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
Joel P Stokdyk
Biography
EDUCATION
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
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
Science and Products
Date published: April 27, 2020
Status: Active 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.
Contacts: Joel P Stokdyk, Kenneth R. Bradbury, Mark A. Borchardt, Maureen A. Muldoon
Date published: January 19, 2019
Status: Active 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.
Contacts: Joel P Stokdyk, Mark Borchardt, Tucker Burch
Date published: January 18, 2019
Status: Completed 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.
Contacts: Joel P Stokdyk, Mark Borchardt, Ken Bradbury, Susan Spencer
Date published: January 18, 2019
Status: Active 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.
Contacts: Joel P Stokdyk, Mark Borchardt
Date published: March 18, 2016
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.
Contacts: Joel P Stokdyk, Mark Borchardt
Attribution: Upper Midwest Water Science Center
Date published: March 17, 2016
Status: Active 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.
Contacts: Joel P Stokdyk, Mark Borchardt
Date published: March 16, 2016
Status: Active 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).
Contacts: Joel P Stokdyk
Date published: March 15, 2016
Status: Active 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.
Contacts: Joel P Stokdyk, Tucker Burch
Year Published: 2021
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,...
Borchardt, Mark A.; Stokdyk, Joel P.; Kieke, Burney A; Muldoon, Maureen A.; Spencer, Susan K.; Firnstahl, Aaron; Bonness, Davina; Hunt, Randall J.; Burch, Tucker R.Attribution: Upper Midwest Water Science Center
Year Published: 2021
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...
Burch, Tucker R.; Stokdyk, Joel P.; Spencer, Susan K.; Kieke, Burney A; Firnstahl, Aaron; Muldoon, Maureen A.; Borchardt, Mark A.Attribution: Upper Midwest Water Science Center
Year Published: 2020
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...
Stokdyk, Joel P.; Firnstahl, Aaron; Walsh, James F. ; Spencer, Susan K.; de Lambert, Jane R.; Anderson, Anita C.; Rezania, Lih-in W.; Kieke, Burney A; Borchardt, Mark A.
Year Published: 2020
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,...
Murphy, Heather; McGinnis, Shannon; Blunt, Ryan; Stokdyk, Joel P.; Wu, Jingwei; Cagle, Alexander; Denno, Donna; Spencer, Susan K.; Firnstahl, Aaron; Borchardt, Mark A.
Year Published: 2019
Reporting 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...
Klymus, Katy E.; Merkes, Christopher M.; Allison, Michael J.; Goldberg, Caren S.; Helbing, Caren C.; Hunter, Margaret; Jackson, Craig; Lance, Richard F.; Mangan, Anna M.; Monroe, Emy M.; Piaggio, Antoinette J.; Stokdyk, Joel P.; Wilson, Chris C.; Richter, Catherine A.
Year Published: 2019
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...
Stokdyk, Joel P.; Bruce, Jennifer L.; Burch, Tucker R.; Spencer, Susan K.; Firnstahl, Aaron; Borchardt, Mark A.Attribution: Upper Midwest Water Science Center, Laboratory for Infectious Disease and the Environment
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Stokdyk, J.P., Bruce, J.L,, Burch, T.R., Spencer, S.K., Firnstahl, A.D., and Borchardt, M.A., 2019, Laboratory for Infectious Disease and the Environment (LIDE): U.S. Geological Survey Fact Sheet 2018-3079, 4 p., https://doi.org/10.3133/fs20183079.
Year Published: 2019
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...
Stokdyk, Joel P.; Spencer, Susan K.; Walsh, James F. ; de Lambert, Jane R.; Fimstahl, Aaron D.; Anderson, Anita C.; Rezania, Lih-in W.; Borchardt, Mark A.
Year Published: 2018
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...
McGinnis, Shannon; Spencer, Susan K.; Firnstahl, Aaron; Stokdyk, Joel P.; Borchardt, Mark A.; McCarthy, David; Murphy, HeatherAttribution: Upper Midwest Environmental Sciences Center, Upper Midwest Water Science Center, Water Resources, Laboratory for Infectious Disease and the Environment
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Shannon McGinnis, Susan Spencer, Aaron Firnstahl, Joel Stokdyk, Mark Borchardt, David T. McCarthy, Heather M. Murphy, Human Bacteroides and total coliforms as indicators of recent combined sewer overflows and rain events in urban creeks, Science of The Total Environment, Volume 630, 15 July 2018, Pages 967-976, ISSN 0048-9697, https://doi.org/10.1016/j.scitotenv.2018.02.108.
Year Published: 2017
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...
Burch, Tucker R.; Spencer, Susan K.; Stokdyk, Joel P.; Kieke, Burney A; Larson, Rebecca A; Firnstahl, Aaron; Rule, Ana M; Borchardt, Mark A.Attribution: Upper Midwest Environmental Sciences Center, Upper Midwest Water Science Center, Water Resources, Laboratory for Infectious Disease and the Environment
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Burch TR, Spencer SK, Stokdyk JP, Kieke BA, Larson RA, Firnstahl AD, Rule AM, Borchardt MA. 2017. Quantitative microbial risk assessment for spray irrigation of dairy manure based on an empirical fate and transport model. Environmental Health Perspectives 125(8). doi: 10.1289/EHP283
Year Published: 2017
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...
Borchardt, Mark A.; Spencer, Susan K.; Hubbard, Laura E.; Firnstahl, Aaron; Stokdyk, Joel P.; Kolpin, Dana W.Attribution: Upper Midwest Environmental Sciences Center, Upper Midwest Water Science Center, Water Resources, Laboratory for Infectious Disease and the Environment
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Borchardt, M.A., Spencer, S.K., Hubbard, L.E., Firnstahl, A.D., Stokdyk, J.P., Kolpin, D.W. 2017. Avian Influenza Virus RNA in Groundwater Wells Supplying Poultry Farms Affected by the 2015 Influenza Outbreak. Environ. Sci. Technol. Lett. DOI: 10.1021/acs.estlett.7b00128
Year Published: 2016
U.S. Geological Survey science strategy for highly pathogenic avian influenza in wildlife and the environment (2016–2020)
IntroductionThrough 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...
Harris, M. Camille; Pearce, John M.; Prosser, Diann J.; White, C. LeAnn; Miles, A. Keith; Sleeman, Jonathan M.; Brand, Christopher J.; Cronin, James P.; De La Cruz, Susan; Densmore, Christine L.; Doyle, Thomas W.; Dusek, Robert J.; Fleskes, Joseph P.; Flint, Paul L.; Guala, Gerald F.; Hall, Jeffrey S.; Hubbard, Laura E.; Hunt, Randall J.; Ip, Hon S.; Katz, Rachel A.; Laurent, Kevin W.; Miller, Mark P.; Munn, Mark D.; Ramey, Andrew M.; Richards, Kevin D.; Russell, Robin E.; Stokdyk, Joel P.; Takekawa, John Y.; Walsh, Daniel P.Attribution: Alaska Science Center, National Wildlife Health Center, Ecosystems, Science Analytics and Synthesis (SAS), Region 11: Alaska, Laboratory for Infectious Disease and the Environment
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Harris, M.C., Pearce, J.M., Prosser, D.J., White, C.L., Miles, A.K., Sleeman, J.M., Brand, C.J., Cronin, J.P., De La Cruz, S., Densmore, C.L., Doyle, T.W., Dusek, R.J., Fleskes, J.P., Flint, P.L., Guala, G.F., Hall, J.S., Hubbard, L.E., Hunt, R.J., Ip, H.S., Katz, R.A., Laurent, K.W., Miller, M.P., Munn, M.D., Ramey, A.M., Richards, K.D., Russell, R.E., Stokdyk, J.P., Takekawa, J.Y., and Walsh, D.P., 2016, U.S. Geological Survey science strategy for highly pathogenic avian influenza in wildlife and the environment (2016–2020): U.S. Geological Survey Open-File Report 2016–1121, 38 p., http://dx.doi.org/10.3133/ofr20161121.
Year Published: 2016
Determining the 95% limit of detection for waterborne pathogen analyses from primary concentration to qPCR
The limit of detection (LOD) for qPCR-based analyses is not consistently defined or determined in studies on waterborne pathogens. Moreover, the LODs reported often reflect the qPCR assay alone rather than the entire sample process. Our objective was to develop an approach to determine the 95% LOD (lowest concentration at which 95% of positive...
Stokdyk, Joel P.; Firnstahl, Aaron; Spencer, Susan K.; Burch, Tucker R; Borchardt, Mark A.Attribution: Upper Midwest Environmental Sciences Center, Upper Midwest Water Science Center, Water Resources, Laboratory for Infectious Disease and the Environment
View Citation
Stokdyk J, Firnstahl AD, Spencer SK, Burch TR, and Borchardt MA. 2016. Determining the 95% limit of detection for waterborne pathogen analyses from primary concentration to qPCR. Water Research 96:105-113.
Pre-USGS Publications
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