10:15am-10:45am
Taxonomic switches and interactions of bacterial species causing blackleg and soft rot of potato in the Northeastern United States
Xiuyan Zhang, University of Maine

               Potato blackleg and soft rot (PBSR) is an important disease, responsible for recent outbreaks in the northeastern United States beginning in 2015. To investigate the temporal dynamics of the disease and potential bacteria-bacteria and bacteria-host interactions, we conducted experiments to: 1) track species switches during recent years 2) evaluate the effect of Dickeya dianthicola inoculation on potato tubers at different timings, 3) examine the effect of mixed inocula of D. dianthicola and P. parmentieri on plant infection, and 4) investigate interactions between the pathogen and host. The taxonomic analysis was performed through DNA sequencing, including amplicon sequencing of potato samples that were submitted to the laboratory for testing as well as sequencing of specific gene regions on isolated bacteria. We found most disease samples contained multiple bacterial species, with D. dianthicola being predominant in the first two years of the outbreak. However, there was a rapid shift in the dominant bacterial species, with D. dianthicola being largely replaced by P. versatile (39%) and P. parmentieri (33%). Dickeya dianthicola was the most aggressive species compared with other PBSR pathogens. When D. dianthicola was co-inoculated with one of some pathogenic species, such as P. carovotorum, P. versatile, especially P. parmentieri, PBSR was much higher than that when inoculated singly. We inoculated potato tubers with D. dianthicola at different stages of storage and then planted these tubers in the following year. The results showed early bacterial inoculation had a higher disease incidence compared to late inoculation just prior to planting. Thus, potato tubers could be infected by contact with infected tubers in storage, but this was less likely when inoculation occurred at planting. The species dynamics may be associated with their interactions driven by weather conditions.

10:45am-11:00am
Field detection and genomic sequencing to characterize the diversity of Streptomyces pathogens that cause potato common scab
Christopher Clarke, USDA Agricultural Research Service

               Common scab is a devastating disease of potato and other tuber and root crops. More than ten species of Streptomyces bacteria that produce the toxin Thaxtomin A can cause common scab. USDA-ARS maintains a collection of more than 1000 phytopathogenic Streptomyces isolates. We are collecting modern isolates and performing genome sequencing on both historic and modern isolates to characterize the diversity of the pathogen. These data are used to determine the distribution of different lineages of the pathogen across the United States and characterize virulence mechanisms. Additionally, transmission patterns of the pathogen may be inferred through genomic epidemiology. We have also developed and deployed a qPCR assay for quantifying pathogen abundance in field soil. Implementation of that assay enables improved understanding of pathogen dynamics across the growing season and the ability to account for heterogeneous disease pressure within field trials. No potato cultivar is fully resistant to common scab, and there are differential resistances dependent on the pathogen species. Therefore, knowledge of the distribution and population structure of the pathogen is critical for growers to make informed planting decisions.

11:00am-11:15am        
Unveiling the Genetic Diversity of Streptomyces spp. from Potato Tubers and Soil: Insights into Pathogenicity and Biocontrol Strategies
Ashish Ranjan, University of Minnesota-Twin Cities

               Streptomyces spp. is a soil-borne gram-positive filamentous bacteria from phylum actinobacteria and is well known for its ability to produce various biologically active compounds. Few of these Streptomyces spp. cause economically important common scab disease of potatoes. Once Streptomyces infests the field, it is difficult to get rid of it. Thus, identifying the pathogenic species of Streptomyces associated with the disease in the field is crucial for its effective management. This study focuses on the genetic diversity of Streptomyces spp. from potato-growing farm in Minnesota. A total of  51 isolates of Streptomyces were retrieved from infected potato tubers and soil samples. 16S rRNA sequencing was performed to identify the species of these isolates. However, with many Streptomyces species sharing a great similarity in 16S rRNA sequences, it is difficult to identify such species. Therefore, we have used multilocus sequence analysis (MLSA) for four well-known housekeeping genes: atpD, gyrB, rpoB, and trpB to determine their species. The pathogenicity of these isolates was also determined based on the presence of pathogenicity island (PAI) genes and their ability to infect radish and potato tubers. Out of 51 isolates, 21 were found to be nonpathogenic. In-vitro dual plate assays using these nonpathogenic isolates confirmed that few isolates possess highly potent biocontrol activity against soil-borne pathogens such as Fusarium graminearum, Pythium ultimum, S.sclerotiorum, and Verticillium dahliae. Further characterization of these strains could lead to devising strategies to control common potato scab disease while deciphering the novel antibiotic properties of these Streptomyces spp.

11:15am-11:30am
Phylogenetic relationships and population structure among global isolates of Colletotrichum coccodes using whole-genome single nucleotide polymorphisms
Marcio Zaccaon, NDSU

               The fungus Colletotrichum coccodes (Wallr.) S. J. Hughes, the causal agent of black dot and part of the early die complex in potato, has been reported from most potato-growing regions of the world.  C. coccodes reduces yield in potato and decreases marketability of tubers destined to table consumption.  Despite the relevance of C. coccodes for the potato industry, single nucleotide polymorphism (SNP) and whole-genome sequencing have never been applied to study C. coccodes.  In the current study, we deployed whole-genome sequence based single nucleotide polymorphisms to provide a general overview of the phylogenetic relationships and population structure among C. coccodes isolates from potato-growing regions in Australia, Chile, South Africa, Europe, and the US.  The resulting WGS-SNP based phylogenetic tree consisted of two major clades which were further divided into four subclades.  Analysis of principal components (DAPC), molecular variance (AMOVA), and principal coordinates (PCoA) supported the clustering of the phylogenetic tree to a great extent.  Isolates belonging to different subclades were separated from each other by substantial nucleotide polymorphisms.  No subclades were exclusive to any particular geographic region.  However, most isolates from a given region tended to belong to the same subclade.  Results suggest some geographic restriction of C. coccodes genotypes; however, global dissemination of this pathogen is present.  We also demonstrate that C. coccodes is amenable to next-generation sequencing technologies and they should be used in place of VCG and AFLP analysis when applicable.  Furthering our understanding of population genetic relatedness will aid in disease management, including identifying host resistance that is functional across all pathogen genotypes