Interaction between Dickeya dianthicola and Pectobacterium parmentieri in Potato Infection under Field Conditions

Dickeya fangzhongdai was prevalent and caused taro soft rot when coexisting with the Pectobacterium complex, with a preference for Araceae plants

Bacterial soft rot caused by coinfection with Dickeya spp. and Pectobacterium spp. in hosts can cause successive changes in fields, and it is difficult to prevent the spread of and control the infection. Pectobacterium spp. are prevalent in the growing areas of tuberous crops, including taro and potato. Recently, Dickeya fangzhongdai has emerged as a virulent pathogen in taro. To determine the prevalence status of the causal agents and evaluate the potential spreading risks of D. fangzhongdai, screening and taxonomic classification were performed on phytopathogenic bacteria collected from different taro-growing areas in Guangdong Province, China, and biological and genomic characteristics were further compared among typical strains from all defined species. The causative agents were verified to be phytobacterial strains of D. fangzhongdai, Pectobacterium aroidearum and Pectobacterium colocasium. P. aroidearum and P. colocasium were found to form a complex preferring Araceae plants and show intensive genomic differentiation, indicating their ancestor had adapted to taro a long time prior. Compared with Pectobacterium spp., D. fangzhongdai was more virulent to taro corms under conditions of exogenous infection and more adaptable at elevated temperatures. D. fangzhongdai strains isolated from taro possessed genomic components of additional T4SSs, which were accompanied by additional copies of the hcp-vgrG genes of the T6SS, and these contributed to the expansion of their genomes. More gene clusters encoding secondary metabolites were found within the D. fangzhongdai strains than within the Pectobacterium complex; interestingly, distinct gene clusters encoding zeamine and arylpolyene were both most similar to those in D. solani that caused potato soft rot. These comparisons provided genomic evidences for that the newly emerging pathogen was potentially equipped to compete with other pathogens. Diagnostic qPCR verified that D. fangzhongdai was prevalent in most of the taro-growing areas and coexisted with the Pectobacterium complex, while the plants enriching D. fangzhongdai were frequently symptomatic at developing corms and adjacent pseudostems and caused severe symptoms. Thus, the emerging need for intensive monitoring on D. fangzhongdai to prevent it from spreading to other taro-growing areas and to other tuberous crops like potato; the adjustment of control strategies based on different pathopoiesis characteristics is recommended.

Surviving the Potato Stems: Differences in Genes Required for Fitness by Dickeya dadantii and Dickeya dianthicola

Bacteria belonging to the genus Dickeya cause blackleg and soft rot symptoms on many plant hosts, including potato. Although there is considerable knowledge about the genetic determinants that allow Dickeya to colonize host plants, as well as the genes that contribute to virulence, much is still unknown. To identify the genes important for fitness in potato stems, we constructed and evaluated randomly barcoded transposon mutant (RB-TnSeq) libraries of Dickeya dadantii and Dickeya dianthicola. We identified 169 and 157 genes important for growth in D. dadantii and D. dianthicola in stems, respectively. This included genes related to metabolic pathways, chemotaxis and motility, transcriptional regulation, transport across membranes, membrane biogenesis, detoxification mechanisms, and virulence-related genes, including a potential virulence cluster srfABC, c-di-GMP modulating genes, and pectin degradation genes. When we compared the results of the stem assay with other datasets, we identified genes important for growth in stems versus tubers and in vitro conditions. Additionally, our data showed differences in fitness determinants for D. dadantii and D. dianthicola. These data provide important insights into the mechanisms used by Dickeya when interacting with and colonizing plants and thus might provide targets for management.

Impact of Homologous Recombination on Core Genome Evolution and Host Adaptation of Pectobacterium parmentieri

Homologous recombination is a major force mechanism driving bacterial evolution, host adaptability, and acquisition of novel virulence traits. Pectobacterium parmentieri is a plant bacterial pathogen distributed worldwide, primarily affecting potatoes, by causing soft rot and blackleg diseases. The goal of this investigation was to understand the impact of homologous recombination on the genomic evolution of P. parmentieri. Analysis of P. parmentieri genomes using Roary revealed a dynamic pan-genome with 3,742 core genes and over 55% accessory genome variability. Bayesian population structure analysis identified 7 lineages, indicating species heterogeneity. ClonalFrameML analysis displayed 5,125 recombination events, with the lineage 4 exhibiting the highest events. fastGEAR analysis identified 486 ancestral and 941 recent recombination events ranging from 43 bp to 119 kb and 36 bp to 13.96 kb, respectively, suggesting ongoing adaptation. Notably, 11% (412 genes) of the core genome underwent recent recombination, with lineage 1 as the main donor. The prevalence of recent recombination (double compared to ancient) events implies continuous adaptation, possibly driven by global potato trade. Recombination events were found in genes involved in vital cellular processes (DNA replication, DNA repair, RNA processing, homeostasis, and metabolism), pathogenicity determinants (type secretion systems, cell-wall degrading enzymes, iron scavengers, lipopolysaccharides (LPS), flagellum, etc.), antimicrobial compounds (phenazine and colicin) and even CRISPR-Cas genes. Overall, these results emphasize the potential role of homologous recombination in P. parmentieri's evolutionary dynamics, influencing host colonization, pathogenicity, adaptive immunity, and ecological fitness.

Soft rot pathogen Dickeya dadantii 3937 produces tailocins resembling the tails of Peduovirus P2

Tailocins are nanomolecular machines with bactericidal activity. They are produced by bacteria to contribute to fitness in mixed communities, and hence, they play a critical role in their ecology in a variety of habitats. Here, we characterized the new tailocin produced by Dickeya dadantii strain 3937, a well-characterized member of plant pathogenic Soft Rot Pectobacteriaceae (SRP). Tailocins induced in D. dadantii were ca. 166 nm long tubes surrounded by contractive sheaths with baseplates having tail fibers at one end. A 22-kb genomic cluster involved in their synthesis and having high homology to the cluster coding for the tail of the Peduovirus P2 was identified. The D. dadantii tailocins, termed dickeyocins P2D1 (phage P2-like dickeyocin 1), were resistant to inactivation by pH (3.5-12), temperature (4-50°C), and elevated osmolarity (NaCl concentration: 0.01-1 M). P2D1 could kill a variety of different Dickeya spp. but not any strain of Pectobacterium spp. tested and were not toxic to Caenorhabditis elegans.

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.

Natural Infections of Potato Plants Grown from Minitubers with Blackleg-Causing Soft Rot Pectobacteriaceae

Information on the infection incidence of blackleg-causing soft rot Pectobacteriaceae (BL-SRP) in potato crops grown from minitubers (PB1-crop) and the distribution of BL-SRP in individual plants was collected during a two-year survey conducted at five potato growers located in the Netherlands. In the last weeks before haulm destruction, leaves, stems, and tubers of 100 or 200 plants were analyzed separately for the presence of Pectobacterium parmentieri, P. brasiliense, P. atrosepticum, and Dickeya spp. Extracted plant parts enriched for BL-SRP were analyzed with TaqMan assays specific for the detection of blackleg-causing BL-SRP. In 2019, low incidences of P. parmentieri (1-6%) in leaves were found at four growing sites. At one farm, reactions were detected in TaqMan assays for D. zeae and D. chrysanthemi in leaves. In 2020, the crops of two growers were largely free from BL-SRP. At one farm, a high infection incidence (21%) was found for D. fangzhongdai in tubers. The isolated pathogen was able to cause potato blackleg. At two other farms, high infection incidences in tubers were found with P. brasiliense (35-39%) and P. parmentieri (12-19%), whereas the incidence of P. brasiliense in leaves was also high (8%). In conclusion, high infection incidences with BL-SRP in potatoes can be found in a PB1 crop at the end of the growing season. Infections in individual plants were found either in tubers or in leaves. The potential sources of initial infection are discussed.

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.

Genome-Wide Identification of Genes Important for Growth of Dickeya dadantii and Dickeya dianthicola in Potato (Solanum tuberosum) Tubers

Dickeya species are causal agents of soft rot diseases in many economically important crops, including soft rot disease of potato (Solanum tuberosum). Using random barcode transposon-site sequencing (RB-TnSeq), we generated genome-wide mutant fitness profiles of Dickeya dadantii 3937, Dickeya dianthicola ME23, and Dickeya dianthicola 67-19 isolates collected after passage through several in vitro and in vivo conditions. Though all three strains are pathogenic on potato, D. dadantii 3937 is a well-characterized model while D. dianthicola strains ME23 and 67-19 are recent isolates. Strain ME23 specifically was identified as a representative strain from a 2014 outbreak on potato. This study generated comparable gene fitness measurements across ecologically relevant conditions for both model and non-model strains. Tubers from the potato cultivars “Atlantic,” “Dark Red Norland,” and “Upstate Abundance” provided highly similar conditions for bacterial growth. Using the homolog detection software PyParanoid, we matched fitness values for orthologous genes in the three bacterial strains. Direct comparison of fitness among the strains highlighted shared and variable traits important for growth. Bacterial growth in minimal medium required many metabolic traits that were also essential for competitive growth in planta, such as amino acid, carbohydrate, and nucleotide biosynthesis. Growth in tubers specifically required the pectin degradation gene kduD. Disruption in three putative DNA-binding proteins had strain-specific effects on competitive fitness in tubers. Though the Soft Rot Pectobacteriaceae can cause disease with little host specificity, it remains to be seen the extent to which strain-level variation impacts virulence.

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.

Quantitative Real-Time PCR Assay for the Detection of Pectobacterium parmentieri, a Causal Agent of Potato Soft Rot

Pectobacterium parmentieri is a plant-pathogenic bacterium, recently attributed as a separate species, which infects potatoes, causing soft rot in tubers. The distribution of P. parmentieri seems to be global, although the bacterium tends to be accommodated to moderate climates. Fast and accurate detection systems for this pathogen are needed to study its biology and to identify latent infection in potatoes and other plant hosts. The current paper reports on the development of a specific and sensitive detection protocol based on a real-time PCR with a TaqMan probe for P. parmentieri, and its evaluation. In sensitivity assays, the detection threshold of this protocol was 10² cfu/mL on pure bacterial cultures and 10²–10³ cfu/mL on plant material. The specificity of the protocol was evaluated against P. parmentieri and more than 100 strains of potato-associated species of Pectobacterium and Dickeya. No cross-reaction with the non-target bacterial species, or loss of sensitivity, was observed. This specific and sensitive diagnostic tool may reveal a wider distribution and host range for P. parmentieri and will expand knowledge of the life cycle and environmental preferences of this pathogen.

Irreplaceable Role of Amendment-Based Strategies to Enhance Soil Health and Disease Suppression in Potato Production

Soilborne diseases are a major constraining factor to soil health and plant health in potato production. In the toolbox of crop management, soil amendments have shown benefits to control these diseases and improve soil quality. Most amendments provide nutrients to plants and suppress multiple soilborne pathogens. Soil amendments are naturally derived materials and products and can be classified into fresh or living plants, organic or inorganic matters, and microbial supplements. Fresh plants have unique functions and continuously exude chemicals to interact with soil microbes. Organic and inorganic matter contain high levels of nutrients, including nitrogen and carbon that plants and soil microorganisms need. Soil microorganisms, whether being artificially added or indigenously existing, are a key factor in plant health. Microbial communities can be considered as a biological reactor in an ecosystem, which suppress soilborne pathogens in various mechanisms and turn soil organic matter into absorbable forms for plants, regardless of amendment types. Therefore, soil amendments serve as an energy input, nutrient source, and a driving force of microbial activities. Advanced technologies, such as microbiome analyses, make it possible to analyze soil microbial communities and soil health. As research advances on mechanisms and functions, amendment-based strategies will play an important role in enhancing soil health and disease suppression for better potato production.