Research

Bacteriophage Ecology & Evolution

Characterizing bacteriophage genotypic and phenotypic diversity in agriculture

Bacteriophage (viruses that infect bacteria) are ubiquitous in the environment and have the potential to influence bacterial populations. Plant pathogenic bacteria can be devastating to crop production with long-term consequences for supply chains. Addressing how bacterial populations are shaped through interactions with microbial community members such as bacteriophage is important to understanding how plant disease occurs and persists.

To study the interaction between bacteria and bacteriophage, I am working on phage associated with Xanthmonas arboricola pv. pruni, casual agent of bacterial spot in Prunus spp. including peach. Using a collection of phage isolates collected from infected peach leaves, I am performing whole genome sequencing to characterize the genetic diversity, incorporating temporal and spatial scales.

Xanthomonas Ecology & Evolution

Characterizing bacterial ecology and evolution in agriculture

Phytopathogenic bacteria are important pests of agricultural crops, causing many devastating diseases and leading to severe yield losses. To develop effective management strategies against bacterial pathogens, we need to understand (1) how these organisms persist in the environment and (2) how interactions with other microorganisms influences bacterial ecology and evolution.

To address these questions, I am researching the interaction between the bacterial plant pathogen, Xanthomonas arboricola pv. pruni (Xap), and associated bacteriophage (phage). Phage are viruses that infect bacteria, often times lysing and killing bacterial cells. The interaction between Xap and virulent phage can shape bacterial populations and drive bacterial evolution. My work focuses on comparing whole genomes of Xap strains to identify specific genetic components that contribute to bacterial susceptibility and resistance to phage infection. Further, I am examining shifts in bacterial genomes at spatiotemporal scales to identify variable regions associated with spatial or temporal differences.

Research Statement

My general statement of research interests including my experience, current projects, and proposed future plans.

Research Statement

Publications

Published, Peer-reviewed (⁺Undergraduate co-author)

D’Amico-Willman, K.M., Prasanna Joglekar*, Emily K. Luna, David F. Ritchie, Jennie Fagen, and Alejandra I Huerta. (2022). Complete genome sequence of Xanthomonas arboricola pv. pruni strain Xcp1 isolated in 1984 from a bacterial spot canker on Prunus persica var. nucipersica cv. “Redgold”. Microbiology Resource Announcements 11. https://doi.org/10.1128/mra.00209-22.

*co-first authors

D’Amico-Willman, K.M., Ouma, W.Z., Meulia, T., Sideli, G.M., Gradziel, T.M., and Fresnedo-Ramirez, J. (2022). Whole-genome sequence and methylome profiling of the almond (Prunus dulcis [Mill.] D.A.Webb) cultivar ‘Nonpareil’. G3 Genes|Genomes|Genetics, jkac065. https://doi.org/10.1093/g3journal/jkac065.

D’Amico-Willman, K.M., Sideli, G.M., Allen, B.J., Anderson, E.S.⁺, Gradziel, T.M. and Fresnedo-Ramirez, J. (2022). Identification of putative markers of noninfectious bud failure in almond (Prunus dulcis) through genome wide DNA methylation profiling and gene expression analysis in an almond peach hybrid population. Frontiers in Plant Science 13, 1-15. https://doi.org/10.3389/fpls.2022.804145.

D’Amico-Willman, K.M., Anderson, E.S.⁺, Gradziel, T.M., and Fresnedo Ramirez, J. (2021). Telomere length and Telomerase Reverse Transcriptase (TERT) expression are associated with age in almond (Prunus dulcis [Mill.] D.A.Webb). Plants 10. https://doi.org/10.3390/plants10020189.

Conrad, A.O., McPherson, B.A., Lopez-Nicora, H., D’Amico, K.M., Wood, D.L., and Bonello, P. (2019). Disease incidence and spatial distribution of host resistance in a coast live oak/sudden oak death pathosystem. Forest Ecology and Management 433, 618-624. https://doi.org/10.1016/j.foreco.2018.11.035.

Chakravarthy, S., Butcher, B., Liu, Y., D’Amico, K., Coster, M.⁺, and Filiatrault, M. (2017). Virulence of Pseudomonas syringae is modulated through the catabolite repression control protein Crc. Molecular Plant-Microbe Interactions 30, 283-294. https://doi.org/10.1094/MPMI-09-16-0196-R.

D’Amico, K., and Filiatrault, M. (2017). The conserved hypothetical protein PSPTO_3957 is essential for virulence in the plant pathogen Pseudomonas syringae pv. tomato DC3000. FEMS Microbiology Letters 364. https://doi.org/10.1093/femsle/fnx004.

Butcher, B., Chakravarthy, S., D’Amico, K., Stoos, K.B., and Filiatrault, M. (2016). Disruption of the carA gene in Pseudomonas syringae results in reduced fitness and alters motility. BMC Microbiology 12, 194-209. https://doi.org/10.1186/s12866-016-0819-z.

D’Amico, K.M., Horton, T.R., Maynard, C.A., Stehman, S.V., Oakes, A.D., and Powell, W.A. (2015). Assessing ectomycorrhizal associations on transgenic American chestnut compared to the wild type, a conventionally-bred hybrid, and related Fagaceae species. Applied and Environmental Microbiology 81, 100-108. https://doi.org/10.1128/AEM.02169-14.

Park, S.H., Bao, Z., Butcher, B.G., D’Amico, K., Xu, Y., Stodghill, P., Schneider, D.J., Cartinhour, S., and Filiatrault, M.J. (2014). Analysis of the small RNA spf in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000. Microbiology 160 941-953. https://doi.org/10.1099/mic.0.076497-0.

Park, S.H., Butcher, B.G., Anderson, Z.⁺, Pellegrini, N.⁺, Bao, Z., D’Amico, K., and Filiatrault, M.J. (2013). Analysis of the small RNA P16/RgsA in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000. Microbiology 159, 296-306. https://doi.org/10.1099/mic.0.063826-0.

Pre-prints, not peer-reviewed

D’Amico-Willman, K.M., Neiderhuth, C.E., Anderson, E.S.⁺, Gradziel, T.M., and Fresnedo-Ramirez, J. (2021). Hypermethylation is associated with increased age in almond (Prunus dulcis [Mill.] D.A.Webb) accessions. bioRxiv. doi: https://doi.org/10.1101/2021.05.02.442365.

D’Amico-Willman, K.M., Neiderhuth, C.E., Willman, M.R., Ouama, W.Z., Meulia, T., Gradziel, T. and Fresnedo-Ramirez, J. (2021). Integrated analysis of the methylome and transcriptome of twin almonds (Prunus dulcis [Mill.] D.A.Webb) reveals genomic features associated with non-infectious bud failure. bioRxiv. doi: https://doi.org/10.1101/2021.02.08.430330.

Page updated

Report abuse