Agricultural & Biosystems Engineering


Home WQRL Projects Publications Group Members Teaching Service


Metagenomic analysis and modeling of environmental resistance to agricultural antibiotics

The goal of this project is to study the vertical transport of antibiotics, antibiotic-resistant bacteria and antibiotic resistance genes at the lab scale.  We are establishing soil columns and will analyze manure, soil, and water samples for a suite of resistant genes using novel metagenomic tools.


Sponsor: CHEEC, USDA

PIs: Adina Howe, Thomas Moorman, Michelle Soupir, Heather Allen, Shannon Hinsa

Project Staff: Liz Luby, Phil Colgan


Bio-electrical augmentation of woodchip bioreactors for enhanced nitrate removal

We are studying the impacts of electrical stimulation on denitrifying bacteria and nitrate removal in woodchip bioreactors.  Experiments are being conducted in temperature controlled chambers at the USDA ARS National Lab for Agriculture and the Environment in Ames.  If successful we plan to pilot this system in the field.    


Sponsor: Iowa Soybean Association

PIs: Michelle Soupir, Natasha Hoover, Tom Moorman

Students: Ji Yeow Law


column bioreactors

Liz and Ross 

Effect of Manure Application Timing and Management on the Persistence and Transport of Antibiotics and Antibiotic-Resistant Bacteria in Corn and Soybean Production Systems

The goal of this project is to inform pork producers of in-field and manure management practices that can be applied to reduce the transport of antibiotics, antibiotic-resistant bacteria and antibiotic resistance genes to surface waters.  We are conducting experiments in the lab and collecting samples at ISU's Nashua Research Farm.


Sponsor: National Pork Board

PIs: Thomas Moorman, Michelle Soupir, Adina Howe, Dan Anderson

Project Staff: Elliot Rossow, Antionette Fowlkes


Water quality monitoring and analysis in Black Hawk Lake Watershed

We will conduct a paired watershed monitoring study in the Black Hawk Lake Watershed beginning fall 2014. The goal of this project is to answer the question, "Are water quality improvement strategies in the Black Hawk Lake Watershed positively impacting water quality?"    


Sponsor: Iowa Department of Natural Resources

PIs: Michelle Soupir, Amy Kaleita, Matt Helmers

Students: Conrad Brendel and Katherine van der Woude

Staff: Leigh Ann Long and Carl Pederson



paper based detection 

Simple and fast detection of pathogens in recreational waters

The objective of this project is to develop a simple dip-stick type test for the detection of fecal indicator bacteria (E. coli) and Salmonella in recreational waters.  We propose using bacteriophages bound to paper to colorimetrically and cheaply detect bacteria in water samples.  We will test our method at recreational beaches in Iowa in collaboration with the Iowa Department of Natural Resources. 



PIs: Rebecca Cademartiri and Michelle Soupir

Student: Miguel Chavez-Santoscoy


Monitoring and Assessment of Closed Depressions in the Des Moines Lobe.

In this project we will monitor the frequency, duration and extent of ponding in several monitored prairie pothole wetlands and use this data to develop an empirical tool for assessing pothole hydrology and connectivity to downstream waterbodies. In the picture to the right our graduate student is collecting data on the extent of ponding after a precipitation event.


Sponsor: Iowa DNR, EPA Region 7, Leopold Center for Sustainable Agriculture, Iowa Nutrient Reduction Center

PIs: Amy Kaleita and Michelle Soupir, Steven Hall, Andy Vanloocke, and Emily Heaton

Students: Ligia De-Oliverira-Serrano, Alex Martin


pothole crew 

pilot reactor study 

Experimental woodchip bioreactor installation and study.

We installed nine pilot scale woodchip bioreactors at the Agricultural Engineering Research Farm near Ames, Iowa.  These experimental bioreactors can be used to test nutrient removal from bioreactors designed with varying hydraulic retention times or receiving varying influent nutrient concentrations.  The reactors can also be modified with different fill materials if desired.  In 2017 we will also be monitoring the bioreactors for monomethylmercury production.


Sponsor: Iowa Nutrient Reduction Center

PIs: Michelle Soupir, Natasha Hoover, Tom Moorman, Tom Isenhart, Bill Crumpton

Students: Morgan Davis


Persistence and Transport of Veterinary Antibiotics and Antibiotic-Resistant Bacteria in Midwestern Farming Systems.

The goal of this project is to study the occurrence and transport of antibiotics, antibiotic-resistant bacteria and antibiotic resistance genes in tile-drained agricultural fields that have received multi-year application of swine, poultry, or beef manure.  We will conduct rainfall simulation experiments and model antibiotic transport using RZWQM.


Sponsor: USDA

PIs: Thomas Moorman, Michelle Soupir, Dennis Busch, Rob Malone

Project Staff: Bailey Sullivan, Maurice Washington, Liz Luby


Field 5 sampling 


Drainage water quality from manure-treated soybean crops: Assessment of woodchip bioreactors for edge-of-field treatment

In collaboration with the ISA we are collecting water samples from installed bioreactors to assess nutrient and fecal indicator bacterial removal.  We are also using column bioreactors to test nutrient and bacteria removal during a range of hydraulic retention times, fill materials, and temperatures.


Sponsor: Iowa Soybean Association

PIs: Michelle Soupir and Natasha Hoover


Genetic and environmental factors driving E. coli attachment to particles in streams.

In this project we will study the impacts of surface proteins and exopolymeric substances (EPS) on E. coli attachment to particles; identify the genes enabling expression of these features; compare attachment and detachment among strains; and asses the mechanisms of attachment to model and stream particulates. We will also develop learning modules for environmental sciences middle school students in Des Moines.


Sponsor: National Science Foundation

PIs: Michelle Soupir, Laura Jarboe, Michael Thompson

Students: Xiao Liang and Chunyu Liao


Xiao and Chunyu 

SWAT flow

Evaluation of pothole wetland impacts on downstream water quantity and quality, and analysis of tile drain management as a potential tool for water resource protection using SWAT.

We will test the pothole functions in the Soil and Water Assessment Tool in the Lyons Creek watershed which is in the Boone River Basin and assess the impacts on downstream hydrology and water quality. 

Sponsor: Agriculture's Clean Water Alliance

PIs: Michelle Soupir, Charles Ikenberry, Phil Gassman


Occurrence and Movement of Antibiotics, Antibiotic Resistant Bacteria and Resistance Genes in Tile-Drained Agricultural Fields Receiving Swine Manure Application.

The goal of this project is to further understanding of the occurrence and transport of antibiotics, antibiotic-resistant bacteria and antibiotic resistance genes in tile-drained agricultural fields that have received multi-year application of liquid swine manure through injection.  We will test the occurrence in soils collected from no-till and chisel plow fields and the transport into tile drainage systems.  We will also examine gene transfer and contaminant concentrations at the watershed scale.

Sponsor: National Pork Board

PIs: Michelle Soupir, Tom Moorman, Matt Helmers

Student: Liz Luby




Sequence analysis of transferable genes encoding bacterial attachment and multi-drug resistance. 

This project will examine potential relationships between genes in E. coli encoding attachment to particles and antibiotic resistance genes; and the possibility that they are found on a common mobile genetic element. We will also explore the possibility of virulence genes and the potential threat to human health through environmental exposure.

Sponsor: Center for Health Effects of Environmental Contamination

PIs: Laura Jarboe, Michelle Soupir, Cathy Logue, Lisa Nolan


Investigation of bacteria transport and resistance mechanisms and implications for water quality from confinement swine and beef grazing production systems in Iowa.

This study combines the long term nutrient monitoring study at Nashua with new monitoring of bacteria transport and phenotypic resistance to human and veterinary antibiotics.  We will also investigate the mechanisms of E. coli and manure particle interactions to better inform the selection of management practices to prevent bacteria transport to surface waters.

Sponsor: Leopold Center for Sustainable Agriculture

PIs: Michelle Soupir, Matt Helmers, Michael Thompson, Laura Jarboe, R. Kanwar, A. Mallarino



HGL Field Day

Hickory Grove Lake Watershed Management Plan

This grant will continue our ongoing work in the Hickory Grove Lake watershed.  In addition to continued monitoring and modeling activities, we will develop a watershed management plan, survey stakeholders, and develop educational materials.  We hosted a field day on September 8th, 2011and the management plan will be completed in fall 2012.

Sponsor: Iowa Department of Natural Resources
Watershed coordinator: Aaron Andrews

PIs: Michelle Soupir and Matt Helmers

Impact of laying hen manure application on water quality under continuous corn

We will test drainflow from field plots receiving laying hen manure for nitrate and dissolved reactive phosphorous concentrations.  This project is a continuation of 12 years of water quality monitoring sponsored by the Iowa Egg Council.

Sponsor: Iowa Egg Council

PIs: Ramesh Kanwar and Michelle Soupir




  PCR image by Trang Hoang

Occurrence and Movement of Antibiotic Resistant Bacteria and Resistance Genes in Tile-Drained Agricultural Fields Receiving Swine Manure Application

The goal of this project is to further understanding of the occurrence and transport of antibiotic-resistant bacteria and antibiotic resistance genes in tile-drained agricultural fields that have received multi-year application of liquid swine manure through injection.  We will test the occurrence in soils collected from no-till and chisel plow fields and the transport into tile drainage systems.

Sponsor: National Pork Board
PIs: Michelle Soupir, Thomas Moorman, Alok Bhandari                            

Improving a Watershed Scale Model to Integrate Wetlands into Watershed Planning

The goal of this project is to increase and improve wetland protection and restoration efforts by developing a tool to integrate wetland protection efforts into watershed plans designed to improve water quality.  We will improve the wetland hydrologic and water quality processes in SWAT and conduct scenarios to optimize placement of new wetlands and prioritize restoration efforts on a watershed scale. 

Sponsor: U.S. EPA Region 7
PI: Michelle Soupir
co-PIs: Bill Crumpton, Phil Gassman, Matt Helmers, and Manoj Jha  Student: Charles Ikenberry



REU logo NSF Research Experience for Undergraduates Site:
Sustainable Production and Processing for
Biomass-Derived Fuels of the Future. 
Coming Summer 2011!!

More details?  Chick

Sponsor: National Science Foundation

PI: Raj Raman
Co-PIs: Michelle Soupir and Alok Bhandari

Hickory Grove Water Quality Improvement

Hickory Grove Lake is experiencing event-driven water quality problems.  In general, the watershed is 85% row crop and has very few elevation changes, and much of the agricultural land is under tile drainage management.  Storm related surface runoff has led to gully erosion, debris, and nitrogen spikes immediately after these events.  We are monitoring the water quality and flow into and out of the lake, modeling the watershed with SWAT, and engaging stakeholders in the water quality improvement process.    

Sponsor: Iowa Department of Natural Resources
PI: Michelle Soupir, Matt Helmers, and Alok Bhandari
Student: Rohith Gali



   rm pp pp ms Improving SWAT for developing TMDLs for bacteria

This project will improve modeling of in-stream bacteria fate and transport processes by incorporating bacteria resuspension and enhancing bacteria decay capabilities of the Soil and Water Assessment Tool (SWAT). 

Sponsor: U.S. EPA Region 7
PI: Michelle Soupir
co-PI: Chris Rehmann
Student: Pramod Pandey

The Potential Role of Poultry Manure Fertilizer in Pathogen and Pharmaceutical Contamination of Soil and Water

We will test drainflow from field plots and matrix flow from lab-scale soil columns, both receiving layer manure application, for the presence of campylobacter, salmonella, indicator bacteria, nutrients, and estrogens.

Sponsor: Iowa Egg Council

PI: Ramesh Kanwar

co-PI: Michelle Soupir

Student: Claire Hruby

Claire soil columns Claire

rm flume  swq

Resuspension of E. coli in sediment laden streams

This project involves laboratory experiments to measure resuspension of E. coli from a sediment bed, development of equations to predict the process, and field experiments in Squaw Creek to test the resuspension relationships developed from the laboratory results. Improved models of the fate and transport of E. coli in streams will improve predictions of conditions where a risk to human health is likely and the implementation of land management practices to reduce bacterial pollution in the nation’s water bodies.

PI: Michelle Soupir
Student: Amy Cervantes
Post doc: Pramod Pandey

Sponsor: National Science Foundation


Release and resuspension of direct fecal deposits in streams

Direct fecal deposits from cattle allowed access to streams can be a leading cause of
E. coli pollution in agricultural watersheds.  Microorganisms in the cowpats can survive in stream sediments for extended periods of time and are resuspended during high flows.  We are using a flume to study the resuspension of E. coli into the water column.

Students: Rachel McDaniel and Ross Tuttle 
rm cp flume

irrig boom  Transport of tylosin resistant bacteria through macropores

The transport of antibiotic resistant enterococci and E. coli into tile lines below no-till and chisel plow field plots was examined following swine manure applications in November 2009 and April 2010.

Student: Trang Hoang

Escherichia coli transport, resistance, and virulence factors from land applied swine slurry 

E. coli collected from swine manure are being examined for attachment to soil and resistance to antibiotics, including tylosin, erythomycin, ampicillan, and chloramphenicol.  Relationships between antibiotic resistance and attachment mechanisms are also being investigated.   

Student: Martha Zwonitzer
counting marth mollypig

SEMdigesters E. coli survival in aerobic and anaerobic digesters

We are comparing the survival of Escherichia coli in lab scale aerobic and anaerobic digesters.  The goal is to optimize the hydraulic retention time in these systems to reduce pathogens in dairy manure before application to agricultural lands.

Student: Pramod Pandey


Projects at Virginia Tech

Transport of pathogen indicators from pasturelands during runoff events

Transport of pathogen indicators to surface waters is a leading cause of water quality impairments in the United States.  Improved understanding of bacterial transport mechanisms will aid in the design and selection of best management practices.
cowpat transport

Die-off of E. coli and enterococci in dairy cowpats

Shortcomings exist in the first order decay equations frequently used to model in-field bacterial die-off.  The goal of this study was to assess E. coli and enterococci re-growth and decay patterns in cowpats applied to pasturelands and model these patterns with higher order time approximations and weather parameters.

marissasmall simulator
Release of pathogen indicators during high-intensity rainfall events

Soil properties have been found to influence attachment of
E. coli and enterococci to particulates.  A portable rainfall simulator was used to examine partitioning in runoff during high intensity rainfall events from cowpats applied to three Virginia soils.

A method to partition between attached and unattached E. coli in runoff from agricultural lands

This laboratory study compared various separation and dispersion techniques to partition between particulate associated and unattached E. coli.   Optimal dispersion was achieved by a 10-minute hand shaker treatment followed by serial dilutions in 1,000 ppm Tween-85 solution and confirmed by fluorescence microcopy.  Fractional filtration separated particulates into sand, silt and clay sized categories.


large simulator

Release and Transport of bacteria and nutrients from livestock manure applied to pasturelands

Pastureland was treated with standard cowpats, liquid dairy manure and poultry litter to compare transport of nutrients and fecal bacteria.   Bacteria, SBP and TN were greatest from plots receiving cowpat treatments while DP was greatest in runoff from turkey litter plots.


Carbon source utilization to identify enterococcus species in runoff and source manure

Identification of transportable species of enterococcus associated with specific source manures could greatly assist in identifying sources of contamination from mixed-landuse watersheds. 



pam plotsrunoff

Effectiveness of PAM in reducing runoff and nutrient losses from construction sites

Polyacrylamide (PAM) was investigated as a temporary erosion control measure during construction activities.  Dry and liquid forms of PAM were applied to plots and compared to untreated bare soils and plots treated with straw mulch and hydroseed.

Grasses reduce nitrate leaching potential

Nitrate leaching was reduced by fescue grass when compared to ryegrass and crabgrass.  Increased waste application rates were reflected in chlorophyll levels.