Pectobacterium carotovorum is a gram-negative phytopathogenic bacterium that causes soft rot disease on diverse plant species. It encodes the type III secretion system effector protein, DspE, and its chaperone, DspF. The DspE family proteins form water and solute channels in plant cells, flooding the apoplast to aid bacterial multiplication. In Pseudomonas syringae, the DspE ortholog, AvrE, upregulates abscisic acid (ABA) expression, leading to stomatal closure. In this study, a P. carotovorum dspEF mutant did not cause leaf cell death in tobacco leaves. This observation is supported by the lower expression of plant cell wall-degrading enzymes such as pelB, pelI, celV, prtW, and the quorum-sensing system transcript expI in tobacco plants prior to visual symptoms (5 h postinoculation). Interestingly, neither dspE/F nor hrpL mutation affected synthesis of quorum-sensing signaling molecule acyl-homoserine lactone under microbiological settings. However, maceration symptoms occurred if leaves infiltrated with the dspEF mutant were kept under high humidity or detached postinfiltration. These leaves showed elevated transcription of ABA synthesis genes compared with infiltrated leaves maintained on the plant under ambient conditions. To validate this involvement, coinfiltration of ABA with the dspEF mutant restored its ability to cause maceration in attached leaves under ambient conditions. Overall, our data suggest that DspE/F facilitates host susceptibility by creating an aqueous apoplast, promoting ABA accumulation and stomata closure.

Potato virus Y (PVY), potato mop-top virus (PMTV), potato virus S (PVS), and tobacco rattle virus (TRV) can be difficult to identify based on visual foliar symptoms. Using tuber samples collected from seven locations and 12 cultivars during 2017 to 2019, we developed a molecular assay using customized Whatman Flinders Technology Associates Plantsaver cards (FTA cards) and a reverse-transcription PCR (RT-PCR) for efficient sample collection and nucleic acid extraction. PMTV and PVY were detected more frequently on the stem end, TRV on the rose end, and PVS was evenly detected across the stem-end to rose-end axis of the tubers. Differences were seen in virus species localization within a tuber, thereby a composite of samples taken from multiple locations on a tuber improved virus detection. Regardless of sampling location on the tuber, tissue excised from the surface to 0.5 cm deep provided the best detection for all four viruses. For PVY, PMTV, and TRV, the proportion of tubers with viruses detected from field samples was highest at 100, 150, and 175 days after harvest, respectively. However, the probability of detecting PMTV and PVY 25 days after harvest was not different than the probability of detection at their peak detection times after harvest. The probability of TRV detection was lower at 25 days after harvest than at 175 days after harvest (P < 0.05).

Potato (Solanum tuberosum) is susceptible to several fungal pathogens, including Alternaria solani, Alternaria alternata, Rhizoctonia solani, and Colletotrichum coccodes, which can significantly reduce yield and tuber quality. Vine-kill is commonly used by potato producers to facilitate harvest, enhance tuber maturation and skin set, and manage tuber size. This study evaluated how different vine-kill methods affect soil DNA levels of these four fungal pathogens, potato virus Y (PVY) incidence in progeny tubers, and tuber yield and size distribution in the San Luis Valley, Colorado. Treatments included pulling, flailing, and chemical desiccation with Reglone (diquat dibromide) combined with either Aim EC (carfentrazone-ethyl) or Super Tin 4L (triphenyltin hydroxide). Vine-kill methods did not significantly affect yield, size profile, or PVY incidence. However, soil pathogen DNA levels measured as DNA copy number by qPCR varied among treatments and year. In 2022, pulling resulted in the lowest levels of A. solani, A. alternata, and R. solani, and the second lowest level of C. coccodes. In 2023, pulling provided no significant benefit, but in 2025, it reduced soil levels of all four pathogens relative to desiccation and natural senescence, while flailing resulted in the lowest soil pathogen DNA levels in 2025 for both R. solani, and C. coccodes. Between the two commonly used practices, flailing generally resulted in lower fungal pathogen DNA levels detected than chemical desiccation. Overall, pulling and flailing reduced soil fungal pathogen DNA levels, suggesting that vine-kill practices might influence disease management in potato production systems.

Potato is an important sector to the U.S. economy, and it created more than $100 billion in economic activity in 2021. The United States exports fresh potatoes to several countries. In certain cases, fresh potato shipments from the United States to the international market requires the crop to be free of potato mop-top virus (PMTV). This increased the need to provide potato growers with an optional, reliable, and large-scale detection method of PMTV, especially in asymptomatic tubers. We developed a duplex immunocapture reverse-transcription quantitative PCR (IC-RT-qPCR) for the large-scale detection of PMTV in dormant tubers. The IC step eliminates the need for RNA extraction kits, making this assay appropriate for large-scale tuber testing. To enhance the reliability of the current assay and reduce the chance of false negatives, a duplex format was used by deploying two primer-probe sets, including a previously reported primer-probe set targeting the RNA-CP and a newly designed primer-probe set targeting a conserved region of RNA-TGB of PMTV genome. We also determined that peels from the stem end of the tubers were more likely to test positive for PMTV than bud end peels or lateral tuber cores. The duplex IC-RT-qPCR will provide a reliable and sensitive tool for the large-scale detection of PMTV in dormant tubers and will help safeguard potato movement in the United States and internationally.

Phytopathogens and plant pests secrete proteases that facilitate virulence and plant-pest interactions through plant cell protein degradation and potentially through modification of extracellular pathogen proteins. In response, plants produce protease inhibitors (PIs) that bind to and neutralize pest and pathogen proteases, thereby contributing to plant resistance. Solanaceous crops such as potato, tomato, and tobacco contain diverse PIs. We analyzed PIs from 23 wild and domesticated varieties of these crops and identified 3,158 PIs, mostly from potato (77%), followed by tomato (15%) and tobacco (8%). Seven PI families were found: cystatins, PTIIPI, PTIPI, KTPI, MCPI, SERPINs, and Kazal-type SPI, with KTPI being the most prevalent PI. Further domain analysis revealed conserved regions and/or reactive center loop motifs in each PI family, with wild species exhibiting greater diversity in bioactive sites of KTPI and PTIPI compared with domesticated species. After screening for signal peptides and comparing with known PIs, we selected 88 PIs for molecular docking with four proteases from key plant pathogens and pests: metallo, aspartic, cysteine, and trypsin proteases from Pectobacterium carotovorum, Fusarium oxysporum, Meloidogyne incognita, and Helicoverpa armigera, respectively. Molecular docking using HADDOCK and AlphaFold3 prioritized 11 PI candidates with potential bioactivity, with six unique to wild species, suggesting potential for plant disease and pest management.

To reduce reliance on time consuming postharvest seed potato grow outs, a Whatman Flinders Technology Associates Plantsaver Cards (FTA)-based pathogen detection protocol based on dormant tubers was developed for four potato viruses. Viruses tested included potato virus Y (PVY), potato virus S (PVS), potato mop-top virus (PMTV), and tobacco rattle virus (TRV). Viruses were also detected from potato tubers, sprouts, and leaves using different experimental test methods and sample collection timings (harvest-FTA, storage-FTA, sprouting-FTA, sprout-enzyme-linked immunosorbent assay [ELISA], sprout-recombinase polymerase amplification [RPA], leaf-RPA, and leaf-ELISA). When compared with the leaf-ELISA, accuracy of the harvest-FTA was 92.9% (PVY) and 93.8% (PVS), and test results were available 90-days earlier than leaf-ELISA. Results from the leaf-ELISA for PMTV and leaf-FTA for TRV grossly underreport detection of these two viruses compared with results obtained using multiple tuber and sprout test methods (harvest-FTA, storage-FTA, sprouting-FTA, sprout-ELISA, and sprout-RPA). In 2020, an on-farm collaboration resulted in field implementation of the FTA card-based tuber test for detecting PVY, PMTV, and TRV from eight seed lots. Accuracy, sensitivity, and specificity for detecting PVY from these eight seed lots using the farm-FTA test method were 89, 92, and 87%, respectively, and the results were provided approximately 3 months earlier than the official results from the state seed potato certification programs. Cost analysis of the FTA card-based detection protocols showed that this approach reduced testing costs for multiple pathogens and allowed growers to use a single sampling pipeline to measure and manage multiple pathogen risks at lower costs.

Necrotrophic bacteria within the order Enterobacterales cause significant agricultural losses, with few effective management options available for producers. These pathogens have evolved at least two distinct strategies for infecting plants. Soft rot pathogens in the family Pectobacteriaceae, such as Dickeya and Pectobacterium, rely on secreting plant cell wall-degrading enzymes. In contrast, Pantoea necrotrophs depend on the production of phosphonate phytotoxins, a type of secondary metabolite, for their pathogenicity. This review summarizes recent discoveries on the virulence mechanisms of bacterial necrotrophs and current knowledge of factors that influence their host range and interactions with plant immune defenses. A deeper understanding of bacterial necrotroph host range determinants could inform the development and deployment of enhanced genetic resistance strategies.

Naringenin, a flavanone from citrus, was studied for its ability to reduce virulence in Pectobacterium, a phytopathogen causing soft rot disease in crop plants. Naringenin downregulated quorum sensing (QS) and suppressed critical virulence determinants in Pectobacterium brasiliense Pb1692, including plant cell wall-degrading enzymes, bacterial motility, and biofilm formation, consequently reducing disease symptoms in two host plants. Molecular docking simulations revealed a plausible binding mode for naringenin within the QS protein ExpI, which were maintained during microsecond-long Molecular Dynamics simulations. These simulations provided atomic-scale insight into specific interactions and estimated binding free energies, supporting naringenin's QS inhibition mode of action. In contrast, S-adenosyl methionine, the natural ligand of ExpI, was unable to maintain a stable binding mode in the ExpI site during simulations. Beyond QS disruption, naringenin induced reactive oxygen species accumulation and compromised DNA repair, indicating a multimodal mechanism of action. Despite these promising findings, naringenin's limited aqueous solubility challenges practical applications.

Most food crops are susceptible to necrotrophic bacteria that cause rotting and wilting diseases in fleshy organs and foods. All varieties of cultivated potato (Solanum tuberosum L.) are susceptible to diseases caused by Pectobacterium species, but resistance has been demonstrated in wild potato relatives including S. chacoense. Previous studies demonstrated that resistance is in part mediated by antivirulence activity of phytochemicals in stems and tubers. Little is known about the genetic basis of antivirulence traits, and the potential for inheritance and introgression into cultivated potato is unclear. Here, the metabolites and genetic loci associated with antivirulence traits in S. chacoense were elucidated by screening a sequenced S. tuberosum x S. chacoense recombinant inbred line (RIL) population for antivirulence traits of its metabolite extracts. Metabolite extracts from the RILs exhibited a quantitative distribution for two antivirulence traits that were positively correlated: quorum sensing inhibition and exo-protease inhibition, with some evidence of transgressive segregation, supporting the role of multiple loci and metabolites regulating these resistance-associated systems. Metabolomics was performed on the highly resistant and susceptible RILs that revealed 30 metabolites associated with resistance, including several alkaloids and terpenes. Specifically, several prenylated metabolites were more abundant in resistant RILs. We constructed a high-density linkage map with 795 SNPs mapped to 12 linkage groups, spanning a length of 1,507 cM and a density of 1 marker per 1.89 cM. Genetic mapping of the antivirulence and metabolite data identified five quantitative trait loci (QTLs) related to quorum sensing inhibition that explained 8-28% of the phenotypic variation and two QTLs for protease activity inhibition that explained 14-19% of the phenotypic variation. Several candidate genes including alkaloid, and secondary metabolite biosynthesis that are related to disease resistance were identified within these QTLs. Taken together, these data support that quorum sensing inhibition and exo-protease inhibition assays may serve as breeding targets to improve resistance to nectrotrophic bacterial pathogens in potato and other plants. The identified candidate genes and metabolites can be utilized in marker assisted selection and genomic selection to improve soft- rot and blackleg disease resistance.

Potato virus Y (PVY) is a major economic threat to potato production worldwide. Understanding the prevalent PVY strains and their dynamics is crucial for effective management. This study investigated PVY trends and diversity in the San Luis Valley (SLV), CO, U.S.A. We leveraged the Colorado Seed Potato Certification Program data (2017 to 2022), revealing a persistent problem with PVY incidence in certified seed lots that fluctuated between 2.6% (2017) and 6.5% (2022). PVYN-Wi was the dominant strain, with others such as PVYO also detected. A complementary field study (2021 to 2022) investigated PVY prevalence and diversity in 600 samples collected from 30 fields. PVYN-Wi was identified as the main strain, followed by PVYO and PVYNTN. Notably, the incidences of dual and triple infections, along with inconclusive samples, increased in both postharvest and field study samples. High-throughput sequencing (HTS) of the inconclusive samples identified from the field study samples determined PVYN-Wi as the predominant strain and identified polymorphisms that may hinder accurate identification by traditional strain typing methods. Beyond PVY, potato virus S (PVS) was the only other major potato-infecting virus detected. HTS revealed diverse nonplant-infecting viruses as well. This study provides valuable insights into the evolving PVY landscape and the complex potato virome in SLV. It highlights the importance of continued surveillance and improved diagnostics to mitigate the impact of viruses on potato production.Copyright (c) 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Spongospora subterranea is a soilborne plasmodiophorid that causes powdery scab and root gall formation in potato. In this study, 18 cover crops suitable for use in dry, high-altitude potato production regions were assessed in potting mix trials to determine whether these cover crops altered S. subterranea population levels. Although S. subterranea appeared to invade roots of all plant species tested, the pathogen was unable to complete its life cycle on 11 of 18 cover crops based on postharvest qPCR and microscopy results. Buckwheat, legumes, and scarlet barley do not appear to support pathogen replication, but the pathogen may be able to complete its life cycle in some mustards. High variability occurred in the experiments and part of this may be due to the natural infestations of peat-based potting mix with S. subterranea. A tomato bioassay was used to confirm that commercial sources of peat-based potting mix were infested with S. subterranea. Dry heat and autoclaving were tested as sanitation methods and multiple rounds of autoclaving were required to reduce viable S. subterranea in potting mix. A second cover crop experiment with autoclaved potting mix was conducted and it confirmed that buckwheat, legumes, and barley do not support S. subterranea replication but that some brassica crops may be hosts of this pathogen. The results suggest that buckwheat, legumes, and barley pose the least risk as cover crops in S. subterranea infested fields and show that peat-based potting mix should not be used in seed potato production.

In response to increasing interest in diploid potato (Solanum tuberosum) breeding and the production of diploid inbred hybrid potato varieties, the Breeding and Genetics section of the Potato Association of America (PAA) organized a symposium on diploid breeding that took place during the 2021 PAA annual meeting. Proceedings from that symposium are documented in this manuscript. Speakers from academia, government and industry presented their unique perspectives. Presentations covered a wide range of topics. Potential advantages of diploid breeding were introduced, and reasons to be skeptical about diploid breeding were highlighted. The impact that diploid breeding might have on the potato seed industry was discussed. Advantages for genetics research were emphasized. Aspects of tomato breeding and production were reviewed and considered as potential models for diploid potato breeding and production activities. Lastly, an industry-centered view of diploid potato breeding was provided. Taken together, these presentations are a snapshot of how diploid potato breeding was viewed in the moment, a vision for how diploid breeding might be implemented, and a thoughtful reflection on how diploid breeding and inbred hybrid varieties might change the potato variety development process and impact the potato industry.

Potato is a major staple crop, and necrotrophic bacterial pathogens such as Pectobacterium spp. are a major threat to global food security. Most lines of cultivated potato (Solanum tuberosum) are susceptible to Pectobacterium spp., but some lines of wild potato are resistant, including Solanum chacoense M6. Despite the discovery of resistance in wild potatoes, specific resistance genes are yet to be discovered. Crude protein extract from M6 had a global effect on Pectobacterium brasiliense Pb1692 (Pb1692) virulence phenotypes. Specifically, M6 protein extracts resulted in reduced Pectobacterium exo-protease activity and motility, induced cell elongation, and affected bacterial virulence and metabolic gene expression. These effects were not observed from protein extracts of susceptible potato S. tuberosum DM1. A proteomics approach identified protease inhibitors (PIs) as candidates for S. chacoense resistance, and genomic analysis showed higher abundance and diversity of PIs in M6 than in DM1. We cloned five PIs that are unique or had high abundance in M6 compared with DM1 and purified the proteins (g18987, g28531, g39249, g40384, g6571). Four of the PIs significantly reduced bacterial protease activity, with strongest effects from g28531 and g6571. Three PIs (g18987, g28531, g6571) inhibited disease when co-inoculated with Pectobacterium pathogens into potato tubers. Two PIs (g28531, g6571) also significantly reduced Pb1692 motility and are promising as resistance genes. These results show that S. chacoense PIs contribute to bacterial disease resistance by inhibiting exo-proteases, motility, and tuber maceration and by modulating cell morphology and metabolism. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

An outbreak of blackleg and soft rot of potato, caused primarily by the bacterial pathogen Dickeya dianthicola, has resulted in significant economic losses in the northeastern United States since 2015. The spread of this seedborne disease is highly associated with seed distribution; therefore, the pathogen likely spread with seed tubers. To describe the blackleg epidemic and track inoculum origins, a total of 1,183 potato samples were collected from 11 states associated with blackleg outbreak from 2015 to 2019. Of these samples, 39.8% tested positive for D. dianthicola. Seventeen isolates of D. dianthicola were recovered from these samples and the genetic diversity of these isolates was examined. Fingerprinting with BOX-A1R-based repetitive extragenic palindromic PCR and phylogenetic analysis based on sequences of the 16S rRNA and gapA genes indicated that D. dianthicola isolates were divided into three genotypes, denoted types I, II, and III. Ninety-five percent of samples from Maine were type I. Type II was found in Maine only in 2015 and 2018. Type II was present throughout the 5 years in some states at a lower percentage than type I. Type III was found in Pennsylvania, New Jersey, and Massachusetts, but not in Maine. Therefore, type I appears to be associated with Maine, but type II appeared to be distributed throughout the northeastern United States. The type II and rarer type III strains were closer to the D. dianthicola type strain isolated from the United Kingdom. This work provides evidence that the outbreak of blackleg of potato in the northeastern United States was caused by multiple strains of D. dianthicola. The geographic origins of these strains remain unknown.

Bacteria use selective membrane transporting strategies to support cell survival in different environments. Of the membrane transport systems, ATP-binding cassette (ABC) transporters, which utilize the energy of ATP hydrolysis to deliver substrate across the cytoplasmic membrane, are the largest and most diverse superfamily. These transporters import nutrients, export molecules, and are required for diverse cell functions, including cell division and morphology, gene regulation, surface motility, chemotaxis, and interspecies competition. Phytobacterial pathogens encode numerous ABC transporter homologs compared with related nonphytopathogens, with up to 160 transporters per genome, suggesting that plant pathogens must be able to import or respond to a greater number of molecules compared with saprophytes or animal pathogens. Despite their importance, ABC transporters have been little examined in plant pathogens. To understand bacterial phytopathogenesis and evolution, we need to understand the roles that ABC transporters play in plant–microbe interactions. In this review, we outline a multitude of roles that bacterial ABC transporters play, using both plant and animal pathogens as examples, to emphasize the importance of exploring these transporters in phytobacteriology.