Dickeya and Pectobacterium: Ecology, Pathology and Plant Protection

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Plant Microbe Interactions".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 39047

Special Issue Editor

Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
Interests: environmental microbiology; microbial ecology; plant microbiology; plant pathology; biocontrol; rhizosphere; Agrobacterium; Pectobacterium; Dickeya; genomics; transcriptomics; Tn-Seq; reverse genetics; quorum-sensing
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Special Issue Information

Dear Colleagues,

Pectinolytic enterobacteria Dickeya and Pectobacterium represent a threat for plant and seed production and trade around the world. This Special Issue offers the opportunity to share recent advances in ecology, evolution, taxonomy and pathogenesis of bacteria of the Pectobacterium and Dickeya genera. This Special Issue will also consider advances in diagnosis and biocontrol approaches and plant breeding to limit propagation of these pathogens and their damage on plants.

Dr. Denis Faure
Guest Editor

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Keywords

  • Dickeya
  • Pectobacterium
  • genomics
  • genetics
  • transcriptomics
  • epidemiology
  • detection
  • adaptation
  • biocontrol
  • aggressiveness
  • host plant
  • reservoir plant

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Published Papers (12 papers)

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Research

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13 pages, 3333 KiB  
Article
Pathogenicity and Relative Abundance of Dickeya and Pectobacterium Species in Switzerland: An Epidemiological Dichotomy
Microorganisms 2021, 9(11), 2270; https://doi.org/10.3390/microorganisms9112270 - 31 Oct 2021
Cited by 4 | Viewed by 1620
Abstract
Pectobacterium and Dickeya species are the causal agents of blackleg and soft rot diseases in potatoes. The main pathogenic species identified so far on potatoes are Dickeya dianthicola, Dickeya solani, Pectobacterium atrosepticum, Pectobacterium brasiliense, Pectobacterium carotovorum, and Pectobacterium [...] Read more.
Pectobacterium and Dickeya species are the causal agents of blackleg and soft rot diseases in potatoes. The main pathogenic species identified so far on potatoes are Dickeya dianthicola, Dickeya solani, Pectobacterium atrosepticum, Pectobacterium brasiliense, Pectobacterium carotovorum, and Pectobacterium parmentieri. Ten years ago, the most prevalent Soft Rot Pectobacteriaceae in Europe were the Dickeya species, P. atrosepticum and P. carotovorum, with some variations among countries. Since then, a drastic increase in the abundance of P. brasiliense has been observed in most European countries. This shift is difficult to explain without comparing the pathogenicity of all Dickeya and Pectobacterium species. The pathogenicity of all the above-mentioned bacterial species was assessed in field trials and in vitro tuber slice trials in Switzerland. Two isolates of each species were inoculated by soaking tubers of cv. Desiree in a suspension of 105 CFU/mL, before planting in the field. For all trials, the Dickeya species were the most virulent ones, but long-term strain surveys performed in Switzerland indicate that P. brasiliense is currently the most frequent species detected. Our results show that the pathogenicity of the species is not the main factor explaining the high prevalence of P. brasiliense and P. parmentieri in the Swiss potato fields. Full article
(This article belongs to the Special Issue Dickeya and Pectobacterium: Ecology, Pathology and Plant Protection)
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24 pages, 1867 KiB  
Article
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(8), 1733; https://doi.org/10.3390/microorganisms9081733 - 14 Aug 2021
Cited by 12 | Viewed by 4407
Abstract
An outbreak of bacterial soft rot and blackleg of potato has occurred since 2014 with the epicenter being in the northeastern region of the United States. Multiple species of Pectobacterium and Dickeya are causal agents, resulting in losses to commercial and seed potato [...] Read more.
An outbreak of bacterial soft rot and blackleg of potato has occurred since 2014 with the epicenter being in the northeastern region of the United States. Multiple species of Pectobacterium and Dickeya are causal agents, resulting in losses to commercial and seed potato production over the past decade in the Northeastern and North Central United States. To clarify the pathogen present at the outset of the epidemic in 2015 and 2016, a phylogenetic study was made of 121 pectolytic soft rot bacteria isolated from symptomatic potato; also included were 27 type strains of Dickeya and Pectobacterium species, and 47 historic reference strains. Phylogenetic trees constructed based on multilocus sequence alignments of concatenated dnaJ, dnaX and gyrB fragments revealed the epidemic isolates to cluster with type strains of D. chrysanthemi, D. dianthicola, D. dadantii, P. atrosepticum, P. brasiliense, P. carotovorum, P. parmentieri, P. polaris, P. punjabense, and P. versatile. Genetic diversity within D. dianthicola strains was low, with one sequence type (ST1) identified in 17 of 19 strains. Pectobacterium parmentieri was more diverse, with ten sequence types detected among 37 of the 2015–2016 strains. This study can aid in monitoring future shifts in potato soft rot pathogens within the U.S. and inform strategies for disease management. Full article
(This article belongs to the Special Issue Dickeya and Pectobacterium: Ecology, Pathology and Plant Protection)
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12 pages, 7450 KiB  
Article
Early Emergence of Dickeya solani Revealed by Analysis of Dickeya Diversity of Potato Blackleg and Soft Rot Causing Pathogens in Switzerland
Microorganisms 2021, 9(6), 1187; https://doi.org/10.3390/microorganisms9061187 - 31 May 2021
Cited by 10 | Viewed by 1958
Abstract
Blackleg and soft rot in potato caused by Pectobacterium and Dickeya enterobacteral genera are among the most destructive bacterial diseases in this crop worldwide. In Europe, over the last century, Pectobacterium spp. were the predominant causal agents of these diseases. As for Dickeya [...] Read more.
Blackleg and soft rot in potato caused by Pectobacterium and Dickeya enterobacteral genera are among the most destructive bacterial diseases in this crop worldwide. In Europe, over the last century, Pectobacterium spp. were the predominant causal agents of these diseases. As for Dickeya, before the large outbreak caused by D. solani in the 2000s, only D. dianthicola was isolated in Europe. The population dynamics of potato blackleg causing soft rot Pectobacteriaceae was, however, different in Switzerland as compared to that in other European countries with a high incidence (60 up to 90%) of Dickeya species (at the time called Erwinia chrysanthemi) already in the 1980s. To pinpoint what may underlie this Swiss peculiarity, we analysed the diversity present in the E. chrysanthemi Agroscope collection gathering potato isolates from 1985 to 2000s. Like elsewhere in Europe during this period, the majority of Swiss isolates belonged to D. dianthicola. However, we also identified a few isolates, such as D. chrysanthemi and D. oryzeae, two species that have not yet been reported in potatoes in Europe. Interestingly, this study allowed the characterisation of two “early” D. solani isolated in the 1990s. Genomic comparison between these early D. solani strains and strains isolated later during the large outbreak in the 2000s in Europe revealed only a few SNP and gene content differences, none of them affecting genes known to be important for virulence. Full article
(This article belongs to the Special Issue Dickeya and Pectobacterium: Ecology, Pathology and Plant Protection)
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17 pages, 1829 KiB  
Article
European Population of Pectobacterium punjabense: Genomic Diversity, Tuber Maceration Capacity and a Detection Tool for This Rarely Occurring Potato Pathogen
Microorganisms 2021, 9(4), 781; https://doi.org/10.3390/microorganisms9040781 - 08 Apr 2021
Cited by 10 | Viewed by 2436
Abstract
Enterobacteria belonging to the Pectobacterium and Dickeya genera are responsible for soft rot and blackleg diseases occurring in many crops around the world. Since 2016, the number of described species has more than doubled. However, some new species, such as Pectobacterium punjabense, [...] Read more.
Enterobacteria belonging to the Pectobacterium and Dickeya genera are responsible for soft rot and blackleg diseases occurring in many crops around the world. Since 2016, the number of described species has more than doubled. However, some new species, such as Pectobacterium punjabense, are often poorly characterized, and little is known about their genomic and phenotypic variation. Here, we explored several European culture collections and identified seven strains of P. punjabense. All were collected from potato blackleg symptoms, sometimes from a long time ago, i.e., the IFB5596 strain isolated almost 25 years ago. We showed that this species remains rare, with less than 0.24% of P. punjabense strains identified among pectinolytic bacteria present in the surveyed collections. The analysis of the genomic diversity revealed the non-clonal character of P. punjabense species. Furthermore, the strains showed aggressiveness differences. Finally, a qPCR Taqman assay was developed for rapid and specific strain characterization and for use in diagnostic programs. Full article
(This article belongs to the Special Issue Dickeya and Pectobacterium: Ecology, Pathology and Plant Protection)
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10 pages, 1661 KiB  
Article
Interaction between Dickeya dianthicola and Pectobacterium parmentieri in Potato Infection under Field Conditions
Microorganisms 2021, 9(2), 316; https://doi.org/10.3390/microorganisms9020316 - 04 Feb 2021
Cited by 11 | Viewed by 2561
Abstract
Dickeya and Pectobacterium spp. both cause blackleg and soft rot of potato, which can be a yield-reducing factor to potato production. The purpose of this study was to examine the interaction between these two bacterial genera causing potato infection, and subsequent disease development [...] Read more.
Dickeya and Pectobacterium spp. both cause blackleg and soft rot of potato, which can be a yield-reducing factor to potato production. The purpose of this study was to examine the interaction between these two bacterial genera causing potato infection, and subsequent disease development and yield responses under field conditions. Analysis of 883 potato samples collected in Northeastern USA using polymerase chain reaction determined that Dickeya dianthicola and P. parmentieri were found in 38.1% and 53.3% of all samples, respectively, and that 20.6% of samples contained both D. dianthicola and P. parmentieri. To further investigate the relationship between the two bacterial species and their interaction, field trials were established. Potato seed pieces of “Russet Burbank”, “Lamoka”, and “Atlantic” were inoculated with bacterial suspension of D. dianthicola at 107 colony-forming unite (CFU)/mL using a vacuum infiltration method, air dried, and then planted in the field. Two-year results showed that there was a high correlation (p < 0.01) between yield loss and percent of inoculated seed pieces. In a secondary field trial conducted in 2018 and 2019, seed pieces of potato “Shepody”, “Lamoka” and “Atlantic” were inoculated with D. dianthicola, P. parmentieri, or mixture of both species, and then planted. In 2019, disease severity index, as measured by the most sensitive variety “Lamoka”, was 16.2 with D. dianthicola inoculation, 10.4 with P. parmentieri, 25.4 with inoculation with both bacteria. Two-year data had a similar trend. Thus, D. dianthicola was more virulent than P. parmentieri, but the co-inoculation of the two species resulted in increased disease severity compared to single-species inoculation with either pathogen. Full article
(This article belongs to the Special Issue Dickeya and Pectobacterium: Ecology, Pathology and Plant Protection)
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22 pages, 5567 KiB  
Article
Host Specificity and Differential Pathogenicity of Pectobacterium Strains from Dicot and Monocot Hosts
Microorganisms 2020, 8(10), 1479; https://doi.org/10.3390/microorganisms8101479 - 26 Sep 2020
Cited by 9 | Viewed by 3110
Abstract
Recent phylogenetic studies have transferred certain isolates from monocot plants previously included in the heterogeneous group of Pectobacteriumcarotovorum (Pc) to a species level termed Pectobacterium aroidearum. The specificity of Pectobacterium associated infections had received less attention, and may be of high [...] Read more.
Recent phylogenetic studies have transferred certain isolates from monocot plants previously included in the heterogeneous group of Pectobacteriumcarotovorum (Pc) to a species level termed Pectobacterium aroidearum. The specificity of Pectobacterium associated infections had received less attention, and may be of high scientific and economic importance. Here, we have characterized differential responses of Pectobacterium isolates from potato (WPP14) and calla lily (PC16) on two typical hosts: Brassica oleracea var. capitata (cabbage) a dicot host; and Zantedeschia aethiopica (calla lily) a monocot host. The results revealed clear host specific responses following infection with the two bacterial strains. This was demonstrated by differential production of volatile organic compounds (VOCs) and the expression of plant defense-related genes (pal, PR-1, lox2, ast). A related pattern was observed in bacterial responses to each of the host’s extract, with differential expression of virulence-related determinants and genes associated with quorum-sensing and plant cell wall-degrading enzymes. The differences were associated with each strain’s competence on its respective host. Full article
(This article belongs to the Special Issue Dickeya and Pectobacterium: Ecology, Pathology and Plant Protection)
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15 pages, 2237 KiB  
Article
Updated Taxonomy of Pectobacterium Genus in the CIRM-CFBP Bacterial Collection: When Newly Described Species Reveal “Old” Endemic Population
Microorganisms 2020, 8(9), 1441; https://doi.org/10.3390/microorganisms8091441 - 20 Sep 2020
Cited by 26 | Viewed by 3152
Abstract
Bacterial collections are invaluable tools for microbiologists. However, their practical use is compromised by imprecise taxonomical assignation of bacterial strains. This is particularly true for soft rotting plant pathogens of the Pectobacterium genus. We analysed the taxonomic status of 265 Pectobacterium strains deposited [...] Read more.
Bacterial collections are invaluable tools for microbiologists. However, their practical use is compromised by imprecise taxonomical assignation of bacterial strains. This is particularly true for soft rotting plant pathogens of the Pectobacterium genus. We analysed the taxonomic status of 265 Pectobacterium strains deposited at CIRM-CFBP collection from 1944 to 2020. This collection gathered Pectobacterium strains isolated in 27 countries from 32 plant species representing 17 botanical families or from nonhost environments. The MLSA approach completed by genomic analysis of 15 strains was performed to update the taxonomic status of these 265 strains. The results showed that the CIRM-CFBP Pectobacterium collection harboured at least one strain of each species, with the exception of P. polonicum. Yet, seven strains could not be assigned to any of the described species and may represent at least two new species. Surprisingly, P. versatile, recently described in 2019, is the most prevalent species among CIRM-CFBP strains. An analysis of P. versatile strains revealed that this species is pandemic and isolated from various host plants and environments. At the opposite, other species gathered strains isolated from only one botanical family or exclusively from a freshwater environment. Our work also revealed new host plants for several Pectobacterium spp. Full article
(This article belongs to the Special Issue Dickeya and Pectobacterium: Ecology, Pathology and Plant Protection)
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17 pages, 2825 KiB  
Article
Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa
Microorganisms 2020, 8(8), 1129; https://doi.org/10.3390/microorganisms8081129 - 27 Jul 2020
Cited by 11 | Viewed by 2412
Abstract
To compare environmental and culture-derived microbial communities, we performed 16S metabarcoding of uncultured samples and their culture-derived bacterial lawns. Microbial communities were obtained from freshwater river samples representative of an anthropization gradient along a river stream. Their culture-derived bacterial lawns were obtained by [...] Read more.
To compare environmental and culture-derived microbial communities, we performed 16S metabarcoding of uncultured samples and their culture-derived bacterial lawns. Microbial communities were obtained from freshwater river samples representative of an anthropization gradient along a river stream. Their culture-derived bacterial lawns were obtained by growing aliquots of the samples on a broad range medium and on two different semi-selective media. The V3–V4 16S rRNA region was amplified and sequenced. The bacterial diversity of water samples decreased from the upper to lower stream sampling sites and, as expected, these differences were mostly suppressed by the culture step. Overall, the diversity of cultured-derived bacterial communities reflected selectivity of each tested medium. Comparison of treatments indicated that the culture selected both detected and rare undetected environmental species. Accurate detection of rare environmental bacteria of the Pectobacterium genus by 16S metabarcoding of the culture lawn was demonstrated. Interestingly, for abundant taxa, such as those of the Pseudomonas genus, the culture/environment ratio varied between sampled sites, indicating the difficulty of comparing cultured-derived taxa abundance between environmental sites. Finally, our study also highlighted media specificity and complementarity: bacterial communities grown on the two selective media, while selecting a small set of specific species, were mostly a subset of the bacterial community observed on the broad range medium. Full article
(This article belongs to the Special Issue Dickeya and Pectobacterium: Ecology, Pathology and Plant Protection)
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16 pages, 2691 KiB  
Article
Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco
Microorganisms 2020, 8(6), 895; https://doi.org/10.3390/microorganisms8060895 - 13 Jun 2020
Cited by 12 | Viewed by 2929
Abstract
Dickeya and Pectobacterium pathogens are causative agents of several diseases that affect many crops worldwide. This work investigated the species diversity of these pathogens in Morocco, where Dickeya pathogens have only been isolated from potato fields recently. To this end, samplings were conducted [...] Read more.
Dickeya and Pectobacterium pathogens are causative agents of several diseases that affect many crops worldwide. This work investigated the species diversity of these pathogens in Morocco, where Dickeya pathogens have only been isolated from potato fields recently. To this end, samplings were conducted in three major potato growing areas over a three-year period (2015–2017). Pathogens were characterized by sequence determination of both the gapA gene marker and genomes using Illumina and Oxford Nanopore technologies. We isolated 119 pathogens belonging to P. versatile (19%), P. carotovorum (3%), P. polaris (5%), P. brasiliense (56%) and D. dianthicola (17%). Their taxonomic assignation was confirmed by draft genome analyses of 10 representative strains of the collected species. D. dianthicola were isolated from a unique area where a wide species diversity of pectinolytic pathogens was observed. In tuber rotting assays, D. dianthicola isolates were more aggressive than Pectobacterium isolates. The complete genome sequence of D. dianthicola LAR.16.03.LID was obtained and compared with other D. dianthicola genomes from public databases. Overall, this study highlighted the ecological context from which some Dickeya and Pectobacterium species emerged in Morocco, and reported the first complete genome of a D. dianthicola strain isolated in Morocco that will be suitable for further epidemiological studies. Full article
(This article belongs to the Special Issue Dickeya and Pectobacterium: Ecology, Pathology and Plant Protection)
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Review

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37 pages, 62283 KiB  
Review
Tailed Lytic Bacteriophages of Soft Rot Pectobacteriaceae
Microorganisms 2021, 9(9), 1819; https://doi.org/10.3390/microorganisms9091819 - 26 Aug 2021
Cited by 6 | Viewed by 3376
Abstract
The study of the ecological and evolutionary traits of Soft Rot Pectobacteriaceae (SRP) comprising genera Pectobacterium and Dickeya often involves bacterial viruses (bacteriophages). Bacteriophages are considered to be a prospective tool for the ecologically safe and highly specific protection of plants and harvests [...] Read more.
The study of the ecological and evolutionary traits of Soft Rot Pectobacteriaceae (SRP) comprising genera Pectobacterium and Dickeya often involves bacterial viruses (bacteriophages). Bacteriophages are considered to be a prospective tool for the ecologically safe and highly specific protection of plants and harvests from bacterial diseases. Information concerning bacteriophages has been growing rapidly in recent years, and this has included new genomics-based principles of taxonomic distribution. In this review, we summarise the data on phages infecting Pectobacterium and Dickeya that are available in publications and genomic databases. The analysis highlights not only major genomic properties that assign phages to taxonomic families and genera, but also the features that make them potentially suitable for phage control applications. Specifically, there is a discussion of the molecular mechanisms of receptor recognition by the phages and problems concerning the evolution of phage-resistant mutants. Full article
(This article belongs to the Special Issue Dickeya and Pectobacterium: Ecology, Pathology and Plant Protection)
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21 pages, 3430 KiB  
Review
Biosensors Used for Epifluorescence and Confocal Laser Scanning Microscopies to Study Dickeya and Pectobacterium Virulence and Biocontrol
Microorganisms 2021, 9(2), 295; https://doi.org/10.3390/microorganisms9020295 - 01 Feb 2021
Cited by 1 | Viewed by 2841
Abstract
Promoter-probe vectors carrying fluorescent protein-reporter genes are powerful tools used to study microbial ecology, epidemiology, and etiology. In addition, they provide direct visual evidence of molecular interactions related to cell physiology and metabolism. Knowledge and advances carried out thanks to the construction of [...] Read more.
Promoter-probe vectors carrying fluorescent protein-reporter genes are powerful tools used to study microbial ecology, epidemiology, and etiology. In addition, they provide direct visual evidence of molecular interactions related to cell physiology and metabolism. Knowledge and advances carried out thanks to the construction of soft-rot Pectobacteriaceae biosensors, often inoculated in potato Solanum tuberosum, are discussed in this review. Under epifluorescence and confocal laser scanning microscopies, Dickeya and Pectobacterium-tagged strains managed to monitor in situ bacterial viability, microcolony and biofilm formation, and colonization of infected plant organs, as well as disease symptoms, such as cell-wall lysis and their suppression by biocontrol antagonists. The use of dual-colored reporters encoding the first fluorophore expressed from a constitutive promoter as a cell tag, while a second was used as a regulator-based reporter system, was also used to simultaneously visualize bacterial spread and activity. This revealed the chronology of events leading to tuber maceration and quorum-sensing communication, in addition to the disruption of the latter by biocontrol agents. The promising potential of these fluorescent biosensors should make it possible to apprehend other activities, such as subcellular localization of key proteins involved in bacterial virulence in planta, in the near future. Full article
(This article belongs to the Special Issue Dickeya and Pectobacterium: Ecology, Pathology and Plant Protection)
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26 pages, 1531 KiB  
Review
Pectobacterium brasiliense: Genomics, Host Range and Disease Management
Microorganisms 2021, 9(1), 106; https://doi.org/10.3390/microorganisms9010106 - 05 Jan 2021
Cited by 25 | Viewed by 6854
Abstract
Pectobacterium brasiliense (Pbr) is considered as one of the most virulent species among the Pectobacteriaceae. This species has a broad host range within horticulture crops and is well distributed elsewhere. It has been found to be pathogenic not only in the field causing [...] Read more.
Pectobacterium brasiliense (Pbr) is considered as one of the most virulent species among the Pectobacteriaceae. This species has a broad host range within horticulture crops and is well distributed elsewhere. It has been found to be pathogenic not only in the field causing blackleg and soft rot of potato, but it is also transmitted via storage causing soft rot of other vegetables. Genomic analysis and other cost-effective molecular detection methods such as a quantitative polymerase chain reaction (qPCR) are essential to investigate the ecology and pathogenesis of the Pbr. The lack of fast, field deployable point-of-care testing (POCT) methods, specific control strategies and current limited genomic knowledge make management of this species difficult. Thus far, no comprehensive review exists about Pbr, however there is an intense need to research the biology, detection, pathogenicity and management of Pbr, not only because of its fast distribution across Europe and other countries but also due to its increased survival to various climatic conditions. This review outlines the information available in peer-reviewed literature regarding host range, detection methods, genomics, geographical distribution, nomenclature and taxonomical evolution along with some of the possible management and control strategies. In summary, the conclusions and a further directions highlight the management of this species. Full article
(This article belongs to the Special Issue Dickeya and Pectobacterium: Ecology, Pathology and Plant Protection)
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