Margarethe A Cooper

Interests

Teaching

Food Safety, Food Microbiology, Microbiology, Parasitology

Courses

Scholarly Contributions

Journals/Publications

• Goforth, M., Cooper, M., Oliver, A., Pinzon, J., Skots, M., Obergh, V., Suslow, T., Flores, G., Huynh, S., Parker, C., Mackelprang, R., & Cooper, K. (2024). Bacterial community shifts of commercial apples, oranges, and peaches at different harvest points across multiple growing seasons. PLoS ONE, 19(4). doi:10.1371/journal.pone.0297453
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  Assessing the microbes present on tree fruit carpospheres as the fruit enters postharvest processing could have useful applications, as these microbes could have a major influence on spoilage, food safety, verification of packing process controls, or other aspects of processing. The goal of this study was to establish a baseline profile of bacterial communities associated with apple (pome fruit), peach (stone fruit), and Navel orange (citrus fruit) at harvest. We found that commercial peaches had the greatest bacterial richness followed by oranges then apples. Time of harvest significantly changed bacterial diversity in oranges and peaches, but not apples. Shifts in diversity varied by fruit type, where 70% of the variability in beta diversity on the apple carposphere was driven by the gain and loss of species (i.e., nestedness). The peach and orange carposphere bacterial community shifts were driven by nearly an even split between turnover (species replacement) and nestedness. We identified a small core microbiome for apples across and between growing seasons that included only Methylobacteriaceae and Sphingomonadaceae among the samples, while peaches had a larger core microbiome composed of five bacterial families: Bacillaceae, Geodermtophilaceae, Nocardioidaceae, Micrococcaeceae, and Trueperaceae. There was a relatively diverse core microbiome for oranges that shared all the families present on apples and peaches, except for Trueperaceae, but also included an additional nine bacterial families not shared including Oxalobacteraceae, Cytophagaceae, and Comamonadaceae. Overall, our findings illustrate the important temporal dynamics of bacterial communities found on major commercial tree fruit, but also the core bacterial families that constantly remain with both implications being important entering postharvest packing and processing.
• Goforth, M., Obergh, V., Park, R., Porchas, M., Crosby, K., Jifon, J., Ravishankar, S., Brierley, P., Leskovar, D., Turini, T., Schultheis, J., Coolong, T., Miller, R., Koiwa, H., Patil, B., Cooper, M., Huynh, S., Parker, C., Guan, W., & Cooper, K. (2024). Bacterial diversity and composition on the rinds of specific melon cultivars and hybrids from across different growing regions in the United States. PLoS ONE, 19(4). doi:10.1371/journal.pone.0293861
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  The goal of this study was to characterize the bacterial diversity on different melon varieties grown in different regions of the US, and determine the influence that region, rind netting, and variety of melon has on the composition of the melon microbiome. Assessing the bacterial diversity of the microbiome on the melon rind can identify antagonistic and protagonistic bacteria for foodborne pathogens and spoilage organisms to improve melon safety, prolong shelf-life, and/or improve overall plant health. Bacterial community composition of melons (n = 603) grown in seven locations over a four-year period were used for 16S rRNA gene amplicon sequencing and analysis to identify bacterial diversity and constituents. Statistically significant differences in alpha diversity based on the rind netting and growing region (p < 0.01) were found among the melon samples. Principal Coordinate Analysis based on the Bray-Curtis dissimilarity distance matrix found that the melon bacterial communities clustered more by region rather than melon variety (R2 value: 0.09 & R2 value: 0.02 respectively). Taxonomic profiling among the growing regions found Enterobacteriaceae, Bacillaceae, Microbacteriaceae, and Pseudomonadaceae present on the different melon rinds at an abundance of ≥ 0.1%, but no specific core microbiome was found for netted melons. However, a core of Pseudomonadaceae, Bacillaceae, and Exiguobacteraceae were found for non-netted melons. The results of this study indicate that bacterial diversity is driven more by the region that the melons were grown in compared to rind netting or melon type. Establishing the foundation for regional differences could improve melon safety, shelf-life, and quality as well as the consumers’ health.
• Zuccolo, A., Joens, L. A., Cooper, M. A., & Cooper, K. K. (2013). Re-sequencing of a virulent strain of Campylobacter jejuni NCTC11168 reveals potential virulence factors.. Research in microbiology, 164(1), 6-11. doi:10.1016/j.resmic.2012.10.002
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  In vitro passage of Campylobacter jejuni strains results in phenotypic changes and a general loss of virulence, as is the case with the genome-sequenced strain C. jejuni NCTC11168. Re-sequencing of a virulent strain of NCTC11168 identified 41 SNPs or indels involving 20 genes, four intergenic regions and three pseudogenes. The genes include six motility genes, two chemotaxis genes, three hypothetical genes and a capsule biosynthesis gene, which might have a critical role in C. jejuni virulence. Additionally, we found an insertion in both Cj0676 and Cj1470c, pseudogenes in avirulent NCTC11168, but functional proteins in virulent NCTC11168.
• Law, B., Zuccolo, A., Law, B., Joens, L. A., Cooper, M. A., & Cooper, K. K. (2011). Complete genome sequence of Campylobacter jejuni strain S3.. Journal of bacteriology, 193(6), 1491-2. doi:10.1128/jb.01475-10
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  Campylobacter jejuni is one of the leading causes of bacterial gastroenteritis in the world; however, there is only one complete genome sequence of a poultry strain to date. Here we report the complete genome sequence and annotation of the second poultry strain, C. jejuni strain S3. This strain has been shown to be nonmotile, to be a poor invader in vitro, and to be a poor colonizer of poultry after minimal in vitro passage.
• Sterling, C. R., Ortega, Y. R., Gilman, R. H., Cooper, M. A., Cama, V., & Adam, R. D. (2010). Molecular analysis of household transmission of Giardia lamblia in a region of high endemicity in Peru.. The Journal of infectious diseases, 202(11), 1713-21. doi:10.1086/657142
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  Giardia lamblia is ubiquitous in multiple communities of nonindustrialized nations. Genotypes A1, A2, and B (Nash groups 1, 2, and 3, respectively) are found in humans, whereas genotypes C and D are typically found in dogs. However, genotypes A and B have occasionally been identified in dogs..Fecal Giardia isolates from 22 families and their dogs, living in Pampas de San Juan, were collected over 7 weeks in 2002 and 6 weeks in 2003. Samples were genotyped, followed by sequencing and haplotyping of many of these isolates by using loci on chromosomes 3 and 5..Human infections were all caused by isolates of genotypes A2 and B. Human coinfections with genotypes A2 and B were common, and the reassortment pattern of different subtypes of A2 isolates supports prior observations that suggested recombination among genotype A2 isolates. All dogs had genotypes C and/or D, with one exception of a dog with a mixed B/D genotype infection..In a region of high endemicity where infected dogs and humans constantly commingle, different genotypes of Giardia are almost always found in dogs and humans, suggesting that zoonotic transmission is very uncommon.
• Sterling, C. R., Worobey, M., Sterling, C. R., Cooper, M. A., & Adam, R. D. (2007). Population genetics provides evidence for recombination in Giardia.. Current biology : CB, 17(22), 1984-8. doi:10.1016/j.cub.2007.10.020
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  Giardia lamblia (syn. Giardia intestinalis, Giardia duodenalis) is an enteric protozoan parasite with two nuclei, and it might be one of the earliest branching eukaryotes. However, the discovery of at least rudimentary forms of certain features, such as Golgi and mitochondria, has refuted the proposal that its emergence from the eukaryotic lineage predated the development of certain eukaryotic features. The recent recognition of many of the genes known to be required for meiosis in the genome has also cast doubt on the idea that Giardia is primitively asexual, but so far there has been no direct evidence of sexual reproduction in Giardia, and population data have suggested clonal reproduction. We did a multilocus sequence evaluation of the genotype A2 reference strain, JH, and five genotype A2 isolates from a highly endemic area in Peru. Loci from different chromosomes yielded significantly different phylogenetic trees, indicating that they do not share the same evolutionary history; within individual loci, tests for recombination yielded significant statistical support for meiotic recombination. These observations provide genetic data supportive of sexual reproduction in Giardia.

Poster Presentations

• Cooper, M. A., Mydosh, J., Sainz, J., Ignat, S., & Li, S. (2022, Summer). SaferFoodCats as a tool to engage students in Food Safety and train interns for Tribal outreach in Food Safety. 2022 Extension Conference.
• Li, S., Cooper, M. A., Sainz, J., Ignat, S., & Fournier, A. J. (2022, August). Increasing Knowledge in IPM and Food Safety among Underserved Communities. 2022 University of Arizona Cooperative Extension Annual Conference. August 10-12, 2022.
• Li, S., Cooper, M. A., Sainz, J., Ignat, S., & Fournier, A. J. (2022, October). Increasing Knowledge in IPM and Food Safety among Underserved Communities. 2022 UArizona Food Safety Conference, October 26-27, 2022.
• Cooper, K. K., Pinzon, J., Cooper, M. A., Skots, M., Flores, G. E., Mackelprang, R., & Suslow, T. V. (2019, July). Characterization of tree fruit bacterial communities during harvest. International Food Protection Association Annual Meeting,. Louisville, KY: International Food Protection Association.
• Lopez, G. U., Christman, K. A., Cooper, M. A., Carstens, R., Thoutt, E., Gonzalez, M., Vasovski, S., Cabrera, D. D., Lonchar, T., Geel, E., Torres, M. A., Lopez, J., Perez, S., & Villa Barbosa, G. (2019, Summer). The University of Arizona Cooperative Extension 4-H Program Collaborating Statewide in Preparing the Next Generation of STEM Innovators. Arizona Cooperative Extension Conference "Pillar of the Community". Tucson, AZ: UA Cooperative Extension.
• Cooper, K. K., Pinzon, J., Cooper, M. A., Skots, M., Flores, G. E., Mackelprang, R., & Suslow, T. V. (2018, September). Characterization of Tree Fruit Bacterial Communities during Harvest. Lake Arrowhead Microbial Genomics Conference. Lake Arrowhead, CA.
• Cooper, K. K., Pinzon, J., Cooper, M. A., Skots, M., Suslow, T. V., Flores, G. E., & Mackelprang, R. (2018, July). Characterization of Tree Fruit Bacterial Communities during Harvest. USDA NIFA "Improving Food Safety" Meeting. Salt Lake City, UT: United State Department of Agriculture, National Institute of Food and Agriculture.

Others

• Cooper, M. A., Li, S., & Woolfolk, C. M. (2022, November). Keeping Food Safe at Home. IPM Newsletter.
• Li, S., Cooper, M. A., & Woolfolk, C. M. (2022, November). Food Safety Resources. IPM Newsletter.