Dickeya Fangzhongdai Research Articles

Genomic characteristics of Dickeya fangzhongdai isolates from pear and the function of type IV pili in the chromosome

Dickeya fangzhongdai, the causal agent of bleeding canker of pear, is a new member of the Dickeya genus and the only one that infects woody plants. Recent studies have reclassified several Dickeya isolates as D. fangzhongdai, which were isolated from various environments, including water, Phalaenopsis sp. and Aglaonema sp. To provide genomic characterization of D. fangzhongdai isolates from pear, the genomes of D. fangzhongdai strain JS5 (=China General Microbiological Culture Collection Center, CGMCC 1.15464T=DSM 101947T), along with two other isolates, LN1 and QZH3, were sequenced and compared to those of other Dickeya spp. Homology greater than 99% was observed among three D. fangzhongdai strains. Plasmid, type IV secretion system (T4SS) and type IV pili (TFPs) were found in genomes of D. fangzhongdai isolates. Comparative analysis of the type III secretion systems (T3SS), type III secretion effectors (T3SE), plant cell wall degradation enzymes (PCWDE) and membrane transport proteins of Dickeya spp. showed some differences which might reflect the variations of virulence, phylogenetic and phenotypic characteristics of Dickeya spp. In addition, deletion mutant of TFP in D. fangzhongdai JS5 showed no twitching motility and reduced virulence and biofilm formation. The fingdings of the distinctive plasmid, T4SS and TFPs, as well as the differences of T3SE, PCWDE and membrane transport proteins make D. fangzhongdai isolates unique. These results also suggested that acquisition of virulence genes by horizontal gene transfer might play some role in the genetic variation of D. fangzhongdai.

Real-time PCR assay for detection of Dickeya fangzhongdai causing bleeding canker of pear disease in China

Bleeding canker, caused by Dickeya fangzhongdai, is a devastating disease of pear in China. The bacterium causes cankers, branch die-back, and eventually kills pear trees. The typical sign of bleeding canker infection is a rusty-brown bacterial ooze that exudes down from cankers onto branches or trunks. However, early symptoms and signs are inconspicuous, which makes effective disease management difficult. Detection and identification of D. fangzhongdai are time-consuming and difficult because no rapid method exists to date. In this study, a TaqMan real-time PCR assay was developed for D. fangzhongdai based on an elongation factor G (fusA) gene. The real-time PCR assay detected 0.2 pg μL−1 DNA and 1×103 CFU mL−1 of D. fangzhongdai. Based on this assay, bleeding canker on asymptomatic pear trees can be diagnosed as early as 5 days after infection. The real-time PCR assay can facilitate disease management by providing early and accurate diagnosis of the bleeding canker disease of pear.

First Report of Dickeya fangzhongdai Causing Soft Rot of Phalaenopsis aphrodite in China

HomePlant DiseaseVol. 103, No. 10First Report of Dickeya fangzhongdai Causing Soft Rot of Phalaenopsis aphrodite in China PreviousNext DISEASE NOTES OPENOpen Access licenseFirst Report of Dickeya fangzhongdai Causing Soft Rot of Phalaenopsis aphrodite in ChinaY. Shen, W. G. Lv, Y. H. Du, Y. X. Zhang, and H. P. LiY. Shen†Corresponding author: Y. Shen; E-mail Address: 763399029@qq.comhttp://orcid.org/0000-0002-2600-3854Shunde Office of Foshan Customs, 528303, Foshan, ChinaSearch for more papers by this author, W. G. LvShunde Office of Foshan Customs, 528303, Foshan, ChinaSearch for more papers by this author, Y. H. DuShunde Office of Foshan Customs, 528303, Foshan, ChinaSearch for more papers by this author, Y. X. ZhangShunde Office of Foshan Customs, 528303, Foshan, ChinaSearch for more papers by this author, and H. P. LiShunde Office of Foshan Customs, 528303, Foshan, ChinaSearch for more papers by this authorAffiliationsAuthors and Affiliations Y. Shen † W. G. Lv Y. H. Du Y. X. Zhang H. P. Li Shunde Office of Foshan Customs, 528303, Foshan, China Published Online:19 Aug 2019https://doi.org/10.1094/PDIS-01-19-0234-PDNAboutSectionsSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Phalaenopsis aphrodite is very popular in China. In the summer of 2017, a soft rot of P. aphrodite was found at the base of Phalaenopsis plants in Foshan city, Guangdong Province, with the incidence of about 10%. The infected leaves displayed water-soaked small round spots initially, and the spots expanded quickly with the increase of humidity and temperature, becoming translucent when facing a light source. Several days later, the inclusions exuded as the lesions decayed. The bacteria further infected the leaf sheath, resulting in the discoloring and perishing of leaf sheaths, falling off of leaves, and even the death of the whole plant. Finally, the leaves became as dry as paper. Five leaves with typical symptoms were randomly collected; after washing with 75% ethanol for 30 s, with 0.1% HgCl2 for 2 min, and with sterile water three times, small pieces of tissues (5 × 5 mm) were removed from lesion borders, plated on LB solid medium, and incubated at 37°C for 24 to 48 h. Thereafter, 10 representative isolates were chosen for further identification. Generally, these strains were gram negative, cultivated at 37°C, and utilized D-arabinose, melibiose, raffinose, and mannitol but not 5-keto-D-gluconate, β-gentiobiose, or casein. A GEN III MicroPlate system (Biolog) was used for examination, and the 10 isolates were identified as Dickeya chrysanthemi (SIM 0.856). PCR was used to amplify the 16S rDNA gene with primers 27f and 1492r (Tillett et al. 2000), recA (Waleron et al. 2002), and dnaX (Sławiak et al. 2009). BLASTn was carried out online, and the underlying phylogeny trees were obtained based on these gene sequences using MEGA 5.05 through 100% bootstrap values. The results showed that representative tested strain FSPAD1, whose sequences were deposited in GenBank under accession numbers MK394174 (16S rDNA), MK405705 (recA), and MK405706 (dnaX), had the highest homology with D. fangzhongdai for 16S rDNA(JN940859), recA (KT992693), and dnaX (KT992713), with the identities of 100, 97, and 97%, respectively. Therefore, this isolate was identified as D. fangzhongdai strain FSPAD1. Pathogenicity tests were performed on healthy tender leaves of P. aphrodite. Sterile filter paper (1 cm in diameter) was used to absorb sterile water and the bacterial suspension (1 × 108 CFU/ml). Then, the paper with sterile water (control) or the bacterial suspension were attached to tender leaves with three acupuncture points in each leaf. All tested plants were incubated at 28°C and kept moist with plastic bags. After 2 days, soft rot symptoms were observed in the pathogen-inoculated leaves, whereas sterile water (control) inoculated leaves exhibited no symptoms. The pathogenicity test was conducted three times. Koch’s postulates were achieved by reisolating D. fangzhongdai from the inoculated leaves. Meanwhile, 16S rDNA sequence alignment confirmed that the new reisolation was consistent with that of the inoculated plant. This pathogenic bacterium has been reported on Pyrus pyrifolia in China (Tian et al. 2016). So far, this is the first report of D. fangzhongdai causing soft rot disease on P. aphrodite.The author(s) declare no conflict of interest.

New bacterial fruit rot disease of jackfruit caused by Dickeya fangzhongdai in Malaysia

New bacterial fruit rot disease of jackfruit caused by Dickeya fangzhongdai in Malaysia

Dickeya undicola sp. nov., a novel species for pectinolytic isolates from surface waters in Europe and Asia.

Strains 2B12T, FVG1-MFV-O17 and FVG10-MFV-A16 were isolated from fresh water samples collected in Asia and Europe. The nucleotide sequences of the gapA barcodes revealed that all three strains belonged to the same cluster within the genus Dickeya. Using 13 housekeeping genes (fusA, rpoD, rpoS, glyA, purA, groEL, gapA, rplB, leuS, recA, gyrB, infB and secY), multilocus sequence analysis confirmed the existence of a new clade. When the genome sequences of these three isolates and other Dickeya species were compared, the in silico DNA-DNA hybridization and average nucleotide identity values were found to be no more than 45.50 and 91.22 %, respectively. The closest relative species was Dickeya fangzhongdai. Genome comparisons also highlighted genetic traits differentiating the new strains from D. fangzhongdai strains DSM 101947T (=CFBP 8607T) and B16. Phenotypical tests were performed to distinguish the three strains from D. fangzhongdai and other Dickeya species. The name Dickeya undicola sp. nov. is proposed with strain 2B12T (=CFBP 8650T=LMG 30903T) as the type strain.

First report of Dickeya fangzhongdai causing soft rot disease of Welsh onion in Taiwan

First report of Dickeya fangzhongdai causing soft rot disease of Welsh onion in Taiwan

Genomic characterisation of the new Dickeya fangzhongdai species regrouping plant pathogens and environmental isolates

BackgroundThe Dickeya genus is part of the Pectobacteriaceae family that is included in the newly described enterobacterales order. It comprises a group of aggressive soft rot pathogens with wide geographic distribution and host range. Among them, the new Dickeya fangzhongdai species groups causative agents of maceration-associated diseases that impact a wide variety of crops and ornamentals. It affects mainly monocot plants, but D. fangzhongdai strains have also been isolated from pear trees and water sources. Here, we analysed which genetic novelty exists in this new species, what are the D. fangzhongdai-specific traits and what is the intra-specific diversity.ResultsThe genomes of eight D. fangzhongdai strains isolated from diverse environments were compared to 31 genomes of strains belonging to other Dickeya species. The D. fangzhongdai core genome regroups approximately 3500 common genes, including most genes that encode virulence factors and regulators characterised in the D. dadantii 3937 model strain. Only 38 genes are present in D. fangzhongdai and absent in all other Dickeyas. One of them encodes a pectate lyase of the PL10 family of polysaccharide lyases that is found only in a few bacteria from the plant environment, soil or human gut. Other D. fangzhongdai-specific genes with a known or predicted function are involved in regulation or metabolism.The intra-species diversity analysis revealed that seven of the studied D. fangzhongdai strains were grouped into two distinct clades. Each clade possesses a pool of 100–150 genes that are shared by the clade members, but absent from the other D. fangzhongdai strains and several of these genes are clustered into genomic regions. At the strain level, diversity resides mainly in the arsenal of T5SS- and T6SS-related toxin-antitoxin systems and in secondary metabolite biogenesis pathways.ConclusionThis study identified the genome-specific traits of the new D. fangzhongdai species and highlighted the intra-species diversity of this species. This diversity encompasses secondary metabolites biosynthetic pathways and toxins or the repertoire of genes of extrachromosomal origin. We however didn’t find any relationship between gene content and phenotypic differences or sharing of environmental habitats.

Genomic analysis of the Phalaenopsis pathogen Dickeya sp. PA1, representing the emerging species Dickeya fangzhongdai

BackgroundDickeya sp. strain PA1 is the causal agent of bacterial soft rot in Phalaenopsis, an important indoor orchid in China. PA1 and a few other strains were grouped into a novel species, Dickeya fangzhongdai, and only the orchid-associated strains have been shown to cause soft rot symptoms.MethodsWe constructed the complete PA1 genome sequence and used comparative genomics to explore the differences in genomic features between D. fangzhongdai and other Dickeya species.ResultsPA1 has a 4,979,223-bp circular genome with 4269 predicted protein-coding genes. D. fangzhongdai was phylogenetically similar to Dickeya solani and Dickeya dadantii. The type I to type VI secretion systems (T1SS–T6SS), except for the stt-type T2SS, were identified in D. fangzhongdai. The three phylogenetically similar species varied significantly in terms of their T5SSs and T6SSs, as did the different D. fangzhongdai strains. Genomic island (GI) prediction and synteny analysis (compared to D. fangzhongdai strains) of PA1 also indicated the presence of T5SSs and T6SSs in strain-specific regions. Two typical CRISPR arrays were identified in D. fangzhongdai and in most other Dickeya species, except for D. solani. CRISPR-1 was present in all of these Dickeya species, while the presence of CRISPR-2 varied due to species differentiation. A large polyketide/nonribosomal peptide (PK/NRP) cluster, similar to the zeamine biosynthetic gene cluster in Dickeya zeae rice strains, was discovered in D. fangzhongdai and D. solani. The D. fangzhongdai and D. solani strains might recently have acquired this gene cluster by horizontal gene transfer (HGT).ConclusionsOrchid-associated strains are the typical members of D. fangzhongdai. Genomic analysis of PA1 suggested that this strain presents the genomic characteristics of this novel species. Considering the absence of the stt-type T2SS, the presence of CRISPR loci and the zeamine biosynthetic gene cluster, D. fangzhongdai is likely a transitional form between D. dadantii and D. solani. This is supported by the later acquisition of the zeamine cluster and the loss of CRISPR arrays by D. solani. Comparisons of phylogenetic positions and virulence determinants could be helpful for the effective quarantine and control of this emerging species.

Diversity within the novel Dickeya fangzhongdai sp., isolated from infected orchids, water and pears

Members of the genus Dickeya are plant pathogens that mostly cause soft‐rot diseases. Diversity within the genus has led to the recent description of three novel species (i.e. a mainly clonal D. solani of economic consequence in potatoes, D. aquatica from water samples and D. fangzhongdai isolated from necrotic pear trees in China). However, multilocus sequence analysis (MLSA) has highlighted the occurrence of seven isolates not related to the defined Dickeya species. These include a previously unclassified group of Dickeya strains isolated from monocotyledonous plants, Dickeya sp. S1, Dickeya sp. B16, and Dickeya sp. NCPPB 3274, as well as Dickeya sp. MK7, a strain isolated from water, and misassigned strains D. solani ND14, D. solani M005 and D. chrysanthemi M074. Here, it is reported that these isolates can be classified as D. fangzhongdai by using average nucleotide identity analysis and MLSA. However, variations in phenotypic characterization featuring colony morphology and carbon utilization assays revealed a diversity of bacterial isolates classified as D. fangzhongdai. Based on the results of the genomic analysis, the classification of Dickeya sp. S1, Dickeya sp. B16, Dickeya sp. MK7, Dickeya sp. NCPPB 3274 to D. fangzhongdai is proposed as well as the reclassification of D. solani ND14, D. solani M005 and D. chrysanthemi M074 to D. fangzhongdai.

Dickeyafangzhongdai sp. nov., a plant-pathogenic bacterium isolated from pear trees (Pyrus pyrifolia).

Gram-stain-negative, pectinolytic bacteria were repeatedly isolated from pear trees displaying symptoms of bleeding canker in China. Three strains, JS5T, LN1 and QZH3, had identical 16S rRNA gene sequences that shared 99 % similarity to the type strain of Dickeya dadantii. Phylogenetic analysis of strains JS5T, LN1 and QZH3 with isolates representing all species of the genus Dickeya and related Pectobacterium species supported their affiliation to Dickeya. Multi-locus sequence typing employing concatenated sequences encoding recA, fusA, gapA, purA, rplB, dnaX and the intergenic spacer illustrated a phylogeny which placed strains JS5T, LN1 and QZH3 as a distinct clade, separate from all other species of the genus Dickeya. Average nucleotide identity values obtained in comparison with all species of the genus Dickeya supported the distinctiveness of strain JS5T within the genus Dickeya. Additionally, all three strains were phenotypically distinguished from other species of the genus Dickeya by failing to hydrolyse casein, and by producing acids from (-)-d-arabinose, (+)melibiose, (+)raffinose, mannitol and myo-inositol, but not from 5-keto-d-gluconate or β-gentiobiose. The name Dickeya fangzhongdai sp. nov. is proposed to accommodate these strains; the type strain is JS5T (=CGMCC 1.15464T=DSM 101947T).