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Multi-regional risk analysis of farm manure use: Balancing soil health and food safety for organic fresh produce production

Oct 13, 2015

SoilsmThis collaboration is a USDA Organic Agriculture Research and Extension Initiative (OREI) funded project to further the study of the use of animal-based manure in organic agricultural practices in order to best prevent the risk of soil pathogens, and includes researchers from the University of California, Davis, University of Minnesota, University of Maine, the USDA Agricultural Research Service’s Beltsville Agricultural Research Center, USDA’s Economic Research Service Resource and Rural Economics Division, Cornell University, and The Organic Center .

The impetus for the proposal of the grant was the ongoing implementation process by the U.S. Food and Drug Administration of the Food Safety Modernization Act (FSMA) to improve food safety. Last fall, FDA issued revised language for its new SoilHealth1smrules implementing the FSMA Produce Safety Rule regulations. Of the revisions, one of the most notable to the organic sector were changes made relating to the use of manure and the required interval that untreated manure could be applied and crops harvested. FDA deferred from its earlier proposed 9-month minimum interval requirement to give the agency time to conduct research into determining an appropriate science-based application interval. FDA expects this process will take at least five years. In the meantime, all organic operations covered under the Produce Safety Rule have continued to follow the established National Organic Program regulations for application of raw manure, with 90- or 120-day application intervals.

Organic agriculture is of of the most strictly regulated system of agriculture, with a rigorously-enforced list of practices by which organic producers adhere. Certified organic producers are prohibited from using synthetic fertilizer on their crops.  Instead they often utilize animal-based soil amendments including manure and compost to improve their soil fertility and quality.

Last year, an OREI planning grant, which was conceived and written in collaboration with The Organic Center (TOC) and The Organic Trade Association (OTA) as well as others, was awarded to UC Davis to explore current practices used by the organic industry related to manure, compost use and rotational grazing. As part of that initiative, UC Davis, The Organic Center, the Organic Trade Association and other collaborators conducted farmer-focused public meetings, as well as online survey and interviews, to allow farmers to voice concerns and beliefs regarding the use of manure and compost and any potential associated food safety risks.

Photo Credit: Ian Barbour

Photo Credit: Ian Barbour

Building on the research plan developed by the planning grant, this project will provide critical information for guidelines on risk mitigation of foodborne pathogens for organic and sustainable agriculture.

Several studies have shown that the use of manure and compost has multiple positive environmental impacts: increased soil health, higher soil biodiversity and reduced erosion. The improved soil health and microbial diversity in organic soils has the potential to control the presence of soil pathogens which can impact food safety. But little research has examined the specific wait periods between manure application and crop harvest required to control pathogens, and how pathogen presence interacts with healthy soil in organic systems.

The specific goals of the project include:

  • Develop a risk analysis of on-farm practices associated with persistence of pathogens on organic farms using manure and compost;
  • Determine the relationship between soil health and pathogen survival in organically managed produce fields treated with animal manure;
  • Develop a comprehensive outreach program to provide technical and systems-based produce safety training.



The awesome researchers from the University of California, Davis get down and dirty in the field collecting spinach for pathogen testing.



Our work continues!  Here are some photos from our field trial at the University of Minnesota Southwest Research and Outreach Center in Lamberton, MN.

These plots are fertilized with either poultry litter, dairy solid manure, horse manure or no manure.  After manure was applied we inoculated the plots
using a generic E. Coli. Soil samples are
collected every 30 days and tested for the presence of E. Coli in order to determine the amount of time the bacteria is able to survive in the soil. The plot that is notwith any manure is our control plot. By comparing differences in E. Coli survival in our
control plot to the plots treated with manure we can better understand how the use ofmanure effects the persistence and survival of pathogens. These trials enable to us to better understand how long a farmer must wait after manure application (used as fertilizer) before they can safely harvest from the plot.  Once the E. Coli has died there is not risk of contamination through contact with the soil. In order to understand how different climates and geography impact our results we have also replicated these trials in California and Maryland. The pictures you see here were taken in the beginning of September and the only visible crop are the tomatoes. We have also planted radish and spinach in the remaining plots but they had not emerged yet.






More photos from day 120 of the experiment in Maine!

Sampling Roma Tomatoes at site ME1 on Day 120.

Irrigation pump at ME1. Notice the river behind the bushes.

Sampling surface irrigation water source from the Saco River at ME1

Field A. To be tilled and planted with greens the next day. Primarily crabgrass that was mowed the day before.

Main irrigation lines running from the pump to the fields.


Here are some images from our organic farm study sites in Maine!  All of our study sites across the country utilize the same techniques to ensure that results are comparable.

Tomato that will be sampled for pathogen contamination

Tomatoes growing on our California farm plots

Data loggers!

Crops growing in our experiment plots

Researcher collecting data

07/18/2017 – 08/09/2017

Research at our organic farm study sites in Maine are trucking along as we near the end of the summer!

At our experimental site, organic farm #3 in Maine, ME: Compost, Manure and Cover Crop strips after tillage prep for fall greens

Maine field site on organic farm #1, Field B: A row of tomatoes with blue flags which mark quadrants from which samples will be collected to test for pathogens. The field surrounding the tomatoes was planted with barley and forage radish cover crop.

A soil sensor box collects data, such as how wet the soil is, in recently mowed weedy bed. Late Fall Greens will be planted shortly.


We’ve been hard at work on our farm study sites! Farm site, ME-2, is a small diversified organic vegetable farm located in Maine’s mid-coast region. This region typically offers advantages to farmers through generally milder weather in Maine’s cold climate and short growing season. The mid-coast also has great market potential due to summer tourism and close geographical proximity to Maine’s largest city Portland, as well as, a plethora of other seasonally burgeoning towns.

ME-2 is one side of a joint farm collaborative. One side of the business raises livestock for various animal products such as meat and milk. While the ME-2 portion of the farm grows organic produce directly marketed to customers through farmer’s markets and their own on-farm market. Additional markets include restaurants and stores specializing in local naturally grown vegetables.

ME 2 manages plant nutrition and soil health in part by animal manure and composts. This, as well as, having animals occupy similar space makes ME-2 fit well into the farm survey of the OREI Manure Project. For 2017, the crop we are sampling will be melons. Here in Maine, melons are typically planted after June 1st when the danger of a frost has likely past.

View of melon plot day 30 before planting

View of farm cleaning shed and high tunnels in the background, perennial herbs/rhubarb in the foreground.

Caterpillar tunnel used for season extension. Crop: beets

Small scale tractor attachments, Allis Chalmer G cultivation tractor on the right.

30 days after manure incorporation still visible manure components on soil surface

Sheep and spring lambs in a adjacent are next to melon plot

Angus sanitizing a soil probe between soil sample locations




More updates and photos from our farm research site, ME-4 in Maine!

Manure was applied on soil surface at ME4, followed by plastic to cover beds until greens can be planted into the untilled field to meet the 120 day waiting period. The plastic is pulled back only for soil sampling. A great snake habitat.

Manure was applied on soil surface at ME4, followed by plastic to cover beds until greens can be planted into the untilled field to meet the 120 day waiting period. The plastic is pulled back only for soil sampling.

Data loggers recording temperature and soil moisture below black plastic. Manure was applied on soil surface at ME4, followed by plastic to cover beds until greens can be planted into the untilled field to meet the 120 day waiting period.

Manure was applied on soil surface at ME4, followed by plastic to cover beds until greens can be planted into the untilled field to meet the 120 day waiting period.


Our research is getting underway! Here are some photos from one of our farm sites in Maine.

Close up of manure pile heavy with waste hey and wood shavings.

Close up of manure pile heavy with waste hay and wood shavings.

Three beds on the left are the sample beds, after manure application. The farm will place a tarp over the beds, without incorporating the manure, for no-till bed preparation for fall greens.

Three beds on the left are the sample beds, after manure application. The farm will place a tarp over the beds, without incorporating the manure, for no-till bed preparation for fall greens.

Loading fresh manure to take to the field

Loading fresh manure to take to the field.

Cow and chicken in front of manure pile.

Cow and chicken in front of manure pile.

Sampling tool box for the project.

Sampling tool box for the project.

2-day old calf with mother.

2-day old calf with mother.



anrThe University of California Division of Agriculture and Natural Resources released a blog about our study! Their post is helping us find farmers in California who are interested in partnering with us on our research.  It’s not too late – we’re still looking for farmers in California.  We’ll be collecting produce, water, soil, and manure samples to test them for bacterial indicators, and in exchange for participating the the two-year study we’re offering a $700 stipend.  Contact Dr. Pires at (530) 754-9855 or, or Dr. Jay-Russell at (530) 219-4628 or if you are interested!



Photo credit: Bob Dass

Photo credit: Bob Dass

We are looking for farms to participate in our research on vegetable production that uses raw manure (dairy or chicken or horse)! The core goal of the study is to validate the 90 days wait period, or potentially provide information on how long it really takes for pathogens to disappear from soil and produce after raw manure application. During the study duration, we would like to collect a soil sample and a manure samples before any manure is applied, a soil sample soon after manure is applied, and 6 soil and produce samples during the growing season, every 30 days, for biological analysis. The study will go on for 2 years and at the end the farmer will be given $700 for participating in the entire 2 year project.  For contact information or more information on how to participate view our California flier if you are located on the West Coast, our Maine flier if you are located in the Northeast, or Maryland flier if you are located on the mid-East Coast, and our Midwest flier if you are located in  Minnesota, Northern Iowa, eastern Dakotas, and western Wisconsin.



We are thrilled to announce that we have been awarded funding for our research from the USDA Organic Research and Extension Initiative.  The grant (exact amount $1,999,848) will support research examining the relationship between manure use in improving soil health and food safety, concentrating on organic fresh produce production. Read the full press release here!


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