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Soil Amendments

Soil amendments are any chemical, biological, or physical materials intentionally added to the soil to improve or support plant growth and development. This definition includes fertilizers as well as materials like manure and compost that add organic matter and enhance soil structure. Food safety risks regarding soil amendments mostly involve raw manure, or other untreated animal-based soil amendments. All animal-based soil amendments can contain pathogenic microorganisms if they are not processed in a way that kills such pathogens. This page will outline the various types of soil amendments and their relative levels of risk, and then will provide recommendations on handling the riskiest soil amendments (raw manure and other untreated animal-based fertilizers).

An important note: If you use composted manure on your farm, you need to ensure that the manure is composted correctly and fully. Otherwise, it should be used as raw manure. Stacked manure or compost that is gathered in an area and left unmonitored for an unspecified amount of time is not equivalent to composted manure and should be handled as raw manure. For more information on raw versus composted manure, how to properly compost, and how to handle raw manure, keep reading.

Types of Soil Amendments

Synthetic fertilizers usually do not pose food safety risks because they are processed in a way that kills pathogens and do not support the growth of human pathogens. However, there have been food-borne illness outbreaks linked to synthesized fertilizers, and so we cannot consider them to be 100% safe. In addition to posing some biological food safety risk, synthetic fertilizers can also pose chemical risks to both consumers and applicators. All workers who work with synthetic fertilizer should be properly trained and should wear appropriate personal protective equipment. Synthetic fertilizers should be applied according to label instructions, clearly labeled and stored in a safe place.
Chemical Storage Log

Animal-based fertilizers – non-manure: Non-manure animal-based fertilizers  include bone, blood, and feather meals, and fish emulsion. These products should be processed to eliminate pathogens and stored in a way that they will not be contaminated with untreated amendments. Commercial production of these types of fertilizers generally involves high heat that will kill any pathogens, so just be sure to get them from a reputable source.  Records and documentation describing how the material was processed and stored can be obtained from the supplier, usually by request.

Compost is a mixture of decayed or decaying organic matter. It can be animal manure-based, or consist only of plant materials such as leaves, grass clippings and vegetable waste. 

Agricultural tea or compost tea is a liquid made from soaking compost or manure in water. Agricultural teas can carry varying amounts of risk, depending on what they are made out of. Agricultural teas made from properly composted materials and potable water are very low risk and do not require specific handling instructions. Agricultural teas that are made from untreated manure, improperly composted manure, or other untreated animal products should be handled as raw manure. Additionally, manure-based teas that have added nutrients (yeast extract, molasses, etc.) must be handled as raw manure, because with such added nutrients, otherwise low levels of human pathogens that may be present can grow into high populations. See “Manure” below for more information on treated versus untreated manure.

Cull piles are usually comprised of discarded plants or produce from fields, greenhouses, or wash/pack facilities. Cull piles are not compost piles. Cull piles are generally static and not aerated and don’t reach the specific temperatures required for composting. Plant material may not completely decompose and pathogens—human and plant—as well as weed seeds will likely survive.  Additionally, cull piles are often havens for animal pests, especially rats, which can carry human pathogens and deposit them in the cull pile in their feces. If you are going to use cull pile material as a soil amendment, you should either compost it fully beforehand, or otherwise treat it as you would raw manure.

Raw manure: Untreated manure is the riskiest soil amendment for produce, as it can contain human pathogens. Composted manure is much less risky, as the composting process, if done correctly, will kill any human pathogens in the manure. “Stacked” manure, or manure that has been gathered into a pile and not monitored, is not composted and should be treated as raw manure. The composting process requires that the composting material meet specific parameters (e.g. 131°F for 3 consecutive days, under aerobic conditions, followed by curing). It’s incredibly important that composted manure is treated correctly and fully—if not, or if there is a question about whether a manure-based fertilizer has been treated completely or properly, it should be considered untreated manure and used as such. For more information on correctly composting manure and how to handle untreated manure, continue reading.

Human waste and biosolids should not be used as soil amendments for produce unless the product meets EPA regulations for biosolids (40 CFR part 503 subpart D). These products pose significant food safety risks as they can contain human pathogens, heavy metals, and pharmaceutical contaminants.

Raw Manure

Raw manure and other untreated animal-based soil amendments pose the greatest food safety risks. The easiest way to reduce these risks is to compost manure before applying it. See the section above for more information on composting. If you do use raw manure or other untreated animal-based soil amendments, use the recommendations below to lower the risk.

Applying Raw Manure

  • Crop selection: Preferentially apply raw manure to fields where agronomic crops and crops that are rarely consumed raw will be grown.
  • Timing: Maximize the time between applying manure and harvest of subsequent crops (the application to harvest interval). Also, apply the material early enough to incorporate before the ground freezes. 
  • Recordkeeping: Keep records of soil amendment applications and soil amendment treatment in case a problem arises.

Handling & Storing Raw Manure

  • Designate specific equipment and tools for handling untreated soil amendments
  • Develop SOPs to clean and sanitize equipment and tools that contact both untreated soil amendments and fresh produce. For more information on tool and equipment sanitation, see our Post-Harvest Handling & Sanitation page.
  • Direct traffic (workers, equipment) around soil amendment storage or processing areas to reduce the risk of cross-contamination.
  • Minimize runoff, leaching, and wind drift that could contaminate crops, harvested produce, and produce handling areas by covering piles, building berms, etc. Don’t store untreated soil amendments in locations that are likely to experience runoff or in areas that are close to water sources.
  • Keep treated soil amendments separate from in-process and raw soil amendments.

Worker Training

Workers who handle soil amendments, both treated and untreated should:

  • Understand SOPs regarding manure, compost, and other soil amendments
  • Make sure clothes, boots, and gloves are clean before handling produce 
  • Wash hands after handling soil amendments, whether treated or untreated


Keep records of the following, in case a problem arises:

  • Type and source of amendments used on your farm
  • Rates and dates of applications
  • Handling and sanitation practices used that reduce risks

Soil Amendments Application Log

Chemical Storage Log


Raw manure can be treated to kill pathogens, making it much less risky. A common treatment is composting. Composting is a specific, controlled process. Stacked manure, or manure that has been gathered in an area and then left unmonitored, is not composted and needs to be considered raw.

General Composting Resources

Waste Management & Composting – UMass

MDAR Guide to Agricultural Composting

Maine Compost School

General Composting Recommendations:

  • Document the composting process that you use (time, temperature, turnings, etc.)
  • Verify and keep records to show that the process parameters are met. Remember, if the correct temperatures/timings/turnings are not met, the manure is not truly composted and can contain human pathogens; handle incompletely or questionably composted manure as raw manure.
  • Monitor the temperature of your compost and keep records of the temperature measurements and the dates the compost was turned. 
  • Request treatment records or certification documentation from any purchased compost. 
  • Keep composted material separate from in-process and raw material. To avoid cross-contamination, designate tools for use in completed compost only.
  • Make sure that compost piles won’t contaminate harvested produce or produce in fields. Consider run off and traffic routes (both foot traffic and vehicles) before you choose the location of your compost piles and/or a new wash/pack facility.
  • If you’re not sure whether manure was composted correctly or completely, treat it as if it was never composted! 
  • Minimize animal access to compost piles to prevent the cross-contamination of the amendment with fecal material.
  • If you purchase composted manure to use on your farm: request documentation from the producer that shows what composting process was used and certifies that the process parameters were met.

Compost Treatment Log

FSMA: Soil Amendments

FSMA regulations focus on “biological soil amendments of animal origin”, abbreviated here as BSAAO, as they pose the most risk to fresh produce. However, there are also risks associated with treated and synthetic soil amendments – see the general recommendations above for more information.

On many farms, the term “biological soil amendments of animal origin” essentially means manure. However, the other materials are included in that definition. The following materials are considered BSAAO:

  • Raw or composted manure
  • Non-fecal animal byproducts, like bone, blood, and feather meal, and fish emulsion
  • Human waste and biosolids
  • Manure-based agricultural teas