Bacterial Soft Rot Research Articles

Comparative Genomics Insights into a Novel Biocontrol Agent Paenibacillus peoriae Strain ZF390 against Bacterial Soft Rot.

Simple SummaryBacterial soft rot, attributed to Pectobacterium brasiliense infection, has caused destructive impacts and colossal economic losses to China’s agricultural industry. Chemical control, which was ubiquitously used, cannot manage this disease as expected, so biocontrol has been followed with interest to date. In this study, we found a Paenibacillus peoriae strain ZF390 that had a potent control efficiency over cucumber plants against Pectobacterium brasiliense, and the comparative genomic analysis revealed biocontrol mechanisms might be involved in the strain ZF390.Bacterial soft rot, caused by Pectobacterium brasiliense, can infect several economically important horticultural crops. However, the management strategies available to control this disease are limited. Plant-growth-promoting rhizobacteria (PGPR) have been considered to be promising biocontrol agents. With the aim of obtaining a strain suitable for agricultural applications, 161 strains were isolated from the rhizosphere soil of healthy cucumber plants and screened through plate bioassays and greenhouse tests. Paenibacillus peoriae ZF390 exhibited an eminent control effect against soft rot disease and a broad antagonistic activity spectrum in vitro. Moreover, ZF390 showed good activities of cellulase, protease, and phosphatase and a tolerance of heavy metal. Whole-genome sequencing was performed and annotated to explore the underlying biocontrol mechanisms. Strain ZF390 consists of one 6,193,667 bp circular chromosome and three plasmids. Comparative genome analysis revealed that ZF390 involves ten gene clusters responsible for secondary metabolite antibiotic synthesis, matching its excellent biocontrol activity. Plenty of genes related to plant growth promotion, biofilm formation, and induced systemic resistance were mined to reveal the biocontrol mechanisms that might consist in strain ZF390. Overall, these findings suggest that strain ZF390 could be a potential biocontrol agent in bacterial-soft-rot management, as well as a source of antimicrobial mechanisms for further exploitation.

Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics.

Bacterial soft rot is a devastating disease for a wide range of crops, vegetables, and ornamental plants including konjac (Amorphophallus konjac). However, the pangenome and genomic plasticity of the konjac soft rot pathogens is little explored. In this study, we reported the complete genome sequences of 11 bacterial isolates that can cause typical soft rot symptoms in konjac by in vitro and in vivo pathogenicity tests. Based on in silico DNA–DNA hybridization, average nucleotide identity and phylogenomic analysis, all 11 isolates were determined to be Pectobacterium aroidearum. In addition, synteny analysis of these genomes revealed considerable chromosomal inversions, one of which is triggered by homologous recombination of ribose operon. Pangenome analysis and COG enrichment analysis showed that the pangenome of P. aroidearum is open and that accessory genes are enriched in replication, recombination, and repair. Variations in type IV secretion system and type VI secretion system were found, while plant cell wall degrading enzymes were conserved. Furthermore, sequence analyses also provided evidence for the presence of a type V secretion system in Pectobacterium. These findings advance our understanding of the pathogenicity determinants, genomic plasticity, and evolution of P. aroidearum.

First Report of Bacterial Soft Rot Caused by Pantoea agglomerans on Chinese yam (Dioscorea opposita) in China.

Chinese yam (Dioscorea opposita Thunb.), which belongs to the family of Dioscorea, is widely naturalized throughout China, due to its high economic and medicinal value. Since 2019, water-soaked lesions were frequently observed in the underground tubers of Chinese yam located in Xinyang City, Henan Province. To identify the causal agent, ten pieces of tissue from the underground tubers with disease symptoms were collected. Those infected tissues (5×5 mm) were crushed in 500 μL sterilized water after surface sterilization and streaked onto Luria-Bertani agar plates. Pale-yellowish, rod-shaped, slimy single bacterial colonies with smooth margin were observed after 24 hours of incubation, and three bacterial colonies (named CY-1, CY-2 and CY-3) were randomly selected for further biochemical and molecular characterization. These bacteria were gram-negative with the cell length of 1.0 to 3.0 μm, width of 0.5 to 1.0 μm, and with peritrichous flagella. Subsequently, the bacteria were biochemically analyzed through BIOLOG (Hayward, CA) and identified as Pantoea agglomerans with 99% probability. Furthermore, the phylogenetic analysis results based on 16S rDNA, DNA gyrase subunit B (gyrB), and RNA polymerase sigma factor (rpoD) showed these three isolates were most closely related to P. agglomerans. The sequence of 16S rDNA, gyrB and rpoD of each strain was submitted to GenBank with the accession numbers MZ541065 MZ541066 and MZ541067 for 16S rDNA; MZ669846, MZ669847 and MZ669848 for gyrB; MZ669849, MZ669850 and MZ669851 for ropD. Pathogenicity test was performed to complete Koch's postulates. Tubers of Chinese yam were wounded by sterile needle and inoculated with 500 μL 108 CFU/mL bacterial suspension. Sterilized water was used as a control. Five pots were inoculated for each isolate. Water-soaked lesions appeared after five days incubation at 25°C in a biochemical incubator and no lesions were observed on the control. Bacteria re-isolated from the lesions were similar in phenotypic and molecular characteristics to the original isolates. In brief, based on colony morphology, biochemical tests, characteristic sequence analysis, and pathogenicity verification, the pathogen responsible for the soft rot of Chinese yam in Henan Province was identified as P. agglomerans. In China, P. agglomerans has been reported to associate with bacterial soft rot on Chinese cabbage (Guo et al., 2020). To our knowledge, this work is the first report of bacterial rot caused by P. agglomerans on Chinese yam.

Isolation and Genome Analysis of Pectobacterium colocasium sp. nov. and Pectobacterium aroidearum, Two New Pathogens of Taro.

Bacterial soft rot is one of the most destructive diseases of taro (Colocasia esculenta) worldwide. In recent years, frequent outbreaks of soft rot disease have seriously affected taro production and became a major constraint to the development of taro planting in China. However, little is known about the causal agents of this disease, and the only reported pathogens are two Dickeya species and P. carotovorum. In this study, we report taro soft rot caused by two novel Pectobacterium strains, LJ1 and LJ2, isolated from taro corms in Ruyuan County, Shaoguan City, Guangdong Province, China. We showed that LJ1 and LJ2 fulfill Koch’s postulates for taro soft rot. The two pathogens can infect taro both individually and simultaneously, and neither synergistic nor antagonistic interaction was observed between the two pathogens. Genome sequencing of the two strains indicated that LJ1 represents a novel species of the genus Pectobacterium, for which the name “Pectobacterium colocasium sp. nov.” is proposed, while LJ2 belongs to Pectobacterium aroidearum. Pan-genome analysis revealed multiple pathogenicity-related differences between LJ1, LJ2, and other Pectobacterium species, including unique virulence factors, variation in the copy number and organization of Type III, IV, and VI secretion systems, and differential production of plant cell wall degrading enzymes. This study identifies two new soft rot Pectobacteriaceae (SRP) pathogens causing taro soft rot in China, reports a new case of co-infection of plant pathogens, and provides valuable resources for further investigation of the pathogenic mechanisms of SRP.

The Effect of Some Wild Grown Plant Extracts and Essential Oils on Pectobacterium betavasculorum: The Causative Agent of Bacterial Soft Rot and Vascular Wilt of Sugar Beet.

The bacterial soft rot and vascular wilt of sugar beet are the major diseases of sugar crops globally induced by Pectobacterium betavasculorum and P. carotovorum subsp. carotovorum (Pcc). The control of this bacterial disease is a severe problem, and only a few copper-based chemical bactericides are available for this disease. Because of the limitations of chemicals to control plant bacterial pathogens, the essential oils and extracts have been considered one of the best alternative strategies for their control. In this study, twenty-seven essential oils and twenty-nine plant extracts were extracted and evaluated for their antibacterial activities against Pectobacterium betavasculorum isolate C3, using the agar diffusion method at 0.01%, 0.1%, and 100% (v/v). Pure Pimpinella anisum L. oil exhibited the most anti-bacterial activity among three different concentrations of essential oils and extracts, followed by Thymus vulgaris L. oil and Rosa multiflora Thunb. extract. The efficacy of effective essential oils and extracts on Ic1 cultivar of sugar beet seeds germination and seedling growth in vivo also were tested. The seed germination of the Ic1 cultivar was inhibited at all the concentrations of essential oils used. Only extracts of Rosa multiflora Thunb., Brassica oleracea L., Lactuca serriola L., Salvia rosmarinus Spenn., Syzygium aromaticum (L.) Merr. and L.M.Perry, Eucalyptus globulus Labill., and essential oils of Ocmium basilicum L., Pimpinella anisum L., and Mentha× piperita L.L. in 0.1% concentration had no inhibition on seed germination and could improve seedling growth. This is the first report of the antibacterial activity of essential oils and extracts on Pectobacterium betavasculorum.

Isolation, identification, and pathogenicity of Lelliottia amnigena causing soft rot of potato tuber in China

Potato (Solanum tuberosum L.) is regarded as the fourth most important food crop because of its economic and nutritional benefits. This crop suffers significant annual losses due to a variety of phytopathogens. Bacterial soft rot disease is one of the most serious diseases that cause significant losses in potato yield all over the world. Therefore, identification of a soft rot pathogen is critical for easy control, as each pathogen has distinct ways of being controlled. Lelliottia amnigena is a subgroup of the genus Enterobacter with many species associated with crop plants, making its classification difficult and complex. Therefore, this study focused on the isolation and identification of a newly L. amnigena from rotten potato tuber obtained from the field after harvest, Lanzhou City, China. Four strains designated as PC2, PC3, PC4 and PC5 were isolated from the same rotting potato tuber. Pathogenicity test showed that strain PC3 induced soft rot symptoms on healthy potato tubers. Koch's postulates were confirmed by re-isolating the strain PC3 in the inoculated tubers. Strain PC3 showed a convex, oval and smooth colony, measuring 0.9–1.3 1.8–3.6 μm under the microscopic observation. Phylogenetic analysis based on 16S rRNA, rpoB and atpD genes showed that strain PC3 species was 99.44%, 97.24%, and 100%, closely related to L. amnigena with accession numbers 240-a-etp (MN208158.1), FDAARGOS (CP023529.1) and R-6 (MN658356.1), respectively. The bacterial strain (PC3) was deposited in the Genbank with the accession number SUB10508072 PC3 OK447935. To the best of our knowledge, this is the first report of L. amnigena causing soft rot on potato tubers in China.

Genomic Comparisons and Phenotypic Diversity of Dickeya zeae Strains Causing Bacterial Soft Rot of Banana in China.

Bacterial soft rot of banana, caused by Dickeya zeae, is spreading rapidly in important banana growing areas in China and seriously threatens banana production. In this study, we sequenced the high-quality complete genomes of three typical banana strains, MS1 (size: 4,831,702-bp; genome coverages: 538x), MS_2014 (size: 4,740,000-bp; genome coverages: 586x) and MS_2018 (size: 4,787,201-bp; genome coverages: 583x), isolated in 2009, 2014, and 2018, respectively. To determine their genomic and phenotypic diversity with respect to their hosts of origin, they were compared with other D. zeae strains, including another representative banana strain MS2 from China. The sequenced strains were similar in utilization of carbon source and chemical substrates, and general genomic features of GC content, and tRNA and rRNA regions. They were also conserved in most virulence determinants, including gene-encoding secretion systems, plant cell wall degrading enzymes, and exopolysaccharides. We further explored their genomic diversity in the predicted genomic islands (GIs). These GIs were rich in integrases and transposases, where some genomic dissimilarity was observed in the flagellar gene cluster and several secondary metabolite gene clusters. Different constituents of core biosynthetic modules were found within the bacteriocin and aryl polyene (APE) pigment gene clusters, and the strains from banana showed different phenotypes with respect to antibiosis effects and colony pigmentation. Additionally, clustered regularly interspaced short palindromic repeat (CRISPR) and prophage elements, such as type I-F and III-A CRISPR arrays and an intact prophage of MS1-P5, contributed to bacterial diversity. Phylogenetic tree analysis and genome-genome nucleotide comparison confirmed the genomic divergence among the strains isolated from banana. Considering these characteristics, MS2 and MS_2014 probably diverged later than MS1, while MS_2018 was different and more similar to foreign strains isolated from other hosts in several characteristics. Strain MS_2018 caused severe symptoms on banana varieties previously considered moderately resistant or moderately susceptible, including varieties of Cavendish (Musa AAA) and Plantain (Musa ABB). Our study of genomic and phenotypic diversity raises public attention to the risk of spreading new pathogenic variants within banana growing regions and supports development of predictive strategies for disease control.

Dickeya Manipulates Multiple Quorum Sensing Systems to Control Virulence and Collective Behaviors.

Soft rot Pectobacteriaceae (SRP), typical of Pectobacterium and Dickeya, are a class of Gram-negative bacterial pathogens that cause devastating diseases on a wide range of crops and ornamental plants worldwide. Quorum sensing (QS) is a cell-cell communication mechanism regulating the expression of specific genes by releasing QS signal molecules associated with cell density, in most cases, involving in the vital process of virulence and infection. In recent years, several types of QS systems have been uncovered in Dickeya pathogens to control diverse biological behaviors, especially bacterial pathogenicity and transkingdom interactions. This review depicts an integral QS regulation network of Dickeya, elaborates in detail the regulation of specific QS system on different biological functions of the pathogens and hosts, aiming at providing a systematic overview of Dickeya pathogenicity and interactions with hosts, and, finally, expects the future prospective of effectively controlling the bacterial soft rot disease caused by Dickeya by quenching the key QS signal.

Genomic and Functional Dissections of Dickeya zeae Shed Light on the Role of Type III Secretion System and Cell Wall-Degrading Enzymes to Host Range and Virulence.

ABSTRACTDickeya zeae is a worldwide destructive pathogen that causes soft rot diseases on various hosts such as rice, maize, banana, and potato. The strain JZL7 we recently isolated from clivia represents the first monocot-specific D. zeae and also has reduced pathogenicity compared to that of other D. zeae strains (e.g., EC1 and MS2). To elucidate the molecular mechanisms underlying its more restricted host range and weakened pathogenicity, we sequenced the complete genome of JZL7 and performed comparative genomic and functional analyses of JZL7 and other D. zeae strains. We found that, while having the largest genome among D. zeae strains, JZL7 lost almost the entire type III secretion system (T3SS), which is a key component of the virulence suite of many bacterial pathogens. Importantly, the deletion of T3SS in MS2 substantially diminished the expression of most type III secreted effectors (T3SEs) and MS2’s pathogenicity on both dicots and monocots. Moreover, although JZL7 and MS2 share almost the same repertoire of cell wall-degrading enzymes (CWDEs), we found broad reduction in the production of CWDEs and expression levels of CWDE genes in JZL7. The lower expression of CWDEs, pectin lyases in particular, would probably make it difficult for JZL7 to break down the cell wall of dicots, which is rich in pectin. Together, our results suggest that the loss of T3SS and reduced CWDE activity together might have contributed to the host specificity and virulence of JZL7. Our findings also shed light on the pathogenic mechanism of Dickeya and other soft rot Pectobacteriaceae species in general.IMPORTANCE Dickeya zeae is an important, aggressive bacterial phytopathogen that can cause severe diseases in many crops and ornamental plants, thus leading to substantial economic losses. Strains from different sources showed significant diversity in their natural hosts, suggesting complicated evolution history and pathogenic mechanisms. However, molecular mechanisms that cause the differences in the host range of D. zeae strains remain poorly understood. This study carried out genomic and functional dissections of JZL7, a D. zeae strain with restricted host range, and revealed type III secretion system (T3SS) and cell wall-degrading enzymes (CWDEs) as two major factors contributing to the host range and virulence of D. zeae, which will provide a valuable reference for the exploration of pathogenic mechanisms in other bacteria and present new insights for the control of bacterial soft rot diseases on crops.

Dickeya solani, Pectobacterium atrosepticum and Pseudomonas asplenii: causal agents of bacterial soft rot in cyclamen plants (Cyclamen persicum Mill.) in Colombia

Cyclamen (Cyclamen persicum Mill.) is an ornamental plant affected by various phytosanitary issues including bacterial soft rots, which cause crop losses of 20% worldwide. In Colombia, however, the symptoms of bacterial soft rots are not well described and the causal agents are unknown. This study aimed to characterize the bacterial soft rot disease according to its symptoms, and identify its causal agents at the species level. For this purpose, we visited nurseries in the municipality of San Antonio del Tequendama, Colombia, and selected diseased plants to describe symptoms, and to isolate and characterize pathogens using morphological, biochemical, and molecular methods. Soft rotting activity in potato tubers and pathogenicity in cyclamen plants also was evaluated. Six symptoms were found to be associated with the disease, namely: wilt, soft corm, bacterial exudates on corms, root rot, soft rot and necrotic soft rot on petioles and peduncles. Of 47 isolates, seven were pathogenic: one from the soft corms; two from petioles with soft rot; two from petioles with necrotic soft rot; and two from root rot. A multiple correspondence analysis clustered isolates in the genera Pseudomonas, Dickeya and Pectobacterium based on the morphological, biochemical, and pathogenic characteristics. A multi-locus analysis (MLSA) based on sequencing of the 16S rDNA region and housekeeping genes (gapA, icdA, mdh, pgi, rpoB and rpoD) confirmed the bacterial species Pseudomonas asplenii, Dickeya solani and Pectobacterium atrosepticum as the causal agents of cyclamen bacterial soft rot in Colombia.

Dickeya dadantii (bacterial wilt and soft rot of ornamentals and potato)

Dickeya dadantii (bacterial wilt and soft rot of ornamentals and potato)

Dickeya dadantii (bacterial wilt and soft rot of ornamentals and potato)

This datasheet on Dickeya dadantii covers Identity, Distribution, Dispersal, Hosts/Species Affected, Diagnosis, Biology & Ecology, Seedborne Aspects, Impacts, Prevention/Control, Further Information.

Enhancing shelf-life of carrot (Daucus carota) during post-harvest processing

The study was carried to find out the effect of physical, chemical and biological treatments on carrot (Daucus carota L.) for enhancing shelf-life during post-harvest processing at Department. of Food Process Engineering, Agricultural Engineering College & Research Institute, Tamil Nadu Agricultural University, Coimbatore. The most significant changes in post-harvest quality were weight loss, bitterness, bacterial deterioration, rotating and sprouting. Losses in carrots are due to Sclerotinia rot Botrytis rot, bacterial soft rot (Erwinia sp.) and sour rot (Geotrichum sp.). The physical, chemical, biological and combination of these methods were studied. Among the different methods, combination of chlorination and ozonization during washing followed by application of Lactobacillus plantarum 020 at the rate of 10 ml/litre of wash water was more effective. Carrots processed with the treatment had a shelf-life of six days under normal room temperature, whereas shelf-life of untreated carrots was two days under normal room temperature

Use of X-ray Mutagenesis to Increase Genetic Diversity of Zantedeschia aethiopica for Early Flowering, Improved Tolerance to Bacterial Soft Rot, and Higher Yield

The development of new cultivars is important for the profitability of the floriculture industry. There is a limited number of cultivars of Zantedeschia aethiopica, an iconic ornamental cut flower, garden plant, and potted plant, because of the incompatibility of interspecific crossings within the genus. Most present-day varieties are the result of spontaneous mutations or classical breeding within the species, followed by a long selection process. Here, Z. aethiopica mutants were generated by treating seeds with 100 Gy of X-ray radiation. The resulting putative mutants were selected based on particular flowering parameters and compared to nonirradiated, control plants. Over two growing seasons, characteristics such as early flowering, flower size and shape, yield, and response to soft-rot disease were monitored, and considerable variation was observed among the mutated lines. Out of 319 mutants, 20 lines were selected based on their phenotypes and then propagated and further analyzed. Within this group, only two phenotypes displayed at least five improved flowering properties under natural Mediterranean conditions. The rest displayed two to four desired combinations of flowering traits, some with great commercial potential.

Antagonistic activity of endophytic actinobacteria from native potatoes (Solanum tuberosum subsp. tuberosum L.) against Pectobacterium carotovorum subsp. carotovorum and Pectobacterium atrosepticum

BackgroundThe native potatoes (Solanum tuberosum subsp. tuberosum L.) grown in Chile (Chiloé) represent a new, unexplored source of endophytes to find potential biological control agents for the prevention of bacterial diseases, like blackleg and soft rot, in potato crops.ResultThe objective of this study was the selection of endophytic actinobacteria from native potatoes for antagonistic activity against Pectobacterium carotovorum subsp. carotovorum and Pectobacterium atrosepticum, and their potential to suppress tissue maceration symptoms in potato tubers. This potential was determined through the quorum quenching activity using a Chromobacterium violaceaum ATCC 12472 Wild type (WT) bioassay and its colonization behavior of the potato plant root system (S. tuberosum) by means of the Double labeling of oligonucleotide probes for fluorescence in situ hybridization (DOPE-FISH) targeting technique. The results showed that although Streptomyces sp. TP199 and Streptomyces sp. A2R31 were able to inhibit the growth of the pathogens, only the Streptomyces sp. TP199 isolate inhibited Pectobacterium sp. growth and diminished tissue maceration in tubers (p ≤ 0.05). Streptomyces sp. TP199 had metal-dependent acyl homoserine lactones (AHL) quorum quenching activity in vitro and was able to colonize the root endosphere 10 days after inoculation.ConclusionsWe concluded that native potatoes from southern Chile possess endophyte actinobacteria that are potential agents for the disease management of soft rot and blackleg.

First Report of Bacterial Soft Rot Disease on Taro Caused by Dickeya fangzhongdai in China.

Taro [Colocasia esculenta (L.) Schott.] is an important root crop in the world with great economic value. In recent years, outbreaks of soft rot were observed on taro plants in several plantation areas located in Shaoguan, Guangdong Province, China (25°7'57" N, 113°19'5" E). Root tubers of taro (Paodan variety) infected by soft rot had water-soaked lesions with a dark brown-black margin including a rotten smell, they also had internal rot that was also found in root tubers with no external symptoms. In some areas, the incidence of soft rot can reach up to 30%. To isolate the causal agent, ten pieces of taro root tubers with typical symptoms were surface-sterilized with 75% ethanol and 0.1% HgCl2 solution and then washed thrice with sterile water. The tuber slices were soaked in 50 ml sterile water and shaken at 28°C, 200 rpm for 2 h, and 100 µl was streaked onto the modified Yeast Extract Beef (YEB) agar medium (1% peptone, 0.5% yeast extract, 0.5% sucrose, 0.5% NaCl, 1 Mmol/L MgSO4•7H2O, 1.5% agar, pH 7.0) plates (Zhou et al. 2011) and incubated at 28°C for 24 h. Single colonies grown on YEB were selected for preliminary inoculation onto healthy taro (Paodan variety) slices. Two of the Gram-negative bacteria, named as ZXC1 and MPC2, developed symptoms consistent in rotted decay inside the root tubers after incubation for 24h at 30°C. ZXC1 and MPC2 were biochemically profiled using a Biolog Gen III MicroPlate (Microlog 3, 5.2) (Shen et al. 2019) and resulted Dickeya sp. (SIM 0.856 and 0.704). To determine the species of the Dickeya isolates, 16S rRNA sequences were amplified by primers 27F and 1492R (Hauben et al. 1998). Housekeeping genes including gyrB, atpD, rpoB, and infB were also amplified using degenerate primers (Brady et al. 2008). Results from the BLASTn analysis of the 16S rRNA (GenBank accession numbers MN853405, MN853406), gyrB (GenBank accession numbers MN866299, MN866303), atpD (GenBank accession numbers MN866298, MN866302), rpoB (GenBank accession numbers MN866301, MN866305), and infB (GenBank accession numbers MN866300, MN866304) genes in the isolates ZXC1 and MPC2 showed 99% identities to those of the previously reported D. fangzhongdai isolates from Phalaenopsis (Zhang et al. 2018). Multilocus sequence analysis (MLSA) by MEGA 7.0 performed with four housekeeping genes (gyrB, atpD, rpoB, infB) showed that they clustered with D. fangzhongdai isolates. Analyses using scanning and transmission electron microscopy showed that ZXC1 and MPC2 bacteria were rod-shaped, 0.5-1.0 μm × 1.0-3.0 µm, with peritrichous flagella. Pathogenicity tests were performed thrice using surface-sterilized 2-month-old taro seedlings (Paodan variety). Six individual seedlings were inoculated using a sterile syringe with ten microliters of bacterial suspension (108 CFU/ml) in Tris buffer (0.1 mol/L Tris and 0.1 mol/L HCl, pH 7.4). Taro seedlings injected with sterile Tris buffer were used as the negative control. These taro seedlings were grown in the greenhouse (30 ± 2°C, 90 ± 5% relative humidity). At the 25th day post inoculation, soft rot symptoms were observed in inoculated taro, while all control taro plants remained symptom-free. Small and pale yellow with irregular margins colonies consistent with morphological characteristics of those of D. fangzhongdai were re-isolated from symptomatic taro tubers and the housekeeping genes presence was verified by sequencing as described above, fulfilling Koch's postulates. D. fangzhongdai is a newly emerging bacterial pathogen, which causes bleeding cankers in pear trees (Tian et al. 2016), and soft rot of Phalaenopsis (Zhang et al. 2018). This is the first report of D. fangzhongdai causing soft rot disease in taro. Considering the high incidence of soft rot, this pathogen might pose a significant threat to taro and other economically important crops. Therefore, further researches are needed to investigate host range of the pathogen and develop appropriate integrated management to contain this disease spreading.

Emergence of bacterial soft rot in calla lily caused by Pectobacterium aroidearum in China

Bacterial soft rot is a destructive disease affecting calla lily production, and it is mainly caused by Pectobacterium carotovorum (Pc). In 2019, this destructive disease was observed in the Shandong and Jiangsu Provinces of China and resulted in serious economic losses for commercial greenhouse producers of ornamental plants. The disease symptoms on leaves and stems were yellow and dark brown patches, and then water-soaked lesions that turned to wet rot occurred on the stems. In total, we obtained twenty-eight calla lily soft rot samples collected from Shandong and Jiangsu. Fifteen colonies on LB medium were milky white, nearly round, with a smooth surface and neat edges. The soft rot symptoms in calla lily caused by artificial inoculation were the same as the natural symptoms in the field. Based on the phenotypic properties determined by morphological, biochemical and physiological analyses, 16S ribosomal DNA gene sequence analysis, and multilocus sequence analysis, the pathogen was identified as P. aroidearum. In addition, all P. aroidearum strains exhibited high virulence and a wide host range on monocotyledonous and dicotyledonous plants. This study is the first official report of P. aroidearum causing calla lily soft rot in China, and the results contribute to a better understanding of the disease.

Occurrence, Characteristics, and PCR-Based Detection of Pectobacterium polaris Causing Soft Rot of Chinese Cabbage in China.

Bacterial soft rot is an important disease of Chinese cabbage (Brassica rapa L. ssp. pekinensis) in China and many other countries. Four pectinolytic bacterial strains (WBC1, WBC6, WBC9, and WBC11) were isolated from soft-rotted Chinese cabbage in Beijing, China. Based on 16S rDNA and pmrA gene sequence analyses, multilocus sequence analysis (MLSA), and genomic average nucleotide identity (ANI) analysis, these four strains were identified as Pectobacterium polaris. This species, previously reported from potato in countries not including China, is a new soft rot pathogen of Chinese cabbage in China. Biochemical characteristics of these P. polaris strains tested by Biolog were mostly consistent with those of P. polaris NIBIO1006T. Their pathogenicity on Chinese cabbage is temperature dependent, with all four strains as well as the type strain exhibiting high pathogenicity at 23°C and 28°C. These four strains infected Lactuca sativa, Daucus carota, Solanum tuberosum, and Capsicum annuum by artificial inoculation. Specific polymerase chain reaction (PCR) and quantitative PCR (qPCR) primers for P. polaris were developed on the basis of its specific gene sequences (determined by genome comparison methods). Both PCR and qPCR detected not only genomic DNA of P. polaris but also the pathogen from diseased plant tissues even before external symptoms appeared. Their detection sensitivities were as low as 1 pg and 100 pg genomic DNA of P. polaris, respectively. To our knowledge, this study is the first to both report the emergence of P. polaris on Chinese cabbage in China and provide rapid and accurate PCR/qPCR-based detection systems specific for P. polaris.

Complete Genome Sequence of Dickeya dadantii subsp. dieffenbachiae Strain S3-1, Isolated from a White-Flowered Calla Lily in Taiwan.

ABSTRACTErwinia chrysanthemi S3-1 is a bacterial soft rot pathogen of the white-flowered calla lily. The complete genome sequence of the strain was determined and used to reclassify the strain as Dickeya dadantii subsp. dieffenbachiae. The sequence will be useful to study plant host-driven speciation in strains of D. dadantii.

Species of Dickeya and Pectobacterium Isolated during an Outbreak of Blackleg and Soft Rot of Potato in Northeastern and North Central United States.

An outbreak of bacterial soft rot and blackleg of potato has occurred since 2014 with the epicenter being in the northeastern region of the United States. Multiple species of Pectobacterium and Dickeya are causal agents, resulting in losses to commercial and seed potato production over the past decade in the Northeastern and North Central United States. To clarify the pathogen present at the outset of the epidemic in 2015 and 2016, a phylogenetic study was made of 121 pectolytic soft rot bacteria isolated from symptomatic potato; also included were 27 type strains of Dickeya and Pectobacterium species, and 47 historic reference strains. Phylogenetic trees constructed based on multilocus sequence alignments of concatenated dnaJ, dnaX and gyrB fragments revealed the epidemic isolates to cluster with type strains of D. chrysanthemi, D. dianthicola, D. dadantii, P. atrosepticum, P. brasiliense, P. carotovorum, P. parmentieri, P. polaris, P. punjabense, and P. versatile. Genetic diversity within D. dianthicola strains was low, with one sequence type (ST1) identified in 17 of 19 strains. Pectobacterium parmentieri was more diverse, with ten sequence types detected among 37 of the 2015–2016 strains. This study can aid in monitoring future shifts in potato soft rot pathogens within the U.S. and inform strategies for disease management.