Res. Plant Dis > Volume 29(3); 2023 > Article
Park, Ten, Back, Hong, Lee, Han, and Jung: First Report of Melon Soft Rot Disease Caused by Pectobacterium brasiliense in Korea


In May 2021, characteristic soft rot symptoms, including soft, watery, slimy, black rot, wilting, and leaf collapse, were observed on melon plants (Cucumis melo) in Gokseong, Jeollanam-do, Korea. A bacterial strain, designated KNUB-06-21, was isolated from infected plant samples, taxonomically classified, and phylogeneti-cally analyzed using 16S rRNA and housekeeping gene sequencing. Strain KNUB-06-21 was also examined for compound utilization using the API ID 32 GN system and strain KNUB-06-21 was identified as Pectobacterium brasiliense. Subsequent melon stem inoculation studies using strain KNUB-06-21 showed soft rot symptoms similar to field plants. Re-isolated strains shared phenotypic and molecular characteristics with the original P. brasiliense KNUB-06-21 strain. To our knowledge, ours is the first report of P. brasiliense causing melon soft rot disease in Korea.

Melon (Cucumis melo) belongs to the family Cucurbita-ceae, subfamily Cucurbitoideae, tribe Melothrieae, subtribe Cucumerinae, and the genus Cucumis. The fruit exhibits many morphological colors, shapes, flavors, and textures, along with diverse biochemical properties that vary de-pending on region and climate (Kim et al., 2021). In Korea, melons are grown on 3,595 hectares of land, with an annual production of 144,834 tons in 2021 (Food and Agriculture Organization Corporate Statistical Database, 2021). However, globally, bacterial diseases can affect melon production and are highly prevalent. In Serbia, Pectobacterium brasiliense has been identified as the causal agent of melon soft rot, while P. carotovorum subsp. carotovorum was identified as the causal agent of melon soft rot in Korea (Yi and Kim, 1996; Zlatković et al., 2019). As a highly aggressive phytopathogen, P. brasiliense has been reported in several global regions, including Asia, Africa, Europe, Oceania, and North and South America (Charkowski, 2018; Gottsberger and Huss, 2016; Hua et al., 2020; Jaramillo et al., 2017; Naas et al., 2018; Panda et al., 2012; Park et al., 2022, 2023).
In May 2021, typical melon soft rot symptoms, including soft, watery, slimy, black rot, wilting, and collapse were observed in Gokseong, Jeollanam-do, Korea. Affected plants showed soft rot symptoms on the infected tissue surfaces and water-soaked lesions on the infected stems (Fig. 1A, B). Disease incidence was approximately 15% of the melons in the investigated region, as observed in the comprehensive survey.
Fig. 1.
Soft rot symptoms caused by Pectobacterium brasiliense KNUB-06-21 on melon stems. (A) Soft rot symptoms on infected tissue surfaces and water-soaked infected stems. (B) Stem surface turned dark brown.
To isolate pathogens from infected plants, the affected stem surfaces sterilized in 1% hypochlorite solution for 90 sec and rinsed in sterile distilled water. Bacterial isolation was car-ried out on selective crystal violet pectate medium (Hyman et al., 2001) at 26°C for 48 hr. Strains positive for pectolytic cavity formation were selected and purified on nutrient agar (NA; Difco, Franklin Lakes, NJ, USA). A total of 2 isolates with identical colony morphology were obtained from the affected stem. Among these isolates, a single colony, designated as KNUB-06-21, was selected in a random manner for further investigation.
Genomic DNA of strain KNUB-06-21 was extracted using a commercial extraction kit (HiGene Genomic DNA Prep Kit, Biofact, Daejeon, Korea) following manufacturer's instructions. The 16S rRNA gene underwent polymerase chain reaction (PCR) using 9F/1512R primers (Weisburg et al., 1991) and yielded a 1,352 base pair (bp) fragment (GenBank no. LC773684), which after sequencing, was BLAST searched in the National Center for Biotechnology Information (NCBI) database. BLAST analyzes revealed 100% 16S rRNA gene similarity with several P. brasiliense strains (GenBank nos. CP009769, CP020350, MK910250, MN393919, and MN393942).
For accurate identification of the strain KNUB-06-21, three housekeeping genes (dnaX, leuS, and recA) were amplified using PCR protocols and primers as described by Portier et al. (2020). A 521 bp fragment was generated for dnaX gene, 511 bp for leuS gene, and 714 bp for recA gene (GenBank nos. LC773681, LC773682, and LC773683). The highest dnaX gene homology was 100% with P. brasiliense (GenBank no. LC717494). Similarly, the strain KNUB-06-21 exhibited a high level of sequence homology 100% with P. brasiliense (GenBank nos. CP059959, LC717493, and MK517247) for the recA gene and with P. brasiliense (GenBank no. LC717495) for the leuS gene, confirming their close genetic relationship. Con-catenated dnaX, leuS, and recA gene sequences were used in phylogenetic analyses and sequences from closely related neighbors were retrieved from NCBI (Table 1). Using MEGA7, a phylogenetic tree was constructed using the maximum-likelihood method with a bootstrap of 1,000 replicates (Kumar et al., 2016). As depicted in Fig. 2, strain KNUB-06-21 grouped with P. brasiliense clade in the phylogenetic tree, ex-hibiting a bootstrap value of 100%. This result indicates that it is a strain belonging to P. brasiliense.
Fig. 2.
Maximum-likelihood phylogenetic tree, based on concatenated sequences (dnaX+ leuS+ recA), shows the phylogenetic position of strain KNUB-06-21 among the closest members of the Pectobacterium. The isoated strain is shown in bold. KNUB-06-21 is in bold. Bootstrap values (based on 1,000 replications) >70% are shown at branch points. Dickeya solani CFBP 7704 was used as an outgroup. Scale bar=0.020 substitutions/nucleotide position.
Table 1.
Pectobacterium species used in this study for phylogenetic analyses and GenBank accession numbers
Species Strain no. GenBank accession no.
dnaX leuS recA
Pectobacterium aroidearum CFBP1457 MT683925 MT684072 MT684219
Pectobacterium aroidearum CFBP 2573 MT683941 MT684088 MT684235
Pectobacterium aroidearum CFBP 6725 MT684029 MT684176 MT684323
Pectobacterium aroidearum CFBP 8737 MT684054 MT684201 MT684348
Pectobacterium atrosepticum CFBP 1526 T MK516904 MK517048 MK517192
Pectobacterium betavasculorum CFBP 1539 T MK516905 MK517049 MK517193
Pectobacterium brasiliense KNUB-06-21 LC773681 LC773682 LC773683
Pectobacterium brasiliense CFBP 5392 MK516927 MK517071 MK517215
Pectobacterium brasiliense CFBP 6607 MK516954 MK517098 MK517242
Pectobacterium brasiliense CFBP 6615 MK516955 MK517099 MK517243
Pectobacterium brasiliense CFBP 6617 T MK516956 MK517100 MK517244
Pectobacterium cacticida CFBP 3628 T MK516923 MK517067 MK517211
Pectobacterium carotovorum subsp. carotovorum CFBP 1364 MK516896 MK517040 MK517184
Pectobacterium carotovorum subsp. carotovorum CFBP 2046 T MK516909 MK517053 MK517197
Pectobacterium carotovorum subsp. carotovorum CFBP 6071 MK516950 MK517094 MK517238
Pectobacterium carotovorum subsp. carotovorum CFBP 7351 MK516962 MK517106 MK517250
Pectobacterium odoriferum CFBP 1878 T MK516907 MK517051 MK517195
Pectobacterium odoriferum CFBP 3259 MK516920 MK517064 MK517208
Pectobacterium odoriferum CFBP 3297 MK516921 MK517065 MK517209
Pectobacterium odoriferum CFBP 5539 MK516929 MK517073 MK517217
Pectobacterium fontis CFBP 8629 T MK516878 MK517022 MK517166
Pectobacterium parmentieri CFBP 8475 T MK516972 MK517116 MK517260
Pectobacterium peruviense CFBP 5834 MK516935 MK517079 MK517223
Pectobacterium polaris CFBP 1403 MK516898 MK517042 MK517186
Pectobacterium polaris CFBP 6058 MK516945 MK517089 MK517233
Pectobacterium polaris CFBP 7360 MT684038 MT684185 MT684332
Pectobacterium polaris CFBP 8603 T MT684046 MT684193 MT684340
Pectobacterium punjabense CFBP 8604 T MK516877 MK517021 MK517165
Pectobacterium versatile CFBP 1118 MK516888 MK517032 MK517176
Pectobacterium versatile CFBP 2138 MK516912 MK517056 MK517200
Pectobacterium versatile CFBP 6051 T MK516938 MK517082 MK517226
Pectobacterium versatile CFBP 8656 MK516973 MK517117 MK517261
Pectobacterium wasabiae CFBP 3304 T MK516922 MK517066 MK517210
Dickeya solani CFBP 7704 MK516970 MK517114 MK517258

T Type strain. The isolated strain is in bold.

The API ID 32 GN system (Biomérieux, Marcy l'Etoile, France) was used to investigate compound utilization by strain KNUB-06-21 according to manufacturer's instructions. KNUB-06-21 responded positively to N-acetyl-glucosamine, L-alanine, D-glucose, inositol, D-maltose, D-mannitol, D-mel-ibiose, L-rhamnose, salicin, L-serine, and sucrose utilization. However, it responded negatively to L-fucose, L-histidine, 3-hydroxybutyric acid, propionic acid, and D-sorbitol utilization. These results were consistent with the characteristics of the type strain of P. brasiliense (Supplementary Table 1) reported by Portier et al. (2019).
Strain KNUB-06-21 pathogenicity was tested by inoculating the strain onto melon plant stems. Bacterial colonies, grown for 48 hr on NA at 26°C, were picked using sterile toothpicks, inserted into stems at 5 cm above the stem base, and inoculation sites covered with vaseline. Control plants were treated with toothpicks dipped in sterile water. Inoculated plants were maintained in greenhouse conditions (25-30°C and relative humidity=80%). Typical soft rot symptoms appeared at 3-4 days after inoculation and were represented by wilting leaves on stems (Fig. 3A), water-soaked lesions on leaves (Fig. 3B), and detailed examination of a cross-section of an infected melon stem revealed the presence of a hollow stalk (Fig. 3C). In contrast, control plants showed no infectious symptoms (Fig. 3D-F). From infected plants, pathogen was successfully re-isolated and, based on its morphological characteristics and the 16S rRNA, dnaX, leuS, and recA gene sequences, was identified as P. brasiliense (data are not shown).
Fig. 3.
Pectobacterium brasiliense KNUB-06-21 pathogenicity results. (A) Inoculated melon plants show leaf wilting symptoms. (B) Water-soaked lesions on melon plants. (C) Cross-section of an infected melon stem showing a hollow stalk. (D-F) Control melon stems showing no infectious symptoms.
P. brasiliense has been reported as a soft rot pathogen on different crops (Meng et al., 2017; Onkendi and Moleleki, 2014). The isolated strain KNUB-06-21 was identified using 16S rRNA and housekeeping gene sequencing, biochemical analyses, and pathogenicity studies on melon stems. To the best of our knowledge, this is the first report of P. brasiliense causing melon soft rot in Korea. Our findings contrib-ute to an increased understanding of P. brasiliense diversity associated with melon, and highlight the importance of early detection and management strategies preventing pathogen spread. Further research is required to investigate P. brasiliense epidemiology and ecology in melon production areas, and develop effective control measures to minimize economic losses caused by this pathogen.

Electronic Supplementary Material

Supplementary materials are available at Research in Plant Disease website (


Conflicts of Interest

No potential conflict of interest relevant to this article was reported.


This research was supported by a fund (Project Code No. PQ20211B003) by Research of Animal and Plant Quarantine Agency, South Korea.


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