Joel Stokdyk is a Biologist with the Laboratory for Infectious Disease and the Environment (LIDE) with the Upper Midwest Water Science Center.
EXPERTISE
Analysis of human and agricultural zoonotic pathogens and fecal indicators in environmental matrices
Quantitative polymerase chain reaction (qPCR)
Large-volume sampling techniques for analysis of viruses and bacteria in water
Human enteric viruses in groundwater
RESEARCH INTERESTS
Occurrence, fate and transport, and health effects of viruses in the environment
Persistence of pathogens in soil, groundwater, and surface water
Plant-soil-microbe interactions
Factors affecting pathogen contamination of drinking water wells
CURRENT PROJECTS
Southwest Wisconsin groundwater and geology (SWIGG) study
Wells and enteric-disease transmission, epidemiological trial
Viral, bacterial, and protozoan pathogens and fecal markers in groundwater for public water supplies in Minnesota
Groundwater contamination occurrence, source, variability with depth to bedrock, and relationship to recharge in Kewaunee County, Wisconsin
Education and Certifications
2014. MS, Natural Resources. University of Wisconsin-Stevens Point
2012. BS, Soil and Land Management with minor in Geographic Information Systems and Spatial Analysis; Wetland Science Certificate. University of Wisconsin-Stevens Point
Science and Products
Well Water Advisory Forecasts for northeast Wisconsin
Assessing the health risk from waterborne pathogens for public users recreating on future Iowa Water Trails recreation sites near Des Moines
Southwest Wisconsin Groundwater and Geology (SWIGG) study
Evaluating the risks of airborne pathogens from manure irrigation
Norovirus outbreak caused by a new septic system
Groundwater viruses in Minnesota drinking water wells
About LIDE
Sampling and analytical capabilities
Real-time quantitative polymerase chain reaction (qPCR)
Quantitative microbial risk assessment (QMRA)
Cumulative antecedent precipitation data associated with well water samples collected in eastern Pennsylvania June-November 2017
Study design and methods of the Wells and Enteric disease Transmission (WET) Trial, a randomised controlled trial
Creek and quarry water quality at Pipestone National Monument and pilot study of pathogen detection methods in waterfall mist at Winnewissa Falls, Pipestone, Minnesota, 2018–19
Microbial source tracking and land use associations for antibiotic resistance genes in private wells influenced by human and livestock fecal sources
Assessing private well contamination in Grant, Iowa, and Lafayette Counties, Wisconsin: The southwest Wisconsin groundwater and geology study
Statewide quantitative microbial risk assessment for waterborne viruses, bacteria, and protozoa in public water supply wells in Minnesota
Quantitative microbial risk assessment for contaminated private wells in the fractured dolomite aquifer of Kewaunee County, Wisconsin
Sources and risk factors for nitrate and microbial contamination of private household wells in the fractured dolomite aquifer of northeastern Wisconsin
Viral, bacterial, and protozoan pathogens and fecal markers in wells supplying groundwater to public water systems in Minnesota, USA
Septic systems and rainfall influence human fecal markers and indicator organisms occurrence in private wells in southeastern Pennsylvania
Reporting the limits of detection and quantification for environmental DNA assays
Laboratory for Infectious Disease and the Environment (LIDE)
Cryptosporidium incidence and surface water influence of groundwater supplying public water systems in Minnesota, USA
Non-USGS Publications**
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
Science and Products
- Science
Well Water Advisory Forecasts for northeast Wisconsin
The fractured bedrock of northeast Wisconsin is vulnerable to groundwater contamination because water and contaminants can move quickly. LIDE is launching a study to predict contamination of private wells in northeast WI using Runoff Risk Advisory Forecasts (RRAF). RRAF is an online tool that forecasts conditions conducive to surface runoff, and the long-term vision is to leverage its forecasts to...Assessing the health risk from waterborne pathogens for public users recreating on future Iowa Water Trails recreation sites near Des Moines
Scientists at LIDE are collaborating with Polk County Conservation in central Iowa to estimate the health risk posed to recreators in the Des Moines River and tributaries. Samples collected over two years are tested for viral, bacterial, and protozoan pathogens, and health risk is estimated using quantitative microbial risk assessment (QMRA). Health risk will also be compared to microbial source...Southwest Wisconsin Groundwater and Geology (SWIGG) study
The fractured bedrock aquifers of southwest Wisconsin are often overlain by shallow soils, so private wells are potentially vulnerable to contamination by nitrate and pathogens from the land surface. The goal of this study is to evaluate the extent and causes of private well water contamination in three southwest Wisconsin counties.Evaluating the risks of airborne pathogens from manure irrigation
Manure irrigation, which is the application of liquid animal manure by irrigation, is increasing. However, the risk of airborne pathogen transmission from manure to humans during spray irrigation is not well-understood. To determine how pathogens can spread using manure irrigation, LIDE measured air concentrations and risk of illness due to exposure to pathogens in the irrigation spray.Norovirus outbreak caused by a new septic system
Patrons and employees of a new restaurant were affected by acute gastroenteritis (vomiting and diarrhea); initial tests were positive for fecal contamination. Investigators utilized a unique combination of epidemiological, microbial, and hydrogeological evidence that identified a new septic system as the source of the contamination.Groundwater viruses in Minnesota drinking water wells
In Minnesota, 74% of the State’s population relies on groundwater to supply their drinking water. Outbreaks of waterborne viral illness have been associated with groundwater, and surveys show that 30 percent of drinking water wells may be contaminated. LIDE is helping the State determine the occurrence of groundwater-borne viruses and the risk of illness in Minnesota groundwater.About LIDE
The Laboratory for Infectious Disease and the Environment (LIDE) is an interagency collaborative effort between the U.S. Geological Survey and the U.S. Department of Agriculture-Agricultural Research Service. As a research laboratory, LIDE’s roles in research-based collaborations range from developing research questions and experimental designs to analyzing samples and interpreting data.Sampling and analytical capabilities
Molecular and culture analysis methods are paired with sampling capabilities across environmental matrices to address a wide range of questions and problems. LIDE collects and analyzes samples from groundwater, surface water, runoff, wastewater, sediments, soil, manure, compost, digestate, and air.Real-time quantitative polymerase chain reaction (qPCR)
Quantitative polymerase chain reaction (qPCR) identifies and quantifies microorganisms in environmental samples by detecting a unique target sequence of nucleic acid (DNA or RNA).Quantitative microbial risk assessment (QMRA)
Quantitative microbial risk assessment (QMRA) is a tool for estimating human health risks from exposure to pathogens via food, water, air, and other environmental routes. - Data
Cumulative antecedent precipitation data associated with well water samples collected in eastern Pennsylvania June-November 2017
The dataset includes aggregated precipitation data from a USGS rain gauge for specified 7- or 8-day time periods between May and November 2017. Daily precipitation measurements were summed to produce 7- or 8-day totals over the specified time period. - Multimedia
- Publications
Filter Total Items: 17
Study design and methods of the Wells and Enteric disease Transmission (WET) Trial, a randomised controlled trial
Introduction: The burden of disease attributed to drinking water from private wells is not well characterised. The Wells and Enteric disease Transmission trial is the first randomised controlled trial to estimate the burden of disease that can be attributed to the consumption of untreated private well water. To estimate the attributable incidence of gastrointestinal illness (GI) associated with prAuthorsDebbie Lee, Donna Denno, Phil Tarr, Jingwei Wu, Joel P. Stokdyk, Mark A. Borchardt, Heather MurphyCreek and quarry water quality at Pipestone National Monument and pilot study of pathogen detection methods in waterfall mist at Winnewissa Falls, Pipestone, Minnesota, 2018–19
Pipestone National Monument is a 301-acre site sacred to many Native American Tribes, providing cultural exhibits and walking trails to Pipestone Creek, Winnewissa Falls, and historical pipestone quarries for numerous visitors each year. However, the Minnesota Pollution Control Agency has determined turbidity and fecal coliform bacteria occur in Pipestone Creek in high enough numbers to be a potenAuthorsAliesha L. Krall, Kerensa A. King, Victoria G. Christensen, Joel P. Stokdyk, Barbara C. Scudder Eikenberry, S. A. StevensonMicrobial source tracking and land use associations for antibiotic resistance genes in private wells influenced by human and livestock fecal sources
Antimicrobial resistance is a growing public health problem that requires an integrated approach among human, agricultural, and environmental sectors. However, few studies address all three components simultaneously. We investigated the occurrence of five antibiotic resistance genes (ARGs) and the class 1 integron gene (intI1) in private wells drawing water from a vulnerable aquifer influenced byAuthorsTucker R. Burch, Joel P. Stokdyk, Aaron Firnstahl, Burney Kieke Jr, Rachel Cook, Sarah Opelt, Sue Spencer, Lisa Durso, Mark A. BorchardtAssessing private well contamination in Grant, Iowa, and Lafayette Counties, Wisconsin: The southwest Wisconsin groundwater and geology study
Rural residents of Grant, Iowa, and Lafayette Counties in Wisconsin rely on private wells for their water. Contaminants like nitrate and bacteria from septic systems, fertilizer, and manure can contaminate the groundwater that residents use. Groundwater is vulnerable to contamination where the soil layer is thin and the bedrock is fractured, which is the case for much of the study region. This stuAuthorsJoel P. Stokdyk, Mark A. Borchardt, Aaron Firnstahl, Ken Bradbury, Moe Muldoon, Burney A KiekeStatewide quantitative microbial risk assessment for waterborne viruses, bacteria, and protozoa in public water supply wells in Minnesota
Infection risk from waterborne pathogens can be estimated via quantitative microbial risk assessment (QMRA) and forms an important consideration in the management of public groundwater systems. However, few groundwater QMRAs use site-specific hazard identification and exposure assessment, so prevailing risks in these systems remain poorly defined. We estimated the infection risk for 9 waterborne pAuthorsTucker R. Burch, Joel P. Stokdyk, Nancy Rice, Anita C. Anderson, James F. Walsh, Sue Spencer, Aaron Firnstahl, Mark A. BorchardtQuantitative microbial risk assessment for contaminated private wells in the fractured dolomite aquifer of Kewaunee County, Wisconsin
Background:Private wells are an important source of drinking water in Kewaunee County, Wisconsin. Due to the region’s fractured dolomite aquifer, these wells are vulnerable to contamination by human and zoonotic gastrointestinal pathogens originating from land-applied cattle manure and private septic systems.Objective:We determined the magnitude of the health burden associated with contamination oAuthorsTucker R. Burch, Joel P. Stokdyk, Susan K. Spencer, Burney A Kieke, Aaron Firnstahl, Maureen A. Muldoon, Mark A. BorchardtSources and risk factors for nitrate and microbial contamination of private household wells in the fractured dolomite aquifer of northeastern Wisconsin
Background:Groundwater quality in the Silurian dolomite aquifer in northeastern Wisconsin, USA, has become contentious as dairy farms and exurban development expand.Objectives:We investigated private household wells in the region, determining the extent, sources, and risk factors of nitrate and microbial contamination.Methods:Total coliforms, Escherichia coli, and nitrate were evaluated by synoptiAuthorsMark A. Borchardt, Joel P. Stokdyk, Burney A Kieke, Maureen A. Muldoon, Susan K. Spencer, Aaron Firnstahl, Davina Bonness, Randall J. Hunt, Tucker R. BurchViral, bacterial, and protozoan pathogens and fecal markers in wells supplying groundwater to public water systems in Minnesota, USA
Drinking water supply wells can be contaminated by a broad range of waterborne pathogens. However, groundwater assessments frequently measure microbial indicators or a single pathogen type, which provides a limited characterization of potential health risk. This study assessed contamination of wells by testing for viral, bacterial, and protozoan pathogens and fecal markers. Wells supplying groundwAuthorsJoel P. Stokdyk, Aaron Firnstahl, James F. Walsh, Susan K. Spencer, Jane R. de Lambert, Anita C. Anderson, Lih-in W. Rezania, Burney A Kieke, Mark A. BorchardtSeptic systems and rainfall influence human fecal markers and indicator organisms occurrence in private wells in southeastern Pennsylvania
In the United States approximately 48 million people are served by private wells. Unlike public water systems, private well water quality is not monitored and there are few studies on the extent and sources of contamination of private wells. We extensively investigated five private wells to understand the variability in microbial contamination, the role of septic systems as sources of contaminatioAuthorsHeather Murphy, Shannon McGinnis, Ryan Blunt, Joel P. Stokdyk, Jingwei Wu, Alexander Cagle, Donna Denno, Susan K. Spencer, Aaron Firnstahl, Mark A. BorchardtReporting the limits of detection and quantification for environmental DNA assays
BackgroundEnvironmental DNA (eDNA) analysis is increasingly being used to detect the presence and relative abundance of rare species, especially invasive or imperiled aquatic species. The rapid progress in the eDNA field has resulted in numerous studies impacting conservation and management actions. However, standardization of eDNA methods and reporting across the field is yet to be fully establisAuthorsKaty E. Klymus, Christopher M. Merkes, Michael J. Allison, Caren S. Goldberg, Caren C. Helbing, Margaret Hunter, Craig Jackson, Richard F. Lance, Anna M. Mangan, Emy M. Monroe, Antoinette J. Piaggio, Joel P. Stokdyk, Chris C. Wilson, Catherine A. RichterLaboratory for Infectious Disease and the Environment (LIDE)
The Laboratory for Infectious Disease and the Environment (LIDE) studies the occurrence, fate and transport, and health effects of human and agricultural zoonotic pathogens in the environment. The LIDE is an interagency collaborative effort between the U.S. Geological Survey and the U.S. Department of Agriculture-Agricultural Research Service that conducts research to inform decision makers and adAuthorsJoel P. Stokdyk, Jennifer L. Bruce, Tucker R. Burch, Susan K. Spencer, Aaron Firnstahl, Mark A. BorchardtCryptosporidium incidence and surface water influence of groundwater supplying public water systems in Minnesota, USA
Regulations for public water systems (PWS) in the U.S. consider Cryptosporidium a microbial contaminant of surface water supplies. Ground- water is assumed free of Cryptosporidium unless surface water is entering supply wells. We determined the incidence of Cryptosporidium in PWS wells varying in surface water influence. Community and noncommunity PWS wells (n = 145) were sampled (n = 964) and analAuthorsJoel P. Stokdyk, Susan K. Spencer, James F. Walsh, Jane R. de Lambert, Aaron D. Fimstahl, Anita C. Anderson, Lih-in W. Rezania, Mark A. BorchardtNon-USGS Publications**
Stokdyk, J., and Herrman, K., 2016, Effects of Frangula alnus on soil microbial communities and biogeochemical processes in Wisconsin forests: Plant and Soil v. 409, n. 1-2, p. 65-75. doi: 10.1007/s11104-016- 2916-zStokdyk, J., and Herrman, K., 2014, Short-term impacts of Frangula alnus litter on forest soil properties: Water, Air, and Soil Pollution v. 225, n. 6, p. 1-9. doi: 10.1007/s11270-014-2000-3**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
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