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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. [ABSTRACT FROM AUTHOR]

Seed potato certification programs aim to limit disease incidence in planting material to levels below a threshold that causes significant losses to seed potato buyers. Records maintained for seed potato certification can be analyzed for trends in seed potato varietal mixture and disease incidences over time. We used logistic regression models to determine effects of year, potato variety, and their interaction on the incidences of potato diseases and disorders based on seed potato certification data collected in Colorado from 2012 to 2016. The effect of seed generation of important varieties on the incidence of common potato diseases was also quantified. Among the documented diseases, mosaic, caused primarily by Potato virus Y, is a persistent problem leading to high percentage of seed lot rejections in both summer and winter inspections, while blackleg, caused by Dickeya spp. and Pectobacterium spp., was a common disease causing summer rejections. The model demonstrated year, potato variety, and their interaction were key factors contributing to incidence of varietal mixture, or one or more potato diseases and disorders. For summer inspections, our models identified 53, 42, and six varieties sensitive to mosaic, blackleg, and leafroll, respectively. There were 17, 15, and six varieties that were tolerant to mosaic, blackleg, and leafroll regardless of pathogen pressures in the environment. For winter inspections, 51 varieties were sensitive to mosaic and three to leafroll, whereas 45 and one were relatively tolerant to mosaic and leafroll. The pattern of seed generation effects of selected potato varieties on mosaic and blackleg incidence was inconsistent across inspection years. In addition, we observed a significant negative correlation between the relative abundance of the green peach aphid, Myzus persicae, and mosaic in winter inspections. Mosaic incidences in summer and leafroll incidences were not influenced by common aphid species captured or total aphids in the valley. These results identify mosaic and blackleg as major causes of seed potato rejections and downgrades, sensitive and tolerant varieties, and provide suggestions for improving integrated crop management practices in Colorado. [ABSTRACT FROM AUTHOR]

The article focuses on the factors influencing the sustainability of the Wisconsin Seed Potato Certification Program (WSPCP) and examines the changes in disease control with changing pathogen epidemiology. It presents the factors responsible for long term stability of these programs which include invention of tractors, synthetic fertilizers, and pesticides. It informs that WSPCP was founded with two aims which include reducing pathogen incidence and providing variety of seeds.

Pectobacteriu,n species cause disease worldwide in many crop and ornamental plants, including potato. A new Pectobacteriu,n subspecies, P carotovorum subsp. brasiliensis was recently described in Brazil and later found in the United States, Israel, and South Africa. Its virulence traits and host range remain unknown. A comparison of three taxa commonly found on potato showed that both P carotovorum subsp. carotovorum and subsp. brasiliensis are more aggressive in causing tuber and stem soft rot than P atrosepticum. Also, despite bacterial growth inhibition in vitro of P carotovorum subsp. carotovorum and P atrosepticum strains by P carotovorum subsp. brasiliensis, this new subspecies and P carorovorum subsp. carotovorurn are able to co-colonize in the same infected tissue. Both subspecies were motile in lesions. Pathogenesis assays showed that host ranges of all three overlap, but are not identical. The host ranges of individual strains of P carobvorum subsp. carotovorum and subsp. brasiliensis are limited, whereas P atrosepticum can macerate many plant species in addition to potato. There was high variability in virulence assays with potato tuber; thus physiological factors were investigated. Tuber size, maturity, and field location had significant effects on susceptibility to soft rot, with larger, more mature tubers being more susceptible. [ABSTRACT FROM AUTHOR]

The advent of genomics has advanced science into a new era, providing a plethora of “toys” for researchers in many related and disparate fields. Genomics has also spawned many new fields, including proteomics and metabolomics, furthering our ability to gain a more comprehensive view of individual organisms and of interacting organisms. Genomic information of both bacterial pathogens and their hosts has provided the critical starting point in understanding the molecular bases of how pathogens disrupt host cells to cause disease. In addition, knowledge of the complete genome sequence of the pathogen provides a potentially broad slate of targets for the development of novel virulence inhibitors that are desperately needed for disease management. Regarding plant bacterial pathogens and disease management, the potential for utilizing genomics resources in the development of durable resistance is enhanced because of developing technologies that enable targeted modification of the host. Here, we summarize the role of genomics studies in furthering efforts to manage bacterial plant diseases and highlight novel genomics-enabled strategies heading down this path. [ABSTRACT FROM AUTHOR]

Pectobacrerium and Dickeva spp. are related broad-host-range enterobacteria! pathogens of angiosperms. A review of the literature shows that these genera each cause disease in species from at least 35% of angiosperm plant orders. The known host ranges of these pathogens partially overlap and, together, these two genera are pathogens of species from 50% of angiosperm plant orders. Notably, there are no reported hosts for either genus in the eudicots dade and no reported Dickeya hosts in the magnoliids or eurosids II clades, although Pectobacterium spp. are pathogens of at least one plant species in the magnoliids and at least one in each of the three eurosids 11 plant orders. In addition, Dickeva but not Pectobacterium spp. have been reported on a host in the rosids dade and, unlike Pectobacterium spp., have been reported on many Poales species. Natural disease among nonangiosperms has not been reported for either genus. Phylogenetic anaIyses of sequences concatenated from regions of seven housekeeping genes (acnA, gapA, icdA, mdh, mtlD, pgi, and proA) from representatives of these genera demonstrated that Dickeya spp. and the related tree pathogens, the genus Brenneria, are more diverse than Pectobacterium spp. and that the Pectobacterium strains can be divided into at least five distinct clades, three of which contain strains from multiple host plants. [ABSTRACT FROM AUTHOR]

Potato is an important sector to the U.S. economy, and it created over $100 billion in economic activity in 2021. The U.S. exports fresh potatoes to several countries. In certain cases, fresh potato shipments from the U.S. 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 Polymerase Chain Reaction (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 U.S. and internationally.

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., Competing Interests: The author(s) declare no conflict of interest.

Dickeya dianthicola has caused an outbreak of blackleg and soft rot of potato in the eastern half of the United States since 2015. To investigate genetic diversity of the pathogen, a comparative analysis was conducted on genomes of D. dianthicola strains. Whole genomes of 16 strains from the United States outbreak were assembled and compared with 16 previously sequenced genomes of D. dianthicola isolated from potato or carnation. Among the 32 strains, eight distinct clades were distinguished based on phylogenomic analysis. The outbreak strains were grouped into three clades, with the majority of the strains in clade I. Clade I strains were unique and homogeneous, suggesting a recent incursion of this strain into potato production from alternative hosts or environmental sources. The pangenome of the 32 strains contained 6,693 genes, 3,377 of which were core genes. By screening primary protein subunits associated with virulence from all U.S. strains, we found that many virulence-related gene clusters, such as plant cell wall degrading enzyme genes, flagellar and chemotaxis related genes, two-component regulatory genes, and type I/II/III secretion system genes, were highly conserved but that type IV and type VI secretion system genes varied. The clade I strains encoded two clusters of type IV secretion systems, whereas the clade II and III strains encoded only one cluster. Clade I and II strains encoded one more VgrG/PAAR spike protein than did clade III. Thus, we predicted that the presence of additional virulence-related genes may have enabled the unique clade I strain to become predominant in the U.S. outbreak.

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.

Seed potato certification data collected in Colorado from 2012 to 2016 was used to rank potato cultivar tolerance to blackleg. Five cultivars with different tolerance levels to blackleg ('Chipeta' ≈ 'Alegria' ≈ 'Lamoka' < 'Classic Russet' < 'Yukon Gem') were tested to determine whether we could validate field data with laboratory assays. A strain isolated from Colorado, Pectobacterium atrosepticum CW1-4, and the P. atrosepticum type strain, 33260, were used to inoculate plants through vacuum infiltration of tubers or stem inoculation. Disease was assessed with time-lapse video and by measuring lesion length and disease incidence. After vacuum infiltration of tubers with P. atrosepticum CW1-4 and 33260, cultivars varied in tolerance to soft rot ('Lamoka' < 'Classic Russet' < 'Alegria' ≈ 'Yukon Gem' < 'Chipeta'). Blackleg tolerance of the five cultivars also varied after vacuum infiltration ('Lamoka' < 'Alegria' ≈ 'Chipeta' < 'Classic Russet' ≈ 'Yukon Gem'). All cultivars were susceptible after stem inoculation with either strain. In this assay, 'Chipeta' had the longest lesions, and 'Lamoka' had the smallest lesions. Time-lapse video was used to assess 'Classic Russet' and 'Yukon Gem.' 'Yukon Gem' developed disease symptoms faster than 'Classic Russet,' but the difference was not significant. These results indicate that relative susceptibility of the five cultivars to P. atrosepticum depends on the assay used and that laboratory and greenhouse results differed from field observations.

Spongospora subterranea is a soilborne plasmodiophorid that causes powdery scab in potato. It also transmits potato mop-top virus (PMTV), which causes necrotic arcs (spraing) in potato tubers. Three field experiments were conducted in naturally S. subterranea -infested soil to investigate the effects of two chemicals, Omega 500F (fluazinam) and FOLI-R-PLUS RIDEZ (biological extract), on powdery scab, PMTV, and changes in S. subterranea inoculum with six different potato cultivars. The efficacy of soil treatment with these two chemicals on tuber lesions, root galling, and pathogen population was also assessed in greenhouse trials. The chemical treatments did not reduce powdery scab, root gall formation, or S. subterranea inoculum in the field or greenhouse trials. Postharvest S. subterranea soil inoculum in fields varied across farms and among potato cultivars but the pathogen population consistently increased by the end of the growing season. The evaluated russet cultivars were more tolerant to powdery scab than the yellow- or red-skinned cultivars but all were susceptible to PMTV. In the field, powdery scab indices and soil inoculum changes were positively correlated, while postharvest S. subterranea inoculum was positively correlated with root galling in both greenhouse trials. Powdery scab and PMTV occurred in noninoculated potting mix, indicating that peat-based potting mix is a source for both pathogens. These results demonstrate that chemical management methods currently used by farmers are ineffective, that S. subterranea and PMTV in potting mix can cause severe epidemics in greenhouses, and that potato cultivar choices impact inoculum increases in soil.

Powdery scab on potato tubers is caused by the obligate soilborne biotroph Spongospora subterranea and is known to cause substantial losses in potato production. The pathogen also infects roots of susceptible hosts, forming galls which can negatively affect root function. S. subterranea is also the vector of Potato mop-top virus , which causes a tuber necrosis disease that can, depending on temperature and cultivar, render potato tubers unmarketable. In this study, we adapted a published protocol to develop a sensitive and robust quantitative real-time PCR (qPCR) assay using specific primers and probes for detecting and quantifying S. subterranea sporosori in soil types that differ in physical properties, including organic matter content and soil pH. For the first time, an external control was utilized and applied directly to the soil prior to DNA extraction, which facilitated normalization of S. subterranea sporosori soil levels from sample to sample. The duplex qPCR protocol was demonstrated to be highly sensitive, capable of detecting and quantifying as few as 1 sporosorus/g of soil, with consistently high qPCR efficiency and the coefficient of determination ( R 2 ) values ranging from 94 to 99% and 0.98 to 0.99, respectively. The protocol was successfully implemented in enumerating S. subterranea sporosori in naturally infested field soil collected from several states and in artificial potting mixes with high organic matter content ranging from 64 to 71%. The qPCR method developed can be useful for potato growers to avoid agricultural soils highly infested with S. subterranea and in the development of risk assessment models in the future that incorporate cultivar susceptibility to powdery scab and soil infestation levels.

Uniqprimer, a software pipeline developed in Python, was deployed as a user-friendly internet tool in Rice Galaxy for comparative genome analyses to design primer sets for PCRassays capable of detecting target bacterial taxa. The pipeline was trialed with Dickeya dianthicola , a destructive broad-host-range bacterial pathogen found in most potato-growing regions. Dickeya is a highly variable genus, and some primers available to detect this genus and species exhibit common diagnostic failures. Upon uploading a selection of target and nontarget genomes, six primer sets were rapidly identified with Uniqprimer, of which two were specific and sensitive when tested with D . dianthicola . The remaining four amplified a minority of the nontarget strains tested. The two promising candidate primer sets were trialed with DNA isolated from 116 field samples from across the United States that were previously submitted for testing. D . dianthicola was detected in 41 samples, demonstrating the applicability of our detection primers and suggesting widespread occurrence of D . dianthicola in North America.