Characterization of Erwinia chrysanthemi by pectinolytic isozyme polymorphism and restriction fragment length polymorphism analysis of PCR-amplified fragments of pel genes

Efficacy of Soft-Rot Disease Biocontrol Agents in the Inhibition of Production Field Pathogen Isolates

The Dickeya and Pectobacterium bacterial species cause blackleg and soft-rot diseases on potato plants and tubers. Prophylactic actions are essential to conserve a high quality of seed potato tubers. Biocontrol approaches are emerging, but we need to know how efficient biocontrol agents are when facing the natural diversity of pathogens. In this work, we sampled 16 production fields, which were excluded from the seed tuber certification scheme, as well as seven experimental parcels, which were planted with seed tubers from those production fields. We collected and characterized 669 Dickeya and Pectobacterium isolates, all characterized using nucleotide sequence of the gapA gene. This deep sampling effort highlighted eleven Dickeya and Pectobacterium species, including four dominant species namely D. solani, D. dianthicola, P. atrosepticum and P. parmentieri. Variations in the relative abundance of pathogens revealed different diversity patterns at a field or parcel level. The Dickeya-enriched patterns were maintained in parcels planted with rejected seed tubers, suggesting a vertical transmission of the pathogen consortium. Then, we retained 41 isolates representing the observed species diversity of pathogens and we tested each of them against six biocontrol agents. From this work, we confirmed the importance of prophylactic actions to discard contaminated seed tubers. We also identified a couple of biocontrol agents of the Pseudomonas genus that were efficient against a wide range of pathogen species.

Two-component system ArcBA modulates cell motility and biofilm formation in Dickeya oryzae

Phytopathogen Dickeya oryzae is a causal agent of rice foot rot disease and the pathogen has an array of virulence factors, such as phytotoxin zeamines, plant cell wall degrading enzymes, cell motility, and biofilms, collectively contributing to the bacterial pathogenesis. In this study, through deletion analysis of predicted regulatory genes in D. oryzae EC1, we identified a two-component system associated with the regulation of bacterial virulence. The two-component system contains a histidine kinase ArcB and a response regulator ArcA, and deletion of their coding genes resulted in changed phenotypes in cell motility, biofilm formation, and bacterial virulence. Electrophoretic mobility shift assay revealed that ArcA bound to the promoters of the bcs operon and bssS, which respectively encode enzymes for the synthesis of celluloses and a biofilm formation regulatory protein. ArcA could also bind to the promoters of three virulence associated transcriptional regulatory genes, i.e., fis, slyA and ohrR. Surprisingly, although these three regulators were shown to modulate the production of cell wall degrading enzymes and zeamines, deletion of arcB and arcA did not seem to affect these phenotypes. Taken together, the findings from this study unveiled a new two-component system associated with the bacterial pathogenesis, which contributes to the virulence of D. oryzae mainly through its action on bacterial motility and biofilm formation.

First report of potato (Solanum tuberosum L.) blackleg disease caused by Dickeya solani in Mayabeque, Cuba

Blackleg, caused by Pectobacterium spp. and Dickeya spp., is an important disease of potatoes. During the period from November 20 and March 2021, stems of potato plants showing necrosis and rot symptoms, and chlorotic leaves, were collected from commercial production areas of the Mayabeque province of Cuba (Fig. 1A). After disinfestation of affected stems, small fragments of the stem were cut and macerated in a sterile 0.85% NaCl solution. Serial dilutions of bacterial suspension were prepared and streaked onto nutrient agar in Petri plates. Two colonies per sample showing the characteristic of "fried egg" were selected for further investigation, and an isolated was selected and named D7. The isolated bacterium was rod shaped, gram-negative, motile, oxidase and indole production negative, with anaerobic growth, and able to use lactose as carbon source in Mac Conkey Agar medium. One colony of the isolate D7 was selected and multiplied. Total DNA of the bacteria cells was extracted and used to amplify the genes pelADE (Nassar et al., 1996) and gapA (Cigna et al., 2017), to differentiate Dickeya from Pectobacterium. The sequence obtained showed 99.75% and 99.88% nucleotide identity with Dickeya solani for pelADE (Genbank accession number ON644347) and gapA (Genbank accession number ON644346), respectively. To confirm the pathogenicity of the isolate D7, four 15-day-old potato plants, including two plants of each 'Otolia' and 'Naima' potatoes were inoculated with a bacterial suspension of the isolate D7 (108 CFU/ml) in sterile water by stabbing. Control plants were stabbed with sterile water. Inoculated plants were maintained at 28°C, relative humidity of about 90%, and at 12 h light/12 h dark, as described by (Chen et al. 2014). After 3 to 5 days, typical blackleg disease symptoms (water-soaked lesions and necrosis) developed at the inoculated areas of plants (Fig. 1B). No symptom was observed in the control plants. Bacterium was re-isolated from symptomatic plants and the isolates had the same cultural, physiological, and biochemical characteristics to the isolate D7. To our knowledge, this is the first report of D. solani causing blackleg in potato fields in Cuba. Further studies to determine the spread of this pathogen in potato producing areas in Cuba is underway.

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

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.

OhrR is a central transcriptional regulator of virulence in Dickeya zeae

Dickeya zeae is the causal agent of rice foot rot disease. The pathogen is known to rely on a range of virulence factors, including phytotoxin zeamines, extracellular enzymes, cell motility, and biofilm, which collectively contribute to the establishment of infections. Phytotoxin zeamines play a critical role in bacterial virulence; signalling pathways and regulatory mechanisms that govern bacterial virulence remain unclear. In this study, we identified a transcriptional regulator OhrR (organic hydroperoxide reductase regulator) that is involved in the regulation of zeamine production in D. zeae EC1. The OhrR null mutant was significantly attenuated in its virulence against rice seed, potato tubers and radish roots. Phenotype analysis showed that OhrR was also involved in the regulation of other virulence traits, including the production of extracellular cellulase, biofilm formation, and swimming/swarming motility. DNA electrophoretic mobility shift assay showed that OhrR directly regulates the transcription of key virulence genes and genes encoding bis-(3'-5')-cyclic dimeric guanosine monophosphate synthetases. Furthermore, OhrR positively regulates the transcription of regulatory genes slyA and fis through binding to their promoter regions. Our findings identify a key regulator of the virulence of D. zeae and add new insights into the complex regulatory network that modulates the physiology and virulence of D. zeae.

Diversity within the Dickeya zeae complex, identification of Dickeya zeae and Dickeya oryzae members, proposal of the novel species Dickeya parazeae sp. nov

The genus Dickeya comprises plant pathogens that cause diseases in a large range of economically important crops and ornamentals. Strains previously assigned to the species Dickeya zeae are major pathogens attacking vital crops such as maize and rice. They are also frequently isolated from surface water. The newly described species Dickeya oryzae is closely related to D. zeae members, so that the limit between the two species can be difficult to define. In order to clearly distinguish the two species, globally described by the term 'D. zeae complex', we sequenced the genome of four new water isolates and compared them to 14 genomes available in databases. Calculation of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values confirmed the phylogenomic classification into the two species D. zeae and D. oryzae. It also allowed us to propose a new species, Dickeya parazeae sp. nov., to characterize a clade distinct from those containing the D. zeae type strain NCPPB2538^T. Strain S31^T (CFBP 8716^T=LMG 32070^T) isolated from water in France is proposed as the type strain of the new species. Phenotypic analysis of eight publically available strains revealed traits common to the five tested D. oryzae members but apparently not shared by the D. oryzae type strain. Genomic analyses indicated that a simple distinction between the species D. zeae, D. parazeae and D. oryzae can be obtained on the basis of the recA sequence. D. oryzae can be distinguished from the two other species by growth on l-tartaric acid. Based on the recA marker, several strains previously identified as D. zeae were re-assigned to the species D. parazeae or D. oryzae. This study also highlighted the broad host range diversity of these three species.

Pathogenicity and Relative Abundance of Dickeya and Pectobacterium Species in Switzerland: An Epidemiological Dichotomy

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.

Genotyping Dickeya dianthicola Causing Potato Blackleg and Soft Rot Outbreak Associated With Inoculum Geography in the United States

An outbreak of blackleg and soft rot of potato, caused primarily by the bacterial pathogen Dickeya dianthicola, has resulted in significant economic losses in the northeastern United States since 2015. The spread of this seedborne disease is highly associated with seed distribution; therefore, the pathogen likely spread with seed tubers. To describe the blackleg epidemic and track inoculum origins, a total of 1,183 potato samples were collected from 11 states associated with blackleg outbreak from 2015 to 2019. Of these samples, 39.8% tested positive for D. dianthicola. Seventeen isolates of D. dianthicola were recovered from these samples and the genetic diversity of these isolates was examined. Fingerprinting with BOX-A1R-based repetitive extragenic palindromic PCR and phylogenetic analysis based on sequences of the 16S rRNA and gapA genes indicated that D. dianthicola isolates were divided into three genotypes, denoted types I, II, and III. Ninety-five percent of samples from Maine were type I. Type II was found in Maine only in 2015 and 2018. Type II was present throughout the 5 years in some states at a lower percentage than type I. Type III was found in Pennsylvania, New Jersey, and Massachusetts, but not in Maine. Therefore, type I appears to be associated with Maine, but type II appeared to be distributed throughout the northeastern United States. The type II and rarer type III strains were closer to the D. dianthicola type strain isolated from the United Kingdom. This work provides evidence that the outbreak of blackleg of potato in the northeastern United States was caused by multiple strains of D. dianthicola. The geographic origins of these strains remain unknown.

European Population of Pectobacterium punjabense: Genomic Diversity, Tuber Maceration Capacity and a Detection Tool for This Rarely Occurring Potato Pathogen

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.

Occurrence and Identification of Pectobacterium carotovorum subsp. brasiliensis and Dickeya dianthicola Causing Blackleg in Some Potato Fields in Serbia

Blackleg outbreaks were noticed on three fields (about 100 ha total) in 2 consecutive years (2018, 2019) in one of the main potato growing areas in Serbia (Bačka region, Vojvodina). The percentage of infected plants reached 40 to 70%, with 10.5 to 44.7% yield reductions. From the three fields, out of 90 samples Pectobacterium carotovorum subsp. brasiliensis was most frequently identified and diagnosed as causal agent of potato blackleg in Serbia for the first time (29 isolates). Dickeya dianthicola was a less frequently causative bacterium, which was also noticed for the first time (nine isolates). A total of 38 isolates were characterized based on their phenotypic and genetic features, including a pathogenicity test on potato. The repetitive element PCR (rep-PCR) using BOX, REP, and ERIC primer pairs differentiated five genetic profiles among 38 tested isolates. Multilocus sequence analysis (MLSA) of four housekeeping genes, acnA, gapA, icdA, and mdh, revealed the presence of three so far unknown P. c. subsp. brasiliensis multilocus genotypes and confirmed clustering into two main genetic clades as determined in other studies. MLSA also revealed the presence of a new genotype of D. dianthicola in Serbia.

First Report of Pectobacterium polaris Causing Soft Rot and Black Leg of Potato in Russia

Blackleg and soft rot of potato (Solanum tuberosum) were monitored in the Central European part of Russia within a period of 2012- 2019. Symptoms included decay of tubers, blackening of stem vascular bundles, and partial yellowing of leaves. The disease causes serious potato yield losses in the field and storage. Pectobacterium parmentieri, P. brasiliense, P. versatile (syn. Ca. Pectobacterium maceratum), P. carotovorum, P. atrosepticum, Dickeya dianthicola, and D. solani are considered as main causal agents of soft rot and blackleg disease in Russia (Voronina et al. 2019, Ngoc Ha et al., 2019, Shirshikov et al. 2018, Kornev et al. 2012). Potato plant samples collected in commercial fields in routine plant health assay were used for bacteria isolation on crystal violet pectate agar (CVP) (Helias et al. 2012) as described previously (Voronina et al. 2019). Bacterial colonies producing pitting on CVP were re-isolated and purified on nutrient broth yeast extract medium. DNA of bacterial isolates was extracted, and polymerase chain reaction (PCR) amplifications were performed using gapA primers (Cigna et al. 2017) followed by sequencing. DNA sequence alignment showed that the isolates F099, F100, F106, F109, and F118 were identical (deposited as part of NCBI Ref.Seq. for F109 NZ_RRYS01000004.1, locus KHDHEBDM_RS06360) and grouped together with the type strain Pectobacterium polaris NIBIO1006T (CP017481), a new species described as a potato pathogen (Dees et al. 2017). These strains were negative in diagnostic PCR assays using specific primers Y45/Y46 for the detection of P. atrosepticum, Br1f and L1r for P. brasiliense (Duarte et al. 2004), and ADE1/ADE2 for Dickeya sp. (Nassar et al. 1996). To further validate the identification, strain F109 of P. polaris was selected for genome sequencing. The genome of P. polaris strain F109, (NCBI Reference Sequence NZ_RRYS00000000.1) reveals >99% sequence similarity with type strain P. polaris IPO_1606 (GenBank accession GCA_902143345.1). The strain F109 was deposited to All-Russian Collection of Microorganisms under number VKM V-3420. Thus, the characterization of five isolates provided evidence that a previously unreported pathogen was present in the surveyed fields. The isolates were uniform in genetic and physiological properties; they were gram negative, facultative anaerobes with pectinolytic activity, negative for oxidase, urease, indole production, gelatin liquefaction. All isolates were catalase positive, produced acid from lactose, rhamnose, saccharose, xylose, and trehalose, and were tolerant to 5% NaCl, unable to utilize malonate and citrate. All the isolates grew at 37°C. All isolates caused soft rot symptoms on 10 inoculated potato tubers. They produced typical black leg rot symptoms in young potato plants inoculated with 107 CFU/ml of the pathogen by stem injection and incubated at 25°C for 48 h. The bacteria were re-isolated successfully from symptomatic potato and pathogen confirmed by gapA sequencing to complete Koch's postulates. To our knowledge, this is the first report of blackleg and soft rot caused by P. polaris on potato in the Russian Federation. According to the data of commercial diagnostic laboratory "PhytoEngineering" (Moscow region), P. polaris occurred in 5% potato seed stocks harvested in 2017-2019 in the Moscow region. This finding may indicate that new Pectobacterium strains have adapted to a diverse environment, which is consistent with widespread distribution of commercial seed potatoes. The author(s) declare no conflict of interest. Funding: This work was supported by Russian Science Foundation grant #16-16-00073.

First Report of Dickeya dianthicola causing blackleg on New Guinea Impatiens (Impatiens hawkeri) in New York State, USA

New Guinea impatiens (NGI), Impatiens hawkeri, has a $54-million wholesale market value in the United States (National Agricultural Statistics Service, 2019) and is highly resistant to Impatiens downy mildew (Plasmopara obducens) according to growers' experience (Warfield, 2011). In March 2019, NGI cv. Petticoat White in a New York greenhouse showed wilting, black stem streaks and vascular discoloration, with a 20% disease incidence. Symptomatic tissue pieces were added to sterile water in a test tube and streaks made on potato dextrose agar (PDA). After incubation at 26oC for two days, the most abundant colony type (mucoid, pale yellow) was transferred to PDA. One representative colony was selected and labeled as isolate 67-19. A single colony of isolate 67-19 was transferred to lysogeny broth (LB) (Bertani, 1951) and cultured at 28oC. Genomic DNA was extracted and polymerase chain reaction (PCR) performed using the 16S rRNA gene universal primers fD2 and rP1 resulting in a partial 16S rRNA amplicon (Weisburg et al., 1991). Basic Local Alignment Search Tool (BLASTn) analysis (Altschul et al., 1990) showed 99% identity with sequences of species belonging to Dickeya. Different primer sets have been developed to detect and identify the genus Dickeya and its various species (Pritchard et al., 2013). The primer sets used for genus identification, dnaX (Sławiak et al., 2009), Df/Dr (Laurila et al., 2010) and ADE1/ADE2 (Nassar et al., 1996), resulted in 500-bp, 133-bp, and 420-bp amplicons, respectively. Results suggested the bacterium was a Dickeya sp. To determine whether the species could be D. dianthicola, the specific primer set DIA-A was used (Pritchard et al., 2013) and the expected product of 150-bp was obtained. BLASTn results showed that the partial dnaX sequence (GenBank accession MT895847) of isolate 67-19 had 99% identity with the sequence of D. dianthicola strain RNS04.9 isolated in 2004 from potato (Solanum tuberosum) in France (GenBank accession CP017638.1). Therefore, this isolate 67-19 was designated as D. dianthicola. The complete genome of D. dianthicola strain 67-19 was generated using Nanopore and Illumina sequencing (GenBank accession CP051429) (Liu et al., 2020). Average nucleotide identity (ANI) determined by FastANI (v1.1) (Jain et al., 2018) showed 97.43% identity between the genome of D. dianthicola strain 67-19 and that of D. dianthicola strain NCPPB 453 (GenBank accession GCA_000365305.1), isolated in 1957 from carnation (Dianthus caryophyllus) in the UK. The pathogenicity of D. dianthicola strain 67-19 was shown on NGI cultivars Petticoat White and Tamarinda White. In July 2020, sterile toothpicks were used to make wounds and to transfer bacteria from a 48-hr PDA culture of D. dianthicola strain 67-19 to the stems of four plants of each cultivar. Four plants of each cultivar were mock inoculated similarly and all wound sites were wrapped with Parafilm before placing plants on a greenhouse bench. Ten days later, stems inoculated with D. dianthicola strain 67-19 showed necrotic lesions similar to the original symptoms, while control plants did not show symptoms. One month after inoculation, bacteria were re-isolated from all symptomatic stems. PCR was performed on the re-isolated bacteria as described. The dnaX sequence (GenBank accession MT895847) was confirmed to match that of D. dianthicola strain 67-19 (GenBank accession CP051429) 100% and fragments of the expected size were amplified (Liu et al., 2020). Stab inoculations of strain 67-19 into potato stems and tubers also resulted in blackleg and soft rot symptoms at the sites of inoculation, while mock-inoculated stem and tuber showed no symptoms. The sequence of the dnaX gene of the re-isolated bacterium from inoculated potatoes was confirmed to match that of D. dianthicola strain 67-19. To our knowledge, this is the first report of blackleg of New Guinea impatiens caused by D. dianthicola in the United States and worldwide. Since the disease caused by D. dianthicola poses a significant threat to the ornamentals and potato industries (Charkowski et al., 2020), further research on genome biology, epidemiology and management options is needed. LITERATURE CITED Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. Journal of Molecular Biology 215:403-410. Bertani, G. 1951. Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. Journal of Bacteriology 62:293-300. Charkowski, A., Sharma, K., Parker, M.L., Secor, G.A., and Elphinstone, J. 2020. Bacterial diseases of potato. Pages 351-388 in: The Potato Crop: Its Agricultural, Nutritional and Social Contribution to Humankind, H. Campos and O. Ortiz, eds. Springer International Publishing, Cham. Jain, C., Rodriguez-R, L.M., Phillippy, A.M., Konstantinidis, K.T., and Aluru, S. 2018. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nature Communications 9:5114. Laurila, J., Hannukkala, A., Nykyri, J., Pasanen, M., Hélias, V., Garlant, L., and Pirhonen, M. 2010. Symptoms and yield reduction caused by Dickeya spp. strains isolated from potato and river water in Finland. European Journal of Plant Pathology 126:249-262. Liu, Y., Helmann, T., Stodghill, P., and Filiatrault, M. 2020. Complete genome sequence resource for the necrotrophic plant-pathogenic bacterium Dickeya dianthicola 67-19 isolated from New Guinea Impatiens. Plant Disease. https://doi.org/10.1094/PDIS-09-20-1968-A. Nassar, A., Darrasse, A., Lemattre, M., Kotoujansky, A., Dervin, C., Vedel, R., and Bertheau, Y. 1996. Characterization of Erwinia chrysanthemi by pectinolytic isozyme polymorphism and restriction fragment length polymorphism analysis of PCR-amplified fragments of pel genes. Applied and Environmental Microbiology 62:2228-2235. National Agricultural Statistics Service. 2019. Floriculture crops 2018 summary. ISSN: 1949-0917. https://downloads.usda.library.cornell.edu/usda-esmis/files/0p0966899/rr1728124/76537c134/floran19.pdf Pritchard, L., Humphris, S., Saddler, G.S., Parkinson, N.M., Bertrand, V., Elphinstone, J.G., and Toth, I.K. 2013. Detection of phytopathogens of the genus Dickeya using a PCR primer prediction pipeline for draft bacterial genome sequences. Plant Pathology 62:587-596. Sławiak, M., van Beckhoven, J.R.C.M., Speksnijder, A.G.C.L., Czajkowski, R., Grabe, G., and van der Wolf, J.M. 2009. Biochemical and genetical analysis reveal a new clade of biovar 3 Dickeya spp. strains isolated from potato in Europe. European Journal of Plant Pathology 125:245-261. Warfield, C.Y. (2011). Downy Mildew of Impatiens. In GrowerTalks. https://www.growertalks.com/Article/?articleid=18921 Weisburg, W.G., Barns, S.M., Pelletier, D.A., and Lane, D.J. 1991. 16S ribosomal DNA amplification for phylogenetic study. Journal of Bacteriology 173:697-703.

Genome-Informed Recombinase Polymerase Amplification Assay Coupled with a Lateral Flow Device for In-Field Detection of Dickeya Species

Dickeya spp. cause blackleg and soft rot diseases of potato and several other plant species worldwide, resulting in high economic losses. Rapid detection and identification of the pathogen is essential for facilitating efficient disease management. Our aim in this research was to develop a rapid and field-deployable recombinase polymerase amplification (RPA) assay coupled with a lateral flow device (LFD) that will accurately detect Dickeya spp. in infected plant tissues without the need for DNA isolation. A unique genomic region (mglA/mglC genes) conserved among Dickeya spp. was used to design highly specific robust primers and probes for an RPA assay. Assay specificity was validated with 34 representative strains from all Dickeya spp. and 24 strains from other genera and species; no false positives or negatives were detected. An RPA assay targeting the internal transcribed spacer region of the host genome was included to enhance the reliability and accuracy of the Dickeya assay. The detection limit of 1 fg was determined by both sensitivity and spiked sensitivity assays; no inhibitory effects were observed when 1 µl of host sap, macerated in Tris-EDTA buffer, was added to each reaction in the sensitivity tests. The developed RPA assay is rapid, highly accurate, sensitive, and fully field deployable. It has numerous applications in routine diagnostics, surveillance, biosecurity, and disease management.

Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

Background

Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae, we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population.

Results

High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani, comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported.

Conclusions

The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.

Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco

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.

Development of PCR-Based Detection System for Soft Rot Pectobacteriaceae Pathogens Using Molecular Signatures

Pectobacterium and Dickeya species, usually referred to as soft rot Enterobacteriaceae, are phytopathogenic genera of bacteria that cause soft rot and blackleg diseases and are responsible for significant yield losses in many crops across the globe. Diagnosis of soft rot disease is difficult through visual disease symptoms. Pathogen detection and identification methods based on cultural and morphological identification are time-consuming and not always reliable. A polymerase chain reaction (PCR)-based detection method with the species-specific primers is fast and reliable for detecting soft rot pathogens. We have developed a specific and sensitive detection system for some species of soft rot Pectobacteriaceae pathogens in the Pectobacterium and Dickeya genera based on the use of species-specific primers to amplify unique genomic segments. The specificities of primers were verified by PCR analysis of genomic DNA from 14 strains of Pectobacterium, 8 strains of Dickeya, and 6 strains of non-soft rot bacteria. This PCR assay provides a quick, simple, powerful, and reliable method for detection of soft rot bacteria.

Development of the Automated Primer Design Workflow Uniqprimer and Diagnostic Primers for the Broad-Host-Range Plant Pathogen Dickeya dianthicola

Uniqprimer, a software pipeline developed in Python, was deployed as a user-friendly internet tool in Rice Galaxy for comparative genome analyses to design primer sets for PCRassays capable of detecting target bacterial taxa. The pipeline was trialed with Dickeya dianthicola, a destructive broad-host-range bacterial pathogen found in most potato-growing regions. Dickeya is a highly variable genus, and some primers available to detect this genus and species exhibit common diagnostic failures. Upon uploading a selection of target and nontarget genomes, six primer sets were rapidly identified with Uniqprimer, of which two were specific and sensitive when tested with D. dianthicola. The remaining four amplified a minority of the nontarget strains tested. The two promising candidate primer sets were trialed with DNA isolated from 116 field samples from across the United States that were previously submitted for testing. D. dianthicola was detected in 41 samples, demonstrating the applicability of our detection primers and suggesting widespread occurrence of D. dianthicola in North America.

Development of a robust, field-deployable loop-mediated isothermal amplification (LAMP) assay for specific detection of potato pathogen Dickeya dianthicola targeting a unique genomic region

Destructive maceration, a wide host range, and longevity in non-plant substrates has established Dickeya dianthicola (blackleg of potato) as a significant threat to potato industries worldwide. To protect these businesses, a specific and sensitive point-of-care D. dianthicola detection tool is necessary. We have developed a loop-mediated isothermal amplification (LAMP) assay for specific, sensitive, and rapid detection of D. dianthicola, which can be streamlined for point-of-care use. The developed LAMP assay targets a unique gene, alcohol dehydrogenase, of D. dianthicola. Assay specificity was assessed using strains present in inclusivity (16 D. dianthicola strains) and exclusivity panels (56 closely related, potato pathogenic, and other bacterial strains). Amplification with strains of inclusivity panel occurred, and cross-reactivity with non-target DNA was not observed. The limit of detection (LOD) was 10 CFU/ml when dilutions were made before isolating the genomic DNA; however, LOD was determined as 1 pg using 10-fold serially diluted D. dianthicola genomic DNA. Similar LOD of 1 pg was observed when serially diluted target genomic DNA was mixed with host genomic DNA. LOD (1 pg) was also calculated with 10-fold serially diluted synthetic DNA fragments containing primer target sites. Naturally and artificially inoculated plant samples were used for field adaptability tests with the field-deployable Optigene Plant Material Lysis Kit and a heat block (65°C); the results were obtained within 20 minutes. Despite the lack of method precision, no false positives or false negatives were observed. Therefore, with prepared reactions and a steady heat source, this assay can be used for rapid point-of-care detection, which is imperative for quarantine, eradication, disease management, and border protection.

Dickeya lacustris sp. nov., a water-living pectinolytic bacterium isolated from lakes in France

The genus Dickeya is an important group of plant pathogens that currently comprises eight recognized species. Although most Dickeya isolates originated from infected cultivated plants, they have also been repeatedly isolated from water. To better understand the natural diversity of Dickeya, a survey was performed in small lakes surrounded by wetlands in the French region of La Dombes. Several Dickeya isolates were obtained from water or plants from lakes protected from direct agricultural inputs. Sequencing of the gapA gene revealed that five isolates, S12, S15, S24, S29^T and S39, belong to a phylogenetic group separated from other Dickeya species. The genomic sequence of strain S29^T clearly established its separation from the other known Dickeya species. The in silico DNA-DNA hybridization (isDDH) and average nucleotide identity (ANI) values (<33 and <88 %, respectively) obtained by comparing strain S29^T with strains of characterized Dickeya species supported the delineation of a novel species. The closest species to strain S29^T is Dickeya aquatica, previously isolated from rivers, suggesting that these strains have a common ancestor adapted to a water environment. Genomic and phenotypic comparisons enabled the identification of traits distinguishing isolates S12, S15, S24, S29^T and S39 from D. aquatica and from other Dickeya species. The name Dickeya lacustris sp. nov. is proposed for this taxon with S29^T (=CFBP 8647^T=LMG 30899^T) as the type strain.

Pectobacterium and Dickeya Responsible for Potato Blackleg Disease in New York State in 2016

Beginning in 2014, outbreaks of blackleg disease compromised potato (Solanum tuberosum) production in the northeastern United States. Disease severity was atypical for plantings with certified seed. During 2016, 43 samples with blackleg symptoms were analyzed, originating from more than 20 farms operating in New York State. A combination of techniques was employed to identify the blackleg pathogens: isolation in vitro, diagnostic PCR assays for Pectobacterium and Dickeya sp., pathogenicity assays, and DNA sequencing. Twenty-three bacterial isolates were obtained, the majority of which were designated D. dianthicola or P. parmentieri; two of the isolates were designated P. atrosepticum. All isolates were pathogenic in stem lesion and tuber soft rot assays and exhibited pectin degrading activity (pitting) in crystal violet pectate agar medium. Phylogenetic analyses of dnaX gene sequences placed all but one of the isolates into clades corresponding to D. dianthicola, P. parmentieri, or P. atrosepticum. One atypical isolate clustered with P. carotovorum subspecies. Data are consistent with the hypothesis that D. dianthicola from New York and the northeast are part of a single clade, and at least three different soft rot bacteria were associated with blackleg during 2016 in New York.

Development of a Loop-Mediated Isothermal Amplification Assay for the Detection of Dickeya spp

Dickeya and Pectobacterium spp. are responsible for soft-rotting diseases of several plant species, some with overlapping host range. On potato, symptoms caused by these pathogens cannot be clearly differentiated. Disease results in the downgrading and rejection of potato seed, thus requiring additional phytosanitary restrictions across Northern Europe and other parts of the world. In an effort to provide a more timely and accurate diagnostic to distinguish these two groups of pathogens, a method for detecting Dickeya spp. using loop-mediated isothermal amplification (LAMP) was developed. The LAMP assay can be used to test crude extracts prepared directly from symptomatic lesions. The entire test can be completed in less than 30 min, making it faster than the current diagnostic standard, the pelADE conventional polymerase chain reaction. Additionally, the LAMP assay was able to detect Dickeya DNA in samples spiked with varying amounts of Pectobacterium DNA, thus demonstrating the highly specific and sensitive nature of the assay, which can be applied on survey samples with mixed soft-rotting bacterial populations.

A gapA PCR-sequencing Assay for Identifying the Dickeya and Pectobacterium Potato Pathogens

Several pectinolytic Pectobacterium and Dickeya species and subspecies are causative agents of blackleg and soft rot diseases on potato plants and tubers. Rapid and accurate identification of these taxa is a crucial issue for the production and international trade of potato seed-tubers. Here, we developed a PCR-sequencing tool to easily characterize the different Pectobacterium and Dickeya taxa. The gapA gene sequences from 53 published genomes were aligned and a phylogeny tree was constructed. A set of 35 signature nucleotides was discovered to distinguish the Pectobacterium and Dickeya genera, species, and subspecies. Then, a PCR-primer couple was designed for amplifying the gapA gene in pectinolytic enterobacteria. The primers were tested on 22 isolates recovered from blackleg symptoms in several potato fields. Amplicons were sequenced and signature-nucleotides were analyzed. A phylogeny that includes gapA sequence specimens confirmed the taxonomical identification of these environmental isolates.

Biodiversity of Dickeya spp. Isolated from Potato Plants and Water Sources in Temperate Climate

Bacteria from the genera Dickeya (formerly Erwinia chrysanthemi) and Pectobacterium (formerly E. carotovora) are the agents of blackleg and soft rot on many important crops. In 2005, Dickeya solani was isolated for the first time in Poland from a symptomatic potato plant. To establish the presence and diversity of Dickeya spp. in Poland, we surveyed potato fields and water sources, including surface waters near potato fields and water from potato-processing facilities and sewage plants. Only D. dianthicola and D. solani were isolated from symptomatic potato, and only D. zeae and D. chrysanthemi were isolated from water sources. The Dickeya spp. isolated from potato formed a relatively homogenous group, while those from water sources were more diverse. To our knowledge, this is the first comprehensive characterization of Dickeya spp. isolated during several years from regions with a temperate climate in Central Europe.

Biocontrol of the Potato Blackleg and Soft Rot Diseases Caused by Dickeya dianthicola

Development of protection tools targeting Dickeya species is an important issue in the potato production. Here, we present the identification and the characterization of novel biocontrol agents. Successive screenings of 10,000 bacterial isolates led us to retain 58 strains that exhibited growth inhibition properties against several Dickeya sp. and/or Pectobacterium sp. pathogens. Most of them belonged to the Pseudomonas and Bacillus genera. In vitro assays revealed a fitness decrease of the tested Dickeya sp. and Pectobacterium sp. pathogens in the presence of the biocontrol agents. In addition, four independent greenhouse assays performed to evaluate the biocontrol bacteria effect on potato plants artificially contaminated with Dickeya dianthicola revealed that a mix of three biocontrol agents, namely, Pseudomonas putida PA14H7 and Pseudomonas fluorescens PA3G8 and PA4C2, repeatedly decreased the severity of blackleg symptoms as well as the transmission of D. dianthicola to the tuber progeny. This work highlights the use of a combination of biocontrol strains as a potential strategy to limit the soft rot and blackleg diseases caused by D. dianthicola on potato plants and tubers.

Characterization of Dickeya and Pectobacterium species by capillary electrophoretic techniques and MALDI-TOF MS

Dickeya and Pectobacterium species represent an important group of broad-host-range phytopathogens responsible for blackleg and soft rot diseases on numerous plants including many economically important plants. Although these species are commonly detected using cultural, serological, and molecular methods, these methods are sometimes insufficient to classify the bacteria correctly. On that account, this study was undertaken to investigate the feasibility of three individual analytical techniques, capillary zone electrophoresis (CZE), capillary isoelectric focusing (CIEF), and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), for reliable classification of Dickeya and Pectobacterium species. Forty-three strains, representing different Dickeya and Pectobacterium species, namely Dickeya dianthicola, Dickeya dadantii, Dickeya dieffenbachiae, Dickeya chrysanthemi, Dickeya zeae, Dickeya paradisiaca, Dickeya solani, Pectobacterium carotovorum, and Pectobacterium atrosepticum, were selected for this purpose. Furthermore, the selected bacteria included one strain which could not be classified using traditional microbiological methods. Characterization of the bacteria was based on different pI values (CIEF), migration velocities (CZE), or specific mass fingerprints (MALDI-TOF MS) of intact cells. All the examined strains, including the undetermined bacterium, were characterized and classified correctly into respective species. MALDI-TOF MS provided the most reliable results in this respect.

Detection of the Bacterial Potato Pathogens Pectobacterium and Dickeya spp. Using Conventional and Real-Time PCR

Blackleg and soft rot of potato, caused by Pectobacterium and Dickeya spp., are major production constraints in many potato-growing regions of the world. Despite advances in our understanding of the causative organisms, disease epidemiology, and control, blackleg remains the principal cause of down-grading and rejection of potato seed in classification schemes across Northern Europe and many other parts of the world. Although symptom recognition is relatively straightforward and is applied universally in seed classification schemes, attributing disease to a specific organism is problematic and can only be achieved through the use of diagnostics. Similarly as disease spread is largely through the movement of asymptomatically infected seed tubers and, possibly in the case of Dickeya spp., irrigation waters, accurate and sensitive diagnostics are a prerequisite for detection. This chapter describes the diagnostic pathway that can be applied to identify the principal potato pathogens within the genera Pectobacterium and Dickeya.

Detection, identification and differentiation of Pectobacterium and Dickeya species causing potato blackleg and tuber soft rot: a review

The soft rot Enterobacteriaceae (SRE) Pectobacterium and Dickeya species (formerly classified as pectinolytic Erwinia spp.) cause important diseases on potato and other arable and horticultural crops. They may affect the growing potato plant causing blackleg and are responsible for tuber soft rot in storage thereby reducing yield and quality. Efficient and cost-effective detection and identification methods are essential to investigate the ecology and pathogenesis of the SRE as well as in seed certification programmes. The aim of this review was to collect all existing information on methods available for SRE detection. The review reports on the sampling and preparation of plant material for testing and on over thirty methods to detect, identify and differentiate the soft rot and blackleg causing bacteria to species and subspecies level. These include methods based on biochemical characters, serology, molecular techniques which rely on DNA sequence amplification as well as several less-investigated ones.

Simultaneous detection of major blackleg and soft rot bacterial pathogens in potato by multiplex polymerase chain reaction

A multiplex polymerase chain reaction (PCR) assay for simultaneous, fast and reliable detection of the main soft rot and blackleg potato pathogens in Europe has been developed. It utilises three pairs of primers and enables detection of three groups of pectinolytic bacteria frequently found in potato, namely: Pectobacterium atrosepticum, Pectobacterium carotovorum subsp. carotovorum together with Pectobacterium wasabiae and Dickeya spp. in a multiplex PCR assay. In studies with axenic cultures of bacteria, the multiplex assay was specific as it gave positive results only with strains of the target species and negative results with 18 non-target species of bacteria that can possibly coexist with pectinolytic bacteria in a potato ecosystem. The developed assay could detect as little as 0.01 ng µL^-1 of Dickeya sp. genomic DNA, and down to 0.1 ng µL^-1 of P. atrosepticum and P. carotovorum subsp. carotovorum genomic DNA in vitro. In the presence of competitor genomic DNA, isolated from Pseudomonas fluorescens cells, the sensitivity of the multiplex PCR decreased tenfold for P. atrosepticum and Dickeya sp., while no change was observed for P. carotovorum subsp. carotovorum and P. wasabiae. In spiked potato haulm and tuber samples, the threshold level for target bacteria was 10¹ cfu mL^-1 plant extract (10² cfu g^-1 plant tissue), 10² cfu mL^-1 plant extract (10³ cfu g^-1 plant tissue), 10³ cfu mL^-1 plant extract (10⁴ cfu g^-1 plant tissue), for Dickeya spp., P. atrosepticum and P. carotovorum subsp. carotovorum/P. wasabiae, respectively. Most of all, this assay allowed reliable detection and identification of soft rot and blackleg pathogens in naturally infected symptomatic and asymptomatic potato stem and progeny tuber samples collected from potato fields all over Poland.

Genomic overview of the phytopathogen Pectobacterium wasabiae strain RNS 08.42.1A suggests horizontal acquisition of quorum-sensing genes

The blackleg and soft-rot diseases caused by pectinolytic enterobacteria such as Pectobacterium and Dickeya are major causes of losses affecting potato crop in the field and upon storage. In this work, we report the isolation, characterization and genome analysis of the Pectobacterium wasabiae (formerly identified as Pectobacterium carotovorum subsp. carotovorum) strain RNS 08.42.1A, that has been isolated from a Solanum tuberosum host plant in France. Comparative genomics with 3 other P. wasabiae strains isolated from potato plants in different areas in North America and Europe, highlighted both a strong similarity at the whole genome level (ANI > 99 %) and a conserved synteny of the virulence genes. In addition, our analyses evidenced a robust separation between these four P. wasabiae strains and the type strain P. wasabiae CFBP 3304(T), isolated from horseradish in Japan. In P. wasabiae RNS 08.42.1A, the expI and expR nucleotidic sequences are more related to those of some Pectobacterium atrosepticum and P. carotovorum strains (90 % of identity) than to those of the other potato P. wasabiae strains (70 to 74 % of identity). This could suggest a recruitment of these genes in the P. wasabiae strain RNS 08.42.1A by an horizontal transfer between pathogens infecting the same potato host plant.

Diversity of Dickeya Strains Collected from Pineapple Plants and Irrigation Water in Hawaii

Bacterial heart rot caused by a yet undetermined species of Dickeya was first observed in December 2003 in Oahu, HI, on a pineapple cultivar (Ananas comosus 'PRI 73-114') recently imported from Central America. Identical symptoms were later seen in the same plantation in fields that had been planted with propagules from the Philippines. Dickeya strains isolated from symptomatic plants and irrigation water collected over subsequent years were identified using bacteriological tests and partial 16S ribosomal DNA sequencing and characterized using repetitive sequence-based polymerase chain reaction (rep-PCR) with the BOXA1R primer (BOX-PCR), pathogenicity on pineapple leaves, and reactivity with two monoclonal antibodies (MAbs). Strains exhibited variability in pathogenicity and in reactivity with MAbs. BOX-PCR separated the plant-isolated Dickeya strains into seven haplotypes that were placed into four fingerprint groups (A to D). Strains from the A and B groups were isolated from the Central American stocks, whereas strains in the D group were identified from Philippine material. Strains from the C group were isolated from both planting materials. Most strains from water sources were placed into three haplotypes that loosely formed group E. BOX-PCR polymorphisms between the Dickeya strains isolated from foreign pineapple plants, a local collection of Dickeya strains, and strains from the plantation's water sources support the possibility that at least two separate introductions of genetically distinct strains occurred via imported planting stocks.

Dickeya aquatica sp. nov., isolated from waterways

Pectinolytic Gram-negative bacteria were isolated from different waterways in the UK and Finland. Three strains (174/2(T), 181/2 and Dw054) had the same 16S rRNA gene sequences which shared 99% sequence similarity to species of the genus Dickeya, and a phylogeny of related genera confirmed attribution to this genus. Fatty acid profile analysis of all three strains found a high proportion of C16 : 1ω7c/C16 : 1ω7c and C16 : 0 fatty acids, and library profile searches found closest matches to Dickeya chrysanthemi. Production of a concatenated phylogeny using six loci, recA, gapA, atpD, gyrB, infB and rpoB, provided a high-resolution phylogeny which placed strains 174/2(T) and 181/2 as a distinct clade, separated from the other species of the genus Dickeya by a relatively long branch-length. DNA-DNA hybridization analysis with a limited number of reference species also supported the distinctiveness of strains 174/2(T) and 181/2 within the genus Dickeya. All three strains could be phenotypically distinguished from other species of the genus by fermentation of melibiose and raffinose but not D-arabinose or mannitol. The name Dickeya aquatica sp. nov. is proposed for the new taxon; the type strain is 174/2(T) ( = NCPPB 4580(T) = LMG 27354(T)).

Identification of Dickeya zeae as a Causal Agent of Bacterial Soft Rot in Banana in China

Bacterial soft rot of banana was first noticed in 2009 in Guangzhou city, China. The disease also was observed on various banana cultivars of different genotypes in several other cities. Symptoms of the disease included leaf wilting, collapse of pseudostems, and unusual odor. Five isolated strains that fulfilled Koch's postulates were used for biochemical testing. The five strains were most similar to Dickeya dadantii or D. zeae, but were much less similar to D. paradisiaca when using several phenotype characteristics. Sequence analysis of 16S rDNA, dnaX, gryB, and recA of a reference strain revealed a similarity of 99% with the sequences of D. zeae, rather than D. paradisiaca. Phylogenic analysis of concatenated sequences of dnaX, gryB, and recA indicated that the banana strain constituted a distinguishable clade with several D. zeae strains involving rice pathogens D. zeae EC1 and ZJU1202 from Guangdong province, but the banana pathogen had several characteristics that distinguished it from the rice pathogens. Therefore, the banana pathogen was determined to be D. zeae. This is the first report of banana soft rot caused by D. zeae in China; however, the pathogen can infect other important crops.

Dickeya solani sp. nov., a pectinolytic plant-pathogenic bacterium isolated from potato (Solanum tuberosum)

Pectinolytic bacteria have been recently isolated from diseased potato plants exhibiting blackleg and slow wilt symptoms found in a number of European countries and Israel. These Gram-reaction-negative, motile, rods were identified as belonging to the genus Dickeya, previously the Pectobacterium chrysanthemi complex (Erwinia chrysanthemi), on the basis of production of a PCR product with the pelADE primers, 16S rRNA gene sequence analysis, fatty acid methyl esterase analysis, the production of phosphatases and the ability to produce indole and acids from α-methylglucoside. Differential physiological assays used previously to differentiate between strains of E. chrysanthemi, showed that these isolates belonged to biovar 3. Eight of the isolates, seven from potato and one from hyacinth, were analysed together with 21 reference strains representing all currently recognized taxa within the genus Dickeya. The novel isolates formed a distinct genetic clade in multilocus sequence analysis (MLSA) using concatenated sequences of the intergenic spacer (IGS), as well as dnaX, recA, dnaN, fusA, gapA, purA, rplB, rpoS and gyrA. Characterization by whole-cell MALDI-TOF mass spectrometry, pulsed field gel electrophoresis after digestion of whole-genome DNA with rare-cutting restriction enzymes, average nucleotide identity analysis and DNA-DNA hybridization studies, showed that although related to Dickeya dadantii, these isolates represent a novel species within the genus Dickeya, for which the name Dickeya solani sp. nov. (type strain IPO 2222(T) = LMG25993(T) = NCPPB4479(T)) is proposed.

Pectobacterium spp. associated with bacterial stem rot syndrome of potato in Canada

Pectobacterium atrosepticum, P. carotovorum subsp. brasiliensis, P. carotovorum subsp. carotovorum, and P. wasabiae were detected in potato stems with blackleg symptoms using species- and subspecies-specific polymerase chain reaction (PCR). The tests included a new assay for P. wasabiae based on the phytase gene sequence. Identification of isolates from diseased stems by biochemical or physiological characterization, PCR, and multi-locus sequence typing (MLST) largely confirmed the PCR detection of Pectobacterium spp. in stem samples. P. atrosepticum was most commonly present but was the sole Pectobacterium sp. detected in only 52% of the diseased stems. P. wasabiae was most frequently present in combination with P. atrosepticum and was the sole Pectobacterium sp. detected in 13% of diseased stems. Pathogenicity of P. wasabiae on potato and its capacity to cause blackleg disease were demonstrated by stem inoculation and its isolation as the sole Pectobacterium sp. from field-grown diseased plants produced from inoculated seed tubers. Incidence of P. carotovorum subsp. brasiliensis was low in diseased stems, and the ability of Canadian strains to cause blackleg in plants grown from inoculated tubers was not confirmed. Canadian isolates of P. carotovorum subsp. brasiliensis differed from Brazilian isolates in diagnostic biochemical tests but conformed to the subspecies in PCR specificity and typing by MLST.

Sequence diversity in the Dickeya fliC gene: phylogeny of the Dickeya genus and TaqMan® PCR for 'D. solani', new biovar 3 variant on potato in Europe

Worldwide, Dickeya (formerly Erwinia chrysanthemi) is causing soft rot diseases on a large diversity of crops and ornamental plants. Strains affecting potato are mainly found in D. dadantii, D. dianthicola and D. zeae, which appear to have a marked geographical distribution. Furthermore, a few Dickeya isolates from potato are attributed to D. chrysanthemi and D. dieffenbachiae. In Europe, isolates of Erwinia chrysanthemi biovar 1 and biovar 7 from potato are now classified in D. dianthicola. However, in the past few years, a new Dickeya biovar 3 variant, tentatively named 'Dickeya solani', has emerged as a common major threat, in particular in seed potatoes. Sequences of a fliC gene fragment were used to generate a phylogeny of Dickeya reference strains from culture collections and with this reference backbone, to classify pectinolytic isolates, i.e. Dickeya spp. from potato and ornamental plants. The reference strains of the currently recognized Dickeya species and 'D. solani' were unambiguously delineated in the fliC phylogram. D. dadantii, D. dianthicola and 'D. solani' displayed unbranched clades, while D. chrysanthemi, D. zeae and D. dieffenbachiae branched into subclades and lineages. Moreover, Dickeya isolates from diagnostic samples, in particular biovar 3 isolates from greenhouse ornamentals, formed several new lineages. Most of these isolates were positioned between the clade of 'D. solani' and D. dadantii as transition variants. New lineages also appeared in D. dieffenbachiae and in D. zeae. The strains and isolates of D. dianthicola and 'D. solani' were differentiated by a fliC sequence useful for barcode identification. A fliC TaqMan®real-time PCR was developed for 'D. solani' and the assay was provisionally evaluated in direct analysis of diagnostic potato samples. This molecular tool can support the efforts to control this particular phytopathogen in seed potato certification.

Classification of plant associated bacteria using RIF, a computationally derived DNA marker

A DNA marker that distinguishes plant associated bacteria at the species level and below was derived by comparing six sequenced genomes of Xanthomonas, a genus that contains many important phytopathogens. This DNA marker comprises a portion of the dnaA replication initiation factor (RIF). Unlike the rRNA genes, dnaA is a single copy gene in the vast majority of sequenced bacterial genomes, and amplification of RIF requires genus-specific primers. In silico analysis revealed that RIF has equal or greater ability to differentiate closely related species of Xanthomonas than the widely used ribosomal intergenic spacer region (ITS). Furthermore, in a set of 263 Xanthomonas, Ralstonia and Clavibacter strains, the RIF marker was directly sequenced in both directions with a success rate approximately 16% higher than that for ITS. RIF frameworks for Xanthomonas, Ralstonia and Clavibacter were constructed using 682 reference strains representing different species, subspecies, pathovars, races, hosts and geographic regions, and contain a total of 109 different RIF sequences. RIF sequences showed subspecific groupings but did not place strains of X. campestris or X. axonopodis into currently named pathovars nor R. solanacearum strains into their respective races, confirming previous conclusions that pathovar and race designations do not necessarily reflect genetic relationships. The RIF marker also was sequenced for 24 reference strains from three genera in the Enterobacteriaceae: Pectobacterium, Pantoea and Dickeya. RIF sequences of 70 previously uncharacterized strains of Ralstonia, Clavibacter, Pectobacterium and Dickeya matched, or were similar to, those of known reference strains, illustrating the utility of the frameworks to classify bacteria below the species level and rapidly match unknown isolates to reference strains. The RIF sequence frameworks are available at the online RIF database, RIFdb, and can be queried for diagnostic purposes with RIF sequences obtained from unknown strains in both chromatogram and FASTA format.

Specificity of monoclonal antibodies to strains of Dickeya sp. that cause bacterial heart rot of pineapple

During a severe outbreak of bacterial heart rot that occurred in pineapple plantations on Oahu, Hawaii, in 2003 and years following, 43 bacterial strains were isolated from diseased plants or irrigation water and identified as Erwinia chrysanthemi (now Dickeya sp.) by phenotypic, molecular, and pathogenicity assays. Rep-PCR fingerprint patterns grouped strains from pineapple plants and irrigation water into five genotypes (A-E) that differed from representatives of other Dickeya species, Pectobacterium carotovorum and other enteric saprophytes isolated from pineapple. Monoclonal antibodies produced following immunization of mice with virulent type C Dickeya sp. showed only two specificities. MAb Pine-1 (2D11G1, IgG1 with kappa light chain) reacted to all 43 pineapple/water strains and some reference strains (D. dianthicola, D. chrysanthemi, D. paradisiaca, some D. dadantii, and uncharacterized Dickeya sp.) but did not react to reference strains of D. dieffenbachiae, D. zeae, or one of the two Malaysian pineapple strains. MAb Pine-2 (2A7F2, IgG3 with kappa light chain) reacted to all type B, C, and D strains but not to any A or E strains or any reference strains except Dickeya sp. isolated from Malaysian pineapple. Pathogenicity tests showed that type C strains were more aggressive than type A strains when inoculated during cool months. Therefore, MAb Pine-2 distinguishes the more virulent type C strains from less virulent type A pineapple strains and type E water strains. MAbs with these two specificities enable development of rapid diagnostic tests that will distinguish the systemic heart rot pathogen from opportunistic bacteria associated with rotted tissues. Use of the two MAbs in field assays also permits the monitoring of a known subpopulation and provides additional decision tools for disease containment and management practices.

Downward vascular translocation of a green fluorescent protein-tagged strain of Dickeya sp. (Biovar 3) from stem and leaf inoculation sites on potato

Translocation of a green fluorescent protein (GFP)-tagged Dickeya sp. from stems or from leaves to underground parts of potato plants was studied in greenhouse experiments. Thirty days after stem inoculation, 90% of plants expressed symptoms at the stem base and 95% of plants showed browning of internal stem tissue. The GFP-tagged Dickeya sp. was detected by dilution plating in extracts of the stem interiors (100%), stem bases (90%), roots (80%), stolons (55%), and progeny tubers (24%). In roots, the GFP-tagged Dickeya sp. was found inside and between parenchyma cells whereas, in stems and stolons, the GFP-tagged Dickeya sp. was found in the xylem vessels and protoxylem cells. In progeny tubers, this strain was detected in the stolon end. Thirty days after leaf inoculation, the GFP-tagged Dickeya sp. was detected in extracts of 75% of the leaves, 88% of the petioles, 63% of the axils, and inside 25% of the stems taken 15 cm above the ground level. UV microscopy confirmed the presence of the GFP-tagged Dickeya sp. inside petioles and in the main leaf veins. No blackleg or aerial stem rot and no translocation of the GFP-tagged Dickeya sp. to underground plant parts was observed. The implications for contamination of progeny tubers are discussed.

Detection of four major bacterial potato pathogens

Ring rot, brown rot and blackleg represent major bacterial pathogens of potato. The methods described below are aimed at basic identification of ring rot, brown rot or blackleg in a tuber sample.

Characterization of Erwinia chrysanthemi from a Bacterial Heart Rot of Pineapple Outbreak in Hawaii

The first reported outbreak of bacterial heart rot of pineapple (Ananas comosus var. comosus) in Hawaii occurred in December 2003. Of immediate concern was the differentiation of heart rot caused by Erwinia chrysanthemi from a soft rot caused by E. carotovora subsp. carotovora because of regulatory issues. Presumptive identifications of the isolated bacteria were made using bacteriological tests (including reactivity with an Erwinia-specific monoclonal antibody, E2) and compared with identifications obtained by two general methods: carbon source utilization profiling (Biolog) and 16S rDNA sequence analysis. The panel of bacteriological tests consistently differentiated E. chrysanthemi from E. carotovora subsp. carotovora and other nonquarantine organisms. BOX-polymerase chain reaction fingerprint patterns further differentiated the pineapple-isolated E. chrysanthemi strains from those obtained from other plants and irrigation water. Pineapple leaf inoculations revealed that only E. chrysanthemi from pineapple produced watersoaking and rot similar to that observed on the original symptomatic plants, thus identifying these strains as the causal agents of the outbreak. In this situation, where rapid identification of an unknown pathogen was necessary, standard bacteriological tests then available in the laboratory provided reliable differentiation of E. chrysanthemi from E. carotovora subsp. carotovora. Additional strain characterization is needed before the pineapple-isolated E. chrysanthemi strains can be classified into a species of the new genus Dickeya.

The acyl-homoserine lactone-type quorum-sensing system modulates cell motility and virulence of Erwinia chrysanthemi pv. zeae

Erwinia chrysanthemi pv. zeae is one of the Erwinia chrysanthemi pathovars that infects on both dicotyledons and monocotyledons. However, little is known about the molecular basis and regulatory mechanisms of its virulence. By using a transposon mutagenesis approach, we cloned the genes coding for an E. chrysanthemi pv. zeae synthase of acyl-homoserine lactone (AHL) quorum-sensing signals (expI(Ecz)) and a cognate response regulator (expR(Ecz)). Chromatography analysis showed that expI(Ecz) encoded production of the AHL signal N-(3-oxo-hexanoyl)-homoserine lactone (OHHL). Null mutation of expI(Ecz) in the E. chrysanthemi pv. zeae strain EC1 abolished AHL production, increased bacterial swimming and swarming motility, disabled formation of multicell aggregates, and attenuated virulence of the pathogen on potato tubers. The mutation also marginally reduced the inhibitory activity of E. chrysanthemi pv. zeae on rice seed germination. The mutant phenotypes were rescued by either exogenous addition of AHL signal or in trans expression of expI(Ecz). These data demonstrate that the AHL-type QS signal plays an essential role in modulation of E. chrysanthemi pv. zeae cell motility and the ability to form multicell aggregates and is involved in regulation of bacterial virulence.

Host range and molecular phylogenies of the soft rot enterobacterial genera pectobacterium and dickeya

ABSTRACT Pectobacterium and Dickeya spp. are related broad-host-range entero-bacterial pathogens of angiosperms. A review of the literature shows that these genera each cause disease in species from at least 35% of angiosperm plant orders. The known host ranges of these pathogens partially overlap and, together, these two genera are pathogens of species from 50% of angiosperm plant orders. Notably, there are no reported hosts for either genus in the eudicots clade and no reported Dickeya hosts in the magnoliids or eurosids II clades, although Pectobacterium spp. are pathogens of at least one plant species in the magnoliids and at least one in each of the three eurosids II plant orders. In addition, Dickeya but not Pectobacterium spp. have been reported on a host in the rosids clade and, unlike Pectobacterium spp., have been reported on many Poales species. Natural disease among nonangiosperms has not been reported for either genus. Phylogenetic analyses of sequences concatenated from regions of seven housekeeping genes (acnA, gapA, icdA, mdh, mtlD, pgi, and proA) from representatives of these genera demonstrated that Dickeya spp. and the related tree pathogens, the genus Brenneria, are more diverse than Pectobacterium spp. and that the Pectobacterium strains can be divided into at least five distinct clades, three of which contain strains from multiple host plants.

Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov

A collection of 75 strains of Pectobacterium chrysanthemi (including all biovars and pathovars) and the type strains of Brenneria paradisiaca (CFBP 4178(T)) and Pectobacterium cypripedii (CFBP 3613(T)) were studied by DNA-DNA hybridization, numerical taxonomy of 121 phenotypic characteristics, serology and 16S rRNA gene-based phylogenetic analyses. From analysis of 16S rRNA gene sequences, it was deduced that P. chrysanthemi strains and B. paradisiaca CFBP 4178(T) formed a clade distinct from the genera Pectobacterium and Brenneria; therefore, it is proposed to transfer all the strains to a novel genus, Dickeya gen. nov. By DNA-DNA hybridization, the strains of P. chrysanthemi were distributed among six genomic species: genomospecies 1 harbouring 16 strains of biovar 3 and four strains of biovar 8, genomospecies 2 harbouring 16 strains of biovar 3, genomospecies 3 harbouring two strains of biovar 6 and five strains of biovar 5, genomospecies 4 harbouring five strains of biovar 2, genomospecies 5 harbouring six strains of biovar 1, four strains of biovar 7 and five strains of biovar 9 and genomospecies 6 harbouring five strains of biovar 4 and B. paradisiaca CFBP 4178(T). Two strains of biovar 3 remained unclustered. Biochemical criteria, deduced from a numerical taxonomic study of phenotypic characteristics, and serological reactions allowed discrimination of the strains belonging to the six genomic species. Thus, it is proposed that the strains clustered in these six genomic species be assigned to the species Dickeya zeae sp. nov. (type strain CFBP 2052(T)=NCPPB 2538(T)), Dickeya dadantii sp. nov. (type strain CFBP 1269(T)=NCPPB 898(T)), Dickeya chrysanthemi comb. nov. (subdivided into two biovars, bv. chrysanthemi and bv. parthenii), Dickeya dieffenbachiae sp. nov. (type strain CFBP 2051(T)=NCPPB 2976(T)), Dickeya dianthicola sp. nov. (type strain CFBP 1200(T)=NCPPB 453(T)) and Dickeya paradisiaca comb. nov., respectively.

Structure and hydrodynamic properties of the extracellular polysaccharide from a mutant strain (RA3W) of Erwinia chrysanthemi RA3

The structure of the extracellular polysaccharide (EPS) produced by Erwinia chrysanthemi strain RA3W, a mutant strain of E. chrysanthemi RA3, has been determined using low pressure size-exclusion and anion-exchange chromatographies, high pH anion-exchange chromatography, glycosyl linkage analysis, and 1D 1H NMR spectroscopy. The polysaccharide is structurally similar, if not identical, to the family of EPS produced by such as E. chrysanthemi strains Ech9, Ech9Sm6, and SR260. The molecular weight of EPS RA3W by ultracentrifugation (sedimentation equilibrium) and light scattering is compared with those of other E. chrysanthami EPSs, as are the viscometric properties.

Analysis of Erwinia chrysanthemi EC16 pelE::uidA, pelL::uidA, and hrpN::uidA mutants reveals strain-specific atypical regulation of the Hrp type III secretion system

The plant pathogen Erwinia chrysanthemi produces a variety of factors that have been implicated in its ability to cause soft-rot diseases in various hosts. These include HrpN, a harpin secreted by the Hrp type III secretion system; PelE, one of several major pectate lyase isozymes secreted by the type II system; and PelL, one of several secondary Pels secreted by the type II system. We investigated these factors in E. chrysanthemi EC16 with respect to the effects of medium composition and growth phase on gene expression (as determined with uidA fusions and Northern analyses) and effects on virulence. pelE was induced by polygalacturonic acid, but pelL was not, and hrpN was expressed unexpectedly in nutrient-rich King's medium B and in minimal salts medium at neutral pH. In contrast, the effect of medium composition on hrp expression in E. chrysanthemi CUCPB1237 and 3937 was like that of many other phytopathogenic bacteria in being repressed in complex media and induced in acidic pH minimal medium. Northern blot analysis of hrpN and hrpL expression by the wild-type and hrpL::omegaCmr and hrpS::omegaCmr mutants revealed that hrpN expression was dependent on the HrpL alternative sigma factor, whose expression, in turn, was dependent on the HrpS putative sigma54 enhancer binding protein. The expression of pelE and hrpN increased strongly in late logarithmic growth phase. To test the possible role of quorum sensing in this expression pattern, the expI/expR locus was cloned in Escherichia coli on the basis of its ability to direct production of acyl-homoserine lactone and then used to construct expI mutations in pelE::uidA, pelL::uidA, and hrpN::uidA Erwinia chrysanthemi strains. Mutation of expI had no apparent effect on the growth-phase-dependent expression of hrpN and pelE, or on the virulence of E. chrysanthemi in witloof chicory leaves. Overexpression of hrpN in E. chrysanthemi resulted in approximately 50% reduction of lesion size on chicory leaves without an effect on infection initiation.

Characterization of Erwinia Populations from Nursery Retention Ponds and Lakes Infecting Ornamental Plants in Florida

Water shortages in Florida are occurring due to intense utilization of the aquifer system by municipalities and agriculture, and because of continued deficits in annual rainfall. Water districts therefore, are, recommending the use of recycled irrigation water, stormwater runoff, reclaimed municipal sewage water, and lakes for agricultural use. With recycled water, however, there is potential for both introducing and concentrating plant pathogens. In Florida, Erwinia soft-rot bacteria (synonym Pectobacterium) cause extensive crop losses in ornamental plant production. To determine Erwinia spp. population levels, samples were taken monthly for 1 year from four hypereutropic lakes and eight nursery retention ponds. Seventy-seven Erwinia strains were collected by both direct plating and by an enrichment process. With the direct plating method, 0 to 29 CFU/ml were detected on sodium polypectate medium. Significantly higher populations of Erwinia were detected in retention ponds of nurseries that were actively reutilizing their water. Erwinia strains were identified to species by fatty acid analysis and biochemical tests. Strains were further characterized by repetitive element-polymerase chain reaction (rep-PCR) and compared with 120 strains of Erwinia collected from ornamentals over a 17-year period in Florida. Using rep-PCR, most strains were clustered into two heterogeneous populations of E. chrysanthemi and E. carotovora subsp. carotovora in a 1:2 and a 1:4 ratio for isolates from ornamentals and from water, respectively. Within each population of E. chrysanthemi and E. carotovora, genetically different subpopulations could be identified that contained high percentages of Erwinia strains from water sources. Even though genetic differences exist, 99% of the strains from water sources were found to be pathogenic on dieffenbachia. Without water treatment of irrigation and stormwater runoff, there is a potential for both introducing and concentrating Erwinia populations within these water sources.

Soft rot erwiniae: from genes to genomes

SUMMARY The soft rot erwiniae, Erwinia carotovora ssp. atroseptica (Eca), E. carotovora ssp. carotovora (Ecc) and E. chrysanthemi (Ech) are major bacterial pathogens of potato and other crops world-wide. We currently understand much about how these bacteria attack plants and protect themselves against plant defences. However, the processes underlying the establishment of infection, differences in host range and their ability to survive when not causing disease, largely remain a mystery. This review will focus on our current knowledge of pathogenesis in these organisms and discuss how modern genomic approaches, including complete genome sequencing of Eca and Ech, may open the door to a new understanding of the potential subtlety and complexity of soft rot erwiniae and their interactions with plants.

TAXONOMY

The soft rot erwiniae are members of the Enterobacteriaceae, along with other plant pathogens such as Erwinia amylovora and human pathogens such as Escherichia coli, Salmonella spp. and Yersinia spp. Although the genus name Erwinia is most often used to describe the group, an alternative genus name Pectobacterium was recently proposed for the soft rot species.

HOST RANGE

Ech mainly affects crops and other plants in tropical and subtropical regions and has a wide host range that includes potato and the important model host African violet (Saintpaulia ionantha). Ecc affects crops and other plants in subtropical and temperate regions and has probably the widest host range, which also includes potato. Eca, on the other hand, has a host range limited almost exclusively to potato in temperate regions only. Disease symptoms: Soft rot erwiniae cause general tissue maceration, termed soft rot disease, through the production of plant cell wall degrading enzymes. Environmental factors such as temperature, low oxygen concentration and free water play an essential role in disease development. On potato, and possibly other plants, disease symptoms may differ, e.g. blackleg disease is associated more with Eca and Ech than with Ecc.

USEFUL WEBSITES

http://www.scri.sari.ac.uk/TiPP/Erwinia.htm, http://www.ahabs.wisc.edu:16080/ approximately pernalab/erwinia/index.htm, http://www.tigr.org/tdb/mdb/mdbinprogress.html, http://www.sanger.ac.uk/Projects/E_carotovora/.