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Welcome to our lab!
The Applied Environmental Microbiology and Exposure Assessment Lab within the University of Maryland School of Public Health focuses on evaluating the complex relationships between environmental microbial exposures and human infectious diseases. Our fearless leader is Dr. Amy R. Sapkota, a Professor of Environmental Health within the Maryland Institute for Applied Environmental Health, and the Director of CONSERVE: A Center of Excellence at the Nexus of Sustainable Water Reuse, Food and Health, funded by the U.S. Department of Agriculture, National Institute of Food and Agriculture. Our group includes undergraduate students, graduate students, post-docs and technicians.
We are always looking for talented undergraduates, graduate students and post-docs to join our group. Please explore our site, and if our group may be a good fit for your interests, please contact Dr. Sapkota at email@example.com.
Rianna Murray got promoted to Assistant Research Professor in MIAEH.
Jessica Chopyk published a paper in Environmental Microbiome https://doi.org/10.1186/s40793-020-00365-8
Prachi Kulkarni published a paper in Frontiers in Environmental Science https://doi.org/10.3389/fenvs.2020.541921
DAWN: Dashboard for Agricultural Water use and Nutrient management
Xin-Zhong Liang (PI). A.R. Sapkota (Co-PI).
Funder: U.S. Department of Agriculture, National Institute of Food and Agriculture.
Total Costs: $10,000,000 Funding Period: 2020-2025
The plan is to develop a Dashboard for Agricultural Water use and Nutrient management (DAWN) that will help maximize corn, soybean and bioenergy crop production in the Midwestern United States. DAWN is expected to identify innovative ways of increasing land- and water-use efficiency given competing resource demands and varying water availability and quality.
For more information, please visit: https://sph.umd.edu/news-item/amy-sapkota-investigator-project-sustain-agricultural-production-funded-10-million-usda
UMD Global STEWARDS: STEM Training at the Nexus of Energy, Water Reuse and Food Systems
Amy R. Sapkota (Principal Investigator).
Funder: National Research Traineeship (NRT) program funded by the National Science Foundation.
Total Costs: $3,000,000 Funding Period: 2018-2023
The program is preparing PhD students from UMD programs in the life and public health sciences, earth system sciences, engineering and computational sciences, social behavioral sciences, natural resource management studies, energy and environmental policy, and other FEW-related programs through hands-on domestic and international experiences, as well as research, professional development, and outreach opportunities.
For more information, please visit the Global Stewards website: http://globalstewards.umd.edu/
CONSERVE: A Center of Excellence at the Nexus of Sustainable Water Reuse, Food & Health
Amy R. Sapkota (Principal Investigator).
Funder: U.S. Department of Agriculture, National Institute of Food and Agriculture.
Total Costs: $10,000,000 Funding Period: 2016-2021
CONSERVE Overview: Climate variability is placing severe stress on high-quality agricultural irrigation sources such as groundwater. As a result, water reuse and exploring nontraditional irrigation water sources (e.g., reclaimed water) have become national priorities for agricultural water security and the sustainable production of our food supply. At the same time, the recent Food Safety Modernization Act is shifting the focus of food safety from responding to foodborne contamination to preventing it. This places great responsibility on agricultural producers, who must meet stricter guidelines for the quality of irrigation water used on food crops. This presents a significant new gap: new sustainable on-farm solutions are needed so that agricultural producers can conserve groundwater through the safe use of nontraditional irrigation water sources.
We are addressing this need through CONSERVE (COordinating NontraditionalSustainable watER Use in Variable climatEs): A Center of Excellence at the Nexus of Sustainable Water Reuse, Food, and Health. CONSERVE research, extension and education activities are developed by a leading team of bioscientists, engineers, economists, social-behavioral scientists, law and policy experts, extension specialists, educational media developers and computer scientists. We extend our findings to stakeholders, including farmers, communities, educators, students, and federal, state, and local governments through outreach and engagement. CONSERVE is focusing on two key regions, the Mid-Atlantic and Southwest, thereby highlighting two diverse climates that are in different stages of need for nontraditional irrigation. Specifically, the Mid-Atlantic is currently not experiencing serious water shortages, and the integration of new on-farm water treatment technologies at this time represents a proactive approach to climate change. In contrast, the Southwest region is experiencing severe water shortage crises, and thereby represents a need for reactive solutions to climate change. Through our innovative efforts, we will facilitate the adoption of transformative on‐farm solutions that enable the safe use of nontraditional irrigation water on food crops and effectively reduce the nation’s agricultural water challenges that are exacerbated by climate change.
For more information, please visit the CONSERVE website: http://conservewaterforfood.org/
Past projects within the past five years:
Rapid Response Characterization of New and Manipulated Tobacco Products (P50 Center, P50CA180523)
P. Clark (PI). R01 within P50 Center, “Exploring tobacco microbial constituents and the oral microbiome of tobacco users.” A.R. Sapkota, E.F. Mongodin (Co-PIs).
Funder: Food and Drug Administration, and National Institutes of Health/National Cancer Institute.
Total Costs: $20,000,000 (Overall Center), $2,700,00 (R01). Funding Period: 2013-2018.
Project Overview: Novel research is needed to improve our understanding of the microbial constituents of tobacco products, and their associated adverse health effects. Research conducted over the past 50 years has provided a firm knowledge base regarding the chemical and physical composition of smokeless tobacco products, smoked tobacco products and cigarette smoke. However, there is a paucity of data regarding the microbial constituents of these products and their impacts on public health. A limited number of microorganisms have been characterized in previous studies, due to the use of traditional culture-based methods. Thus, our long-term goal is to harness the power of next-generation sequencing technologies to comprehensively characterize 1) the bacterial flora of a range of conventional, new and manipulated tobacco products and smoke; 2) the influence of specific groups of bacteria on the production of tobacco-specific N-nitrosamines (TSNAs); and 3) the impacts of tobacco bacterial flora on the oral microbiome of tobacco users. The central hypothesis of our project is that tobacco products are characterized by bacterial populations that may influence not only the chemical constituents of tobacco products, but also the health of tobacco users. Our rationale for exploring this hypothesis is that, to our knowledge, no studies have comprehensively characterized the microbial diversity of tobacco products and their subsequent public health effects. As a result, there is a critical knowledge gap with regard to 1) the diversity of tobacco microbial constituents; and 2) whether these constituents should be regulated by FDA. Our specific aims address these critical issues: Aim 1: To explore the bacterial microbiome of conventional, new and manipulated smoked and smokeless tobacco products and smoke, and examine the role of specific genera in TSNA production; Aim 2: To provide novel, baseline data on the composition of the oral microbiome and its associated expressed activities in smokers and smokeless tobacco users compared with that of non-users; Aim 3: To characterize the transient changes--bacterial community composition and expressed metabolic activities--in the oral microbiome after single-use of new and manipulated smoked and smokeless tobacco products. The novel science generated in this study is directly relevant to the Family Smoking Prevention and Tobacco Control Act because it can be used immediately to inform potential new microbial-related tobacco regulations that have never before been considered despite the reality that the microbiology of tobacco has been of interest to the tobacco industry for the past 60 years.
For more information, please visit our website at: https://tcors.umd.edu/
Suhana Chattopadhyay is a Senior Faculty Specialist. She received her BS and MS in Botany from India. She completed her MS in Ecology from Kent State University, Ohio and joined University of Maryland in 2014.
Contact: Building: School of Public Health | Room: 0110N Phone: (301) 405-5559 | Email: firstname.lastname@example.org
Leena Malayil is a Research Associate for CONSERVE, a Center of Excellence at the Nexus of Sustainable Water Reuse, Food, and Health. successfully defended her PhD dissertation as student in the Toxicology and Environmental Health program. She received her triple major BS (Chemistry, Zoology and Microbiology) and MS (Microbiology) in India. She also has a MS in Toxicology from University of Georgia (2009) and recently graduated with a PhD in Toxicology and Environmental Health from University of Maryland in 2019.
Contact: Building: School of Public Health | Room: 0110N Phone: (301) 405-5559 | Email: email@example.com
Michele Morgado is graduate student in Environmental Health Sciences. She received her BS (Marine Biology and Fisheries) in Portugal and earned an MS in Oceanography/Coastal Zone Management from Nova Southeastern University (2007). She also attended Johns Hopkins University and received a post-master’s graduate certificate in Environmental Engineering, Science and Planning (2014). Previously, she worked as an oceanographic technician and adjunct faculty at the U.S. Naval Academy, and taught Oceanography at Anne Arundel Community College.
Contact: Building: School of Public Health | Room: 0110N Phone: (301) 405-5559 | Email: firstname.lastname@example.org
Rianna Murray, is an Assistant Research Professor in MIAEH and Program Manager of the UMD Global STEWARDS program. She received her BSc. with a double major in Biochemistry and Chemistry from the University of the West Indies in Trinidad & Tobago. She graduated from the University of Maryland School of Public Health in 2019 with a PhD in Toxicology and Environmental Health. She also earned her Master of Public Health degree with a concentration in Environmental Health Sciences from the University of Maryland School of Public Health in 2013. Her research interests lie in the fields of environmental health, global health, environmental justice, food safety, and water quality. Her dissertation investigated the influence of private drinking water wells and their proximity to animal agricultural operations on the incidence of foodborne illness in Maryland. Rianna's passion for global health took her to Sierra Leone in 2014 and 2016 with the UMD student-led group Public Health Without Borders, where she worked with a rural community to conduct community needs assessments and health and hygiene workshops, and investigated the impact of the 2014-2016 Ebola epidemic on the community.
Contact: Building: School of Public Health | Room: 0110N Phone: (301) 405-5559 | Email: email@example.com
Post doctoral scholars:
Leena Malayil (PhD, 2019)
Hillary Craddock (PhD, 2019)
Jessica Chopyk (PhD, 2019)
Rianna Murray (PhD, 2018)
Prachi Kulkarni (PhD, 2016)
Rhodel Bradshaw (MPH, 2017)
Kelsey Babik (MPH, 2015 )
Molly Reid (MPH, 2015)
Rachel Rosenberg Goldstein (PhD, 2013)
Anthony Quang-Vinh Bui
Selected Publications From Our Group Within the Past Five Years (†denotes corresponding author; § denotes shared first or senior authorship; #denotes advised undergraduate students; *denotes advised graduate students; **denotes advised post-doctoral students):
Kulkarni P**, Olson ND*, Paulson JN, Pop M, Maddox C, Claye E, Rosenberg Goldstein RE, Sharma M, Gibbs SG, Mongodin EF, Sapkota AR†. 2018. Conventional wastewater treatment and reuse site practices modify bacterial community structure but do not eliminate some opportunistic pathogens in reclaimed water. Science of the Total Environment.
Murray R, Rosenberg Goldstein R, Maring E, Pee D, Aspinwall K, Wilson S, Sapkota A. Prevalence of Microbiological and Chemical Contaminants in Private Drinking Water Wells in Maryland, USA. International Journal of Environmental Research and Public Health. 2018;15(8):1686. doi:10.3390/ijerph15081686
Chopyk J, Nasko DJ, Allard S, Bui A, Treangen T, Pop M, Mongodin EF, Sapkota AR†. 2020 Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications. Water Research, 169:115250.
Chopyk J, Nasko CJ, Allard S, Callahan MT, Bui A, Ferelli AMC, Chattopadhyay S, Mongodin EF, Pop M, Micallef S, Sapkota AR†. 2020. Metagenomic analysis of bacterial and viral assemblages from a freshwater creek and irrigated field reveals temporal and spatial dynamics. Science of the Total Environment, 205:135395. doi: 10.1016/j.scitotenv.2019.135395.
Craddock HA, Panthi S, Rjoub Y, Lipchin C, Sapkota A, Sapkota AR†. 2020. Antibiotic and herbicide concentrations in household greywater reuse systems and pond water used for food crop irrigation: West Bank, Palestinian Territories. Science of the Total Environment, 699:134205.
Malayil L, Chattopadhyay S, Kulkarni P, Hittle LE, Clark P, Mongodin EF, Sapkota AR. 2020. Mentholation triggers brand-specific shifts in the bacterial microbiota of commercial cigarette products. Applied Microbiology and Biotechnology, 1-11.
Murray, R.T., Cruz-Cano, R., Nasko, D., Blythe, D., Ryan, P., Boyle, M., Wilson, S.M., Sapkota, A.R. (2020). Association between Private Drinking Water Wells and the Incidence of Campylobacteriosis in Maryland: An Ecological Analysis Using Foodborne Diseases Active Surveillance Network (FoodNet) Data (2007-2016). Environmental Research, 188:109773. https://doi.org/
Craddock HA, Chattopadhyay S, Rjoub Y, Rosen D, Greif J, Lipchin C, Mongodin EF, Sapkota AR. 2020. Antibiotic-resistant Escherichia coli and Klebsiella sp. in greywater reuse systems and pond water used for agricultural irrigation in the West Bank, Palestinian Territories. Environmental Research. https://doi.org/10.1016/j.envres.2020.109777
Kulkarni P, Olson ND, Bui AQ, et al. Zero-Valent Iron Sand Filtration Can Reduce Human and Plant Pathogenic Bacteria While Increasing Plant Growth Promoting Bacteria in Reclaimed Water. Frontiers in Environmental Science. 2020;8:203. doi:10.3389/fenvs.2020.541921
Chopyk, J., Nasko, D.J., Allard, S. et al. Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond. Environmental Microbiome 15, 18 (2020). https://doi.org/10.1186/s40793-020-00365-8
Our laboratories are fully equipped for processing and analyzing large numbers of environmental and human clinical samples with regard to the presence of bacterial and viral pathogens, as well as total bacterial and vrial diversity (using both culture-based techniques and sophisticated culture-independent, next-generation sequencing methods). Specifically, our laboratories include a 1000 ft2 biosafety level II environmental microbiology and molecular biology laboratory, a 500 ft2 biosafety level two field laboratory, and a 500 ft2 biosafety level two post-polymerase chain reaction (PCR) laboratory. Major items of equipment available in these labs include: 1 Beckman Coulter high-capacity centrifuge; refrigerated microcentrifuges; 2 Baker SterilGARDIII Advance biological safety cabinets; 2 chemical fume hoods; 1 NanoDrop ND-1000 spectrophotometer; 1 MP Biomedicals FastPrep bead beater; 2 Sensititre autoinoculators; multiple deli-style refrigerators; 6 -20°C freezers; 4 -80°C freezers; 2 environmental chambers; and 8 incubators. In addition to these items, the following pieces of equipment are also housed in our laboratories: air sampling equipment; a membrane filtration system; conventional and real-time thermocyclers; gel electrophoresis units and power supplies; a gel documentation system; a rotisserie hybridization oven; an ultraviolet light crosslinker; water baths and small table top instruments. A glassware, media and autoclave facility is located next to these laboratories.