Joel P Stokdyk
Joel Stokdyk is a Research Biologist with the Laboratory for Infectious Disease and the Environment (LIDE) with the Upper Midwest Water Science Center.
RESEARCH SUMMARY
I study the occurrence, fate and transport, and health effects of pathogens in the environment at LIDE. My research includes analysis of viruses, bacteria, and protozoa to characterize pathogen occurrence combined with microbial source tracking to identify pathogen sources. Studies address public health and resource management aspects of groundwater and surface water by assessing the factors that contribute to contamination and by characterizing relationships among pathogens, microbial indicators, and human health risk. Projects include collaboration with public agencies and other researchers to study public and private well water, recreational water, drinking water, and other environmental matrices.
EXPERTISE
Analysis of human and agricultural zoonotic pathogens and microbial source tracking markers in environmental matrices
Quantitative polymerase chain reaction (qPCR) and associated lab quality control
Large-volume sampling techniques for analysis of viruses and bacteria in water
Enteric viral, bacterial, and protozoan pathogens in groundwater
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
Filter Total Items: 25
Statewide quantitative microbial risk assessment for waterborne viruses, bacteria, and protozoa in public water supply wells in Minnesota Statewide 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...
Authors
Tucker R. Burch, Joel Stokdyk, Nancy Rice, Anita C. Anderson, James Walsh, Sue Spencer, Aaron Firnstahl, Mark Borchardt
Quantitative microbial risk assessment for contaminated private wells in the fractured dolomite aquifer of Kewaunee County, Wisconsin Quantitative 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...
Authors
Tucker R. Burch, Joel Stokdyk, Susan Spencer, Burney Kieke, Aaron Firnstahl, Maureen Muldoon, Mark Borchardt
Sources and risk factors for nitrate and microbial contamination of private household wells in the fractured dolomite aquifer of northeastern Wisconsin Sources 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...
Authors
Mark Borchardt, Joel Stokdyk, Burney Kieke, Maureen Muldoon, Susan Spencer, Aaron Firnstahl, Davina Bonness, Randall J. Hunt, Tucker R. Burch
Viral, bacterial, and protozoan pathogens and fecal markers in wells supplying groundwater to public water systems in Minnesota, USA Viral, 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...
Authors
Joel Stokdyk, Aaron Firnstahl, James Walsh, Susan Spencer, Jane de Lambert, Anita C. Anderson, Lih-in Rezania, Burney Kieke, Mark Borchardt
Septic systems and rainfall influence human fecal markers and indicator organisms occurrence in private wells in southeastern Pennsylvania Septic 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
Authors
Heather Murphy, Shannon McGinnis, Ryan Blunt, Joel Stokdyk, Jingwei Wu, Alexander Cagle, Donna Denno, Susan Spencer, Aaron Firnstahl, Mark Borchardt
Reporting the limits of detection and quantification for environmental DNA assays Reporting the limits of detection and quantification for environmental DNA assays
Background Environmental 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...
Authors
Katy Klymus, Christopher Merkes, Michael Allison, Caren Goldberg, Caren Helbing, Margaret Hunter, Craig Jackson, Richard Lance, Anna M. Mangan, Emy Monroe, Antoinette Piaggio, Joel Stokdyk, Chris Wilson, Catherine Richter
Laboratory for Infectious Disease and the Environment (LIDE) Laboratory 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...
Authors
Joel Stokdyk, Jennifer Bruce, Tucker R. Burch, Susan Spencer, Aaron Firnstahl, Mark Borchardt
Cryptosporidium incidence and surface water influence of groundwater supplying public water systems in Minnesota, USA Cryptosporidium 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...
Authors
Joel Stokdyk, Susan K. Spencer, James Walsh, Jane de Lambert, Aaron D. Fimstahl, Anita C. Anderson, Lih-in Rezania, Mark Borchardt
Human Bacteroides and total coliforms as indicators of recent combined sewer overflows and rain events in urban creeks Human Bacteroides and total coliforms as indicators of recent combined sewer overflows and rain events in urban creeks
Combined sewer overflows (CSOs) are a known source of human fecal pollution and human pathogens in urban water bodies, which may present a significant public health threat. To monitor human fecal contamination in water, bacterial fecal indicator organisms (FIOs) are traditionally used. However, because FIOs are not specific to human sources and do not correlate with human pathogens...
Authors
Shannon McGinnis, Susan Spencer, Aaron Firnstahl, Joel Stokdyk, Mark Borchardt, David McCarthy, Heather Murphy
Quantitative microbial risk assessment for spray irrigation of dairy manure based on an empirical fate and transport model Quantitative microbial risk assessment for spray irrigation of dairy manure based on an empirical fate and transport model
BACKGROUND: Spray irrigation for land-applying livestock manure is increasing in the United States as farms become larger and economies of scale make manure irrigation affordable. Human health risks from exposure to zoonotic pathogens aerosolized during manure irrigation are not well understood. OBJECTIVES: We aimed to a) estimate human health risks due to aerosolized zoonotic pathogens...
Authors
Tucker R. Burch, Susan Spencer, Joel Stokdyk, Burney Kieke, Rebecca A Larson, Aaron Firnstahl, Ana Rule, Mark Borchardt
Avian influenza virus RNA in groundwater wells supplying poultry farms affected by the 2015 influenza outbreak Avian influenza virus RNA in groundwater wells supplying poultry farms affected by the 2015 influenza outbreak
During the 2015 outbreak of highly pathogenic avian influenza virus (HPAI) on poultry farms in the midwestern United States, concern was raised about the potential for HPAI to contaminate groundwater. Our study objective was to evaluate the occurrence of HPAI in the groundwater supply wells on 13 outbreak-affected poultry farms in Iowa and Wisconsin. We sampled 20 wells, six waste...
Authors
Mark Borchardt, Susan Spencer, Laura Hubbard, Aaron Firnstahl, Joel Stokdyk, Dana Kolpin
U.S. Geological Survey science strategy for highly pathogenic avian influenza in wildlife and the environment (2016–2020) U.S. Geological Survey science strategy for highly pathogenic avian influenza in wildlife and the environment (2016–2020)
Introduction Through the Science Strategy for Highly Pathogenic Avian Influenza (HPAI) in Wildlife and the Environment, the USGS will assess avian influenza (AI) dynamics in an ecological context to inform decisions made by resource managers and policymakers from the local to national level. Through collection of unbiased scientific information on the ecology of AI viruses and wildlife...
Authors
M. Harris, John Pearce, Diann Prosser, C. White, A. Miles, Jonathan Sleeman, Christopher Brand, James Cronin, Susan De La Cruz, Christine Densmore, Thomas Doyle, Robert Dusek, Joseph P. Fleskes, Paul Flint, Gerald F. Guala, Jeffrey Hall, Laura Hubbard, Randall Hunt, S. Ip, Rachel Katz, Kevin Laurent, Mark Miller, Mark Munn, Andrew Ramey, Kevin D. Richards, Robin Russell, Joel P. Stokdyk, John Takekawa, Daniel Walsh
Non-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-z
Stokdyk, 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.
Science and Products
Filter Total Items: 25
Statewide quantitative microbial risk assessment for waterborne viruses, bacteria, and protozoa in public water supply wells in Minnesota Statewide 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...
Authors
Tucker R. Burch, Joel Stokdyk, Nancy Rice, Anita C. Anderson, James Walsh, Sue Spencer, Aaron Firnstahl, Mark Borchardt
Quantitative microbial risk assessment for contaminated private wells in the fractured dolomite aquifer of Kewaunee County, Wisconsin Quantitative 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...
Authors
Tucker R. Burch, Joel Stokdyk, Susan Spencer, Burney Kieke, Aaron Firnstahl, Maureen Muldoon, Mark Borchardt
Sources and risk factors for nitrate and microbial contamination of private household wells in the fractured dolomite aquifer of northeastern Wisconsin Sources 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...
Authors
Mark Borchardt, Joel Stokdyk, Burney Kieke, Maureen Muldoon, Susan Spencer, Aaron Firnstahl, Davina Bonness, Randall J. Hunt, Tucker R. Burch
Viral, bacterial, and protozoan pathogens and fecal markers in wells supplying groundwater to public water systems in Minnesota, USA Viral, 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...
Authors
Joel Stokdyk, Aaron Firnstahl, James Walsh, Susan Spencer, Jane de Lambert, Anita C. Anderson, Lih-in Rezania, Burney Kieke, Mark Borchardt
Septic systems and rainfall influence human fecal markers and indicator organisms occurrence in private wells in southeastern Pennsylvania Septic 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
Authors
Heather Murphy, Shannon McGinnis, Ryan Blunt, Joel Stokdyk, Jingwei Wu, Alexander Cagle, Donna Denno, Susan Spencer, Aaron Firnstahl, Mark Borchardt
Reporting the limits of detection and quantification for environmental DNA assays Reporting the limits of detection and quantification for environmental DNA assays
Background Environmental 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...
Authors
Katy Klymus, Christopher Merkes, Michael Allison, Caren Goldberg, Caren Helbing, Margaret Hunter, Craig Jackson, Richard Lance, Anna M. Mangan, Emy Monroe, Antoinette Piaggio, Joel Stokdyk, Chris Wilson, Catherine Richter
Laboratory for Infectious Disease and the Environment (LIDE) Laboratory 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...
Authors
Joel Stokdyk, Jennifer Bruce, Tucker R. Burch, Susan Spencer, Aaron Firnstahl, Mark Borchardt
Cryptosporidium incidence and surface water influence of groundwater supplying public water systems in Minnesota, USA Cryptosporidium 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...
Authors
Joel Stokdyk, Susan K. Spencer, James Walsh, Jane de Lambert, Aaron D. Fimstahl, Anita C. Anderson, Lih-in Rezania, Mark Borchardt
Human Bacteroides and total coliforms as indicators of recent combined sewer overflows and rain events in urban creeks Human Bacteroides and total coliforms as indicators of recent combined sewer overflows and rain events in urban creeks
Combined sewer overflows (CSOs) are a known source of human fecal pollution and human pathogens in urban water bodies, which may present a significant public health threat. To monitor human fecal contamination in water, bacterial fecal indicator organisms (FIOs) are traditionally used. However, because FIOs are not specific to human sources and do not correlate with human pathogens...
Authors
Shannon McGinnis, Susan Spencer, Aaron Firnstahl, Joel Stokdyk, Mark Borchardt, David McCarthy, Heather Murphy
Quantitative microbial risk assessment for spray irrigation of dairy manure based on an empirical fate and transport model Quantitative microbial risk assessment for spray irrigation of dairy manure based on an empirical fate and transport model
BACKGROUND: Spray irrigation for land-applying livestock manure is increasing in the United States as farms become larger and economies of scale make manure irrigation affordable. Human health risks from exposure to zoonotic pathogens aerosolized during manure irrigation are not well understood. OBJECTIVES: We aimed to a) estimate human health risks due to aerosolized zoonotic pathogens...
Authors
Tucker R. Burch, Susan Spencer, Joel Stokdyk, Burney Kieke, Rebecca A Larson, Aaron Firnstahl, Ana Rule, Mark Borchardt
Avian influenza virus RNA in groundwater wells supplying poultry farms affected by the 2015 influenza outbreak Avian influenza virus RNA in groundwater wells supplying poultry farms affected by the 2015 influenza outbreak
During the 2015 outbreak of highly pathogenic avian influenza virus (HPAI) on poultry farms in the midwestern United States, concern was raised about the potential for HPAI to contaminate groundwater. Our study objective was to evaluate the occurrence of HPAI in the groundwater supply wells on 13 outbreak-affected poultry farms in Iowa and Wisconsin. We sampled 20 wells, six waste...
Authors
Mark Borchardt, Susan Spencer, Laura Hubbard, Aaron Firnstahl, Joel Stokdyk, Dana Kolpin
U.S. Geological Survey science strategy for highly pathogenic avian influenza in wildlife and the environment (2016–2020) U.S. Geological Survey science strategy for highly pathogenic avian influenza in wildlife and the environment (2016–2020)
Introduction Through the Science Strategy for Highly Pathogenic Avian Influenza (HPAI) in Wildlife and the Environment, the USGS will assess avian influenza (AI) dynamics in an ecological context to inform decisions made by resource managers and policymakers from the local to national level. Through collection of unbiased scientific information on the ecology of AI viruses and wildlife...
Authors
M. Harris, John Pearce, Diann Prosser, C. White, A. Miles, Jonathan Sleeman, Christopher Brand, James Cronin, Susan De La Cruz, Christine Densmore, Thomas Doyle, Robert Dusek, Joseph P. Fleskes, Paul Flint, Gerald F. Guala, Jeffrey Hall, Laura Hubbard, Randall Hunt, S. Ip, Rachel Katz, Kevin Laurent, Mark Miller, Mark Munn, Andrew Ramey, Kevin D. Richards, Robin Russell, Joel P. Stokdyk, John Takekawa, Daniel Walsh
Non-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-z
Stokdyk, 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.