Poultry Mortality Freezer Units: Better BMP, Better Biosecurity, Better Bottom Line.

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Why Tackle Mortality Management?  It’s Ripe for Revolution.

The poultry industry has enjoyed a long run of technological and scientific advancements that have led to improvements in quality and efficiency.  To ensure its hard-won prosperity continues into the future, the industry has rightly shifted its focus to sustainability.  For example, much money and effort has been expended on developing better management methods and alternative uses/destinations for poultry litter.

In contrast, little effort or money has been expended to improve routine mortality management – arguably one of the most critical aspects of every poultry operation.  In many poultry producing areas of the country, mortality management methods have not changed in decades – not since the industry was forced to shift from the longstanding practice of pit burial.  Often that shift was to composting (with mixed results at best).  For several reasons – improved biosecurity being the most important/immediate – it’s time that the industry shift again.

The shift, however, doesn’t require reinventing the wheel, i.e., mortality management can be revolutionized without developing anything revolutionary.  In fact, the mortality management practice of the future owes its existence in part to a technology that was patented exactly 20 years ago by Tyson Foods – large freezer containers designed for storing routine/daily mortality on each individual farm until the containers are later emptied and the material is hauled off the farm for disposal.

Despite having been around for two decades, the practice of using on-farm freezer units has received almost no attention.  Little has been done to promote the practice or to study or improve on the original concept, which is a shame given the increasing focus on two of its biggest advantages – biosecurity and nutrient management.

Dusting off this old BMP for a closer look has been the focus of our work – and with promising results.  The benefits of hitting the reset button on this practice couldn’t be more clear:

  1. Greatly improved biosecurity for the individual grower when compared to traditional composting;
  2. Improved biosecurity for the entire industry as more individual farms switch from composting to freezing, reducing the likelihood of wider outbreaks;
  3. Reduced operational costs for the individual poultry farm as compared to more labor-intensive practices, such as composting;
  4. Greatly reduced environmental impact as compared to other BMPs that require land application as a second step, including composting, bio-digestion and incineration; and
  5. Improved quality of life for the grower, the grower’s family and the grower’s neighbors when compared to other BMPs, such as composting and incineration.

What Did We Do?

We basically took a fresh look at all aspects of this “old” BMP, and shared our findings with various audiences.

That work included:

  1. Direct testing with our own equipment on our own poultry farm regarding
    1. Farm visitation by animals and other disease vectors,
    2. Freezer unit capacity,
    3. Power consumption, and
    4. Operational/maintenance aspects;
  2. Field trials on two pilot project farms over two years regarding
    1. Freezer unit capacity
    2. Quality of life issues for growers and neighbors,
    3. Farm visitation by animals and other disease vectors,
    4. Operational and collection/hauling aspects;
  3. Performing literature reviews and interviews regarding
    1. Farm visitation by animals and other disease vectors
    2. Pathogen/disease transmission,
    3. Biosecurity measures
    4. Nutrient management comparisons
    5. Quality of life issues for growers and neighbors
  4. Ensuring the results of the above topics/tests were communicated to
    1. Growers
    2. Integrators
    3. Legislators
    4. Environmental groups
    5. Funding agencies (state and federal)
    6. Veterinary agencies (state and federal)

What Have We Learned?

The breadth of the work at times limited the depth of any one topic’s exploration, but here is an overview of our findings:

  1. Direct testing with our own equipment on our own poultry farm regarding
    1. Farm visitation by animals and other disease vectors
      1. Farm visitation by scavenger animals, including buzzards/vultures, raccoons, foxes and feral cats, that previously dined in the composting shed daily slowly decreased and then stopped entirely about three weeks after the farm converted to freezer units.
      2. The fly population was dramatically reduced after the farm converted from composting to freezer units.  [Reduction was estimated at 80%-90%.]
    2. Freezer unit capacity
      1. The test units were carefully filled on a daily basis to replicate the size and amount of deadstock generated over the course of a full farm’s grow-out cycle.
      2. The capacity tests were repeated over several flocks to ensure we had accurate numbers for creating a capacity calculator/matrix, which has since been adopted by the USDA’s Natural Resources Conservation Service to determine the correct number of units per farm based on flock size and finish bird weight (or number of grow-out days) in connection with the agency’s cost-share program.
    3. Power consumption
      1. Power consumption was recorded daily over several flocks and under several conditions, e.g., during all four seasons and under cover versus outside and unprotected from the elements.
      2. Energy costs were higher for uncovered units and obviously varied depending on the season, but the average cost to power one unit is only 90 cents a day.  The total cost of power for the average farm (all four units) is only $92 per flock.  (See additional information for supporting documentation and charts.)
    4. Operational/maintenance aspects;
      1. It was determined that the benefits of installing the units under cover (e.g., inside a small shed or retrofitted bin composter) with a winch system to assist with emptying the units greatly outweighed the additional infrastructure costs.
      2. This greatly reduced wear and tear on the freezer component of the system during emptying, eliminated clogging of the removable filter component, as well as provided enhanced access to the unit for periodic cleaning/maintenance by a refrigeration professional.
  2. Field trials on two pilot project farms over two years regarding
    1. Freezer unit capacity
      1. After tracking two years of full farm collection/hauling data, we were able to increase the per unit capacity number in the calculator/matrix from 1,500 lbs. to 1,800 lbs., thereby reducing the number of units required per farm to satisfy that farm’s capacity needs.
    2. Quality of life issues for growers and neighbors
      1. Both farms reported improved quality of life, largely thanks to the elimination or reduction of animals, insects and smells associated with composting.
    3. Farm visitation by animals and other disease vectors
      1. Both farms reported elimination or reduction of the scavenging animals and disease-carrying insects commonly associated with composting.
    4. Operational and collection/hauling aspects
      1. With the benefit of two years of actual use in the field, we entirely re-designed the sheds used for housing the freezer units.
      2. The biggest improvements were created by turning the units so they faced each other rather than all lined up side-by-side facing outward.  (See additional information for supporting documentation and diagrams.)  This change then meant that the grower went inside the shed (and out of the elements) to load the units.  This change also provided direct access to the fork pockets, allowing for quicker emptying and replacement with a forklift.
  3. Performing literature reviews and interviews regarding
    1. Farm visitation by animals and other disease vectors
      1. More research confirming the connection between farm visitation by scavenger animals and the use of composting was recently published by the USDA National Wildlife Research Center:
        1. “Certain wildlife species may become habituated to anthropogenically modified habitats, especially those associated with abundant food resources.  Such behavior, at least in the context of multiple farms, could facilitate the movement of IAV from farm to farm if a mammal were to become infected at one farm and then travel to a second location.  …  As such, the potential intrusion of select peridomestic mammals into poultry facilities should be accounted for in biosecurity plans.”
        2. Root, J. J. et al. When fur and feather occur together: interclass transmission of avian influenza A virus from mammals to birds through common resources. Sci. Rep. 5, 14354; doi:10.1038/ srep14354 (2015) at page 6 (internal citations omitted; emphasis added).
    2. Pathogen/disease transmission,
      1. Animals and insects have long been known to be carriers of dozens of pathogens harmful to poultry – and to people.  Recently, however, the USDA National Wildlife Research Center demonstrated conclusively that mammals are not only carriers – they also can transmit avian influenza virus to birds.
        1. The study’s conclusion is particularly troubling given the number and variety of mammals and other animals that routinely visit composting sheds as demonstrated by our research using a game camera.  These same animals also routinely visit nearby waterways and other poultry farms increasing the likelihood of cross-contamination, as explained in this the video titled Farm Freezer Biosecurity Benefits.
        2. “When wildlife and poultry interact and both can carry and spread a potentially damaging agricultural pathogen, it’s cause for concern,” said research wildlife biologist Dr. Jeff Root, one of several researchers from the National Wildlife Research Center, part of the USDA-APHIS Wildlife Services program, studying the role wild mammals may play in the spread of avian influenza viruses.
    3. Biosecurity measures
      1. Every day the grower collects routine mortality and stores it inside large freezer units. After the broiler flock is caught and processed, but before the next flock is started – i.e. when no live birds are present,  a customized truck and forklift empty the freezer units and hauls away the deadstock.  During this 10- to 20- day window between flocks biosecurity is relaxed and dozens of visitors (feed trucks, litter brokers, mortality collection) are on site in preparation for the next flock.
        1. “Access will change after a production cycle,” according to a biosecurity best practices document (enclosed) from Iowa State University. “Empty buildings are temporarily considered outside of the [protected area and even] the Line of Separation is temporarily removed because there are no birds in the barn.”
    4. Nutrient management comparisons
      1. Research provided by retired extension agent Bud Malone (enclosed) provided us with the opportunity to calculate nitrogen and phosphorous numbers for on-farm mortality, and therefore, the amount of those nutrients that can be diverted from land application through the use of freezer units instead of composting.
      2. The research (contained in an enclosed presentation) also provided a comparison of the cost-effectiveness of various nutrient management BMPs – and a finding that freezing and recycling is about 90% more efficient than the average of all other ag BMPs in reducing phosphorous.
    5. Quality of life issues for growers and neighbors
      1. Local and county governments in several states have been compiling a lot of research on the various approaches for ensuring farmers and their residential neighbors can coexist peacefully.
      2. Many of the complaints have focused on the unwanted scavenger animals, including buzzards/vultures, raccoons, foxes and feral cats, as well as the smells associated with composting.
      3. The concept of utilizing sealed freezer collection units to eliminate the smells and animals associated with composting is being considered by some government agencies as an alternative to instituting deeper and deeper setbacks from property lines, which make farming operations more difficult and costly.

Future Plans

We see more work on three fronts:

  • First, we’ll continue to do monitoring and testing locally so that we may add another year or two of data to the time frames utilized initially.
  • Second, we are actively working to develop new more profitable uses for the deadstock (alternatives to rendering) that could one day further reduce the cost of mortality management for the grower.
  • Lastly, as two of the biggest advantages of this practice – biosecurity and nutrient management – garner more attention nationwide, our hope would be to see more thorough university-level research into each of the otherwise disparate topics that we were forced to cobble together to develop a broad, initial understanding of this BMP.

Corresponding author (name, title, affiliation)

Victor Clark, Co-Founder & Vice President, Legal and Government Affairs, Farm Freezers LLC and Greener Solutions LLC

Corresponding author email address


Other Authors

Terry Baker, Co-Founder & President, Farm Freezers LLC and Greener Solutions LLC

Additional Information


Farm Freezer Biosecurity Benefits

One Night in a Composting Shed


Transmission Pathways

Avian flu conditions still evolving (editorial)

USDA NRCS Conservation fact sheet Poultry Freezers

Nature.com When fur and feather occur together: interclass transmission of avian influenza A virus from mammals to birds through common resources

How Does It Work? (on-farm freezing)

Influenza infections in wild raccoons (CDC)

Collection Shed Unit specifications

Collection Unit specifications

Freezing vs Composting for Biosecurity (Render magazine)

Manure and spent litter management: HPAI biosecurity (Iowa State University)


Bud Malone, retired University of Delaware Extension poultry specialist and owner of Malone Poultry Consulting

Bill Brown, University of Delaware Extension poultry specialist, poultry grower and Delmarva Poultry Industry board member

Delaware Department of Agriculture

Delaware Nutrient Management Commission

Delaware Office of the Natural Resources Conservation Service

Maryland Office of the Natural Resources Conservation Service

The authors are solely responsible for the content of these proceedings. The technical information does not necessarily reflect the official position of the sponsoring agencies or institutions represented by planning committee members, and inclusion and distribution herein does not constitute an endorsement of views expressed by the same. Printed materials included herein are not refereed publications. Citations should appear as follows. EXAMPLE: Authors. 2017. Title of presentation. Waste to Worth: Spreading Science and Solutions. Cary, NC. April 18-21, 2017. URL of this page. Accessed on: today’s date.

Elimination of Equine Streptococci from Soiled Equine Bedding

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Streptococcus equi subspecies equi (S. equi), causes the potentially fatal respiratory disease in horses known as “strangles”, while the closely related Streptococcus equi subspecies zooepidemicus (S. zooepidemicus) causes potentially fatal infections in humans. A study was undertaken to determine the survival of these 2 organisms in compost and soiled bedding.

What did we do? 

Dacron bags were filled with a feedstock mixture of soiled equine bedding and feed waste at ratios of 3:1 (C:N ratio 40.6), 1:1 (C:N ratio 31.9), and 1:4 (C:N ratio 25.4). The Dacron bags were inoculated with S. zooepidemicus, and placed in 3 compost windrows of the same 3 feedstock ratios 24 h later. Streptococci were quantified at different time points. Next, S. equi was inoculated into Dacron bags then placed into a compost windrow of the same feedstock ratio. Streptococci were quantified. To rule out killing of both Streptococcal species by microflora during the 24 h storage period, samples of soiled equine bedding, both autoclaved and non-autoclaved, were inoculated with S. zooepidemicus and periodically sampled. A repeated study was conducted with S. equi. To determine the role of moisture on the killing of S. equi in equine waste, soiled equine bedding was dried at 37 °C for 48 h and sterile water then added to dried bedding.

What have we learned?             

Microbes in soiled equine bedding may eliminate Streptococci, indicating that normal compost microflora may provide sustainable methods for the control of human and animal pathogens.

Future Plans    

Future studies could assess the role of individual bacterial species in the abatement of Streptococci, and possible additives to a compost pile which might increase numbers of streptocidal organisms. In addition, compost could be examined to discover novel antibiotics or bacteriophages which may be used for disease control.

Corresponding author, title, and affiliation        

Alexandria Garcia, Graduate Student, University of Maine

Corresponding author email    


Other authors   

Dr. Robert Causey, Associate Professor at University of Maine, Scott Mitchell, Student, Kathleen Harvey, Student, Ashley Myer, Student, Mark Hutchison, Extension Professor, and Martin Stokes, Professor

Additional information               

Garcia, Alexandria, “Abatement of Streptococcus equi in Equine Compost” (2016). Electronic Theses and Dissertations. 2435.



Maine Agricultural Center, Dr. M. Susan Erich, Mark Hutchinson


The authors are solely responsible for the content of these proceedings. The technical information does not necessarily reflect the official position of the sponsoring agencies or institutions represented by planning committee members, and inclusion and distribution herein does not constitute an endorsement of views expressed by the same. Printed materials included herein are not refereed publications. Citations should appear as follows. EXAMPLE: Authors. 2017. Title of presentation. Waste to Worth: Spreading Science and Solutions. Cary, NC. April 18-21, 2017. URL of this page. Accessed on: today’s date.

Manure Treatment and Natural Inactivation of Porcine Epidemic Diarrhea Virus in Soils

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The porcine epidemic diarrhea virus (PEDv) outbreak in North America has substantially impacted swine production, causing nearly 100% mortality in infected newborn piglets. Because manure may remain a source of reinfection, proper manure management practices to limit outbreaks need to be developed and evaluated. Two laboratory studies simulating manure pit treatment with increasing amounts of quicklime were conducted to determine PEDv susceptibility to increasing pH. Additionally, two laboratory soil incubation studies contrasting manure liming, multiple soil types, and two antecedent soil moistures were conducted over several months with incubation conditions mimicking the climates in Minnesota, Missouri, and Oklahoma to determine whether current manure application practices reduce the potential for PEDv reinfection via manure-amended soil. Quantitative PCR and live swine bioassays were used to enumerate PED virus and to determine whether manure and soil samples contained infectious PEDv.

What did we do?

Quicklime-Manure Slurry Incubations: An initial short-term manure slurry study was conducted on fresh PEDv-positive manure slurry collected in 2015 from the shallow pit of a commercial swine facility in southeast Nebraska. Manure was sampled prior to treatment (0 h) and then distributed among glass beakers (250 mL) to accommodate triplicates of three treatments: liming to pH 10, liming to pH 12, and unlimed manure. Following pH adjustment, aliquots of each sample were collected at 1 and 10 h, immediately neutralized with 10 mM HCl and stored at -80°C for subsequent analysis. In a second manure slurry incubation, triplicate PEDv-positive manure samples collected from a commercial swine operation in south central Nebraska site in December 2016 were mixed in equal portion (w:v) with distilled water to mimic manure slurry consistency observed in swine production pit storages. Quicklime was added stepwise (0.25 g addition) to each manure slurr! y sample with continuous stirring to gradually increase manure slurry pH. After each addition of quicklime, pH was measured and an aliquot of manure slurry was collected for subsequent quantitative PCR PEDv enumeration and infectivity in a pig bioassay.

Long-term manure and soil incubation. Initial tests determined appropriate initial soil moisture contents (representing a ‘dry’ and ‘moist’ soil condition) and manure:soil ratios (1 g slurry:3 g soil) to best represent the manure:soil within an injection furrow when slurry is injected into soil, and appropriate liming source (ag lime vs. quicklime). PEDv-positive manure slurry collected from a commercial swine operation in southeast Nebraska was divided between two 3-L containers, one for limed treatment (LIME) and the other for the control, or no-lime, treatment (CNL). Quicklime (30 g) was added to one 3 L portion (equivalent to an application of 80 lbs. quicklime per 1000 gallons of slurry) to achieve a final pH of 12. Both treated and untreated slurry stocks were incubated at room temperature for 24 hours. Distilled water was added to two soils, a silty clay loam (pH 7.0) and a loamy fine sand (pH 6.9), to attain 10% and 30% water holding capacity! (dry and moist soil condition). Thirty grams (dry weight) of soil was apportioned to multiple 50 mL screw top conical tubes and a cavity was made in the center of the soil by pressing a 10 mL pipet tip into the soil. Ten mL of slurry (LIME or CNL) were then added to each soil tube via pipet. Four replicate tubes were immediately frozen at -80°C for each combination of soil, moisture, and manure treatment to represent initial soil application (day 0). The tubes were loosely capped and placed into one of three incubators operated independently throughout the trial to simulate soil temperatures between November 1 and May 1 at one of three geographic locations: southern Minnesota, northern Missouri, and central Oklahoma (Figure 1). Twenty replicate tubes were created for each combination of soil, moisture, incubation, and manure treatment, and a set of four tubes were collected for each treatment combination on days 30, 60, 90, 120 and 150 of the incubation and immediately transfer! red to a -80°C freezer for storage.

Molecular detection and quantification of PEDv. Prior to analysis, soil and manure samples were removed from -80°C storage and allowed to thaw at room temperature. The RNA in each sample was extracted using the RNA PowerSoil Total RNA Isolation kit (Mo Bio, Carlsbad, CA). PEDv was detected in samples by reverse transcription and quantitative polymerase chain reaction (RT-qPCR).

Swine bioassay. To confirm that conditions yielding a PCR negative result actually inactivated the PED virus and rendered the manure non-infectious, a live pig bioassay was conducted with the limed and non-limed manure slurry samples from the initial short-term manure slurry incubation (quicklime addition). Fifteen pigs, approximately 21 days old, were sourced from a high-health facility whose dams tested negative for PEDv antibodies and virus by PCR. Piglets were tested for PEDv upon arrival and confirmed negative. Piglets were randomly assigned to individual housing in BSL-2 rooms at the University of Nebraska-Lincoln Life Sciences Annex as follows: control (3 piglets), pH 10 (6 piglets), and pH 12 (6 piglets), and allowed to acclimate for three days. Each pig was then administered a 10-mL oral gavage of manure slurry: three piglets in the control room received one of the three un-limed slurry samples; six piglets in the pH 10 room received one of the six limed (pH 10) sl! urry samp les (three limed for 1 h and three limed for 10 h); and six pigs in the pH 12 room received one of the six limed (pH 12) slurry samples (three limed for 1 h and three limed for 10 h). Piglets were monitored for fecal shedding of PEDv for four days until control animals began to demonstrate clinical signs of PEDv infection, at which time all piglets were humanely euthanized. Fecal swabs, and duodenum, ileum, jejunum, and cecum samples were collected from each animal and fixed in formalin. All fecal and tissue samples were analyzed for the presence of detectable PED virus by immunohistochemistry and PCR.

PEDv, log # g soil

What have we learned?

Manure Slurry Incubation: Manure limed to pH 10 and pH 12 for 1 and 10 h yielded no detectable PEDv RNA. Live swine bioassay results confirmed that these samples were not infective while control samples resulted in PEDv infection of piglets. These results indicate that a final manure slurry pH of 10 (equivalent to 50 lbs. of quicklime added to 1000 gallons manure slurry) is sufficient to reduce PEDv RNA to an undetectable concentration after 1 hour of contact time. All pigs receiving limed manure (pH 10 or 12 maintained for 1 or 10 h) during the live swine bioassay tested negative for PEDv infection while control pigs (un-limed treatment) all tested positive for PEDv infection (Figure 1). The pig bioassay results confirmed that the PCR assay is a reliable predictor for the presence of infectious PEDv in these matrices and that lime addition to achieve pH 10 for just one hour is sufficient to deactivate the virus in stored manure.

Soil Incubations: At the completion of the long-term (150-day) soil incubation, a subset of the frozen samples (LIME and CON soil samples collected on day 0 and 30) was selected for RNA extraction and qPCR analysis. The qPCR results from days 0 and 30 yielded no detectable PEDv RNA in either the limed or un-limed manure-amended soils (Figure 1). Furthermore, manure-amended soils did not differ from soil-only controls even though PEDv RNA was still detectable in the original manure slurry at high concentrations. No differences in PEDv abundance were detected on either day when initial soil moisture (10% vs 30% water holding capacity), incubation condition (MN vs. MO vs. OK), or soil type (silty clay loam and loamy fine sand) were varied. For these soils, the concentration of PEDv in limed or un-limed manure decreased immediately to a non-detectable level. These results indicate that manure-amended soil with pH 6.9 or greater is not a vector for transmission of the PED virus.

A consistent finding from all of the studies is that pH of media (slurry or soil) strongly influences PED virus survival.

Future Plans

Additional studies are underway to identify the lowest pH at which the PED virus is rendered non-infectious in slurry manure.

Corresponding author, title, and affiliation

Amy Millmier Schmidt, Assistant Professor, Departments of Biological Systems Engineering and Animal Science, University of Nebraska – Lincoln

Corresponding author email


Other authors

Stevens, E., A. Schmidt, D. Miller, J.D. Loy and V. Jin

Additional information

Dr. Amy Millmier Schmidt, corresponding author, can also be reach at (402) 472-0877.


Funding for this research was provided by the National Pork Board. Gratitude is extended to Ashley Schmit for assistance with laboratory activities and animal care. Special thanks to the Nebraska pork producers who granted access to their farms for collection of PEDv-positive manure.

Integrating Small Scale Digestion Systems in Developing Regions

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People in developing countries regularly lack access to energy or their energy source is not reliable. Low cost anaerobic digestion systems have the potential to provide methane to be used in a variety of end uses. Unfortunately, many low cost systems are not evaluated and it is unclear if they are living up to the expectations of the end users or those that are promoting or financially supporting their installation.

What did we do? 

We have evaluated multiple small scale anaerobic digestion systems in Uganda and Bolivia to assess their energy production potential, impact of digestate as a fertilizer (using plot studies), pathogen reduction through the digester, and impact to kitchen air quality when biogas stoves replace firewood. Based on feedback we have also designed, tested and implemented a low cost separation system for handling digestate to recycle separated liquids and improve handling of solids. We have also modified an absorption chiller to run on biogas and are in the process of wider spread adoption and evaluation.

What have we learned? 

Throughout this assessment we have learned that many institutional level digestion systems in developing countries are not meeting the biogas demands of the end users. While they like the improved cooking time and reduced air quality impacts in the kitchen, only small households are producing enough gas to realize many of these benefits. Biogas poses a reduction in PM2.5 (fine particulates) within kitchens when compared to firewood stoves. However, when any amount of firewood is used in the kitchens (when there is not enough biogas), much of this benefit is lost. Therefore it is critical to improve the biogas production of these systems.

Maize plot trials show that compared to control plots digestate applied in any form (slurry or separated solids) significantly improves yields. When compared to inorganic fertilizer applications the grain yields are statistically similar but the stover yields increase significantly. End users show a preference for using the separated solids and the reduction in water needed to operate the systems. While these benefits seem appealing, there may be concern for the risks associated with pathogens in the digestate when applied to food crops. While digesters showed a significant reduction in pathogen related to the system retention time, pathogen remained in the effluent and must be handled properly to limit transfer to food and the human health risks after ingestion.

Increasing the end use of biogas beyond cooking to chillers has shown great potential for implementation and has high demand for end users. Systems have been able to provide cooling at multiple locations for extended periods with low biogas demands. Additional materials are needed to provide end users with guidance on troubleshooting and operation.

Future Plans    

Based on the results of these studies we are moving forward with farmer trials of the digestate to assess end user issues and motivations. In addition, we are currently designing a low cost heating system to improve biogas production efficiency in order to meet end user needs or decrease the size of digesters. Finally we are working on an evaluation of chiller biogas needs and providing training on all aspects of the digestion systems.

Corresponding author, title, and affiliation      

Rebecca Larson, Assistant Professor at the University of Wisconsin-Madison

Corresponding author email    


Other authors   

A. McCord, Associate Director at University of Wisconsin-Madison, Vianney Tumwesige, CEO at GreenHeat Uganda, Dorothy Lsoto at W2E Uganda

Additional information              



McCord, A.I., S.A. Stefanos, V. Tumwesige, D. Lsoto, A. Meding, A. Adong, J.J. Schauer, and R.A. Larson. 2017. Biogas and the impacts of fuel choice on institutional kitchen air quality in Kampala, Uganda. Indoor Air. In Review, revisions requested.

McCord, A.I., S.A. Stefanos, V. Tumwesige, D.T. Lsoto, M. Kawala, J. Mutebi, I. Nansubuga, and R.A. Larson. 2017. Anaerobic digestion and public sanitation in Kampala: risks and opportunities. In Review.

Effectiveness of Different Dairy Manure Management Practices in Controlling the Spread of Antibiotics and Antibiotic Resistance

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Even when antibiotics are used judiciously, antibiotic residues, antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG) can accumulate in human waste and manure and contribute to the spread of antibiotic resistance. Modern U.S. dairy farms use antibiotics for disease treatment and prevention according to the guidance of veterinary physicians. While dairy manure handling and treatment systems may effectively mitigate antibiotic resistance, the fate of antibiotic residues, ARB and ARG through these systems has not been adequately investigated. 

What did we do? 

Working cooperatively with 11 dairies in 3 states (NY, PA, MD) our multi-institutional (U. Buffalo, Cornell, U. Maryland, U. Michigan), interdisciplinary team is investigating the effect different manure management practices (e.g. long-term storage, composting, anaerobic digestion, etc.) have on antibiotic residue levels, ARB and ARG. Every 6 weeks for 2 years manure is being collected pre- and post- each treatment step of the various manure handling systems used by each farm. All samples are being characterized and tested for select antibiotic residues (tetracyclines, macrolides, sulfonamides, penicillins and ceftiofurs), with select samples also analyzed for ARB and ARG. To guide these efforts, antibiotic usage and manure treatment system operational data are also being collected for each farm.

What have we learned? 

A year of samples has been collected with analysis of antibiotic residues, ARB and ARG on-going. Based on the preliminary data, antibiotic residues are detectable at low-concentrations (< 200 mg/L) in each farm’s manure. Antibiotic residue levels are generally lower in treated manure compared to levels in raw manure, though mitigation efficacy is variable. Early findings show some composting systems have the capacity to lower antibiotic residue levels. Antibiotic residue levels are also lower in separated manure solids, with evidence for partitioning of soluble antibiotic residues into separated manure liquids. At this time, the effects of anaerobic digestion and long-term anaerobic manure storage on antibiotic residue levels remain unclear. Select samples are currently being analyzed for ARB and ARG.

Future Plans 

We are entering our second year of field monitoring and ARB and ARG analysis is on-going. Laboratory efforts are also beginning to test the effectiveness of specific anaerobic digester operational parameters at mitigating antimicrobial resistance. Extension/outreach meetings with stakeholder groups are also being planned. The ultimately project goals are to discern the fate of antibiotic residues, ARB and ARG as they move through dairy manure handling systems, identify the efficacy of different manure treatment systems at mitigating antibiotic resistance and extending this knowledge to dairy operators.

Corresponding author, title, and affiliation      

Jason Oliver, Postdoctoral Associate at Dept. of Animal Science, Cornell University

Corresponding author email    


Other authors   

Curt Gooch, Senior Extension Associate at Cornell University, Dept. of Animal Science, PRO-DAIRY

Additional information               

Additional project information can be found on the dairy environmental system webpage: www.manuremanagement.cornell.edu


This material is based upon work that is supported by the National Institute of Food and Agriculture, U.S. Department of Agriculture, under award number 2016-68003-24601. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture.

Project collaborators include: (PD) Diana Aga, University of Buffalo, Dept. of Chemistry (Co-PI); her students Mitch Mayville and Jarod Hurst; (Co-PD) Lauren Sassoubre , University of Buffalo, Dept. of Civil, Structural & Environmental Engineering; (Co-PDs) Stephanie Lansing and Gary Felton, Associate Professors at University of Maryland, Dept. of Environmental Science & Technology; their student Jenna Schueler; (Co-PD) Krista Wigginton, Assistant Professor at University of Michigan, Dept. of Civil & Environmental Engineering; Lutgarde Raskin, Professor at University of Michigan, Dept. of Civil & Environmental Engineering; and their student Emily Crossette.


The authors are solely responsible for the content of these proceedings. The technical information does not necessarily reflect the official position of the sponsoring agencies or institutions represented by planning committee members, and inclusion and distribution herein does not constitute an endorsement of views expressed by the same. Printed materials included herein are not refereed publications. Citations should appear as follows. EXAMPLE: Authors. 2017. Title of presentation. Waste to Worth: Spreading Science and Solutions. Cary, NC. April 18-21, 2017. URL of this page. Accessed on: today’s date.

Archived Pathogen Pages

Question or concerns, contact John Brooks (john.brooks@ars.usda.gov)

Research Summaries




E. coli diversity in livestock manures


Cook, K.L., Bolster, C.H., Ayers, K.A., Reynolds, D.N. 2011. Escherichia coli diversity in livestock manures and agriculturally impacted stream waters. Current Microbiology. 63(5):439–449.


Escherichia coli (E. coli) is a dominant intestinal commensal organism, an important fecal indicator bacterium (FIB), a pathogen and a target for microbial source tracking (MST). Strain level differences (genotypic and phenotypic) influence E. coli fate and transport and therefore have important implications for its validity as an FIB and for MST. The goals of this study were to (1) determine the diversity of E. coli in manures from livestock and stream-water samples taken following dry and wet weather events; (2) determine the profile of virulence-associated genes and; (3) evaluate the effect of strain level differences on the attachment and transport of E. coli. To evaluate diversity, 1346 E. coli isolates were obtained from three livestock species and seventeen stream-water samples. We found that many E. coli strains isolated from water sources had DNA fingerprints that were significantly different than those from stream-water in a predominantly agricultural area. Furthemore, significant differences were also seen between E. coli isolates from stream-water samples taken following wet and dry weather events. Wide diversity in the attachment efficiency of E. coli isolates from different sources occurred and those differences corresponded with the occurrence of virulence factors often correlated with adhesion. These findings underscore the genetic variation inherent to this important indicator organism. The influence of diversity on genetic exchange and the concomitant effect on the organisms’ fitness and adaptation to in situ environmental conditions require further investigation. The resultant issues for purposes of modeling, source tracking and risk assessment require careful consideration in future research studies.

Transport behaviors of E. coli

Bolster, C.H., Cook, K.L., Marcus, I.M., Haznedaroglu, B.Z., Walker, S.L. 2010. Correlating Transport Behavior with Cell Properties for Eight Porcine Escherichia coli Isolates. Environmental Science and Technology. 44(13):5008–5014.


Infiltration of fecal material into the subsurface can result in the contamination of ground water supplies by pathogenic microorganisms such as bacteria, viruses, and protozoa, thereby posing a threat to public health. To assess whether a ground water source is at risk for fecal contamination, agencies responsible for monitoring water supplies generally test for the presence of nonpathogenic as indicator organisms. One of the most commonly used indicator organisms in ground water systems is E coli. To improve our understanding of the mechanisms controlling E. coli movement in the environment, we conducted a set of transport studies to better understand the factors that control E. coli attachment to sediment surfaces. For quartz sand we found that E .coli attachment, and thus transport, was controlled by the surface charge of the cell. For Fe-coated sand a mild correlation between cell width and attachment was observed. These findings will help improve our understanding of the mechanisms controlling E .coli in the environment.

Broiler litter application and E. coli

Sistani, K.R., Torbert III, H.A., Way, T.R., Bolster, C.H., Pote, D.H., Warren, J.G. 2009. Broiler Litter Application Method and Runoff Timing Effects on Nutrient and Escherichia coli Losses from Tall Fescue Pasture. Journal of Environmental Quality. 38(3):1216-1223


Over two-thirds of the total U.S. Broiler chicken production is located in the southeastern United States, which is a major segment of the farm economy in the region. Poultry litter is generally surface applied to pastures and hay fields year-round to supply plant nutrients, particularly nitrogen (N) and phosphorus (P). Runoff from litter-applied land has the potential to transport nutrients and pathogenic microorganisms to nearby surface water. Proper land application of animal manure is critical to water quality in watersheds with significant livestock numbers. With regard to permanent pasture systems, inability to incorporate waste materials leads to increased nutrient concentration such as phosphorus, nitrogen, copper, and zinc and pathogenic microorganisms near the soil surface. Currently, broadcasting is a common method of litter application on soil in many parts of U.S. The objectives of this study were (i) to compare the effect of broiler litter application method on nutrient and E. coli losses in runoff from tall fescue pasture in the Appalachian Plateau, and (ii) to determine the impact of antecedent time (time between litter application and the first runoff event) on nutrient and E. coli losses. Inorganic N and E. coli concentrations in runoff were significantly greater from broadcast litter application than subsurface litter application, while fertilizer treatment had runoff with greater NH4-N but smaller NO3-N than litter application treatments. The loss of total phosphorus, NO3-N, and total suspended solids from broadcast litter application was 83.5%, 64%, and 68% greater than subsurface litter application, respectively. About 81% of the runoff total phosphorus concentration was in the form of dissolved reactive phosphorus for both litter-application methods.

Methods to reduce pathogen loads following application of broiler litter

Brooks, J.P., McLaughlin, M.R., Adeli, A., Miles, D.M. 2012. The effect of poultry manure application rate and AlCl3 treatment on bacterial fecal indicators in runoff. Journal of Water and Health. 10:619-628.


Land application of poultry litter is a beneficial method of using this fertilizer source. It can provide high levels of N and organic C. However, the protection of water sources following land application of any fertilizer is necessary since many of the US surface water supply has been compromised due to the presence of fecal bacteria like Escherichia coli (E. coli) or anoxic, a condition in which the presence of nutrient runoff can lead to conditions which kill fish. The purpose of this study was to determine a suitable fecal indicator for poultry litter runoff following large-scale rain events. A previous greenhouse study determined that there are other poultry-litter fecal indicators more suitable for runoff than traditional indicators such as E. coli; this study confirms those results and found that of all treatments receiving poultry litter, two indicators proved to be useful. Over a two year period, field plots were land applied with various combinations of poultry litter or inorganic fertilizers and rained upon with an artificial rain maker. The results suggested that Clostridium perfringens and staphylococci were more useful as an indicator of poultry litter horizontal movement than all others. This persisted for up to 30 days following land application of poultry litter. The presence of these two indicators may signal a change for regulators and environmental monitors when investigating poultry litter fecal pollution.

Risk assessment of pathogens in manure

Brooks, J.P., McLaughlin, M.R., Gerba, C.P., Pepper, I.L. 2012. Land application of manure and class B biosolids: an occupational and public quantitative microbial risk assessment. Journal of Environmental Quality. 41:2009-2023.


The land application of wastes, such as wastewater treatment plant biosolids and manures, has been practiced for years and serves as a method to dispose and treat these wastes. The presence of bacterial, viral, and parasitic pathogens in these wastes can further complicate issues and reduce public confidence in their disposal. Typically the concern and hence the regulations governing their land application and use have revolved around controlling nutrient runoff and public contact with these microbial pathogens. The recent foodborne outbreaks involving bacterial and viral pathogens has brought into question the use of these wastes and potential for public exposures. To properly assess the use of these wastes a quantitative microbial risk assessment was conducted comparing the use of manure and municipal biosolids using current pathogen data and simulating potential public exposures following a variety of exposures ranging from fresh food crop consumption to aerosol exposures. A comparison of the risks demonstrated that public health risks are relatively low during non-intentional exposures such as fresh food crop or aerosol exposures and fall below the USEPA recommended annual 1 per 10,000 risk of infection. Only exposures in which intentional consumption of soil contaminated with fecal matter yielded risks which were greater. Risks were far below occupational exposures for the most part and demonstrated that risks between the two types of wastes were similar. Infectious risks from biosolids were greater from viral pathogens, while bacterial pathogens presented the greatest risks from manure. This study demonstrated that given typical conditions, the risk of infection from land application and use of either of these types of wastes are acceptable given time between application and exposures.

Microorganisms in dairy wastewater

Dungan, R.S., Leytem, A.B. 2013. The characterization of microorganisms in dairy wastewater storage ponds. Journal of Environmental Quality. 42:1583-1588.


Idaho is the third largest dairy state in the United States. With over 500,000 milk cows, a vast quantity of solid and liquid manure is generated, much of which is land applied. Given the fact that cattle feces contain a variety of microorganisms, we undertook a study using a culture-independent approach (i.e. no cultivation) to characterize microbial communities in wastewaters from south-central Idaho. After the microbial DNA was extracted from the wastewaters, it was amplified and then a sequence library was created for identification of putative matches. In general, the dairy wastewaters contained a variety of microorganisms affiliated with the domains Archaea and Bacteria. However, a statistical analysis of the data revealed that an insufficient number of sequences were obtained to sufficiently characterize microbial diversity at the species level. Despite this limitation, the results from our study enhanced our understanding of microbial species and communities in dairy wastewaters more so then if culture-dependent techniques were utilized.

Bioaerosols and open-freestall dairy operations

Dungan, R.S. 2012. Use of a culture-independent approach to characterize aerosolized bacteria near an open-freestall dairy operation. Environment International. 41(2012):8-14.


Animal manures are known to harbor a variety of pathogens that can potentially be transmitted to humans in the form of airborne particles. In this study, air samples were collected downwind from a 10,000 cow open-freestall dairy and nearby fields being sprinkler irrigated with wastewater. Nucleic acids (DNA) were extracted from the air samples, then a highly conserved gene was sequenced for bacterial identification. Of the 191 gene sequences, none were affiliated with bacteria known to be pathogenic to healthy humans. Our results suggest that there is a low incidence of airborne bacterial pathogens immediately downwind from the dairy and wastewater irrigation sites.

Poultry Digestion – Emerging Farm-Based Opportunity

While EPA AGSTAR has long supported the adoption of anaerobic digestion on dairies and swine farms, they have not historically focused on the use of anaerobic digestion on egg laying and other poultry facilities. This has been because the high solids and ammonia concentrations within the manure make anaerobic digestion in a slurry-based system problematic. Development of enhanced downstream ammonia and solids recovery systems is now allowing for effective digestion without ammonia toxicity. The process also generates dilution water, avoiding the need for fresh water consumption, and eliminating unwanted effluent that needs to be stored or disposed of to fields. The system produces high-value bio-based fertilizers. In this presentation, a commercial system located in Fort Recovery Ohio will be used to detail the process flow, its technologies, and the co-products sold.

Why Examine Anaerobic Digestion on Poultry Farms?

The purpose of this presentation is to supply a case study on a commercial poultry digestion project for production of combined heat and power as well as value-added organic nutrients on a 1M egg-layer facility in Ohio.

What did we do?

In this study we used commercial farm information to demonstrate that poultry digestion is feasible in regard to overcoming ammonia inhibition while fitting well into an existing egg-layer manure management system. Importantly, during the treatment process a significant portion of nutrients within the manure are concentrated for value-added sales, ammonia losses to the environment are reduced, and wastewater production is minimized due to recycle of effluent as dilution water.

What have we learned?

In this study, commercial data shows that ammonia and solids/salts levels that are potentially inhibitory to the biology of the digestion process can be controlled. The control is through a post-digestion treatment that includes ammonia stripping and recovery as ammonium sulfate as well as fine solids separation using a dissolved air flotation process with the addition of a polymer. The resulting treated effluent is sent back to the front of the digester as dilution water for the high solids poultry manure. The separated fine solids and the ammonium sulfate solution are dried using waste engine heat to produce a nutrient-rich fertilizer for off-farm sales. The stable anaerobic digestion process resulting from the control of potential inhibitors that might accumulate in the return water, if no post-treatment occurred, leads to production of a significant supply of electrical power for sales to the grid.

Demonstration at commercial scale shows the promise anaerobic digestion with post-digestion treatment and effluent recycle can play in a more sustainable poultry manure treatment system including managing nutrients for export out of impacted watersheds.

Future Plans

Future plans include continued work with industry in developing and/or providing extension capabilities around novel digestion and post-treatment processes for a variety of manures and on-farm situations. Expansion of such processes to poultry and other on-farm business plans will allow for improved reductions in wastewater production, concentrate nutrients for export out of impacted watersheds and do so within a positive economic business plan.


Craig Frear, Assistant Professor at Washington State University cfrear@wsu.edu

Quanbao Zhao, Project Engineer DVO Incorporated, Steve Dvorak, President DVO Incorporated

Additional information

Additional information about the corresponding author can be found at http://www.csanr.wsu.edu while information about the poultry project and the industry developer can be found at http://www.dvoinc.net. Numerous articles related to anaerobic digestion, nutrient recovery and separation technologies for climate, air, water and human health improvements can be found at the WSU website using their searchable articles function.


This research was supported by funding from USDA National Institute of Food and Agriculture, Contract #2012-6800219814; National Resources Conservation Service, Conservation Innovation Grants #69-3A75-10-152; and Biomass Research Funds from the WSU Agricultural Research Center. 

The authors are solely responsible for the content of these proceedings. The technical information does not necessarily reflect the official position of the sponsoring agencies or institutions represented by planning committee members, and inclusion and distribution herein does not constitute an endorsement of views expressed by the same. Printed materials included herein are not refereed publications. Citations should appear as follows. EXAMPLE: Authors. 2015. Title of presentation. Waste to Worth: Spreading Science and Solutions. Seattle, WA. March 31-April 3, 2015. URL of this page. Accessed on: today’s date.