Characterization of Dickeya strains isolated from potato grown under hot‐climate conditions

Dickeya strains isolated in Israel in 2006–2010 were characterized by dnaX sequence analysis, pulsed‐field gel electrophoresis (PFGE), biochemical assays and pectolytic activity, and found to be homogeneous: most of them could be classified as ‘Dickeya solani’. Of the 34 strains isolated from imported seed tubers or potato plants grown from imported seed, 32 were typed as ‘D. solani’ and only two were characterized as Dickeya dianthicola. Biovar typing indicated that all ‘D. solani’ strains were biovar 3. ‘Dickeya solani’ strains were most closely related to Dickeya dadantii subsp. dieffenbachiae according to PFGE and dnaX analyses and both species exhibited high pectolytic activity. Expression levels of two putative virulence genes, pelL (encoding a pectic enzyme) and dspE (encoding a type III effector) were significantly induced in ‘D. solani’ strains isolated from potato plants or tubers grown in hot climates such as the Negev region in Israel, compared to those isolated from seed tubers imported from the Netherlands, France or Germany. Results of this study support the hypothesis that ‘D. solani’ strains isolated in Israel are also clonal; however, they appear to be more virulent than strains isolated in Europe.     

Virulence of ‘Dickeya solani’ and Dickeya dianthicola biovar‐1 and ‐7 strains on potato (Solanum tuberosum)

Studies were conducted to explain the relative success of ‘Dickeya solani’, a genetic clade of Dickeya biovar 3 and a blackleg‐causing organism that, after recent introduction, has spread rapidly in seed potato production in Europe to the extent that it is now more frequently detected than D. dianthicola. In vitro experiments showed that both species were motile, had comparable siderophore production and pectinolytic activity, and that there was no antagonism between them when growing. Both ‘D. solani’ and biovar 1 and biovar 7 of D. dianthicola rotted tuber tissue when inoculated at a low density of 10³ CFU mL^?1. In an agar overlay assay, D. dianthicola was susceptible to 80% of saprophytic bacteria isolated from tuber extracts, whereas ‘D. solani’ was susceptible to only 31%, suggesting that ‘D. solani’ could be a stronger competitor in the potato ecosystem. In greenhouse experiments at high temperatures (28°C), roots were more rapidly colonized by ‘D. solani’ than by biovar 1 or 7 of D. dianthicola and at 30 days after inoculation higher densities of ‘D. solani’ were found in stolons and progeny tubers. In co‐inoculated plants, fluorescent protein (GFP or DsRed)‐tagged ‘D. solani’ outcompeted D. dianthicola in plants grown from vacuum‐infiltrated tubers. In 3 years of field studies in the Netherlands with D. dianthicola and ‘D. solani’, disease incidence varied greatly annually and with strain. In summary, ‘D. solani’ possesses features which allow more efficient plant colonization than D. dianthicola at high temperatures. In temperate climates, however, tuber infections with ‘D. solani’ will not necessarily result in a higher disease incidence than infections with D. dianthicola, but latent seed infection could be more prevalent.     

Dickeya species: an emerging problem for potato production in Europe

Dickeya species (formerly Erwinia chrysanthemi) cause diseases on numerous crop and ornamental plants world‐wide. Dickeya spp. (probably D. dianthicola) were first reported on potato in the Netherlands in the 1970s and have since been detected in many other European countries. However, since 2004–5 a new pathogen, with the proposed name ‘D. solani’, has been spreading across Europe via trade in seed tubers and is causing increasing economic losses. Although disease symptoms are often indistinguishable from those of the more established blackleg pathogen Pectobacterium spp., Dickeya spp. can initiate disease from lower inoculum levels, have a greater ability to spread through the plant’s vascular tissue, are considerably more aggressive, and have higher optimal temperatures for disease development (the latter potentially leading to increased disease problems as Europe’s climate warms). However, they also appear to be less hardy than Pectobacterium spp. in soil and other environments outside the plant. Scotland is currently the only country in Europe to enforce zero tolerance for Dickeya spp. in its potato crop in an attempt to keep its seed tuber industry free from disease. However, there are a number of other ways to control the disease, including seed tuber certification, on‐farm methods and the use of diagnostics. For diagnostics, new genomics‐based approaches are now being employed to develop D. dianthicola‐ and ‘D. solani’‐specific PCR‐based tests for rapid detection and identification. It is hoped that these diagnostics, together with other aspects of ongoing research, will provide invaluable tools and information for controlling this serious threat to potato production.     

Detection of phytopathogens of the genus Dickeya using a PCR primer prediction pipeline for draft bacterial genome sequences

This study used a novel computational pipeline to exploit draft bacterial genome sequences in order to predict, automatically and rapidly, PCR primer sets for Dickeya spp. that were unbiased in terms of diagnostic gene choice. This pipeline was applied to 16 draft and four complete Dickeya genome sequences to generate >700 primer sets predicted to discriminate between Dickeya at the species level. Predicted diagnostic primer sets for both D. dianthicola (DIA‐A and DIA‐B) and ‘D. solani’ (SOL‐C and SOL‐D) were validated against a panel of 70 Dickeya reference strains, representative of the known diversity of this genus, to confirm primer specificity. The classification of the four previously sequenced strains was re‐examined and evidence of possible misclassification of three of these strains is presented.     

Distribution of <Emphasis Type="Italic">Dickeya</Emphasis> spp. and <Emphasis Type="Italic">Pectobacterium carotovorum</Emphasis> subsp. <Emphasis Type="Italic">carotovorum</Emphasis> in naturally infected seed potatoes

Detailed studies were conducted on the distribution of Pectobacterium carotovorum subsp. carotovorum and Dickeya spp. in two potato seed lots of different cultivars harvested from blackleg-diseased crops. Composite samples of six different tuber sections (peel, stolon end, and peeled potato tissue 0.5, 1.0, 2.0 and 4.0 cm from the stolon end) were analysed by enrichment PCR, and CVP plating followed by colony PCR on the resulting cavity-forming bacteria. Seed lots were contaminated with Dickeya spp. and P. carotovorum subsp. carotovorum (Pcc), but not with P. atrosepticum. Dickeya spp. and Pcc were found at high concentrations in the stolon ends, whereas relatively low densities were found in the peel and in deeper located potato tissue. Rep-PCR, 16S rDNA sequence analysis and biochemical assays, grouped all the Dickeya spp. isolates from the two potato seed lots as biovar 3. The implications of the results for the control of Pectobacterium and Dickeya spp., and sampling strategies in relation to seed testing, are discussed.     

Biochemical and genetical analysis reveal a new clade of biovar 3 <Emphasis Type="Italic">Dickeya</Emphasis> spp. strains isolated from potato in Europe

Sixty-five potato strains of the soft rot-causing plant pathogenic bacterium Dickeya spp., and two strains from hyacinth, were characterised using biochemical assays, REP-PCR genomic finger printing, 16S rDNA and dnaX sequence analysis. These methods were compared with nineteen strains representing six Dickeya species which included the type strains. A group of twenty-two potato strains isolated between 2005-2007 in the Netherlands, Poland, Finland and Israel were characterised as belonging to biovar 3. They were 100% identical in REP-PCR, dnaX and 16S rDNA sequence analysis. In a polyphasic analysis they formed a new clade different from the six Dickeya species previously described, and may therefore constitute a new species. The strains were very similar to a Dutch strain from hyacinth. On the basis of dnaX sequences and biochemical assays, all other potato strains isolated in Europe between 1979 and 1994 were identified as D. dianthicola (biovar 1 and 7), with the exception of two German strains classified as D. dieffenbachia (biovar 2) and D. dadantii (biovar 3), respectively. Potato strains from Peru were classified as D. dadantii, from Australia as D. zeae and from Taiwan as D. chrysanthemi bv. parthenii, indicating that different Dickeya species are found in association with potato.     

Assessment of recent outbreaks of <Emphasis Type="Italic">Dickeya</Emphasis> sp. (syn. <Emphasis Type="Italic">Erwinia chrysanthemi</Emphasis>) slow wilt in potato crops in Israel

Suspected Dickeya sp. strains were obtained from potato plants and tubers collected from commercial plots. The disease was observed on crops of various cultivars grown from seed tubers imported from the Netherlands during the spring seasons of 2004–2006, with disease incidence of 2–30% (10% in average). In addition to typical wilting symptoms on the foliage, in cases of severe infection, progeny tubers were rotten in the soil. Six strains were characterised by biochemical, serological and PCR-amplification. All tests verified the strains as Dickeya sp. The rep-PCR and the biochemical assays showed that the strains isolated from blackleg diseased plants in Israel were very similar, if not identical to strains isolated from Dutch seed potatoes, suggesting that the infection in Israel originated from the Dutch seed. The strains were distantly related to D. dianthicola strains, typically found in potatoes in Western Europe, and were similar to biovar 3 D. dadanti or D. zeae. This is the first time that the presence of biovar 3 strains in potato in the Netherlands is described. One of the strains was used for pathogenicity assays on potato cvs Nicola and Mondial. Symptoms appeared 2 to 3 days after stem inoculation, and 7 to 10 days after soil inoculation. The control plants treated with water, or plants inoculated with Pectobacterium carotovorum, did not develop any symptoms with either method of inoculation. The identity of Dickeya sp. and P. carotovorum re-isolated from inoculated plants was confirmed by PCR and ELISA.     

Virulence of Pectobacterium carotovorum subsp. brasiliense on potato compared with that of other Pectobacterium and Dickeya species under climatic conditions prevailing in the Netherlands

In western Europe, Pectobacterium carotovorum subsp. brasiliense is emerging as a causal agent of blackleg disease. In field experiments in the Netherlands, the virulence of this pathogen was compared with strains of other Dickeya and Pectobacterium species. In 2013 and 2014, seed potato tubers were vacuum infiltrated with high densities of bacteria (10⁶ CFU mL^?1) and planted in clay soil. Inoculation with P. carotovorum subsp. brasiliense and P. atrosepticum resulted in high disease incidences (75–95%), inoculation with D. solani and P. wasabiae led to incidences between 5% and 25%, but no significant disease development was observed in treatments with P. carotovorum subsp. carotovorum, D. dianthicola or the water control. Co‐inoculations of seed potatoes with P. carotovorum subsp. brasiliense and D. solani gave a similar disease incidence to inoculation with only P. carotovorum subsp. brasiliense. However, co‐inoculation of P. carotovorum subsp. brasiliense with P. wasabiae resulted in a decrease in disease incidence compared to inoculation with only P. carotovorum subsp. brasiliense. In 2015, seed potatoes were inoculated with increasing densities of P. carotovorum subsp. brasiliense, D. solani or P. atrosepticum (10³–10⁶ CFU mL^?1). After vacuum infiltration, even a low inoculum density resulted in high disease incidence. However, immersion without vacuum caused disease only at high bacterial densities. Specific TaqMan assays were evaluated and developed for detection of P. carotovorum subsp. brasiliense, P. wasabiae and P. atrosepticum and confirmed the presence of these pathogens in progeny tubers of plants derived from vacuum‐infiltrated seed tubers.     

Putative new species of the genus Dickeya as major soft rot pathogens in Phalaenopsis orchid production

Bacterial soft rots are a serious limitation to the production of orchids and other horticultural plants. Here, the characterization of causative bacteria isolated from Phalaenopsis orchids showing symptoms, from a commercial production site, is reported. The most commonly isolated bacteria were identified as Dickeya spp. Partial sequencing of 16S rDNA, fliC and dnaX showed diversity among the isolates and divided the isolates into two groups, with greatest similarity to previously reported undefined Dickeya lineages from orchids (UDL‐3 and UDL‐4). Two isolates (B16, S1) were sequenced using next‐generation sequencing, which has provided draft genomes of these two isolates for further studies (Ali? et al., 2015 ). Newly developed fliC‐based lineage‐specific quantitative real‐time PCR assays were used to distinguish among the lineages and to assess their relative abundances in diseased tissues. Virulence and aggressiveness comparison tests in vivo on Phalaenopsis orchids, potato plants and witloof chicory leaves indicated high virulence and extreme maceration potential of these novel Dickeya isolates, compared to a reference panel of other Dickeya spp. Pantoea cypripedii (formerly Pectobacterium cypripedii), which has previously been reported as a soft rot pathogen of orchids, was not detected, and isolates obtained from culture collections did not cause symptoms on artificially infected Phalaenopsis orchids.     

Studies on the interaction between the biocontrol agent,Serratia plymuthica A30, and blackleg‐causing Dickeya sp. (biovar 3) in potato (Solanum tuberosum)

Interactions between Serratia plymuthica A30 and a blackleg‐causing biovar 3 Dickeya sp. were examined. In a potato slice assay, S. plymuthica A30 inhibited tissue maceration caused by Dickeya sp. IPO2222 when co‐inoculated at a density at least 10 times greater than that of the pathogen. In glasshouse experiments, population dynamics of the antagonist and of the pathogen in planta were studied by dilution plating and confocal laser scanning microscopy (CLSM) using fluorescent protein‐tagged strains. Pathogen‐free minitubers were vacuum‐infiltrated with DsRed‐tagged Dickeya sp. IPO2222 and superficially treated during planting with a water suspension containing GFP‐tagged S. plymuthica A30. A30 reduced the blackleg incidence from 55% to 0%. Both the pathogen and the antagonist colonized the seed potato tubers internally within 1 day post‐inoculation (dpi). Between 1 and 7 dpi, the population of A30 in tubers increased from 10¹ to c. 10³ CFU g^?1 and subsequently remained stable until the end of the experiment (28 dpi). Populations of A30 in stems and roots increased from c. 10² to c. 10⁴ CFU g^?1 between 7 and 28 dpi. Dilution plating and CLSM studies showed that A30 decreased the density of Dickeya sp. populations in plants. Dilution plating combined with microscopy allowed the enumeration of strain A30 and its visualization in the vascular tissues of stem and roots and in the pith of roots, as well as its adherence to and colonization of the root surface. The implications of these finding for the use of S. plymuthica A30 as a biocontrol agent are discussed.     

Temperature‐responsive genetic loci in pectinolytic plant pathogenic Dickeya solani

Fifty‐four Dickeya solani thermoregulated genes were identified using Tn5 transposon mutagenesis with an inducible gusA reporter system; 45 genes were up‐regulated at 37 °C, whereas nine were up‐regulated at 18 °C. The relative level of gene up‐regulation ranged from 2–1200 and 5–650 U/mg total proteins at 18 and 37 °C, respectively. Among the temperature‐regulated loci, genes coding for proteins involved in fundamental bacterial metabolism, membrane‐related proteins and pathogenicity‐corresponding factors and several hypothetical unknown proteins were found. The mutants were tested for their pathogenicity in planta and for features known to be important for D. solani virulence viz. production of pectinolytic enzymes, cellulases, proteases, siderophores and auxins as well as for motility and the ability to form a biofilm. Eight Tn5 mutants, four up‐regulated at high and four up‐regulated at low temperature, expressed visible phenotypes including the decreased ability to cause symptoms on potato tubers and chicory leaves, impairment in phospholipase production and/or deficiency in biofilm formation. The implications of environmental temperature on the ability of D. solani to cause disease symptoms in potato are discussed.     

A new ‘forma specialis’ of Fusarium solani causing leaf yellowing of Phalaenopsis

The pathogenicity of 35 Fusarium solani isolates obtained from diseased leaves of greenhouse‐grown Phalaenopsis plants in Taiwan was tested on different orchids, including Phalaenopsis sp., Cymbidium spp., Oncidium sp., Dendrobium sp. and Cattleya sp., plus pea (Pisum sativum), chrysanthemum (Chrysanthemum indicum) and cucurbit [melon (Cucumis melo) and cucmber (C. sativus)] plants. Isolates of F. solani from Phalaenopsis spp. caused severe leaf yellowing on Phalaenopsis and mild symptoms on Cymbidium spp., but no visual symptoms on Oncidium sp., Dendrobium sp., Cattleya sp., pea, chrysanthemum or melon. Fusarium solani isolates collected from Phalaenopsis, pea and cucurbits were molecularly characterized by internal transcribed spacer (ITS), intergenic spacer (IGS) and β‐tubulin gene analyses. Phylogenetic trees constructed by distance and parsimony methods indicated that isolates from Phalaenopsis were grouped into one type based on ITS, IGS and β‐tubulin sequences with high bootstrap value (> 84%) support, compared to ‘formae speciales’ of F. solani from the other hosts. These analyses show that isolates of F. solani from Phalaenopsis are distinct from F. solani isolates from other hosts in Taiwan. Therefore, it is proposed that F. solani isolates that incite Phalaenopsis leaf yellowing be designated F. solani f. sp. phalaenopsis.     

Biological control of potato soft rot caused by Dickeya solani and the survival of bacterial antagonists under cold storage conditions

Dickeya and Pectobacterium are responsible for causing blackleg of plants and soft rot of tubers in storage and in the field, giving rise to losses in seed potato production. In an attempt to improve potato health, biocontrol activity of known and putative antagonists was screened using in vitro and in planta assays, followed by analysis of their persistence at various storage temperatures. Most antagonists had low survival on potato tuber surfaces at 4 °C. The population dynamics of the best low-temperature tolerant strain and also the most efficient antagonist, Serratia plymuthica A30, along with Dickeya solani as target pathogen, was studied with TaqMan real-time PCR throughout the storage period. Tubers of three potato cultivars were treated in the autumn with the antagonist and then inoculated with D. solani. Although the cell densities of both strains decreased during the storage period in inoculated tubers, the pathogen population was always lower in the presence of the antagonist. The treated tubers were planted in the field the following growing season to evaluate the efficiency of the bacterial antagonist for controlling disease incidence. The potato endophyte S. plymuthica A30 protected potato plants by reducing blackleg development on average by 58.5% and transmission to tuber progeny as latent infection by 47–75%. These results suggest that treatment of potato tubers with biocontrol agents after harvest can reduce the severity of soft rot disease during storage and affect the transmission of soft rot bacteria from mother tubers to progeny tubers during field cultivation.     

Simultaneous and selective detection of two major soft rot pathogens of potato: Pectobacterium atrosepticum (Erwinia carotovora subsp. atrosepticum) and Dickeya spp. (Erwinia chrysanthemi)

Dickeya spp. and Pectobacterium atrosepticum are major pathogens of potato. Current methods to detect these soft-rotting bacteria require separate identification steps. Here we describe a simple method allowing simultaneous detection of both pathogens based on multiplex PCR. The sensitivity of the primer sets was first examined on purified genomic DNA of the type strains Dickeya chrysanthemi 2048^T and P. atrosepticum 1526^T. The specificity and detection limits of the primer sets were successfully tested on 61 strains belonging to various Dickeya and Pectobacterium species, on artificially inoculated and on naturally contaminated potato plants. This new method provides a gain in time and materials, the main advantages for large-scale processes such as pathogen-free seed certification.     

Characterization of bacterial isolates from rotting potato tuber tissue showing antagonism to Dickeya sp. biovar 3 in vitro and in planta

Possibilities for biocontrol of biovar 3 Dickeya sp. in potato were investigated, using bacteria from rotting potato tissue isolated by dilution plating on nonselective agar media. In a plate assay, 649 isolates were screened for antibiosis against Dickeya sp. IPO2222 and for the production of siderophores. Forty‐one isolates (6·4%) produced antibiotics and 112 isolates (17·3%) produced siderophores. A selection of 41 antibiotic‐producing isolates and 41 siderophore‐producing isolates were tested in a potato slice assay for control of the Dickeya sp. Isolates able to reduce rotting of potato tuber tissue by at least 50% of the control were selected. Isolates were characterized by 16S rDNA analysis as Bacillus, Pseudomonas, Rhodococcus, Serratia, Obesumbacterium and Lysinibacillus genera. Twenty‐three isolates belonging to different species and genera, 13 producing antibiotics and 10 producing siderophores, were further characterized by testing acyl‐homoserine lactone (AHL) production, quorum quenching, motility, biosurfactant production, growth at low (4·0) and high (10·0) pH, growth at 10°C under aerobic and anaerobic conditions and auxin production. In replicated greenhouse experiments, four selected antagonists based on the in vitro tests were tested in planta using wounded or intact minitubers of cv. Kondor subsequently inoculated by vacuum infiltration with an antagonist and a GFP (green fluorescent protein)‐tagged biovar 3 Dickeya sp. strain. A potato endophyte A30, characterized as S. plymuthica, protected potato plants by reducing blackleg development by 100% and colonization of stems by Dickeya sp. by 97%. The potential use of S. plymuthica A30 for the biocontrol of Dickeya sp. is discussed.     

The effect of temperature on the phenotypic features and the maceration ability of <Emphasis Type="Italic">Dickeya solani</Emphasis> strains isolated in Finland,Israel and Poland

Pectinolytic bacteria from the genus Dickeya (former Erwinia chrysanthemi), belonging to Dickeya dianthicola and Dickeya solani species, are causative agents of blackleg and soft rot diseases in Europe. Recently, D. solani have been isolated most frequently from potato plants with the symptoms of blackleg and soft rot. D. solani strains were shown to cause more severe disease symptoms on potato plants than D. dianthicola especially at the higher temperature. They are also able to develop blackleg disease from lower inoculum levels. In the presented study we not only compared phenotypic features of fifteen D. solani strains isolated in countries having different climatic conditions, Poland, Finland and Israel, but also we examined three D. dianthicola strains. The comparison was performed to determine the influence of the strain origin and the temperature of incubation on the ability of the strains to macerate potato tissue and on their major virulence factors such as: pectinolytic, cellulolytic and proteolytic activities, siderophore production and motility. Polish D. solani strains showed higher activities of cell wall degrading enzymes than the Finnish and Israeli strains at all the tested temperatures: 18, 27, 37 °C. This observation is correlated with the higher ability of Polish D. solani strains to cause soft rot. In addition, D. solani strains exhibited higher activity of the above mentioned enzymes and caused more severe potato tuber maceration in laboratory tests than the tested D. dianthicola strains. The collected results indicate that although D. solani strains from different climatic conditions have identical Pulse Field Gel Electrophoresis (PFGE) profiles in addition to the same fingerprint profiles obtained by the repetitive sequence-based polymerase chain reaction (REP, ERIC and BOX repetitive sequences), they differ in the examined phenotypic features, especially in the activities of pectinolytic, cellulolytic and proteolytic enzymes and their capacity to macerate potato tuber tissue.     

Survey on the prevalence of Rhizoctonia spp. in European soils and determination of the baseline sensitivity towards sedaxane

The prevalence of Rhizoctonia spp. in European soils was determined by analysing soil samples from 282 locations. Rhizoctonia spp. were found in 68% of these samples from France, Germany, the UK, Poland, Italy, Spain, Hungary and the Czech Republic. Samples from 136 locations were further analysed by pyrosequencing. Seventy‐six percent of the isolates were Rhizoctonia solani and 24% binucleate Rhizoctonia spp. Rhizoctonia solani anastomosis group (AG) 5 was detected most frequently (25%), followed by AG 9 (16%) and AG 4 (13%). For the binucleate Rhizoctonia spp., AG E was most prevalent (13%). Rhizoctonia cerealis was not detected in soil samples. Soil type or cropping history had no effect on the type of Rhizoctonia observed. Rhizoctonia solani AG 5 was the most frequently detected AG irrespective of the previous crop. The spectrum of AGs detected was similar for France, Germany and Poland but was significantly different for the UK (P = 0·0016). Finally, the baseline sensitivity towards sedaxane, a new active ingredient for seed treatment, was analysed for all isolates. The results indicate a low baseline sensitivity (average EC₅₀ of 0·028 p.p.m.) for all Rhizoctonia AGs. No difference in sensitivity was observed with the isolates obtained from different countries.     

Biochemical,physiological, and molecular characterization of <Emphasis Type="Italic">Dickeya dianthicola</Emphasis> (formerly named <Emphasis Type="Italic"> Erwinia chrysanthemi</Emphasis>) causing potato blackleg disease in Japan

The taxonomic assignment of Japanese potato blackleg isolates of Dickeya spp. has not been confirmed after the changes in their former name, Erwinia chrysanthemi. Therefore, we investigated and identified 23 representative isolates of Dickeya spp. from symptomatic stems of potatoes in Japan, with biochemical tests and phylogenetic sequence analysis using recA, dnaX, rpoD, gyrB, and 16S rDNA sequences. Results of our biochemical tests showed that all isolates can be assigned to phenon 5 and biovar 1, which are associated with D. dianthicola. Based on the recA, dnaX, rpoD, gyrB, and 16S rDNA sequences, all isolates are in the same clade with D. dianthicola and were clearly distinguished from D. chrysanthemi, D. dadantii, D. dadantii subsp. dieffenbachiae, D. solani, D. zeae, and D. paradisiaca. Therefore, we conclude that Dickeya spp. isolated from potatoes with blackleg symptoms in Japan are D. dianthicola.     

Phenotypic diversity,host range and molecular phylogeny of <Emphasis Type="Italic">Dickeya</Emphasis> isolates from Spain

Six Dickeya spp. strains representative of a larger group of bacteria isolated from potato, onion and irrigation water in Spain between years 2003–2005, were characterised by biochemical, serological, molecular and pathogenicity assays. Biochemical and serological differences, as well as pathogenic behaviour in host range and virulence levels, were observed among the strains. They were classified into biovars 3 and 6. Phylogenetic analysis and comparison of the isolates with type strains of Dickeya species characterised to date were performed using concatenated partial sequences of the housekeeping genes gapA and mdh. One of the Spanish strains was identified as D. dieffenbachiae, whereas the other ones did not fit clearly into the previously described six Dickeya species, and may therefore constitute novel species. Isolation of dissimilar pathogenic strains in different rivers and irrigation water sources supports the idea that Dickeya species is commonly present in such an environment, and contaminated water is a potential source of inoculum for the disease in different crops.