Study on the preservation effect of 60Co-γ ray irradiation on potatoes.

To evaluate the effect of irradiation on the preservation of potatoes, fresh potatoes were selected as the irradiation objects, and irradiated with 60Co-γ radiation source for 0, 100, 200, 500 and 1000 Gy, respectively. During the irradiation, the well-packaged Y1.79Bi0.01Eu0.2MgTiO6 novel thermoluminescence dosimeter material was placed together with the potatoes at the same position. Then, the potatoes were stored in the same temperature and humidity environment, and the quality changes of the potatoes were observed. The Y1.79Bi0.01Eu0.2MgTiO6 material had good performance indicators, and was used to measure the irradiation dose of the potatoes. The experiment showed that irradiation could appropriately extend the storage time of potatoes, and gamma irradiation of about 1000 Gy could achieve the best preservation effect. The main pathogenic fungi that cause dry rot of potatoes were Fusarium solani and Fusarium oxysporum, and the appropriate dose of 60Co-γ irradiation could effectively inhibit the spread and growth of these fungi.

Transcriptome analysis unravels the biocontrol mechanism of Serratia plymuthica A30 against potato soft rot caused by Dickeya solani.

Endophytic bacterium Serratia plymuthica A30 was identified as a superior biocontrol agent due to its effective colonization of potato tuber, tolerance to cold conditions, and strong inhibitory action against various soft rot pathogens, including Dickeya solani. We characterized transcriptome changes in potato tubers inoculated with S. plymuthica A30, D. solani, or both at the early and the late phases of interaction. At the early phase and in the absence of the pathogen, A30 influenced the microbial recognition system to initiate plant priming. In the presence of the pathogen alongside biocontrol strain, defense signaling was highly stimulated, characterized by the induction of genes involved in the detoxification system, reinforcement of cell wall structure, and production of antimicrobial metabolites, highlighting A30's role in enhancing the host resistance against pathogen attack. This A30-induced resistance relied on the early activation of jasmonic acid signaling and its production in tubers, while defense signaling mediated by salicylic acid was suppressed. In the late phase, A30 actively interferes with plant immunity by inhibiting stress- and defense-related genes expression. Simultaneously, the genes involved in cell wall remodeling and indole-3-acetic acid signaling were activated, thereby enhancing cell wall remodeling to establish symbiotic relationship with the host. The endophytic colonization of A30 coincided with the induction of genes involved in the biosynthesis and signaling of ethylene and abscisic acid, while downregulating those related to gibberellic acid and cytokinin. This combination suggested fitness benefits for potato tubers by preserving dormancy, and delaying sprouting, which affects durability of tubers during storage. This study contributes valuable insights into the tripartite interaction among S. plymuthica A30, D. solani, and potato tubers, facilitating the development of biocontrol system for soft rot pathogens under storage conditions.

Long intergenic non-coding RNAs modulate proximal protein-coding gene expression and tolerance to Candidatus Liberibacter spp. in potatoes.

Long intergenic non-coding RNAs (lincRNAs) are emerging as regulators of protein-coding genes (PCGs) in many plant and animal developmental processes and stress responses. In this study, we characterize the genome-wide lincRNAs in potatoes responsive to a vascular bacterial disease presumably caused by Candidatus Liberibacter solanacearum (CLso). Approximately 4397 lincRNAs were detected in healthy and infected potato plants at various stages of zebra chip (ZC) disease progression. Of them, ~65% (2844) were novel lincRNAs, and less than 1% (9) were orthologs of Arabidopsis and rice based on reciprocal BLAST analysis, suggesting species-specific expansion. Among the proximal lincRNAs within 50 kbp from a PCG, ~49% were transcribed from the same strand, while ~39% and ~15% followed convergent (head-to-head) and divergent (tail-to-tail) orientations, respectively. Approximately 30% (1308) were differentially expressed following CLso infection, with substantial changes occurring 21 days after infection (DAI). Weighted Gene Co-expression Network Analysis (WGCNA) of lincRNAs and PCGs identified 46 highly correlated lincRNA-PCG pairs exhibiting co-up or co-downregulation. Furthermore, overexpression of selected lincRNAs in transgenic potato hairy roots resulted in perturbation of neighboring PCG expression and conferred tolerance to CLso infection. Our results provide novel insights into potato lincRNAs' identity, expression dynamics, and functional relevance to CLso infection.

Phenazines are involved in the antagonism of a novel subspecies of Pseudomonas chlororaphis strain S1Bt23 against Pythium ultimum.

Long-term use of chemical fungicides to control plant diseases caused by fungi and oomycetes has led to pathogen resistance and negative impacts on public health and environment. There is a global search for eco-friendly methods and antagonistic bacteria are emerging as alternatives. We isolated a potent antagonistic bacterial strain (S1Bt23) from woodland soil in Québec, Canada. Taxonomic characterization by 16S rRNA, multi-locus sequence analysis, pairwise whole-genome comparisons, phylogenomics and phenotypic data identified strain S1Bt23 as a novel subspecies within Pseudomonas chlororaphis. In dual culture studies, strain S1Bt23 exhibited potent mycelial growth inhibition (60.2-66.7%) against Pythium ultimum. Furthermore, strain S1Bt23 was able to significantly bioprotect potato tuber slices from the development of necrosis inducible by P. ultimum. Annotations of the whole genome sequence of S1Bt23 revealed the presence of an arsenal of secondary metabolites including the complete phenazine biosynthetic cluster (phzABCDEFG). Thin-layer (TLC) and high-performance liquid (HPLC) chromatographic analyses of S1Bt23 extracts confirmed the production of phenazines, potent antifungal compounds. CRISPR/Cas9-mediated deletion of phzB (S1Bt23ΔphzB) or phzF (S1Bt23ΔphzF) gene abrogated phenazine production based on TLC and HPLC analyses. Also, S1Bt23ΔphzB and S1Bt23ΔphzF mutants lost antagonistic activity and bioprotection ability of potato tubers against P. ultimum. This demonstrated that phenazines are involved in the antagonistic activity of S1Bt23 against P. ultimum. Finally, based on genotypic and phenotypic data, we taxonomically conclude that S1Bt23 represents a novel subspecies for which the name Pseudomonas chlororaphis subsp. phenazini is proposed.

Evolution of Phytophthora infestans on its potato host since the Irish potato famine.

Phytophthora infestans is a major oomycete plant pathogen, responsible for potato late blight, which led to the Irish Potato Famine from 1845-1852. Since then, potatoes resistant to this disease have been bred and deployed worldwide. Their resistance (R) genes recognize pathogen effectors responsible for virulence and then induce a plant response stopping disease progression. However, most deployed R genes are quickly overcome by the pathogen. We use targeted sequencing of effector and R genes on herbarium specimens to examine the joint evolution in both P. infestans and potato from 1845-1954. Currently relevant effectors are historically present in P. infestans, but with alternative alleles compared to modern reference genomes. The historic FAM-1 lineage has the virulent Avr1 allele and the ability to break the R1 resistance gene before breeders deployed it in potato. The FAM-1 lineage is diploid, but later, triploid US-1 lineages appear. We show that pathogen virulence genes and host resistance genes have undergone significant changes since the Famine, from both natural and artificial selection.

Differences in the constituents of bacterial microbiota of soils collected from two fields of diverse potato blackleg and soft rot diseases incidences, a case study.

The presence of bacteria from the Dickeya spp. and Pectobacterium spp. in farmlands leads to global crop losses of over $420 million annually. Since 1982, the scientists have started to suspect that the development of disease symptoms in crops might be inhibited by bacteria present in the soil. Here, we characterized in terms of physicochemical properties and the composition of bacterial soil microbiota two fields differing, on the basis of long-term studies, in the occurrence of Dickeya spp.- and Pectobacterium spp.-triggered infections. Majority, i.e. 17 of the investigated physicochemical features of the soils collected from two fields of either low or high potato blackleg and soft rot diseases incidences turned out to be similar, in contrast to the observed 4 deviations in relation to Mg, Mn, organic C and organic substance contents. By performing microbial cultures and molecular diagnostics-based identification, 20 Pectobacterium spp. strains were acquired from the field showing high blackleg and soft rot incidences. In addition, 16S rRNA gene amplicon sequencing followed by bioinformatic analysis revealed differences at various taxonomic levels in the soil bacterial microbiota of the studied fields. We observed that bacteria from the genera Bacillus, Rumeliibacillus, Acidobacterium and Gaiella turned out to be more abundant in the soil samples originating from the field of low comparing to high frequency of pectinolytic bacterial infections. In the herein presented case study, it is shown for the first time that the composition of bacterial soil microbiota varies between two fields differing in the incidences of soft rot and blackleg infections.

Early asymptomatic prediction of potato soft rot disease using phytohormone-induced volatile biomarkers.

Potatoes (Solanum tuberosum L.) are one of the world's major staple crops. In stored potatoes, Pectobacterium carotovorum subsp carotovorum causes soft rot. As a result of the rapid spread of the disease during post-harvest storage, potato production suffers huge losses. By detecting disease early and controlling it promptly, losses can be minimized. The profile of volatiles of plants can be altered by phytopathogens. Identifying unique volatile organic compounds (VOCs) as biomarkers for early disease detection has attracted considerable research attention. This study compared the VOC profiles of healthy and soft rot inoculated potatoes (cv. "Kufri Pukhraj") over a time course using gas chromatography-mass spectrometry (GC-MS). It was found that there was a differential emission of 27 VOCs between healthy non-inoculated potatoes and soft rot inoculated potatoes. Among 27 VOCs, only five (1-octen-3-ol, 2-methylisoborneol, 3-octanone, 1,4-dimethyladamantane, and 2-methyl-2-bornene) were found exclusively in soft rot inoculated potatoes, suggesting them potential biomarker for non-destructive prediction of soft rot disease in potatoes. Reactive oxygen species (H2O2) and phytohormone methyl-jasmonate (MeJa) levels increased transiently on infection with soft rot. The analysis of the primary metabolism of soft rot infected tubers at three different stages suggests metabolic reprogramming that occurs at the early stage of infection, possibly leading to biomarker volatile emission. Based on these results, it appears that the initial potato-soft rot bacteria interaction initiates metabolic reprogramming mainly through H2O2 and the MeJa signalling pathway. In asymptomatic potatoes, these biomarkers may be promising candidates for non-destructive detection of soft rot at an early stage. These biomarkers can be used to develop an e-nose sensor to predict soft rot in the future.

The StPti5 ethylene response factor acts as a susceptibility factor by negatively regulating the potato immune response to pathogens.

Ethylene response factors (ERFs) have been associated with biotic stress in Arabidopsis, while their function in non-model plants is still poorly understood. Here we investigated the role of potato ERF StPti5 in plant immunity. We show that StPti5 acts as a susceptibility factor. It negatively regulates potato immunity against potato virus Y and Ralstonia solanacearum, pathogens with completely different modes of action, and thereby has a different role than its orthologue in tomato. Remarkably, StPti5 is destabilised in healthy plants via the autophagy pathway and accumulates exclusively in the nucleus upon infection. We demonstrate that StEIN3 and StEIL1 directly bind the StPti5 promoter and activate its expression, while synergistic activity of the ethylene and salicylic acid pathways is required for regulated StPti expression. To gain further insight into the mode of StPti5 action in attenuating potato defence responses, we investigated transcriptional changes in salicylic acid deficient potato lines with silenced StPti5 expression. We show that StPti5 regulates the expression of other ERFs and downregulates the ubiquitin-proteasome pathway as well as several proteases involved in directed proteolysis. This study adds a novel element to the complex puzzle of immune regulation, by deciphering a two-level regulation of ERF transcription factor activity in response to pathogens.

Isolation and identification of entomopathogenic fungi strains for Colorado potato beetle (Leptinotarsa decemlineata) control.

AIMS: The Colorado potato beetle, Leptinotarsa decemlineata (Say) (Coleoptera: Chrysomelidae) is the most widespread insect pest that causes major economic losses, especially on potatoes. Due to heavy insecticide use, this species now resists most pesticides, posing a significant control challenge. Frequent pesticide application also harms non-target organisms, the environment, and human health. Hence, utilizing biocontrol agents like entomopathogenic fungi (EPF) offers a viable alternative for pest management. The aim of this study was to identify and characterize new EPF strains isolated from soil samples and evaluate their efficacy against adult L. decemlineata under laboratory conditions. METHODS AND RESULTS: Soil samples were collected in potato fields or uncultivated areas adjacent to the field in the Czech Republic and the EPF strains were isolated using a modified Tenebrio bait method. A total of 20 fungal strains were isolated and identified using morphological and molecular markers based on the 28S rRNA, ITS, and elongation factor 1-alpha gene sequences as Beauveria bassiana (Bals.-Criv.) Vuill., Beauveria brongniartii (Sacc.) Petch, and Cordyceps fumosorosea (Wize) Kepler, B. Shrestha & Spatafora (Hypocreales: Cordycipitaceae), Purpureocillium lilacinum (Thom.) Luangsa-ard, Houbraken, Hywel-Jones & Samson (Hypocreales: Ophiocordycipitaceae), Metarhizium brunneum (Petch), and Metarhizium robertsii Bisch., Rehner & Humber (Hypocreales: Clavicipitaceae). The bioassays revealed high variability among virulence of these strains against L. decemlineata with the shortest median time to death (LT50 = 5 days) in M. robertsii strain MAN3b. CONCLUSIONS: Results shown that some EPF strains, particularly those of genera Metarhizium, can be promising biocontrol agents against the Colorado potato beetle.

Ribosomal S6 kinases 2 mediates potato resistance to late blight, through WRKY59 transcription factor.

Potato late blight is the most devastating pre- and post-harvest crop disease in the world, which is widespread and difficult to control, causing serious economic losses. Cultivating resistant varieties is a major way to prevent and control late blight in a green way. However, due to the rapid evolution of pathogens, the plant resistance is losing. Therefore, mining effective and durable genes involved in disease resistance is crucial for breeding resistant varieties against late blight. In this study, we took "potato-Phytophthora infestans" as the "host-pathogen" model system to discover the potential disease resistance-related genes and elucidate their molecular functional mechanism. Through yeast two-hybridization, bimolecular fluorescence complementation, Co-immunoprecipitation assays, and gene function validation etc., we found that ribosomal protein S6 kinase 2 (StS6K2) is a key resistant protein, which is interacted with StWRKY59 transcription factor. Overexpression of StS6K2 and StWRKY59 both enhanced the plants resistance to P. infestans, and promoted the host immune response, such as ROS burst and callose deposition. In OEStWRKY59 lines, DEGs involved in secondary metabolites synthesis, plant hormone signaling transduction and plant-pathogen interaction were significantly enriched. These findings provide novel genetic resources for the breeding of resistant varieties.

Mycotoxin Accumulation in Dry Rot Potato Tubers from Algeria and Toxigenic Potential of Associated Isolates of Fusarium Genus.

The presence of different mycotoxins in 232 tuber samples exhibiting dry rot symptoms and their associated Fusarium strains from two production sites in Algeria was investigated. LC-MS/MS was used to simultaneously detect and quantify 14 mycotoxins, including trichothecenes and non-trichothecenes. A total of 49 tubers were contaminated with at least one mycotoxins, including T-2, HT-2, Diacetoxyscirpenol (DAS), 15-acetoxyscirpenol (15-AS) and Beauvericin (BEA). Positive samples from the Bouira region had a significantly higher level of toxin contamination compared to Ain Defla (56.34% and 5.59%, respectively). A total of 283 Fusarium strains were isolated: 155 from Bouira and 128 from Ain Defla. These strains were evaluated for their ability to produce the targeted mycotoxins. The results showed that 61.29% and 53.9% of strains originate from Bouira and Ain Defla regions were able to produce Nivalenol, Fusarenone-X, DAS, 15-AS, Neosolaniol, BEA and Zearalenone. The phylogenetic analysis of the conserved ribosomal internal transcribed spacer (ITS) sequences of 29 Fusarium strains, representative of the recorded mycotoxins profiles, was distributed into 5 Fusarium species complexes (SC): F. incarnatum-equiseti SC (FIESC), F. sambucinum SC (FSAMSC), F. oxysporum SC (FOSC), F. tricinctum SC (FTSC) and F. redolens SC (FRSC). This is the first study determining multiple occurrences of mycotoxins contamination associated to Fusarium dry rot of potato in Algeria and highlights fungal potential for producing trichothecene and non-trichothecens mycotoxins.

Biocontrol potential and growth-promoting effect of endophytic fungus Talaromyces muroii SD1-4 against potato leaf spot disease caused by Alternaria alternata.

BACKGROUND: Alternaria alternata is the primary pathogen of potato leaf spot disease, resulting in significant potato yield losses globally. Endophytic microorganism-based biological control, especially using microorganisms from host plants, has emerged as a promising and eco-friendly approach for managing plant diseases. Therefore, this study aimed to isolate, identify and characterize the endophytic fungi from healthy potato leaves which had great antifungal activity to the potato leaf spot pathogen of A. alternata in vitro and in vivo. RESULTS: An endophytic fungal strain SD1-4 was isolated from healthy potato leaves and was identified as Talaromyces muroii through morphological and sequencing analysis. The strain SD1-4 exhibited potent antifungal activity against the potato leaf spot pathogen A. alternata Lill, with a hyphal inhibition rate of 69.19%. Microscopic and scanning electron microscope observations revealed that the strain SD1-4 grew parallel to, coiled around, shrunk and deformed the mycelia of A. alternata Lill. Additionally, the enzyme activities of chitinase and ß-1, 3-glucanase significantly increased in the hyphae of A. alternata Lill when co-cultured with the strain SD1-4, indicating severe impairment of the cell wall function of A. alternata Lill. Furthermore, the mycelial growth and conidial germination of A. alternata Lill were significantly suppressed by the aseptic filtrate of the strain SD1-4, with inhibition rates of 79.00% and 80.67%, respectively. Decrease of leaf spot disease index from 78.36 to 37.03 was also observed in potato plants treated with the strain SD1-4, along with the significantly increased plant growth characters including plant height, root length, fresh weight, dry weight, chlorophyll content and photosynthetic rate of potato seedlings. CONCLUSION: The endophyte fungus of T. muroii SD1-4 isolated from healthy potato leaves in the present study showed high biocontrol potential against potato leaf spot disease caused by A. alternata via direct parasitism or antifungal metabolites, and had positive roles in promoting potato plant growth.

Biocontrol Mechanisms of Three Plant Essential Oils Against Phytophthora infestans Causing Potato Late Blight.

Late blight, caused by the notorious pathogen Phytophthora infestans, poses a significant threat to potato (Solanum tuberosum) crops worldwide, impacting their quality as well as yield. Here, we aimed to investigate the potential use of cinnamaldehyde, carvacrol, and eugenol as control agents against P. infestans and to elucidate their underlying mechanisms of action. To determine the pathogen-inhibiting concentrations of these three plant essential oils (PEOs), a comprehensive evaluation of their effects using gradient dilution, mycelial growth rate, and spore germination methods was carried out. Cinnamaldehyde, carvacrol, and eugenol were capable of significantly inhibiting P. infestans by hindering its mycelial radial growth, zoospore release, and sporangium germination; the median effective inhibitory concentration of the three PEOs was 23.87, 8.66, and 89.65 µl/liter, respectively. Scanning electron microscopy revealed that PEOs caused the irreversible deformation of P. infestans, resulting in hyphal shrinkage, distortion, and breakage. Moreover, propidium iodide staining and extracellular conductivity measurements demonstrated that all three PEOs significantly impaired the integrity and permeability of the pathogen's cell membrane in a time- and dose-dependent manner. In vivo experiments confirmed the dose-dependent efficacy of PEOs in reducing the lesion diameter of potato late blight. Altogether, these findings provide valuable insight into the antifungal mechanisms of PEOs vis-à-vis late blight-causing P. infestans. By utilizing the inherent capabilities of these natural compounds, we could effectively limit the harmful impacts of late blight on potato crops, thereby enhancing agricultural practices and ensuring the resilience of global potato food production.

Chitosan as an Antimicrobial, Anti-Insect, and Growth-Promoting Agent for Potato (Solanum tuberosum L.) Plants.

A growing trend in plant protection is replacing chemical preparations with environmentally friendly biological compositions. Chitosan, due to its biocompatibility, biodegradability, and bioactivity, is an effective agent against plant diseases. The purpose of the study was to evaluate chitosan as a potential biopesticide for potato plants. Three variants of chitosan were tested: high (310-375 kDa, >75% deacetylated), medium (190-310 kDa, 75-85% deacetylated), and low (50-190 kDa, 75-85% deacetylated) molecular weight. The chitosan variants were dissolved in lactic and succinic acids and tested for antibacterial and antifungal properties against eight strains of mould and two strains of bacteria responsible for potato diseases. The possible cytotoxicity of chitosan was evaluated against different cell lines: insect Sf-9, human keratinocyte HaCaT, and human colon carcinoma Caco-2. The bioprotective activities of the chitosan were also evaluated in situ on potato tubers. Chitosan inhibited the growth of almost all the selected phytopathogens. The most active was medium molecular chitosan in lactic acid. This formula was characterized by low toxicity towards human cells and high toxicity towards Sf-9 cells. It was also found to have positive effects on the growth of stems and roots, gas exchange, and chlorophyll index in potato plants. Selected chitosan formulation was proposed as a functional biopesticide for potato protection against phytopathogens.

Biocontrol potential of endophytic fungi against phytopathogenic nematodes on potato (Solanum tuberosum L.).

Root-knot nematodes (RKNs) are a vital pest that causes significant yield losses and economic damage to potato plants. The use of chemical pesticides to control these nematodes has led to environmental concerns and the development of resistance in the nematode populations. Endophytic fungi offer an eco-friendly alternative to control these pests and produce secondary metabolites that have nematicidal activity against RKNs. The objective of this study is to assess the efficacy of Aspergillus flavus (ON146363), an entophyte fungus isolated from Trigonella foenum-graecum seeds, against Meloidogyne incognita in filtered culture broth using GC-MS analysis. Among them, various nematicidal secondary metabolites were produced: Gadoleic acid, Oleic acid di-ethanolamide, Oleic acid, and Palmitic acid. In addition, biochemical compounds such as Gallic acid, Catechin, Protocatechuic acid, Esculatin, Vanillic acid, Pyrocatechol, Coumarine, Cinnamic acid, 4, 3-indol butyl acetic acid and Naphthyl acetic acid by HPLC. The fungus was identified through morphological and molecular analysis, including ITS 1-4 regions of ribosomal DNA. In vitro experiments showed that culture filtrate of A. flavus had a variable effect on reducing the number of egg hatchings and larval mortality, with higher concentrations showing greater efficacy than Abamectin. The fungus inhibited the development and multiplication of M. incognita in potato plants, reducing the number of galls and eggs by 90% and 89%, respectively. A. flavus increased the activity of defense-related enzymes Chitinas, Catalyse, and Peroxidase after 15, 45, and 60 days. Leaching of the concentrated culture significantly reduced the second juveniles' stage to 97% /250 g soil and decreased the penetration of nematodes into the roots. A. flavus cultural filtrates via soil spraying improved seedling growth and reduced nematode propagation, resulting in systemic resistance to nematode infection. Therefore, A. flavus can be an effective biological control agent for root-knot nematodes in potato plants. This approach provides a sustainable solution for farmers and minimizes the environmental impact.

Transcriptome analysis reveals genes associated with late blight resistance in potato.

Late blight is a serious disease of potato worldwide. Our study aimed to unveil genes involved in late blight resistance in potato by RNA-seq analysis after artificial inoculation under controlled conditions. In this study, two potato somatic hybrids (P7 and Crd6) and three varieties such as Kufri Girdhari, Kufri Jyoti and Kufri Bahar (control) were used. Transcriptiome analysis revealed statistically significant (p < 0.05) differentially expressed genes (DEGs), which were analysed into up-regulated and down-regulated genes. Further, DEGs were functionally characterized by the Gene Ontology annotations and the Kyoto Encyclopedia of Genes and Genomes pathways. Overall, some of the up-regulated genes in resistant genotypes were disease resistance proteins such as CC-NBS-LRR resistance protein, ankyrin repeat family protein, cytochrome P450, leucine-rich repeat family protein/protein kinase family, and MYB transcription factor. Sequence diversity analysis based on 38 peptide sequences representing 18 genes showed distinct variation and the presence of three motifs in 15 amino acid sequences. Selected genes were also validated by real-time quantitative polymerase chain reaction analysis. Interestingly, gene expression markers were developed for late blight resistant genotypes. Our study elucidates genes involved in imparting late blight resistance in potato, which will be beneficial for its management strategies in the future.

A novel genus of Pectobacterium bacteriophages display broad host range by targeting several species of Danish soft rot isolates.

The bacterial diseases black leg and soft rot in potatoes cause heavy losses of potatoes worldwide. Bacteria within the genus Pectobacteriaceae are the causative agents of black leg and soft rot. The use of antibiotics in agriculture is heavily regulated and no other effective treatment currently exists, but bacteriophages (phages) have shown promise as potential biocontrol agents. In this study we isolated soft rot bacteria from potato tubers and plant tissue displaying soft rot or black leg symptoms collected in Danish fields. We then used the isolated bacterial strains as hosts for phage isolation. Using organic waste, we isolated phages targeting different species within Pectobacterium. Here we focus on seven of these phages representing a new genus primarily targeting P. brasiliense; phage Ymer, Amona, Sabo, Abuela, Koroua, Taid and Pappous. TEM image of phage Ymer showed siphovirus morphotype, and the proposed Ymer genus belongs to the class Caudoviricetes, with double-stranded DNA genomes varying from 39 kb to 43 kb. In silico host range prediction using a CRISPR-Cas spacer database suggested both P. brasiliense, P. polaris and P. versatile as natural hosts for phages within the proposed Ymer genus. A following host range experiment, using 47 bacterial isolates from Danish tubers and plants symptomatic with soft rot or black leg disease verified the in silico host range prediction, as the genus as a group were able to infect all three Pectobacterium species. Phages did, however, primarily target P. brasiliense isolates and displayed differences in host range even within the species level. Two of the phages were able to infect two or more Pectobacterium species. Despite no nucleotide similarity with any phages in the NCBI database, the proposed Ymer genus did share some similarity at the protein level, as well as gene synteny, with currently known phages. None of the phages encoded integrases or other genes typically associated with lysogeny. Similarly, no virulence factors nor antimicrobial resistance genes were found, and combined with their ability to infect several soft rot-causing Pectobacterium species from Danish fields, demonstrates their potential as biocontrol agents against soft rot and black leg diseases in potatoes.

Functional and evolutionary comparative analysis of the DIR gene family in Nicotiana tabacum L. and Solanum tuberosum L.

BACKGROUND: The dirigent (DIR) genes encode proteins that act as crucial regulators of plant lignin biosynthesis. In Solanaceae species, members of the DIR gene family are intricately related to plant growth and development, playing a key role in responding to various biotic and abiotic stresses. It will be of great application significance to analyze the DIR gene family and expression profile under various pathogen stresses in Solanaceae species. RESULTS: A total of 57 tobacco NtDIRs and 33 potato StDIRs were identified based on their respective genome sequences. Phylogenetic analysis of DIR genes in tobacco, potato, eggplant and Arabidopsis thaliana revealed three distinct subgroups (DIR-a, DIR-b/d and DIR-e). Gene structure and conserved motif analysis showed that a high degree of conservation in both exon/intron organization and protein motifs among tobacco and potato DIR genes, especially within members of the same subfamily. Total 8 pairs of tandem duplication genes (3 pairs in tobacco, 5 pairs in potato) and 13 pairs of segmental duplication genes (6 pairs in tobacco, 7 pairs in potato) were identified based on the analysis of gene duplication events. Cis-regulatory elements of the DIR promoters participated in hormone response, stress responses, circadian control, endosperm expression, and meristem expression. Transcriptomic data analysis under biotic stress revealed diverse response patterns among DIR gene family members to pathogens, indicating their functional divergence. After 96 h post-inoculation with Ralstonia solanacearum L. (Ras), tobacco seedlings exhibited typical symptoms of tobacco bacterial wilt. The qRT-PCR analysis of 11 selected NtDIR genes displayed differential expression pattern in response to the bacterial pathogen Ras infection. Using line 392278 of potato as material, typical symptoms of potato late blight manifested on the seedling leaves under Phytophthora infestans infection. The qRT-PCR analysis of 5 selected StDIR genes showed up-regulation in response to pathogen infection. Notably, three clustered genes (NtDIR2, NtDIR4, StDIR3) exhibited a robust response to pathogen infection, highlighting their essential roles in disease resistance. CONCLUSION: The genome-wide identification, evolutionary analysis, and expression profiling of DIR genes in response to various pathogen infection in tobacco and potato have provided valuable insights into the roles of these genes under various stress conditions. Our results could provide a basis for further functional analysis of the DIR gene family under pathogen infection conditions.

Elucidating the impact of environmental factors on the growth of Colletotrichum coccodes strains isolated from potato tubers in Great Britain.

Black dot and silver scurf caused by Colletotrichum coccodes and Helminthosporium solani, respectively, are tuber blemish diseases affecting quality in the fresh and pre-pack potato industry. In the last 20 years, the importance of high-quality tuber appearance has increased considerably due to the growing demand for washed and pre-packed potatoes in the UK. Changing climate characterised by rising temperatures and wetter summers is a threat as this will favour the development of pathogens such as C. coccodes in the soil increasing the risk of food spoilage. Moreover, both diseases can develop not only in the field but also after harvest, with postharvest storage temperatures being a crucial factor in controlling fungal growth. Furthermore, anecdotal evidence showed differences on the aggressiveness of black dot depending on its origin (i.e. England and Scotland) on potato tubers. Silver scurf and black dot are difficult to differentiate as they present similar phenotypes characterised by silvery lesions making it challenging for managers to take the necessary corrective action during storage. Hence, the aim of this study was to give a general insight into the ecological conditions affecting the establishment of the causal agent of potato black dot in the field, and black dot and silver scurf during the supply chain. Therefore, invitro experiments were designed to study the growth rate and lag times simulating both scenarios respectively: on soil extract agar (SEA) media at different temperatures (4, 11, 15 °C) and matric potentials (control [unmodified] and - 1.4 MPa [modified]); and on natural potato dextrose agar (NPDA) for different temperatures (4, 11, 15 and 20 °C) at 99 % relative humidity (RH) for 25 days. When simulating the field environment, drier conditions (matric potential = -1.4 MPa) reduced fungal growth for both isolates by 0.1 cm day-1 at the temperature of 15 °C, suggesting temperature as the main limiting factor for the growth of C. coccodes in the soil. The causal agent of black dot exhibited a faster growth rate under retailer-like conditions (i.e., 15 °C) compared to H. solani. Understanding the environmental influence on both the pathogen and the crop is vital for proper disease management to help reduce food loss and waste.

Differential expression of "Candidatus Liberibacter solanacearum" genes and prophage loci in different life stages of potato psyllid.

Psyllid species, including the potato psyllid (PoP) Bactericera cockerelli (Sulc) (Triozidae) serve as host and vector of "Candidatus Liberibacter spp." ("Ca. Liberibacter"), which also infects diverse plant hosts, including citrus and tomato. Psyllid transmission of "Ca. Liberibacter" is circulative and propagative. The time of "Ca. Liberibacter" acquisition and therefore vector life stage most competent for bacterial transmission varies by pathosystems. Here, the potato psyllid-"Ca. Liberibacter solanacearum" (CLso) pathosystem was investigated to dissect CLso-prophage interactions in the tomato plant and PoP-psyllid host by real-time quantitative reverse transcriptase amplification of CLso genes/loci with predicted involvement in host infection and psyllid-CLso transmission. Genes/loci analyzed were associated with (1) CLso-adhesion, -invasion, -pathogenicity, and -motility, (2) prophage-adhesion and pathogenicity, and (3) CLso-lysogenic cycle. Relative gene expression was quantified by qRT-PCR amplification from total RNA isolated from CLso-infected 1st-2nd and 4th-5th nymphs and teneral adults and CLso-infected tomato plants in which CLso infection is thought to occur without SC1-SC2 replication. Gene/loci expression was host-dependent and varied with the psyllid developmental stage. Loci previously associated with repressor-anti-repressor regulation in the "Ca Liberibacter asiaticus"-prophage pathosystem, which maintains the lysogenic cycle in Asian citrus psyllid Diaphorina citri, were expressed in CLso-infected psyllids but not in CLso-infected tomato plants.