Back to top

Soil Amendments

Soil Amendments Tree graphicSoil Amendments Decision Tree (Full Portfolio)


A soil amendment refers to any material added to the soil to improve its physical or chemical properties. With fresh fruits and vegetables, food safety concerns are most often associated with biological contamination by pathogens in manure-based soil amendments. However, chemical hazards associated with inorganic fertilizers can represent a chemical risk to crops as well as to those who apply the fertilizers. Many inorganic fertilizers are federally regulated so the first rule is to always follow the label because the label is the law. Proper storage practices and controlling access to these chemicals is also important to meet federal requirements and reduce the chance of chemical contamination on the farm.

Manure-based soil amendments can harbor pathogens that can cause illness in humans and may contaminate produce when introduced into the production environment. This overview is intended to provide general guidelines and recommendations to reduce the likelihood of produce microbial contamination when using manure-based soil amendments.

  • If it is unknown whether the manure-based soil amendment is raw or fully composted, it should be considered raw manure.
  • Recommended time intervals from application of raw manure to the harvest of the produce crop vary from 90 days to 1 year. These recommendations are discussed in more detail below.
  • Composting manure can significantly reduce the risk of contamination.
  • Recordkeeping is important for all soil amendment applications. Document what, where, when, how, and how much was applied. For compost, the composting process including monitoring time, temperatures, and turnings should also be documented.

Raw Manure

When a crop is grown on land on which raw manure has recently been applied, there is a risk that the crop could be contaminated because of the likelihood of foodborne illness pathogens being present and the increased risk of crop contamination. If raw manure is used as a soil amendment or fertilizer, it should never be applied during the growing season and always be incorporated into the soil within 72 hours after application. The interval between raw manure application and harvest should be maximized. The required time frame between application and harvest varies throughout the industry. The Leafy Greens Marketing Agreement (LGMA)1 requires an interval of at least one year. The National Organic Program7 (Rule 7 CFR Part 205.203) recommends applications be at least 90 days before harvest for crops that have edible portions which do not come in contact with the soil and at least 120 days before harvest of crops that have edible portions which do come in contact with the soil (crops in or near the soil are most vulnerable to contamination). The proposed Food Safety Modernization Act (FSMA)13 Produce Rule would require nine months between a raw manure application and harvest of a produce crop covered by the rule. Some research even shows that pathogens can persist in the soil well beyond this time frame2,3,4,5 and therefore some leafy green buyers require a five year interval.6

Aside from raw manure purposely applied to fields, it is important to consider manure that may enter the field through runoff, wildlife animal intrusion, or movement from adjacent lands that have domesticated farm animals. Please see the Wildlife and Animal Management and Land Use Decision Trees to assess these risks.


Composting animal manure can reduce microbial pathogens and greatly reduce the risk of contamination to fruit and vegetable crops. Simply piling manure without actively managing and monitoring it, or using an anaerobic system (also called 'aging'), is not composting and therefore must be considered raw manure. If the same equipment or tools are used on raw, cured, or curing piles, be sure to clean and sanitize them after use on raw manure to avoid recontamination of the other piles.

Compost must maintain a temperature of between 131 and 170°F for 3 days (enclosed system) or 15 days (windrow system), during which period the composting materials must be turned a minimum of five times. After these steps, the compost pile should cure for 45 days. Finished and curing compost piles should be covered in order to prevent recontamination. Acceptable organic materials for compost include, but are not limited to: animal manure, by-products of agricultural commodities processing, yard debris, and kitchen wastes. Detailed records should be kept of pile type (aerobic vs. anaerobic, enclosed, windrow, etc.), temperature and moisture management, dates turned, and the duration of high temperatures. The Northeast Recycling Council11, and the Cornell Waste Management Institute's Compost Fact Sheet Series 1–812 provide specific guidelines and tips for composting manure to assure its safe and effective use as a fertilizer. Furthermore, if commercial compost is treated by a scientifically valid controlled physical or chemical process, or combination of these processes, in accordance with the FSMA requirements to meet the microbial standard, there is a 0 day interval between application and harvest.

Leachates and Teas

Leachates and teas are used as foliar fertilizers and soil amendments to suppress pests and diseases, as well as enhance soil biology. Compost leachate is the liquid coming out of compost when water from irrigation, rain, or snow filters through the compost. Compost tea is made from compost steeped in water. There are two basic types of compost tea, aerated and non-aerated.

  • Aerated tea = manure/compost mixed with water (1:10-50) and then aerated by injection or re-circulated water for 12–24 hours.15
  • Non-aerated tea = manure/compost mixed with water (1:3-10) and left untouched for several days (1–3 weeks).15

To reduce the risk of pathogen contamination of produce:

  1. Use potable water when mixing compost teas. The proposed FSMA Produce Rule requires any tea be mixed with water that is free of generic E. coli determined through testing.
  2. Use properly composted manure. There is no application restriction on using compost tea made from properly composted manure, though it should only contact the soil and not the edible portion of the crop.
  3. Raw manure teas can only be applied to soil and not directly to plants, and should follow the one-year harvest interval.
  4. Additives (molasses, yeast, etc.) must follow the same one-year application to harvest interval as raw manure.
  5. Compost leachate may be applied to the soil with the 90/120 day rule. It may NOT be applied directly to plant.
  6. Teas may NOT be applied to edible seed sprouts.15


Recordkeeping should always be part of your food safety program. Developing a recordkeeping system that is easy to use will encourage soil amendment applicators to properly document their activities and support the implementation of a farm food safety plan. Documentation should include:

  • Type of soil amendment being applied
  • Composting method and microbial testing (if applicable)
  • Fields receiving application
  • Date of application
  • Rate (quantity applied per acre)
  • Method of application
  • What crops will be planted


  1. Leafy Greens Marketing Agreement. 2010. Commodity Specific Food Safety Guidelines for the Production and Harvest of Lettuce and Leafy Greens. Pg 25.
  2. Fukushima, H., K. Hoshina, and M. Gomyoda. 1999. Long-Term Survival of Shiga Toxin-Producing Escherichia coli O26, O111, and O157 in Bovine Feces. Applied and Environmental Microbiology 65(11): 5177-5181.
  3. Gagliardi, J. V., and J. S. Karns. 2000. Leaching of Escherichia coli O157:H7 in Diverse Soils under Various Agricultural Management Practices. Applied and Environmental Microbiology 66(3): 877-883.
  4. Islam, M., M. P. Doyle, S. C. Phatak, P. Millner, and X. Jiang. 2005. Survival of Escherichia coli O157:H7 in Soil and on Carrots and Onions Grown in Fields Treated with Contaminated Manure Composts or Irrigation Water. Food Microbiology 22: 63-70.
  5. Wang, G., T. Zhao, and M.P. Doyle. 1996. Fate of enterohemorrhagic Escherichia coliO157:H7 in bovine feces. Journal of Applied and Environmental Microbiology62(7):2567-2570.
  6. Bihn, Elizabeth A. 2011. Survey of Current Water Use Practices on Fresh Fruit and Vegetable Farms and Evaluation of Microbiological Quality of Surface Waters Intended for Fresh Produce Production. Thesis (Ph.D.), Cornell University, August 2011.
  7. National Organic Program. 2012. Rule 7 CFR part 205.203. Soil fertility and crop nutrient management practice standard
  8. National Resources Conservation Service. 2012. Code 590, Nutrient Management.
  9. Food and Drug Administration. 1998. Guide to Minimize Microbial Food Safety Hazards for Fresh Fruits and Vegetables. p. 19-26. 
  10. GLOBAL GAP Program. 2013. Integrated Farm Assurance, All Farm Base, Crops Base, Fruit and Vegetables. CB 5.5. p. 33.
  11. Northeast Recycling Council. 2008. Manure management for small hobby farms.
  12. Cornell Waste Management Institute factsheets
  13. Food and Drug Administration. 2013. Proposed Food Safety Modernization Act Rules. Federal Register vol. 78, no. 11, p. 3503.
  14. Leafy Green Guidance Handbook
  15. National Organic Standards Board. 2004. Compost Task Force Report. 21 p. 
  16. Erickson, M., F. Critzer and M. Doyle. 2010. Composting Criteria for Animal Manure. Produce Safety Project Issue Brief on Composting of Animal Manures. 13 p. 

The information in the template food safety plan, SOPs, and recordkeeping logs are examples you can use. They are not intended to be used directly. Tailor each to fit your farm operation and practices. These documents are guidance for risk reduction and for educational use only. These documents are not regulatory and are not intended to be used as audit metrics. These documents are subject to change without notice based on the best available science.