Room Number: 
2234P
Director: 
Office Phone Number: 
301-405-1772
Email: 
ars@umd.edu

 

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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 ars@umd.edu.

Spring 2019

Hillary Craddock Kelbick (a PhD candidate in our group) defending her dissertation titled "Water reuse for food production in the West Bank and Israel: Assessing the efficacy of household greywater treatment systems, and consumer perceptions of reuse applications" on March 29.

Jessica Chopyk (a PhD candidate in our group) successfully defended her PhD dissertation "Diversity, dynamics, and dissemination of microbial communities in reclaimed and untreated surface waters used for agricultural irrigation" on March 21. 

Sarah Allard, PhD (a post-doctoral fellow in our group) just published a paper in Environmental research, https://www.sciencedirect.com/science/article/pii/S0013935119300969. She also authored another publication in Science of The Total Environmenthttps://www.sciencedirect.com/science/article/pii/S0048969719306679.

Leena Malayil (a PhD candidate in our group) defending her dissertation on May 6. 

Suhana Chattopadhyay (senior research assistant in our group) published a paper in Plos Onehttps://journals.plos.org/plosone/article/comments?id=10.1371/journal.po....

 

Our lab is currently engaged in research under two different areas described below:

UMD Global STEWARDSSTEM 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: $xxx. Funding Period: 2018-2023

The UMD Global STEWARDS graduate training fellowship, funded by the National Science Foundation Research Traineeship (NRT) program, is preparing future leaders focused on innovations at the nexus of food, energy and water (FEW) systems. UMD Global STEWARDS focus on a range of topics in three integrated FEW nexus research areas: Agriculture resilience through energy-efficient water reuse, Food safety and security in variable climate scenarios, and Decision support systems to advance food-energy-water adaptation strategies. 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: 2016-2020

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:

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/

Amy R. Sapkota

Dr. Sapkota is the Director of CONSERVE: A Center of Excellence at the Nexus of Sustainable Water Reuse, Food & Health, a multi-institution Center funded by the U.S. Department of Agriculture, National Institute of Food and Agriculture (2016-2020). She is also the Principal Investigator of UMD Global STEWARDS (STEM Training at the Nexus of Energy, Water Reuse and Food Systems), a National Research Traineeship (NRT) program funded by the National Science Foundation (2018-2023). The mission of CONSERVE is to facilitate the adoption of transformative on‐farm water treatment solutions that enable the safe use of nontraditional irrigation water (e.g. reclaimed water, return flows) on food crops. And the overarching goal of the UMD Global STEWARDS program is for graduate trainees to become adept at working and communicating across food-energy-water (FEW) disciplines, enabling transformative discoveries that can only be realized through transdisciplinary approaches and systems-based thinking. 

Dr. Sapkota received a PhD in Environmental Health Sciences from the Johns Hopkins Bloomberg School of Public Health, and an MPH in Environmental Health Sciences from the Yale School of Public Health. After completing her doctorate, she engaged in post-doctoral fellowships at the Johns Hopkins Bloomberg School of Public Health and the Environmental Microbial Genomics Group at Ecole Centrale de Lyon in Lyon, France.

She is the recipient of the 2012 Eric Mood New Professional Award from the Yale School of Public Health that recognizes the career of a Yale alumnus/a who demonstrates outstanding leadership potential and creativity in the practice of public health. Dr. Sapkota is also the recipient of the 2015 Jerry P. Wrenn Outstanding Service Award and the 2018 Research and Development Award from the University of Maryland School of Public Health. In 2017, she represented the Core Fulbright U.S. Scholar Program and the United States as a Fulbright Senior Researcher in Chitwan, Nepal.

Dr. Sapkota's research interests lie in the areas of environmental microbiology, environmental microbial genomics, exposure assessment and environmental epidemiology.  Her research group evaluates the complex relationships between environmental microbial exposures and human infectious diseases, with a special focus on assessing the public health impacts associated with water reuse. Much of her group's work seeks to 1) characterize the microbiome of recycled water sources, and 2) understand how direct and indirect exposures to these sources can impact the human microbiome and infectious disease risk.

Sarah Allard is a Research Associate for CONSERVE, a Center of Excellence at the Nexus of Sustainable Water Reuse, Food, and Health. Sarah began her research career as an undergraduate, investigating the pollination efficiency and diversity of native bees on watermelon fields in the mid-Atlantic. After receiving her B.A. in Biology from Haverford College in 2009, she began an ORISE fellowship in the Division of Microbiology at the FDA's Center for Food Safety and Applied Nutrition. At FDA, she participated in environmental sampling for foodborne pathogens, evaluation of a food safety biological control agent, and optimization of Salmonella detection methods from environmental samples. As a graduate student in Plant Science at the University of Maryland, she studied the influence of farming practices and environmental conditions on the lives of microbes, including foodborne pathogens, in the complex agricultural environment. As part of the CONSERVE team based in the UMD School of Public Health, she is primarily working to characterize the microbiomes of nontraditional irrigation water sources including surface water and reclaimed wastewater. She is passionate about working towards the adoption of agricultural practices that are microbiologically safe, environmentally sustainable, and economically viable. Contact: Building: School of Public Health | Room: 0110N Phone: (301) 405-2164 | Email: sallard@umd.edu

 

Suhana Chattopadhyay is a Senior Research Assistant. 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: suhanac@umd.edu

 

 

 

 

Jessica Chopyk successfully defended her PhD dissertation as student in the Toxicology and Environmental Health program and COMBINE: (Computation and Mathematics for Biological Networks) fellow. Previously, she obtained a Master’s degree in Plant and Soil Sciences at the University of Delaware exploring the commensal microbial communities that exist along with Shiga toxin-producing E. coli (STEC) on cattle hide during beef   processing. Her current research is aimed at utilizing next generation sequencing technologies to explore bacterial and viral community structure, dynamics,   and dissemination in nontraditional sources of irrigation water.

 Contact: Building: School of Public Health | Room: 0110N Phone: (301) 405-   5559 | Email: jchopyk@umd.edu

 

 

Hillary A. Craddock (PhD Candidate in Environmental Health Science) completed her BS in Biology at the Pennsylvania State University and her MPH in Epidemiology at the University of Michigan. For   her doctoral work, she is   investigating the microbial quality of non-traditional irrigation water sources, the persistence of antibiotics in small-scale wastewater treatment systems, and consumer perceptions   regarding the use of treated wastewater for   agricultural irrigation. She works in the United States and the Middle East. She is also a Graduate Fellow for the UMD National Socio-Environmental Synthesis   Center, where she supports initiatives to improve the teaching and   learning of socio-environmental synthesis. She is passionate about using interdisciplinary science and environmental health research to   improve food safety and tackle issues of environmental justice. 

 Contact: Building: School of Public Health | Room: 0110N Phone: (301) 405-5559 | Email: hcrad1@umd.edu

 

Leena Malayil (PhD. Candidate in Toxicology and Environmental Health) 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 joined University of Maryland in 2015 to pursue her PhD.  For her doctoral work, she is   exploring the metabolically active bacterial communities associated with tobacco products and water samples from the mid-Atlantic region by coupling DNA labelling and   next generation sequencing techniques.

 Contact: Building: School of Public Health | Room: 0110N Phone: (301) 405-5559 | Email: lmalayil@umd.edu

 

 

Rianna Murray,  is a Research Associate for CONSERVE and 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 in 2018 with a PhD in Toxicology and Environmental Health at the University of Maryland School of Public Health where she also received her Master of Public Health degree. Her research interests lie in the fields of environmental health, global health, environmental justice, food safety, and water quality. Her dissertation investigates the influence of private drinking water wells and their proximity to animal agricultural operations on the incidence of foodborne illness in Maryland. Rianna also works on the USDA-NIFA supported CONSERVE Center of Excellence that investigates transformative on‐farm treatment solutions that enable the safe use of nontraditional irrigation water on food crops. Her 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: rmurray@umd.edu

 

Former Members:

  • Post doctoral scholars:

           Eoghan Smyth 

           Kristi Shaw

           Sutyajeet Soneja

           Shirley Micallef

  • Graduate Students

          Prachi Kulkarni (PhD, 2016)

          Rachel Rosenberg Goldstein (PhD, 2013)

          Kelsey Babik (MPH, 2015 )

          Molly Reid (MPH, 2015)

          Rhodel Bradshaw (MPH, 2017)

  • Undergraduate Students

          Anthony Quang-Vinh Bui 

          Emma Claye

          Shamar Rundhawa 

          Robin Cagle 

          Mansi Panse

          Daniella Portal

          Isabel Burick

         Jackie Taylor

 

 

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):

Jiang C, Shaw KS, Upperman CR, Blythe D, Mitchell C, Murtugudde R, Sapkota AR, Sapkota A. 2015. Climate change, extreme events and increased risk of salmonellosis in Maryland, USA: Evidence for coastal vulnerability. Environment International. 83:58-62. 

Carey SA*, Rosenberg Goldstein RE**, Gibbs SG, Claye E, He, X, Sapkota AR. 2016. Occurrence of vancomycin-resistant and –susceptible Enterococcus spp. in reclaimed water used for spray irrigation. Environmental Research. 147:350-355. 

Shaw KS**, Cruz-Cano R, Jiang C, Malayil L, Palmer A, Blythe D, Ryan P, Sapkota AR2016. Presence of animal feeding operations and community socioeconomic factors impact salmonellosis incidence rates: Foodborne diseases active surveillance network (FoodNet), 2004-2010. Environmental Research. 150:166-172. 

Rosenberg Goldstein RE**, Cruz-Cano R, Jiang C, Palmer A, Blythe D, Ryan P, Hogan B, White B, Dunn JR, Libby T, Tobin-D’Angelo M, Huang J, McGuire S, Scherzinger K, Lee MLT, Sapkota AR.  2016. Association between community socioeconomic factors, animal feeding operations and Campylobacteriosis incidence rates: Foodborne diseases active surveillance network (FoodNet), 2004-2010. BMC Infectious Diseases. 16:354. 

Rosenberg Goldstein RE**, Cruz-Cano R, Jiang C, Palmer A, Blythe D, Ryan P, Hogan B, White B, Dunn JR, Libby T, Tobin-D’Angelo M, Huang J, McGuire S, Scherzinger K, Lee MLT, Sapkota AR.  2016. Association between community socioeconomic factors, animal feeding operations and Campylobacteriosis incidence rates: Foodborne diseases active surveillance network (FoodNet), 2004-2010. BMC Infectious Diseases. 16:354.

Chopyk J*, Chattopadhyay S*, Kulkarni P*, Claye E*, Babik KR*, Reid MC*, Smyth EM**, Hittle LE, Paulson JN, Cruz-Cano R, Pop M, Clark PI, Sapkota AR§Mongodin EF§,†. 2017. Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens. Microbiome. 15;5(1):22. 

Chopyk J*, Chattopadhyay S, Kulkarni P*, Smyth EM**, Hittle LE, Paulson JN, Pop M, Clark PI, Mongodin EF§Sapkota AR§,†. 2017. Temporal variations in cigarette tobacco bacterial community composition and tobacco-specific nitrosamine content are influenced by brand and storage conditions. Frontiers in Microbiology. 7(8):358. 

Boyle M*, Sutyajeet S**, Quiros-Alcala L, Dalemarre L, Sapkota AR, Sangaramoorthy T, Wilson S, Miton D, Sapkota A. 2017. A pilot study to assess residential noise exposure near natural gas compressor stations. 2017. PLoSOne. 12(4): e0174310. 

Rosenberg Goldstein RE**†, Kleinfelter L*, He X, Micallef SA, George A, Gibbs SG, Sapkota AR. 2017. Higher prevalence of coagulase-negative staphylococci carriage among reclaimed water spray irrigators. Science of the Total Environment. 595(1):35-40. 

Rosenberg Goldstein RE**†, Kleinfelter L*, He X, Micallef SA, George A, Gibbs SG, Sapkota AR. 2017. Higher prevalence of coagulase-negative staphylococci carriage among reclaimed water spray irrigators. Science of the Total Environment. 595(1):35-40.

Smyth EM**, Kulkarni P*, Claye E*, Stanfill S, Tyx R, Mongodin EF, Sapkota AR†. 2017. Smokeless tobacco products harbor diverse bacterial communities that differ across products and brands. Applied Microbiology and Biotechnology. Jul;101(13):5391-5403. 

Kulkarni P*, Olson N*, Raspanti G*, Rosenberg Goldstein R**, Gibbs SG, Sapkota A, Sapkota AR2017. Antibiotic concentrations decrease during wastewater treatment but persist at low levels in reclaimed water. International Journal of Environmental Research and Public Health. Jun 21;14(6).

Huang JY, Patrick ME, Manners J, Sapkota AR, Scherzinger KJ, Tobin-D’Angelo M, Henao OL, Cole DJ, Vieira AR. 2017. Association between wetland presence and incidence of Salmonella enterica serotype Javiana infections in selected US sites, 2005-2011. Epidemiology and Infection, 145(14):2991-2997.

Chopyk J*, Allard S**, Nasko DJ**, Bui A, Mongodin EF, Sapkota AR.  2018. Agricultural freshwater pond supports diverse and dynamic bacterial and viral populations. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2018.00792.

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

Allard SM, Callahan MT, Bui A, Ferelli AMC, Chopyk J, Chattopadhyay S, Mongodin EF, Micallef SA, Sapkota AR; Creek to Table: Tracking fecal indicator bacteria, bacterial pathogens, and total bacterial communities from irrigation water to kale and radish crops. Science of The Total Environment 2019.

Sarah M Allard, Sultana Solaiman, Mary Theresa Callahan, Anthony Bui, Hillary Craddock, Joseph Haymaker, Derek Foust, Rico Duncan, Eoghan Smyth, Emmanuel F Mongodin, Fawzy Hashem, Eric May, Shirley A Micallef, Amy R SapkotaQuenching by sodium thiosulfate does not influence 16S rRNA gene sequencing profiles of reclaimed water from three sites in the Mid-Atlantic, United StatesEnvironmental research 2019.

Sapkota ARWater reuse, food production and public health: Adopting transdisciplinary, systems-based approaches to achieve water and food security in a changing climate. Environmental research, 2019.

Prachi Kulkarni, Greg A Raspanti, Anthony Q Bui, Rhodel N Bradshaw, Kalmia E Kniel, Pei C Chiu, Manan Sharma, Amir Sapkota, Amy R SapkotaZerovalent iron-sand filtration can reduce the concentration of multiple antimicrobials in conventionally treated reclaimed water. Environmental research, 2019.

Prachi Kulkarni, Greg A Raspanti, Anthony Q Bui, Rhodel N Bradshaw, Kalmia E Kniel, Pei C Chiu, Manan Sharma, Amir Sapkota, Amy R SapkotaImpact of conventional wastewater treatment and reuse site practices on the bacterial community structure of reclaimed water. Science of the Total Environment 2019

Suhana Chattopadhyay, Eoghan M Smyth, Prachi Kulkarni, Kelsey R Babik, Molly Reid, Lauren E Hittle, Pamela I Clark, Emmanuel F Mongodin, Amy R SapkotaLittle cigars and cigarillos harbor diverse bacterial communities that differ between the tobacco and the wrapper. PloS one, 2019.

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.