M.; Bonants, P.J.M.; Vreeburg, R.A.M.; Bollema, R.; de Haan, J.R.; Berke, L.; Smit, S.; et al. The Pectobacterium Pangenome, with a Focus on Pectobacterium brasiliense, Shows a Robust Core and Extensive Exchange of Genes from a Shared Gene Pool. BMC Genom. 2021, 22, 265. [Google Scholar] [CrossRef]
- Oulghazi, S.; Cigna, J.; Lau, Y.Y.; Moumni, M.; Chan, K.G.; Faure, D. Transfer of the Waterfall Source Isolate Pectobacterium carotovorum M022 to Pectobacterium fontis sp. nov., a Deep-Branching Species within the Genus Pectobacterium. Int. J. Syst. Evol. Microbiol. 2019, 69, 470–475. [Google Scholar] [CrossRef]
- Pédron, J.; Bertrand, C.; Taghouti, G.; Portier, P.; Barny, M.-A. Pectobacterium aquaticum sp. nov., Isolated from Waterways. Int. J. Syst. Evol. Microbiol. 2019, 69, 745–751. [Google Scholar] [CrossRef] [PubMed]
- Waleron, M.; Misztak, A.; Waleron, M.; Jonca, J.; Furmaniak, M.; Waleron, K. Pectobacterium polonicum sp. nov. Isolated from Vegetable Fields. Int. J. Syst. Evol. Microbiol. 2019, 69, 1751–1759. [Google Scholar] [CrossRef] [PubMed]
- Ben Moussa, H.; Pédron, J.; Bertrand, C.; Hecquet, A.; Barny, M.-A. Pectobacterium quasiaquaticum sp. nov., Isolated from Waterways. Int. J. Syst. Evol. Microbiol. 2021, 71, 005042. [Google Scholar] [CrossRef] [PubMed]
- du Raan, S.; Coutinho, T.A.; van der Waals, J.E. Cardinal Temperature Differences, Determined in Vitro, between Closely Related Species and Subspecies of Pectinolytic Bacteria Responsible for Blackleg and Soft Rot on Potatoes. Eur. J. Plant Pathol. 2016, 144, 361–369. [Google Scholar] [CrossRef] [Green Version]
- Pasanen, M.; Laurila, J.; Brader, G.; Palva, E.T.; Ahola, V.; van Der Wolf, J.; Hannukkala, A.; Korhonen, M. Characterisation of Pectobacterium Wasabi and Pectobacterium carotovorum subsp. Carotovorum Isolates from Diseased Potato Plants in Finland. Ann. Appl. Biol. 2013, 163, 403–419. [Google Scholar] [CrossRef]
- van der Merwe, J.J.; Coutinho, T.A.; Korsten, L.; van der Waals, J.E. Pectobacterium carotovorum subsp. Brasiliensis Causing Blackleg on Potatoes in South Africa. Eur. J. Plant Pathol. 2010, 126, 175–185. [Google Scholar] [CrossRef] [Green Version]
- De Boer, S.H. PCR Detection of Erwinia carotovora subsp. Atroseptica Associated with Potato Tissue. Phytopathology 1995, 85, 854. [Google Scholar] [CrossRef]
- Duarte, V.; De Boer, S.; Ward, L.; De Oliveira, A.M.R. Characterization of Atypical Erwinia Carotovora Strains Causing Blackleg of Potato in Brazil. J. Appl. Microbiol. 2004, 96, 535–545. [Google Scholar] [CrossRef]
- De Boer, S.H.; Li, X.; Ward, L.J. Pectobacterium spp. Associated with Bacterial Stem Rot Syndrome of Potato in Canada. Phytopathology 2012, 102, 937–947. [Google Scholar] [CrossRef] [Green Version]
- Darrasse, A.; Priou, S.; Kotoujansky, A.; Bertheau, Y. PCR and Restriction Fragment Length Polymorphism of a Pel Gene as a Tool to Identify Erwinia Carotovora in Relation to Potato Diseases. Appl. Environ. Microbiol. 1994, 60, 1437–1443. [Google Scholar] [CrossRef] [Green Version]
- Nabhan, S.; De Boer, S.H.; Maiss, E.; Wydra, K. Taxonomic Relatedness between Pectobacterium carotovorum subsp. Carotovorum, Pectobacterium carotovorum subsp. Odoriferum and Pectobacterium carotovorum subsp. Brasiliense subsp. nov. J. Appl. Microbiol. 2012, 113, 904–913. [Google Scholar] [CrossRef] [PubMed]
- Versalovic, J.; Koeuth, T.; Lupski, J.R. Distribution of Repetitive DNA Sequences in Eubacteria and Application to Fingerprinting of Bacterial Genomes. Nucleic Acids Res. 1991, 19, 6823–6831. [Google Scholar] [CrossRef] [PubMed]
- Nassar, A.; Darrasse, A.; Lemattre, M.; Kotoujansky, A.; Dervin, C.; Vedel, R.; Bertheau, Y. Characterization of Erwinia Chrysanthemi by Pectinolytic Isozyme Polymorphism and Restriction Fragment Length Polymorphism Analysis of PCR-Amplified Fragments of Pel Genes. Appl. Environ. Microbiol. 1996, 62, 2228–2235. [Google Scholar] [CrossRef] [Green Version]
- Portier, P.; Pédron, J.; Taghouti, G.; Dutrieux, C.; Barny, M.-A. Updated Taxonomy of Pectobacterium Genus in the CIRM-CFBP Bacterial Collection: When Newly Described Species Reveal “Old” Endemic Population. Microorganisms 2020, 8, 1441. [Google Scholar] [CrossRef]
- Waleron, M.; Waleron, K.; Lojkowska, E. Application of RecA PCR-RFLP for Differentiation of Erwinia Carotovora Associated with Potato Plants in Tuber. In Plant Pathogenic Bacteria, Proceedings of the 10th International Conference on Plant Pathogenic Bacteria, Charlottetown, Prince Edward Island, Canada, 23–27 July 2000; Kluwer: Dordrecht, The Netherlands, 2001; pp. 385–388. ISBN 978-94-010-3858-4. [Google Scholar]
- Waleron, M.; Waleron, K.; Podhajska, A.J.; Łojkowska, E. Genotyping of Bacteria Belonging to the Former Erwinia Genus by PCR-RFLP Analysis of a RecA Gene Fragment. Microbiology 2002, 148, 583–595. [Google Scholar] [CrossRef] [Green Version]
- Ben Moussa, H.; Bertrand, C.; Rochelle-Newall, E.; Fiorini, S.; Pédron, J.; Barny, M.-A. The Diversity of Soft Rot Pectobacteriaceae along the Durance River Stream in the South-East of France Revealed by Multiple Seasonal Surveys. Phytopathology 2022. [Google Scholar] [CrossRef] [PubMed]
- Ashmawy, N.A.; Jadalla, N.M.; Shoeib, A.A.; El-Bebany, A.F. Identification and Genetic Characterization of Pectobacterium spp. and Related Enterobacteriaceae Causing Potato Soft Rot Diseases in Egypt. J. Pure Appl. Microbiol. 2015, 9, 1847–1858. [Google Scholar]
- Oulghazi, S.; Moumni, M.; Khayi, S.; Robic, K.; Sarfraz, S.; Lopez-Roques, C.; Vandecasteele, C.; Faure, D. Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco. Microorganisms 2020, 8, 895. [Google Scholar] [CrossRef]
- Zaczek-Moczydłowska, M.A.; Fleming, C.C.; Young, G.K.; Campbell, K.; O’Hanlon, R. Pectobacterium and Dickeya Species Detected in Vegetables in Northern Ireland. Eur. J. Plant Pathol. 2019, 154, 635–647. [Google Scholar] [CrossRef] [Green Version]
- Curland, R.D.; Mainello, A.; Perry, K.L.; Hao, J.; Charkowski, A.O.; Bull, C.T.; McNally, R.R.; Johnson, S.B.; Rosenzweig, N.; Secor, G.A.; et al. Species of Dickeya and Pectobacterium Isolated during an Outbreak of Blackleg and Soft Rot of Potato in Northeastern and North Central United States. Microorganisms 2021, 9, 1733. [Google Scholar] [CrossRef]
- Tsror (Lahkim), L.; Hélias, V.; Mordechai-Lebiush, S.; Erlich, O.; Hazanovsky, M.; Chalupowicz, L.; Reuven, M.; Dror, O.; Valinsky, L.; Laurent, A.; et al. Characterization of Pectobacterium Brasiliense Strains from Potato and Vegetables in Israel. Plant Pathol. 2021, 70, 2179–2187. [Google Scholar] [CrossRef]
- Laurila, J.; Ahola, V.; Lehtinen, A.; Joutsjoki, T.; Hannukkala, A.; Rahkonen, A.; Pirhonen, M. Characterization of Dickeya Strains Isolated from Potato and River Water Samples in Finland. Eur. J. Plant Pathol. 2008, 122, 213–225. [Google Scholar] [CrossRef]
- Degefu, Y. Co-Occurrence of Latent Dickeya and Pectobacterium Species in Potato Seed Tuber Samples from Northern Finland. Agric. Food Sci. 2021, 30, 1–7. [Google Scholar] [CrossRef]
- Dees, M.W.; Lebecka, R.; Perminow, J.I.S.; Czajkowski, R.; Grupa, A.; Motyka, A.; Zoledowska, S.; Śliwka, J.; Lojkowska, E.; Brurberg, M.B. Characterization of Dickeya and Pectobacterium Strains Obtained from Diseased Potato Plants in Different Climatic Conditions of Norway and Poland. Eur. J. Plant Pathol. 2017, 148, 839–851. [Google Scholar] [CrossRef]
- Waleron, M.; Waleron, K.; Lojkowska, E. First Report of Pectobacterium carotovorum subsp. Brasiliense Causing Soft Rot on Potato and Other Vegetables in Poland. Plant Dis. 2015, 99, 1271. [Google Scholar] [CrossRef]
- Waleron, M.; Waleron, K.; Lojkowska, E. Occurrence of Pectobacterium Wasabiae in Potato Field Samples. Eur. J. Plant Pathol. 2013, 137, 149–158. [Google Scholar] [CrossRef] [Green Version]
- Waleron, M.; Misztak, A.; Jońca, J.; Waleron, K. First Report of Pectobacterium Polaris Causing Soft Rot of Potato in Poland. Plant Dis. 2019, 103, 144. [Google Scholar] [CrossRef]
- Waleron, M.; Misztak, A.; Jońca, J.; Furmaniak, M.; Waleron, M.M.; Waleron, K. First Report of ‘Candidatus Pectobacterium Maceratum’ Causing Soft Rot of Potato in Poland. Plant Dis. 2019, 103, 1409. [Google Scholar] [CrossRef]
- Del, M.; Marquez-Villavicencio, P.; Charkowski, A. Soft Rot Disease Severity Is Affected by Potato Physiology and Pectobacterium Taxa. Plant Dis. 2011, 95, 232–241. [Google Scholar] [CrossRef] [Green Version]
- Shyntum, D.Y.; Nkomo, N.P.; Shingange, N.L.; Gricia, A.R.; Bellieny-Rabelo, D.; Moleleki, L.N. The Impact of Type VI Secretion System, Bacteriocins and Antibiotics on Bacterial Competition of Pectobacterium carotovorum subsp. Brasiliense and the Regulation of Carbapenem Biosynthesis by Iron and the Ferric-Uptake Regulator. Front. Microbiol. 2019, 10, 2379. [Google Scholar] [CrossRef]
- Niemi, O.; Laine, P.; Koskinen, P.; Pasanen, M.; Pennanen, V.; Harjunpää, H.; Nykyri, J.; Holm, L.; Paulin, L.; Auvinen, P.; et al. Genome Sequence of the Model Plant Pathogen Pectobacterium carotovorum SCC1. Stand. Genom. Sci. 2017, 12, 87. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Queenan, A.M.; Bush, K. Carbapenemases: The Versatile β-Lactamases. Clin. Microbiol. Rev. 2007, 20, 440–458. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Cohen, M.L. Epidemiology of Drug Resistance: Implications for a Post-Antimicrobial Era. Science 1992, 257, 1050–1055. [Google Scholar] [CrossRef] [PubMed]
- Livermore, D.M. Has the Era of Untreatable Infections Arrived? J. Antimicrob. Chemother. 2009, 64 (Suppl. 1), i29–i36. [Google Scholar] [CrossRef] [Green Version]
- Jonca, J.; Waleron, M.; Czaplewska, P.; Bogucka, A.; Steć, A.; Dziomba, S.; Jasiecki, J.; Rychłowski, M.; Waleron, K. Membrane Vesicles of Pectobacterium as an Effective Protein Secretion System. Int. J. Mol. Sci. 2021, 22, 12574. [Google Scholar] [CrossRef]
- Royer, G.; Dixit, Z.; Pédron, J.; Pierrat, G.; Demontant, V.; Berçot, B.; Rodriguez, C.; Barny, M.-A.; Jacquier, H.; Woerther, P.-L. Genetic and Phenotypic Study of the Pectobacterium versatile Beta-Lactamase, the Enzyme Most Similar to the Plasmid-Encoded TEM-1. Appl. Environ. Microbiol. 2022, 88, e00220-22. [Google Scholar] [CrossRef]
- Haas, A.R.C. pH Determination in plant tissue. Plant Physiol. 1941, 16, 405–409. [Google Scholar] [CrossRef] [Green Version]
- Masoero, G.; Cugnetto, A. The Raw PH in Plants: A Multifaceted Parameter. J. Agron. Res. 2018, 1, 18–34. [Google Scholar] [CrossRef] [Green Version]
- Hélias, V.; Hamon, P.; Huchet, E.; Wolf, J.V.D.; Andrivon, D. Two New Effective Semiselective Crystal Violet Pectate Media for Isolation of Pectobacterium and Dickeya. Plant Pathol. 2012, 61, 339–345. [Google Scholar] [CrossRef]
- Pinheiro, J.; Bates, D.; DebRoy, S.; Sarkar, D.; R Core Team. NLME: Linear and Nonlinear Mixed Effects Models. 2021. Available online: https://CRAN.R-project.org/package=nlme (accessed on 20 May 2022).
- William, S.; Feil, H.; Copeland, A. Bacterial Genomic DNA Isolation Using CTAB; Protocols. Joint Genome Institute, 2012. Available online: http://jgi.doe.gov/collaborate-with-jgi/pmo-overview/protocols-sample-preparation-information/ (accessed on 20 May 2022).
- Kearse, M.; Moir, R.; Wilson, A.; Stones-Havas, S.; Cheung, M.; Sturrock, S.; Buxton, S.; Cooper, A.; Markowitz, S.; Duran, C.; et al. Geneious Basic: An Integrated and Extendable Desktop Software Platform for the Organization and Analysis of Sequence Data. Bioinformatics 2012, 28, 1647–1649. [Google Scholar] [CrossRef]
Figure 1.
The recA gene sequences-based phylogeny of Pectobacterium and Dickeya strains isolated from asymptomatic plants. The maximum likelihood tree based on recA gene sequences reflecting the phylogenetic position of 73 newly isolated Pectobacterium and 1 Dickeya strains originated from asymptomatic plant samples and 18 strains originated from symptomatic plants. For comparison, the 44 sequences of type strains and reference strains from both genera were retrieved from Genbank and were included in the analysis. The number in the brackets indicates the number of newly isolated strains present in each clade. The bootstrap value was equal to 1000 replicates. The recA gene sequence of Erwinia amylovora was used as an outgroup. Bootstrapping values < 50% were cut off.
Figure 1.
The recA gene sequences-based phylogeny of Pectobacterium and Dickeya strains isolated from asymptomatic plants. The maximum likelihood tree based on recA gene sequences reflecting the phylogenetic position of 73 newly isolated Pectobacterium and 1 Dickeya strains originated from asymptomatic plant samples and 18 strains originated from symptomatic plants. For comparison, the 44 sequences of type strains and reference strains from both genera were retrieved from Genbank and were included in the analysis. The number in the brackets indicates the number of newly isolated strains present in each clade. The bootstrap value was equal to 1000 replicates. The recA gene sequence of Erwinia amylovora was used as an outgroup. Bootstrapping values < 50% were cut off.
Figure 2.
Percentage share of individual Pectobacterium species and other genera of pectinolytic bacteria detected in the tested samples of vegetables and ornamental plants that did not show any disease symptoms.
Figure 2.
Percentage share of individual Pectobacterium species and other genera of pectinolytic bacteria detected in the tested samples of vegetables and ornamental plants that did not show any disease symptoms.
Figure 3.
Comparison of the potato tissue maceration ability of the 26 strains isolated from asymptomatic plant samples in contrast to 21 strains originating from plants with disease symptoms. Strains abbreviations: * strains isolated from symptomatic plants, T—type strains. Means ± SD of diameters of the rotten tissues is depicted. Three independent experiments with three replications were conducted.
Figure 3.
Comparison of the potato tissue maceration ability of the 26 strains isolated from asymptomatic plant samples in contrast to 21 strains originating from plants with disease symptoms. Strains abbreviations: * strains isolated from symptomatic plants, T—type strains. Means ± SD of diameters of the rotten tissues is depicted. Three independent experiments with three replications were conducted.
Figure 4.
Comparison of the chicory tissue maceration ability of the 26 strains isolated from asymptomatic plant samples in contrast to 18 strains originating from plants with disease symptoms. Strain abbreviations: * strains isolated from symptomatic plants, T—type strains. Means ± SD of diameters of the rotten tissues is depicted. Three independent experiments with three replications were conducted.
Figure 4.
Comparison of the chicory tissue maceration ability of the 26 strains isolated from asymptomatic plant samples in contrast to 18 strains originating from plants with disease symptoms. Strain abbreviations: * strains isolated from symptomatic plants, T—type strains. Means ± SD of diameters of the rotten tissues is depicted. Three independent experiments with three replications were conducted.
Figure 5.
Comparison of the (A) potato tuber and (B) chicory leaves tissue maceration ability of the strains isolated from asymptomatic and symptomatic plant samples. p = 0.02.
Figure 5.
Comparison of the (A) potato tuber and (B) chicory leaves tissue maceration ability of the strains isolated from asymptomatic and symptomatic plant samples. p = 0.02.
Table 1.
Host plant, geographical origin, year of isolation, recA PCR, sequence accession numbers specific PCR applied, and ERIC profile of the studied Pectobacterium isolates.
Table 1.
Host plant, geographical origin, year of isolation, recA PCR, sequence accession numbers specific PCR applied, and ERIC profile of the studied Pectobacterium isolates.
| Plant Sample No. | Strain Designation | Isolation Source | Geographic Origin of Sample | Year of Isolation | Darrasse PCR/ Nassar PCR (P/D) | Reca PCR Sequence Accession No | #Species Specific PCR | ERIC Profile |
|---|---|---|---|---|---|---|---|---|
| Pectobacterium atrosepticum | ||||||||
| mw1 | IFB5094 | Garlic | Poland | 2002 | P+ | + This work | Pba | A1 |
| mw2 | IFB5095 | Parsley | Poland | 2002 | P+ | + This work | Pba | A1 |
| 39 | a DPMP134 | Potato tuber | Belgium | 2015 | P+ | + | Pba | A1 |
| 45 | DPMP148 | Parsley | Poland | 2015 | P+ | + This work | Pba | A2 |
| 73 | DPMP275 | Potato tuber | Norway | 2016 | P+ | + This work | Pba | A1 |
| 73 | j DPMP278 | Potato tuber | Norway | 2016 | P+ | + | Pba | A1 |
| 61 | DPMP226 | Ginger | Poland | 2016 | P+ | + | Pba | A3 |
| 61 | DPMP227 | Ginger | Poland | 2016 | P+ | + | Pba | A3 |
| 92 | DPMP330 | Weed | Poland | 2016 | P+ | + | Pba | A1 |
| 92 | DPMP332 | Weed | Poland | 2016 | P+ | + | Pba | A1 |
| 96 | DPMP340a | Fennel | Poland | 2016 | P+ | + | Pba | A1 |
| 98 | b DPMP350 | Potato stem | Poland | 2016 | P+ | + | Pba | A1 |
| 98 | DPMP366 | Potato stem | Poland | 2016 | P+ | + | Pba | A1 |
| 101 | DPMP371 | Potato tuber | United Kingdom | 2016 | P+ | + | Pba | A3 |
| 106 | DPMP381 | Sugar beet | Poland | 2016 | P+ | + | Pba | A1 |
| 125A | DPMP442 | Potato stem | Poland | 2017 | P+ | + | Pba | A1 |
| 149 | DPMP623 | Diffenbachia | Poland | 2018 | P+ | + | Pba | A1 |
| 147 | DPMP617 | Diffenbachia | Poland | 2018 | P+ | + | Pba | A1 |
| 155 | c DPMP634 | Potato tuber | Kazakhstan | 2018 | P+ | + | Pba | A2 |
| *75B1 | *DPMP759 | Potato tuber | Poland | 1996 | P+ | + | Pba | A3 |
| *16A1 | *IFB5050 | Potato stem | Poland | 1996 | P+ | AY217078 | Pba | A1 |
| *SCRI1043 | Potato stem | Scotland UK | 1985 | P+ | BX950851 | Pba | A3 | |
| *CFBP1526 | Potato | United Kingdom | 1957 | P+ | JQHK00000000 | Pba | A1 | |
| *57A1 | *IFB5205 | Potato stem | Poland | 1996 | P+ | + This work | Pba | A1 |
| Pectobacterium brasiliense | ||||||||
| 2 | DPMP17 | Potato tuber | Cyprus | 2013 | P+ | + This work | - | B3 |
| 6 | DPMP32 | Cabbage | Poland | 2015 | P+ | + This work | Pbr | B1 |
| 7 | DPMP33 | Leek | Poland | 2015 | P+ | + | Pbr | B1 |
| 16 | d DPMP55 | Potato tuber | Morocco | 2013 | P+ | + | Pbr | B1 |
| 21 | DPMP81 | Potato tuber | Spain Tenerife | 2014 | P+ | + | Pbr | B2 |
| 38 | DPMP132 | Sweet Potato | USA | 2015 | P+ | + | Pbr | B2 |
| 25 | DPMP135 | Rhubarb | Poland | 2015 | P+ | + | Pbr | B2 |
| 44 | e DPMP152 | Potato tuber | Morocco | 2015 | P+ | + | Pbr | B2 |
| 46 | DPMP153 | Potato tuber | Israel | 2015 | P+ | + This work | Pbr | B2 |
| 46 | DPMP154 | Potato tuber | Israel | 2015 | P+ | + | Pbr | B2 |
| 60 | DPMP224 | Potato tuber | Portugal | 2016 | P+ | + This work | Pbr | B2 |
| 66 | DPMP255 | Celery | Poland | 2016 | P+ | + | Pbr | B2 |
| 101 | DPMP372 | Potato tuber | United Kingdom | 2016 | P+ | + | Pbr | B2 |
| 103 | DPMP374 | Potato tuber | Brasil | 2016 | P+ | + This work | Pbr | B2 |
| 103 | DPMP375 | Potato tuber | Brasil | 2016 | P+ | + | Pbr | B2 |
| 103 | DPMP377 | Potato tuber | Brasil | 2016 | P+ | + | Pbr | B2 |
| 103.2 | DPMP378 | Potato tuber | Brasil | 2016 | P+ | + | Pbr | B2 |
| 111 | f DPMP394 | Sugar beet | Poland | 2016 | P+ | + This work | - | B2 |
| 112 | g DPMP396 | Bittersweet | Poland | 2016 | P+ | + This work | - | B2 |
| 156 | DPMP678 | Rhubarb | Poland | 2018 | P+ | + | Pbr | B4 |
| 156 | DPMP679 | Rhubarb | Poland | 2018 | P+ | + | Pbr | B4 |
| 156 | DPMP680 | Rhubarb | Poland | 2018 | P+ | + This work | Pbr | B4 |
| 156 | DPMP681 | Rhubarb | Poland | 2018 | P+ | + | Pbr | B4 |
| 157 | DPMP682 | Potato tuber | The Netherlands | 2018 | P+ | + | Pbr | B4 |
| 29 | DPMP120 | Zucchini | Poland | 2016 | P+ | + This work | Pbr | B2 |
| mkw16 | MKW16 | Potato tuber | Cyprus | 2013 | P+ | + This work | Pbr | B3 |
| mkw33 | MKW33 | Potato tuber | Morocco | 2013 | P+ | + This work | Pbr | B1 |
| *mw3 | IFB5258 | Sugar beet | Poland | 2002 | P+ | KP762589 | Pbr | B2 |
| *MN9 | *IFB5164 | Parsley | Poland | 2002 | P+ | + This work | Pbr | B3 |
| *110-6B | *IFB5369 | Potato | Poland | 2011 | P+ | KP762587 | Pbr | B2 |
| *LMG2137T | Potato | Brazil | 1999 | P+ | JQOE01000000 | Pbr | B4 | |
| Pectobacterium carotovorum | ||||||||
| 10 | DPMP60 | Prickly pear | Tunisia | 2016 | P+ | + | - | C3 |
| 44 | e DPMP146 | Potato tuber | Morocco | 2015 | P+ | + | - | C1 |
| 51.1 | DPMP189 | Potato tuber | Egypt | 2015 | P+ | + This work | - | C2 |
| 51.5 | DPMP199 | Potato tuber | Egypt | 2016 | P+ | + This work | - | C2 |
| 51.3 | DPMP200 | Potato tuber | Egypt | 2016 | P+ | + This work | - | C2 |
| 51.4 | DPMP262 | Potato tuber | Egypt | 2016 | P+ | + | - | C1 |
| 77 | DPMP292 | Onion | Poland | 2016 | P+ | + | - | C1 |
| 87 | DPMP323 | Prickly pear | Italy | 2016 | P+ | + | - | C3 |
| 98 | DPMP346 | Potato stem | Poland | 2016 | P+ | + | - | C2 |
| 98 | DPMP351 | Potato stem | Poland | 2016 | P+ | + | - | C2 |
| 99.1 | DPMP356 | Potato tuber | Poland | 2016 | P+ | + | - | C2 |
| 99.3 | DPMP357 | Potato tuber | Poland | 2016 | P+ | + | - | C2 |
| 99.3 | DPMP358 | Potato tuber | Poland | 2016 | P+ | + | - | C2 |
| 100 | h DPMP369 | Potato tuber | Cyprus | 2016 | P+ | + | - | C3 |
| 102 | DPMP373 | Broccoli | Poland | 2016 | P+ | + | - | C2 |
| 109 | DPMP389 | Potato tuber | Japan | 2016 | P+ | + | - | C1 |
| 113 | DPMP398 | Sugar beet | Poland | 2016 | P+ | + This work | - | C3 |
| 113 | DPMP399 | Sugar beet | Poland | 2016 | P+ | + This work | - | C3 |
| 113 | DPMP400 | Sugar beet | Poland | 2016 | P+ | + This work | - | C3 |
| 113 | DPMP401 | Sugar beet | Poland | 2016 | P+ | + This work | - | C3 |
| 119 | DPMP417 | Leek | Poland | 2016 | P+ | + | - | C1 |
| 119 | DPMP418 | Leek | Poland | 2016 | P+ | + | - | C1 |
| 109 | DPMP421 | Potato tuber | Japan | 2016 | P+ | + | - | C1 |
| 141 | DPMP598 | Potato tuber | Georgia | 2017 | P+ | + | - | C1 |
| 142 | DPMP607 | Alpine violet | Poland | 2018 | P+ | + | - | C2 |
| 143 | DPMP608 | Alpine violet | Poland | 2018 | P+ | + | - | C2 |
| 145 | DPMP613 | Alpine violet | Poland | 2018 | P+ | + | - | C1 |
| 146 | DPMP615 | Diffenbachia | Poland | 2018 | P+ | + | - | C1 |
| 147 | DPMP616 | Diffenbachia | Poland | 2018 | P+ | + | - | C1 |
| 147 | DPMP618 | Diffenbachia | Poland | 2018 | P+ | + | - | C2 |
| 148 | DPMP619 | Diffenbachia | Poland | 2018 | P+ | + | - | C2 |
| 148 | DPMP622 | Diffenbachia | Poland | 2018 | P+ | + | - | C1 |
| 155 | c DPMP631 | Potato tuber | Kazakhstan | 2018 | P+ | + | - | C1 |
| *134A2 | *DPM510 | Potato stem | Poland | 1996 | P+ | AY264792 | - | C4 |
| *LMG2401 | Carot | USA | 1967 | P+ | + | - | C1 | |
| *LMG2404T | Potato | Danemark | 1952 | P+ | JQHJ00000000 | - | nt | |
| Pectobacterium odoriferum | ||||||||
| 4 | DPMP27 | Celery | Poland | 2015 | P+ | + This work | - | O1 |
| 78 | DPMP293 | Celery | Poland | 2016 | P+ | + This work | - | O1 |
| MN6 | *IFB5295 | Carrot | Poland | 1999 | P+ | AY264791 | - | O1 |
| L9 | *IFB5300 | Leek | Poland | 1995 | P+ | KF704816 | - | O1 |
| *CFBP1878T | Chicory | France | 1979 | P+ | KF704811 | - | O1 | |
| Pectobacterium parmentieri | ||||||||
| 40 | DPMP136 | Potato tuber | Poland | 2015 | P+ | + This work | Ppar | Pa1 |
| 96 | DPMP340b | Fennel | Poland | 2016 | P+ | + | Ppar | Pa1 |
| 60 | DPMP225 | Potato tuber | Portugal | 2016 | P+ | + | Ppar | Pa1 |
| 98.2 | DPMP347 | Potato stem | Poland | 2016 | P+ | + | Ppar | Pa1 |
| 99.1 | k DPMP353 | Potato tuber | Poland | 2016 | P+ | + This work | Ppar | Pa2 |
| 99.1 | DPMP354 | Potato tuber | Poland | 2016 | P+ | + | Ppar | Pa2 |
| 99.3 | DPMP355 | Potato tuber | Poland | 2016 | P+ | + | Ppar | Pa2 |
| 99.1 | DPMP362 | Potato tuber | Poland | 2016 | P+ | + | Ppar | Pa2 |
| 99.1 | DPMP363 | Potato tuber | Poland | 2016 | P+ | + | Ppar | Pa1 |
| 99.2 | DPMP364 | Potato tuber | Poland | 2016 | P+ | + | Ppar | Pa1 |
| 100 | h DPMP370 | Potato tuber | Cyprus | 2016 | P+ | + | Ppar | Pa1 |
| 109 | DPMP390 | Potato tuber | Japan | 2016 | P+ | + | Ppar | Pa1 |
| *SCC3193 | Potato stem | Finland | 1980s | P+ | CP003415 | Ppar | Pa1 | |
| *IFB5322 | Potato sten | Poland | 1996 | P+ | AY217080 | Ppar | Pa1 | |
| Pectobacterium parvum | ||||||||
| mkw18 | i DPMP20 | Potato tuber | Cyprus | 2013 | P+ | + This work | - | Pv1 |
| 20 | DPMP78 | Peppers | Spain Tenerife | 2014 | P+ | + | - | Pv1 |
| 53 | DPMP223 | Ginger | Poland | 2016 | P+ | + | - | Pv1 |
| *so421 | Potato stem | Finland | 2005 | P+ | OANP00000000 | - | Pv1 | |
| 38A1 | *IFB5220 | Potato stem | Poland | 1996 | P+ | PHSZ00000000 | - | Pv1 |
| Pectobacterium polaris | ||||||||
| 73 | j DPMP280 | Potato tuber | Norway | 2016 | P+ | + | - | Po1 |
| 76 | DPMP286 | Potato tuber | Finland | 2016 | P+ | + This work | - | Po1 |
| 76 | DPMP290 | Potato tuber | Finland | 2016 | P+ | + | - | Po1 |
| 106 | DPMP380 | Sugar beet | Poland | 2016 | P+ | + This work | - | Po2 |
| 112 | g DPMP397 | Bittersweet | Poland | 2016 | P+ | + This work | - | Po2 |
| 111 | f DPMP403 | Sugar beet | Poland | 2016 | P+ | + This work | - | Po3 |
| 114 | DPMP404 | Rutabaga | Poland | 2016 | P+ | + This work | - | Po3 |
| 114 | DPMP405 | Rutabaga | Poland | 2016 | P+ | + This work | - | Po3 |
| 16 | d DPMP730 | Potato tuber | Morocco | 2013 | P+ | + | - | Po4 |
| mw10 | IFB5223 | Black nightshade | Poland | 2002 | P+ | + This work | - | Po3 |
| mkw36 | MKW36 | Potato tuber | Morroco | 2013 | P+ | + This work | - | Po4 |
| 104B2 | *IFB5252 | Potato tuber | Poland | 1996 | P+ | KU510113 | - | Po3 |
| 119A1 | *IFB5222 | Potato stem | Poland | 1996 | P+ | KU510110 | - | Po4 |
| 129A1 | *IFB5225 | Potato stem | Poland | 1996 | P+ | KU510111 | - | Po4 |
| *NBIO1006T | Potato tuber | Norway | 2010 | P+ | CP017481 | - | Po3 | |
| Pectobacterium versatile | ||||||||
| k19 | IFB5176 | Cabbage | Poland | 1999 | P+ | + This work | - | V2 |
| p36 | IFB5178 | Parsley | Poland | 1999 | P+ | + This work | - | V2 |
| p42 | IFB5179 | Parsley | Poland | 1999 | P+ | + This work | - | V2 |
| ce42 | IFB5181 | Celery | Poland | 1999 | P+ | + This work | - | V2 |
| mw6 | IFB5212 | Rose | Poland | 2002 | P+ | + This work | - | V2 |
| mw57 | IFB5215 | Garlic | Germany | 1999 | P+ | + This work | - | V1 |
| mw8l | IFB5213 | Bittersweet | Poland | 2002 | P+ | + This work | - | V1 |
| mw8b | IFB5214 | Bittersweet | Poland | 2002 | P+ | + This work | - | V1 |
| mkw18 | i MKW18 | Potato tuber | Cyprus | 2013 | P+ | + This work | - | V2 |
| mkw32 | MKW32 | Potato tuber | Morocco | 2013 | P+ | + This work | - | V1 |
| 5 | DPMP28 | Leek | Poland | 2015 | P+ | + | - | V2 |
| 9 | DPMP35 | Leek | Poland | 2015 | P+ | + | - | V2 |
| 27.5p | DPMP98 | Potato tuber | Israel | 2015 | P+ | + This work | - | V4 |
| 27.5p | DPMP100 | Potato tuber | Israel | 2015 | P+ | + This work | - | V4 |
| 27.3p | DPMP102 | Potato tuber | Israel | 2015 | P+ | + | - | V3 |
| 32 | DPMP114 | Potato tuber | Morocco | 2013 | P+ | + | - | V3 |
| 29 | DPMP106 | Zucchini | Poland | 2016 | P+ | + | - | V3 |
| 28 | DPMP105 | Iris | Poland | 2016 | P+ | + This work | - | V3 |
| 28 | DPMP108 | Iris | Poland | 2016 | P+ | + This work | - | V3 |
| 31 | DPMP112 | Iris | Poland | 2016 | P+ | + This work | - | V3 |
| 39 | a DPMP133 | Potato tuber | Belgium | 2015 | P+ | + | - | V1 |
| 42 | DPMP140 | Potato tuber | Poland | 2015 | P+ | + | - | V1 |
| 44 | e DPMP155 | Potato tuber | Morocco | 2015 | P+ | + | - | V3 |
| 45 | DPMP156 | Parsley | Poland | 2015 | P+ | + This work | - | V3 |
| 29 | DPMP181 | Zucchini | Poland | 2016 | P+ | + This work | - | V2 |
| 52 | DPMP198 | Cactus | Poland | 2016 | P+ | + This work | - | V2 |
| 52 | DPMP202 | Cactus | Poland | 2016 | P+ | + This work | - | V2 |
| 54 | DPMP204 | Potato tuber | France | 2016 | P+ | + This work | - | V3 |
| 57 | DPMP217 | Potato tuber | Spain | 2016 | P+ | + | - | V3 |
| 58 | DPMP228 | Potato tuber | Spain | 2016 | P+ | + This work | - | V3 |
| 62 | DPMP234 | Onion | Poland | 2016 | P+ | + This work | - | V3 |
| 65.1p | DPMP238 | Potato tuber | Cyprus | 2016 | P+ | + This work | - | V2 |
| 65.2.p | DPMP240 | Potato tuber | Cyprus | 2016 | P+ | + | - | V2 |
| 65.1p | DPMP248 | Potato tuber | Cyprus | 2016 | P+ | + This work | - | V2 |
| 67 | DPMP256 | Potato stem | Poland | 2016 | P+ | + This work | - | V3 |
| 80t | DPMP299 | Tomato | Poland | 2016 | P+ | + This work | - | V2 |
| 81p | DPMP300 | Potato tuber | Poland | 2016 | P+ | + This work | - | V2 |
| 96 | DPMP337 | Fenel | Poland | 2016 | P+ | + | - | V1 |
| 98 | b DPMP344 | Potato stem | Poland | 2016 | P+ | + This work | - | V2 |
| 99.1 | k DPMP352 | Potato tuber | Poland | 2016 | P+ | + This work | - | V1 |
| 94 | DPMP334 | Bean | Poland | 2016 | P+ | + | - | V4 |
| 95 | DPMP335 | Peppers | Morocco | 2016 | P+ | + This work | - | V4 |
| 106 | DPMP383 | Sugar beet | Poland | 2016 | P+ | + | - | V2 |
| 108 | DPMP387 | Beetroot | Poland | 2016 | P+ | + This work | - | V2 |
| 114 | DPMP402 | Beetroot | Poland | 2016 | P+ | + This work | - | V2 |
| 130 | DPMP500 | Bittersweet | Poland | 2002 | P+ | + | - | V1 |
| 130 | DPMP501 | Bittersweet | Poland | 2002 | P+ | + This work | - | V1 |
| 137 | DPMP546 | Iris | Poland | 2016 | P+ | + This work | - | V3 |
| 155 | c DPMP632 | Potato tuber | Kazakhstan | 2018 | P+ | + This work | - | V4 |
| 155 | c DPMP633 | Potato tuber | Kazakhstan | 2018 | P+ | + This work | - | V4 |
| 61A1 | *IFB5206 | Potato stem | Poland | 1996 | P+ | MK024782 | - | V1 |
| 75B5 | *IFB5208 | Potato tuber | Poland | 1996 | P+ | MK024779 | - | V1 |
| 25A3 | *IFB5169 | Potato stem | Poland | 1996 | P+ | MK024780 | - | V4 |
| 143A1 | *IFB5266 | Potato stem | Poland | 1996 | P+ | MK024781 | - | V1 |
| *IFB5462 | Potato tuber | Poland | 1996 | P+ | KU510133 | - | V1 | |
| *SCC1 | Potato tuber | Finland | 1982 | P+ | CP021894 | - | V2 | |
| Pectobacterium zantedeschiae | ||||||||
| *9MT | Calla lily | Poland | 2018 | P+ | MH367240 | - | ||
| Dickeya dadantii | ||||||||
| 150 | DPMP624 | Diffenbachia | Poland | 2018 | D+ | + | - | D1 |
| 151 | DPMP625 | Diffenbachia | Poland | 2018 | D+ | + This work | - | D1 |
| 152 | DPMP626 | Diffenbachia | Poland | 2018 | D+ | + | - | D1 |
| 153 | DPMP627 | Diffenbachia | Poland | 2018 | D+ | + | - | D1 |
| *3937 | African violet | France | 1980 | D+ | CP002038 | - | D1 | |
* Strains isolated from plants with disease symptoms used as reference in this research; #Pba positive result of PCR with Eca1/Eca2 primers [29]; Pbr positive result of PCR with Br1f/L1r primers [30]; Ppar positive result of PCR with PhF/PhR primers [31]; a—potato tuber sample Liege 2/2015; b—potato stem Lodyga3/16; c—potato tuber sample Szymkent 215, d—potato tuber sample Maroko13, e—potato tuber sample Maroko15; f—Sugar beet sample BC16; g—Bittersweet sample SD16; h—potato tuber sample Cypr103; i—potato tuber sample Cypr4/1; Darrasse—a PCR test for Pectobacterium spp. using Y1, Y2 primers [32]; j—potato tuber sample Norwegia28; k—potato tuber sample Patków99; T—type strain; P+—the strain was identified as Pectobacterium; Nassar PCR with primers specific for Dickeya genus [35] D+—the strain was identified as Dickeya.
Table 2.
List of Pectobacterium strains classified into different species that were co-isolated from the same plant sample.
Table 2.
List of Pectobacterium strains classified into different species that were co-isolated from the same plant sample.
| Plant Sample No/Name | Host Plant | Geographic Origin of Plant | Detected Pectobacterium species | Year of Isolation |
|---|---|---|---|---|
| 111/BC16 | Sugar beet | Poland | P. brasiliense DPMP394 P. polaris DPMP403 | 2016 |
| 112/SD16 | Bittersweet | Poland | P. brasiliense DPMP396 P. polaris DPMP397 | 2016 |
| 155/Maroko2013 | Potato tuber | Morocco | P. brasiliense DPMP55 P. polaris DPMP730 | 2013 |
| 39/Łodyga3/16 | Potato stem | Poland | P. atrosepticum DPMP350 P. versatile DPMP344 | 2016 |
| 39/Liege 2/2015 | Potato tuber | Belgium | P. atrosepticum DPMP134 P. versatile DPMP133 | 2015 |
| 73/Norwegia28 | Potato tuber | Norway. | P. atrisepticum DPMP278 P. polaris DPMP280 | 2016 |
| 99.1/Patków 99 | Potato tuber | Poland | P. versatile DPMP352 P. parmentieri DPMP353 | 2016 |
| 100/Cypr103 | Potato tuber | Cyprus | P. parmentieri DPMP370 P. carotovorum DPMP369 | 2016 |
| mkw18/Cypr 4/1 | Potato tuber | Cyprus | P. parvum DPMP20 P. versatile MKW18 | 2013 |
| 98/Szymkent215 | Potato tuber | Kazakhstan | P. atrosepticum DPMP634 P. versatile DPMP632 and DPMP633 P. carotovorum DPMP631 | 2013 |
| 44/Maroko2015 | Potato tuber | Morocco | P. brasilense DPMP152 P. carotovorum DPMP146 P. versatile DPMP155 | 2015 |
Table 3.
Measurement of pH effect on bacteria growth.
| pH Value | ||||||||
|---|---|---|---|---|---|---|---|---|
| Strain | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 |
| P. atrosepticum | ||||||||
| DPMP275 | X | OPT | ||||||
| DPMP442 | X | OPT | ||||||
| *IFB5050 | OPT | |||||||
| *SCRI1043 | X | OPT | X | |||||
| *ICMP1526T | OPT | |||||||
| P. brasiliense | ||||||||
| DPMP55 | OPT | |||||||
| DPMP224 | X | OPT | ||||||
| DPMP372 | X | OPT | ||||||
| DPMP374 | X | OPT | ||||||
| DPMP396 | X | OPT | X | |||||
| DPMP680 | X | OPT | ||||||
| *IFB5369 | X | OPT | X | |||||
| *LMG21371T | X | X | OPT | |||||
| P. carotovorum | ||||||||
| DPMP199 | V | OPT | ||||||
| DPMP200 | V | OPT | ||||||
| DPMP323 | X | OPT | ||||||
| DPMP399 | X | OPT | ||||||
| *DPMP510 | X | OPT | ||||||
| P. parmentieri | ||||||||
| DPMP390 | X | OPT | ||||||
| * IFB5322 | X | OPT | ||||||
| * SCC3193 | X | OPT | ||||||
| P. parvum | ||||||||
| DPMP20 | X | OPT | ||||||
| *IFB5220 | X | OPT | ||||||
| P. polaris | ||||||||
| DPMP286 | OPT | |||||||
| DPMP403 | X | OPT | X | |||||
| DPMP397 | X | OPT | ||||||
| *IFB5222 | X | OPT | ||||||
| *IFB5252 | OPT | |||||||
| P. versatile | ||||||||
| DPMP198 | OPT | |||||||
| DPMP202 | OPT | |||||||
| *IFB5266 | X | OPT | ||||||
| *IFB5258 | X | OPT | ||||||
| DPMP633 | X | OPT | ||||||
| *DPMP5169 | X | OPT | ||||||
| P. zantedeschiae | ||||||||
| *9MT | X | OPT | ||||||
The symbol “X” means no bacterial growth in the spot test, “V” means the presence of viable bacterial cells in spot test. The “OPT” symbol indicates the optimum at which the strain reached the highest OD value. * reference strains and strains that were isolated from plants with disease symptoms. T—Type Strain. The following colours indicate average OD ranges of two measurements. Black: <0.03, grey: 0.03–0.3, blue: 0.3–0.7, white: >0.7.
Table 4.
Growth in various salinity conditions.
| Concentration of Sodium Chloride [%] | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Strain | 0% | 1% | 2% | 3% | 4% | 6% | 7% | 8% | 11% |
| P. atrosepticum | |||||||||
| DPMP275 | OPT | V | V | V | |||||
| DPMP442 | OPT | V | V | X | X | ||||
| *IFB5050 | OPT | X | X | ||||||
| *SCRI1043 | OPT | ||||||||
| *ICMP1526T | OPT | X | X | X | X | ||||
| P. brasiliense | |||||||||
| DPMP55 | OPT | V | |||||||
| DPMP224 | OPT | V | V | ||||||
| DPMP372 | OPT | V | V | V | |||||
| DPMP374 | OPT | V | V | V | |||||
| DPMP396 | OPT | V | V | V | |||||
| DPMP680 | OPT | V | V | V | X | ||||
| *IFB5369 | OPT | V | V | V | X | ||||
| *LMG21371T | OPT | V | V | V | X | ||||
| P. carotovorum | |||||||||
| DPMP199 | OPT | V | V | V | |||||
| DPMP200 | OPT | V | V | X | |||||
| DPMP323 | OPT | V | V | V | X | ||||
| DPMP399 | OPT | V | V | V | |||||
| *DPMP510 | OPT | X | X | X | |||||
| P. parmentieri | |||||||||
| DPMP390 | OPT | X | X | X | X | X | |||
| *IFB5322 | OPT | X | X | X | X | X | |||
| *SCC3193 | OPT | X | X | X | X | X | |||
| P. parvum | |||||||||
| DPMP20 | OPT | V | V | X | |||||
| *IFB5220 | OPT | V | V | V | X | ||||
| P. polaris | |||||||||
| DPMP286 | OPT | V | V | V | X | ||||
| DPMP403 | OPT | V | V | X | |||||
| DPMP397 | OPT | V | X | ||||||
| *IFB5222 | OPT | V | X | X | |||||
| *IFB5252 | OPT | V | V | ||||||
| P. versatile | |||||||||
| DPMP198 | OPT | V | X | ||||||
| DPMP202 | OPT | V | V | X | |||||
| IFB402 | OPT | V | V | ||||||
| DPMP633 | OPT | V | V | X | |||||
| *IFB5266 | OPT | V | V | V | V | ||||
| *IFB5169 | OPT | X | X | X | |||||
| P. zantedeschiae | |||||||||
| *9MT | OPT | V | V | X | |||||
The symbol “X” means no bacterial growth in the spot test, “V” means the presence of viable bacterial cells in a spot test. The “OPT” symbol indicates the optimum at which the strain reached the highest OD value. * reference strains and strains that were isolated from plants with disease symptoms. T—Type Strain. The average OD ranges are highlighted in the same color as in Table 3.
Table 5.
The tolerance for limited water availability.
| Concentration Polyethylene Glycol [g/L] | ||||||||
|---|---|---|---|---|---|---|---|---|
| Strain | 0 g/L | 50 g/L | 75 g/L | 100 g/L | 200 g/L | 300 g/L | 400 g/L | 500 g/L |
| P. atrosepticum | ||||||||
| DPMP275 | OPT | V | X | X | X | |||
| DPMP442 | OPT | X | X | X | X | |||
| *IFB5050 | X | X | X | |||||
| *SCRI1043 | OPT | X | X | X | ||||
| *CFBP1526T | X | X | X | |||||
| P. brasiliense | ||||||||
| DPMP55 | OPT | V | X | X | ||||
| DPMP224 | OPT | V | X | X | X | |||
| DPMP372 | OPT | V | X | X | X | |||
| DPMP374 | OPT | V | X | X | X | |||
| DPMP396 | OPT | V | X | X | X | |||
| DPMP680 | OPT | V | X | X | X | |||
| *IFB5369 | OPT | V | X | X | X | |||
| *LMG21371T | OPT | X | X | X | ||||
| P. carotovorum | ||||||||
| DPMP199 | OPT | V | X | |||||
| DPMP200 | OPT | V | X | |||||
| DPMP323 | OPT | X | X | X | X | |||
| DPMP399 | OPT | V | X | X | X | |||
| *DPMP510 | OPT | X | X | X | X | |||
| P. parmentieri | ||||||||
| DPMP390 | OPT | X | X | X | X | |||
| *IFB5322 | OPT | X | X | X | X | |||
| *SCC3193 | OPT | X | X | X | X | |||
| P. parvum | ||||||||
| DPMP20 | OPT | X | X | X | X | |||
| *IFB5220 | OPT | X | X | X | X | |||
| P. polaris | ||||||||
| DPMP286 | OPT | V | X | X | X | |||
| DPMP403 | OPT | V | X | X | X | |||
| DPMP397 | OPT | X | X | X | X | |||
| *IFB5222 | OPT | X | X | |||||
| *IFB5252 | OPT | V | V | |||||
| P. versatile | ||||||||
| DPMP198 | OPT | V | X | |||||
| DPMP202 | OPT | V | ||||||
| DPMP402 | OPT | V | V | X | X | |||
| DPMP633 | OPT | X | X | X | X | |||
| *IFB5169 | OPT | X | X | X | X | |||
| *IFB5266 | OPT | V | X | X | X | |||
| P. zantedeschiae | ||||||||
| *9MT | OPT | V | V | X | X | |||
The symbol “X” means no bacterial growth in the spot test, “V” means the presence of viable bacterial cells in spot test. The “OPT” symbol indicates the optimum at which the strain reached the highest OD value. * reference strains and strains that were isolated from plants with disease symptoms. T—Type Strain. The average OD ranges are highlighted in the same colour as in Table 3.
Table 6.
Antibiotic susceptibility results.
| Strain | Antibiotics Susceptibility | ESBL Type Resistance Assay | Carbapenemase Resistance Assay | |||||
|---|---|---|---|---|---|---|---|---|
| Ampicillin 10 µg | Erythromycin 15 µg | Gentamicin 300 µg | Kanamycin 30 µg | Streptomycin 100 µg | Tetracycline 15 µg | |||
| Zone of growth inhibition [mm] | ||||||||
| P. atrosepticum | ||||||||
| DPMP134 | 0 | 0 | 31 | 35 | 20 | 25 | - | - |
| DPMP275 | 30 | 16 | 30 | 24 | 16 | 25 | - | - |
| DPMP366 | 12 | 19 | 38 | 15 | 0 | 20 | - | - |
| DPMP371 | 30 | 12 | 30 | 34 | 21 | 30 | - | - |
| P. brasiliense | ||||||||
| DPMP55 | 11 | 10 | 34 | 18 | 16 | 26 | - | - |
| DPMP224 | 30 | 12 | 36 | 27 | 15 | 26 | - | - |
| DPMP372 | 31 | 14 | 36 | 26 | 28 | 32 | - | - |
| DPMP374 | 34 | 16 | 37 | 27 | 24 | 34 | - | - |
| DPMP396 | 18 | 14 | 40 | 32 | 18 | 27 | - | - |
| DPMP120 | 0 | 12 | 30 | 30 | 26 | 30 | + | - |
| DPMP135 | 10 | 10 | 24 | 22 | 14 | 26 | - | - |
| DPMP152 | 10 | 0 | 24 | 26 | 13 | 27 | - | - |
| *IFB5369 | 31 | 19 | 45 | 34 | 22 | 37 | nt | nt |
| P. carotovorum | ||||||||
| DPMP189 | 10 | 8 | 13 | 0 | 11 | 30 | - | - |
| DPMP199 | 0 | 7 | 8 | 5 | 2 | 7 | + | - |
| DPMP200 | 8 | 7 | 12 | 10 | 11 | 5 | - | - |
| DPMP323 | 35 | 17 | 35 | 26 | 24 | 34 | - | - |
| DPMP399 | 30 | 15 | 38 | 27 | 20 | 29 | - | - |
| P. odoriferum | ||||||||
| DPMP293 | 0 | 10 | 30 | 30 | 25 | 24 | - | + |
| P. parmentieri | ||||||||
| DPMP136 | 0 | 11 | 30 | 27 | 20 | 20 | - | + |
| P. parvum | ||||||||
| DPMP20 | 10 | 13 | 30 | 30 | 20 | 25 | - | - |
| *IFB5220 | 30 | 13 | 37 | 32 | 24 | 28 | nt | nt |
| P. polaris | ||||||||
| DPMP286 | 0 | 0 | 35 | 33 | 20 | 21 | - | - |
| DPMP403 | 16 | 16 | 38 | 26 | 25 | 37 | - | nt |
| P. versatile | ||||||||
| DPMP78 | 15 | 10 | 25 | 15 | 11 | 16 | - | - |
| DPMP105 | 0 | 10 | 30 | 28 | 15 | 28 | - | - |
| DPMP108 | 0 | 9 | 30 | 30 | 25 | 32 | - | + |
| DPMP112 | 0 | 4 | 8 | 5 | 11 | 0 | - | + |
| DPMP181 | 0 | 4 | 10 | 9 | 9 | 7 | - | + |
| DPMP198 | 0 | 4 | 6 | 2 | 0 | 0 | + | - |
| DPMP202 | 0 | 4 | 6 | 4 | 0 | 0 | + | - |
| DPMP204 | 35 | 7 | 35 | 32 | 25 | 30 | - | - |
| DPMP633 | 0 | 5 | 10 | 5 | 2 | 0 | + | - |
| P. zantedeschiae | ||||||||
| * 9MT | 8 | 0 | 15 | 29 | 18 | 25 | - | - |
* Strains isolated from plants with disease symptoms used as reference in this research. The symbol nt—means that strain was not tested; +/- strain was able to grow/did not grow on ESBL and CARBA chromagar plates.
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. |
© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
MDPI and ACS Style
Smoktunowicz, M.; Jonca, J.; Stachowska, A.; May, M.; Waleron, M.M.; Waleron, M.; Waleron, K. The International Trade of Ware Vegetables and Orna-Mental Plants—An Underestimated Risk of Accelerated Spreading of Phytopathogenic Bacteria in the Era of Globalisation and Ongoing Climatic Changes. Pathogens 2022, 11, 728. https://doi.org/10.3390/pathogens11070728
AMA Style
Smoktunowicz M, Jonca J, Stachowska A, May M, Waleron MM, Waleron M, Waleron K. The International Trade of Ware Vegetables and Orna-Mental Plants—An Underestimated Risk of Accelerated Spreading of Phytopathogenic Bacteria in the Era of Globalisation and Ongoing Climatic Changes. Pathogens. 2022; 11(7):728. https://doi.org/10.3390/pathogens11070728
Chicago/Turabian StyleSmoktunowicz, Magdalena, Joanna Jonca, Aneta Stachowska, Michal May, Michal Mateusz Waleron, Malgorzata Waleron, and Krzysztof Waleron. 2022. "The International Trade of Ware Vegetables and Orna-Mental Plants—An Underestimated Risk of Accelerated Spreading of Phytopathogenic Bacteria in the Era of Globalisation and Ongoing Climatic Changes" Pathogens 11, no. 7: 728. https://doi.org/10.3390/pathogens11070728
APA StyleSmoktunowicz, M., Jonca, J., Stachowska, A., May, M., Waleron, M. M., Waleron, M., & Waleron, K. (2022). The International Trade of Ware Vegetables and Orna-Mental Plants—An Underestimated Risk of Accelerated Spreading of Phytopathogenic Bacteria in the Era of Globalisation and Ongoing Climatic Changes. Pathogens, 11(7), 728. https://doi.org/10.3390/pathogens11070728
Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.
